通过基因组测序获取人类自身具有基因敲除效应的突变，并用于新药研发。 最近几十年来，生物学家多通过在小鼠或其它实验动物身上失活某个基因，来观察这个基因的功能。现在，这种基因敲除研究功能的模式又有了新的更理想的物种材料：人类自身。 这种方法可不是在实验室中通过基因工程制备基因突变的人，研究人员通过扫描成千上万的人基因组序列，来找寻自然发生的突变所致特定基因的失活。通过观察这些突变如何影响健康，研究者希望获得疾病的生物学根源并找到新的治疗方式。 上周，在加州圣地亚哥美国人类遗传学会（American Society of Human Genetics）会议的分会上，遗传学家们讨论了几个这种大规模（测序数据）的效应。来自波士顿马省总医院（Massachusetts General Hospital）的基因组学家Daniel MacArthur说，我们现在所有认知都是基于小鼠和大鼠的，而不是基于人。他的研究组通过扫描超过9万人的基因组蛋白编码区，已经确定了大约15万自然发生的敲除基因。“现在我们发现了拥有某特定失活的基因或者特定修饰的基因，我们可以直接利用他们来检验我们的假设。” 平均每个人都携带不少的基因突变，这些突变导致至少1/200基因出现单拷贝失活，导致大约1/20基因出现双拷贝失活。然而，要得到任何一个基因的敲除突变却很难，因此需要大人口规模来研究其效应。这类功能缺失突变在特定疾病中，例如囊肿性纤维化，被广泛采用。多数突变对健康并无损害，一些突变甚至对携带者有益。“（很多突变不导致疾病，因而）我们不会在临床上看到，但是他们在生物学上依旧很有价值”，MacArthur说。MacArthur及其研究组将关注的焦点放在基因组数据上，他们现在也开始通过患者—健康记录来确定哪些相对微弱突变导致的效应。在一项有超过36000芬兰人参与的研究中(发表于PLoS Genet. 10, e1004494; 2014)，MacArthur的团队发现缺失LPA基因可能有心脏保护作用，另一种敲除突变，在芬兰人中有2.4%的人为该突变的单拷贝携带者，这种突变如果以双拷贝形式出现则容易引起流产。 来自休斯敦德克萨斯健康科学中心大学（University of Texas Health Science Center）的Bing Yu在会上说，他的团队将1300多人的基因敲除突变数据与血液中300多分子数据进行了比较，发现基因SLCO1B1上的突变与高脂肪酸有关，高脂肪酸是心衰的风险因子。英国Hinxton之Wellcome Trust Sanger研究所的一个研究组报道：在小鼠中失活具有致死效应的43个基因，在人体这些基因失活时人却看上去很健康，并不呈现致死效应。 宣传海报 循此方式可以揭开人类成千未知功能基因的作用。并可能通过确认具有保护性（让人免受疾病困扰）的基因或生物通路来辅助药物研发。 人类基因敲除效应的宣传海报（poster child）是一类新型、可阻止PCSK9基因的药物(Nature 496, 152–155; 2013)。PCSK9基因于本世纪早期在高胆固醇的法国人家族中被发现。研究人员很快发现：在PCSK9单拷贝失活这样一种罕见突变的人群中，胆固醇含量低，少有心脏病发生。首个阻止PCSK9的药物将在明年问世，并预计将在未来五年中产生250亿美元的销量收入。 加利福尼亚La Jolla 的Scripps转化科学研究所（Scripps Translational Science Institute）领导人Eric Topol说：“将来会有成百，甚至成千个像PCSK9基因样的故事出现”。药物可以模拟功能缺失型突变。耶鲁大学的生物信息学家Mark Gerstein则认为人类基因突变在研发对抗衰老性疾病上尤其重要。“你可以想象状况，某个基因在你25岁的时候对你有益，而当你75岁的时候，它或许对你有害了。” “通过这些基因敲除数据，你可以很容易的理解为什么现在越来越多的人通过基因组测序来寻求自己所患疾病的解决方案了吧。” 伦敦肿瘤研究所的医学遗传学家Nazneen Rahman说。Rahman在会上展示了她的团队对1000个英国人基因敲除突变的分析结果，这些信息确切无疑的表明发生在人类的基因突变比我们先前想象的多许多。 当利用人类基因组测序确认某神秘疾病的原因时，任何敲除型突变都是可疑原因。拥有这些突变的完整清单以及它们的健康效应（或缺失效应）将有助于确定疾病的真是原因，Rahman说。 MacArthur团队上周刚释放了约63000人的敲除及其它信息，已经有人在利用这些数据了。“当我看到这些数据时，我做的第一件事就是查看我所关注的严重疾病有关基因，看是否有什么人在这数据库中，我还真发现了他们”，休斯敦Baylor医学院的医学遗传学家John Belmont说。（在这批人中）他发现了11个人携带有马凡氏综合征相关基因突变，这种疾病累及结缔组织，如果不予处理，可能引起突发性心力衰竭。 这些人可能属于潜伏的病例，他们可能具有保护性、防止发病的机制或是存在测序错误。Belmont说：“携带致病的突变基因而不发病，这太迷人了，我们将好好关注它，这或许预示着马凡氏综合征的新治疗方式。 链接： http://www.nature.com/news/geneticists-tap-human-knockouts-1.16239 文题：Geneticists tap human knockouts Sequenced genomes reveal mutations that disable single genes and can point to new drugs. Ewen Callaway For decades, biologists have studied gene function by inactivating the gene in question in mice and other lab animals, and then observing how it affects the organism. Now researchers studying such gene ‘knockouts’ have another, ideal model at their disposal: humans. The approach does not involve genetically engineering mutant people in the lab, as is done in mice. Instead, researchers scan the genomes of thousands or millions of people, looking for naturally occurring mutations that inactivate a particular gene. By observing how these mutations affect health, researchers hope to gain insight into basic biology and to unearth new disease treatments. Geneticists discussed several such large-scale efforts during a packed session at the American Society of Human Genetics meeting in San Diego, California, last week. “So much of what we know is based on mice and rats, and not humans,” says Daniel MacArthur, a genomicist at Massachusetts General Hospital in Boston, whose team identified around 150,000 naturally knocked-out genes by trawling the protein-coding portion of the genome, or exome, in more than 90,000 people. “Now we can find people who actually have a particular gene inactivated or somehow modified, and that allows us to test hypotheses directly.” On average, every person carries mutations that inactivate at least one copy of 200 or so genes and both copies of around 20 genes. However, knockout mutations in any particular gene are rare, so very large populations are needed to study their effects. These ‘loss of function’ mutations have long been implicated in certain debilitating diseases, such as cystic fibrosis. Most, however, seem to be harmless — and some are even beneficial to the persons carrying them. “These are people we’re not going to find in a clinic, but they’re still really informative in biology,” says MacArthur. His group and others had been focusing on genome data, but they are now also starting to mine patient-health records to determine the — sometimes subtle — effects of the mutations. In a study of more than 36,000 Finnish people, published in July (E. T. Lim et al. PLoS Genet. 10, e1004494; 2014), MacArthur and his team discovered that people lacking a gene called LPA might be protected from heart disease, and that another knockout mutation, carried in one copy of a gene by up to 2.4% of Finns, may cause fetuses to miscarry if it is present in both copies. Bing Yu of the University of Texas Health Science Center in Houston told the meeting how he and his collaborators had compared knockout mutations found in more than 1,300 people with measurements of around 300 molecules in their blood. The team found that mutations in one gene, called SLCO1B1, were linked to high levels of fatty acids, a known risk factor for heart failure. And a team from the Wellcome Trust Sanger Institute in Hinxton, UK, reported that 43 genes whose inactivation is lethal to mice were found to be inactivated in humans who are alive and apparently well. Poster child Following up on such insights will help researchers to unpick the functions of the thousands of human genes about which little or nothing is known, say MacArthur and others. It might even aid drug discovery by identifying genes or biological pathways that could protect against disease. The poster child for human-knockout efforts is a new class of drugs that block a gene known as PCSK9 (see Nature 496, 152–155; 2013). The gene was discovered in French families with extremely high cholesterol levels in the early 2000s. But researchers soon found that people with rare mutations that inactivate one copy of PCSK9 have low cholesterol and rarely develop heart disease. The first PCSK9-blocking drugs should hit pharmacies next year, with manufacturers jostling for a share of a market that could reach US$25 billion in five years. “I think there are hundreds more stories like PCSK9 out there, maybe even thousands,” in which a drug can mimic an advantageous loss-of-function mutation, says Eric Topol, director of the Scripps Translational Science Institute in La Jolla, California. Mark Gerstein, a bio-informatician at Yale University in New Haven, Connecticut, predicts that human knockouts will be especially useful for identifying drugs that treat diseases of ageing. “You could imagine there’s a gene that is beneficial to you as a 25-year-old, but the thing is not doing a good job for you when you’re 75.” The human-knockout data presented last week will also make it easier to interpret the growing number of genomes being sequenced from people seeking treatment, says Nazneen Rahman, a medical geneticist at the Institute for Cancer Research in London. Rahman told the meeting about her team’s analysis of knockout mutations in 1,000 British people. “The take-home message is that these types of mutations occur much more commonly than people thought,” she says. When a person’s genome is sequenced to identify the cause of a mysterious illness, any knockout mutations that turn up are obvious suspects. Having a complete list of such mutations and their health effects (or lack thereof) should help to identify the true causes of a disease, Rahman says. To that end, MacArthur’s team last week released knockout and other data from some 63,000 people — and others are already making use of this trove. “One of the first things I did when they released the data was to look at all my favourite genes for very severe diseases, to see if there are people in those databases — and there are,” says John Belmont, a medical geneticist at Baylor College of Medicine in Houston. He found 11 people with mutations associated with Marfan syndrome, a disorder that affects connective tissue and that can cause sudden heart failure if left untreated. However, these people may be silent cases, they might somehow be protected against the disease or their genomes might have been sequenced incorrectly. People who carry disease-causing mutations but don’t get sick are especially intriguing, he says. “We should pay attention to them,” Belmont says. “They may hold a key for new treatments.” 上文由群晓科苑翻译整理，科学推广，服务民众。他人或机构如需使用，请提供该原始链接地址。 北京群晓科苑生物技术有限公司主要经营生物医药领域的试剂、耗材和仪器。群晓生物致力于为用户提供优质的材料、技术和实验整体性解决方案，完美配合用户的科研创意和灵感。群晓生物立志把一流的产品、专业的技术和完善的售后服务献给广大用户。 北京群晓科苑生物技术有限公司 www.qbioscience.com www.qbiotec.com Tel: 010-84504282/64880108 qbioscience@126.com
Study Finds Honey Bees Originated from Asia, not Africa 体会： 1、重新审视蜜蜂（Apis mellifera）在亚洲的进化历史和迁移路径； 2、审视少数基因片段信息在系统学上的局限性； 3、重视基因组数据在种群和物种水平上的应用。 Title: A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera Authors: Andreas Wallberg , Fan Han , Gustaf Wellhagen , Bjørn Dahle , Masakado Kawata , Nizar Haddad , Zilá Luz Paulino Simões , Mike H Allsopp , Irfan Kandemir , Pilar De la Rúa , Christian W Pirk Matthew T Webster Abstract: The honeybee Apis mellifera has major ecological and economic importance. We analyze patterns of genetic variation at 8.3 million SNPs, identified by sequencing 140 honeybee genomes from a worldwide sample of 14 populations at a combined total depth of 634×. These data provide insight into the evolutionary history and genetic basis of local adaptation in this species. We find evidence that population sizes have fluctuated greatly, mirroring historical fluctuations in climate, although contemporary populations have high genetic diversity, indicating the absence of domestication bottlenecks. Levels of genetic variation are strongly shaped by natural selection and are highly correlated with patterns of gene expression and DNA methylation. We identify genomic signatures of local adaptation, which are enriched in genes expressed in workers and in immune system– and sperm motility–related genes that might underlie geographic variation in reproduction, dispersal and disease resistance. This study provides a framework for future investigations into responses to pathogens and climate change in honeybees. August 25, 2014 by Entomology Today Leave a Comment Photo by Alexander Wild. http://www.alexanderwild.com In a study published in Nature Genetics, researchers from Uppsala University present the first global analysis of genome variation in honey bees. The findings show a surprisingly high level of genetic diversity in honey bees, and indicate that the species most probably originates from Asia, and not from Africa as previously thought. “The evolutionary tree we constructed from genome sequences does not support an origin in Africa,” said Matthew Webster, one of the authors. “This gives us new insight into how honey bees spread and became adapted to habitats across the world.” Another unexpected result was that honey bees seem to be derived from an ancient lineage of cavity-nesting bees that arrived from Asia around 300,000 years ago and rapidly spread across Europe and Africa. Extensive losses of honey bee colonies in recent years are a major cause for concern. Honey bees face threats from disease, climate change, and management practices. To combat these threats, it is important to understand the evolutionary history of honey bees and how they have adapted to different environments across the world. “We have used state-of-the-art, high-throughput genomics to address these questions, and have identified high levels of genetic diversity in honey bees,” Webster said. “In contrast to other domestic species, management of honey bees seems to have increased levels of genetic variation by mixing bees from different parts of the world. The findings may also indicate that high levels of inbreeding are not a major cause of global colony losses.” Also hidden in the patterns of genome variation are signals that indicate that climate change has strongly impacted honey bee populations historically. “Populations in Europe appear to have contracted during ice ages, whereas African populations have expanded at those times, suggesting that environmental conditions there were more favorable,” said Webster. The researchers also identified specific mutations in genes that are important in adaptation to factors such as climate and pathogens, including those involved in morphology, behavior, and innate immunity. “The study provides new insights into evolution and genetic adaptation, and establishes a framework for investigating the biological mechanisms behind disease resistance and adaptation to climate — knowledge that could be vital for protecting honey bees in a rapidly changing world,” Webster said. Read more at: - A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera
3月3日，以四川农业大学为第一作者单位、玉米所作物遗传育种学博士生覃成为第一作者，玉米所沈亚欧研究员为共同第一作者，玉米所张志明研究员为最后责任作者，联合遵义市农业科学研究院、华南农业大学、深圳华大基因研究院、墨西哥生物多样性基因组学国家重点实验室等13家科研院所合作完成的辣椒基因组研究成果发表在国际著名期刊Proceedings of the National Academy of Sciences USA(PNAS)》(《美国国家科学院院刊》)(该期刊2013年影响因子为9.737)上，文章题目为“栽培辣椒和野生种辣椒的全基因组测序揭示了辣椒属的驯化和特异性”。该研究公布了我国辣椒(Capsicum annuum L.)种质资源遵辣1号的基因组测序结果(http://peppersequence.genomics.cn)。辣椒是全球最重要的经济作物之一，开展辣椒基因组学研究，深入挖掘与利用辣椒重要功能基因，将加快分子育种和全基因组育种的进程。辣椒基因组的成功解析及其群体遗传学研究，将为培育高产、优质和抗病的新品种辣椒奠定坚实的遗传学基础，同时也为该物种的基础生物学研究提供宝贵的资源。
Provider: Quertle (www.quertle.info) Content: text/plain; charset=UTF-8 TY- JOUR TI- Genome of a songbird unveiled AU- Pinaud, Raphael PY- 2011 T2- Journal of Biology J2- J Biol UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871510/ VL- 9 IS- 3 SP- 19-19 DO- 10.1186/jbiol222 C2- 2871510 N2- An international collaborative effort has recently uncovered the genome of the zebra finch, a songbird model that has provided unique insights into an array of biological phenomena. See research articles , ,and N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Reprogramming of the non-coding transcriptome during brain development AU- Valadkhan, Saba AU- Nilsen, Timothy W PY- 2011 T2- Journal of Biology J2- J Biol UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871522/ VL- 9 IS- 1 SP- 5-5 DO- 10.1186/jbiol197 C2- 2871522 N2- A recent global analysis of gene expression during the differentiation of neuronal stem cells to neurons and oligodendrocytes indicates a complex pattern of changes in the expression of both protein-coding transcripts and long non-protein-coding RNAs. See research article . N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- LINE-1 Retrotransposition Activity in Human Genomes AU- Beck, Christine R AU- Collier, Pamela AU- Macfarlane, Catriona AU- Malig, Maika AU- Kidd, Jeffrey M AU- Eichler, Evan E AU- Badge, Richard M AU- Moran, John V PY- 2011 T2- Cell J2- Cell UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013285/ VL- 141 IS- 7 SP- 1159-1170 DO- 10.1016/j.cell.2010.05.021 C2- 3013285 N2- Summary: Long Interspersed Element-1 (LINE-1 or L1) sequences comprise the bulk of retrotransposition activity in the human genome; however, the abundance of highly active or hot L1s in the human population remains largely unexplored. Here, we used a fosmid-based, paired-end DNA sequencing strategy to identify 68 full-length L1s which are differentially present among individuals but are absent from the human genome reference sequence. The majority of these L1s were highly active in a cultured cell retrotransposition assay. Genotyping 26 elements revealed that two L1s are only found in Africa and that two more are absent from the H952 subset of the Human Genome Diversity Panel. Therefore, these results suggest that hot L1s are more abundant in the human population than previously appreciated, and that ongoing L1 retrotransposition continues to be a major source of inter-individual genetic variation. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Lrp12/Mig13a Reveals Changing Patterns of Preplate Neuronal Polarity during Corticogenesis that Are Absent in Reeler Mutant Mice AU- Schneider, Stephanie AU- Gulacsi, Alexandra AU- Hatten, Mary E PY- 2011 T2- Cerebral Cortex (New York, NY) J2- Cereb Cortex UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000567/ VL- 21 IS- 1 SP- 134-144 DO- 10.1093/cercor/bhq070 C2- 3000567 N2- During corticogenesis, the earliest generated neurons form the preplate, which evolves into the marginal zone and subplate. Lrp12/Mig13a, a mammalian gene related to the Caenorhabditis elegans neuroblast migration gene mig-13, is expressed in a subpopulation of preplate neurons that undergo ventrally directed tangential migrations in the preplate layer and pioneer axon projections to the anterior commissure. As the preplate separates, Lrp12/Mig13a-positive neurons polarize in the radial plane and form a pseudocolumnar pattern, prior to moving to a deeper position within the emerging subplate layer. These changes in neuronal polarity do not occur in reeler mutant mice, revealing the earliest known defect in reeler cortical patterning and suggesting that the alignment of preplate neurons into a pseudolayer facilitates the movement of later-born radially migrating neurons into the emerging cortical plate. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- ENCODE whole-genome data in the UCSC genome browser (2011 update) AU- Raney, Brian J AU- Cline, Melissa S AU- Rosenbloom, Kate R AU- Dreszer, Timothy R AU- Learned, Katrina AU- Barber, Galt P AU- Meyer, Laurence R AU- Sloan, Cricket A AU- Malladi, Venkat S AU- Roskin, Krishna M AU- Suh, Bernard B AU- Hinrichs, Angie S AU- Clawson, Hiram AU- Zweig, Ann S AU- Kirkup, Vanessa AU- Fujita, Pauline A AU- Rhead, Brooke AU- Smith, Kayla E AU- Pohl, Andy AU- Kuhn, Robert M AU- Karolchik, Donna AU- Haussler, David AU- Kent, W James PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013645/ VL- 39 IS- Database issue SP- D871-D875 DO- 10.1093/nar/gkq1017 C2- 3013645 N2- The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. This data helps illuminate transcription factor-binding sites, histone marks, chromatin accessibility, DNA methylation, RNA expression, RNA binding and other cell-state indicators. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser (). ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC () provides information about the ENCODE data and links for access. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- BACs as Tools for the Study of Genomic Imprinting AU- Tunster, S J AU- Van De Pette, M AU- John, R M PY- 2011 T2- Journal of Biomedicine and Biotechnology J2- J Biomed Biotechnol UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3010669/ VL- 2011 DO- 10.1155/2011/283013 C2- 3010669 N2- Genomic imprinting in mammals results in the expression of genes from only one parental allele. Imprinting occurs as a consequence of epigenetic marks set down either in the father's or the mother's germ line and affects a very specific category of mammalian gene. A greater understanding of this distinctive phenomenon can be gained from studies using large genomic clones, called bacterial artificial chromosomes (BACs). Here, we review the important applications of BACs to imprinting research, covering physical mapping studies and the use of BACs as transgenes in mice to study gene expression patterns, to identify imprinting centres, and to isolate the consequences of altered gene dosage. We also highlight the significant and unique advantages that rapid BAC engineering brings to genomic imprinting research. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera AU- Munoz-Torres, Monica C AU- Reese, Justin T AU- Childers, Christopher P AU- Bennett, Anna K AU- Sundaram, Jaideep P AU- Childs, Kevin L AU- Anzola, Juan M AU- Milshina, Natalia AU- Elsik, Christine G PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013718/ VL- 39 IS- Database issue SP- D658-D662 DO- 10.1093/nar/gkq1145 C2- 3013718 N2- The Hymenoptera Genome Database (HGD) is a comprehensive model organism database that caters to the needs of scientists working on insect species of the order Hymenoptera. This system implements open-source software and relational databases providing access to curated data contributed by an extensive, active research community. HGD contains data from 9 different species across 200 million years in the phylogeny of Hymenoptera, allowing researchers to leverage genetic, genome sequence and gene expression data, as well as the biological knowledge of related model organisms. The availability of resources across an order greatly facilitates comparative genomics and enhances our understanding of the biology of agriculturally important Hymenoptera species through genomics. Curated data at HGD includes predicted and annotated gene sets supported with evidence tracks such as ESTs/cDNAs, small RNA sequences and GC composition domains. Data at HGD can be queried using genome browsers and/or BLAST/PSI-BLAST servers, and it may also be downloaded to perform local searches. We encourage the public to access and contribute data to HGD at: . N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing AU- Martelli, Pier L AU- D'Antonio, Mattia AU- Bonizzoni, Paola AU- Castrignan, Tiziana AU- D'Erchia, Anna M AU- D'Onorio De Meo, Paolo AU- Fariselli, Piero AU- Finelli, Michele AU- Licciulli, Flavio AU- Mangiulli, Marina AU- Mignone, Flavio AU- Pavesi, Giulio AU- Picardi, Ernesto AU- Rizzi, Raffaella AU- Rossi, Ivan AU- Valletti, Alessio AU- Zauli, Andrea AU- Zambelli, Federico AU- Casadio, Rita AU- Pesole, Graziano PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013677/ VL- 39 IS- Database issue SP- D80-D85 DO- 10.1093/nar/gkq1073 C2- 3013677 N2- Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256939 protein variants from 17191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at . N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology AU- Hong, Dongwan AU- Park, Sung-Soo AU- Ju, Young Seok AU- Kim, Sheehyun AU- Shin, Jong-Yeon AU- Kim, Sujung AU- Yu, Saet-Byeol AU- Lee, Won-Chul AU- Lee, Seungbok AU- Park, Hansoo AU- Kim, Jong-Il AU- Seo, Jeong-Sun PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013693/ VL- 39 IS- Database issue SP- D883-D888 DO- 10.1093/nar/gkq1101 C2- 3013693 N2- High-throughput genomic technologies have been used to explore personal human genomes for the past few years. Although the integration of technologies is important for high-accuracy detection of personal genomic variations, no databases have been prepared to systematically archive genomes and to facilitate the comparison of personal genomic data sets prepared using a variety of experimental platforms. We describe here the Total Integrated Archive of Short-Read and Array (TIARA; ) database, which contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). At present, 36 individual genomes have been archived and may be displayed in the database. TIARA supports a user-friendly genome browser, which retrieves read-depths (RDs) and log2 ratios from NGS and CGH arrays, respectively. In addition, this database provides information on all genomic variants and the raw data, including short reads and feature-level CGH data, through anonymous file transfer protocol. More personal genomes will be archived as more individuals are analyzed by NGS or CGH array. TIARA provides a new approach to the accurate interpretation of personal genomes for genome research. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Primate and Rodent Specific Intron Gains and the Origin of Retrogenes with Splice Variants AU- Szcze?niak, Micha? W AU- Ciomborowska, Joanna AU- Nowak, Witold AU- Rogozin, Igor B AU- Maka?owska, Izabela PY- 2011 T2- Molecular biology and evolution J2- Mol Biol Evol UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002245/ VL- 28 IS- 1 SP- 33-37 DO- 10.1093/molbev/msq260 C2- 3002245 N2- Retroposition, a leading mechanism for gene duplication, is an important process shaping the evolution of genomes. Retrogenes are also involved in the gene structure evolution as a major player in the process of intron deletion. Here, we demonstrate the role of retrogenes in intron gain in mammals. We identified one case of intronization, the transformation of exonic sequences into an intron, in the primate specific retrogene RNF113B and two independent intronization events in the retrogene DCAF12L2, one in the common ancestor of primates and rodents and another one in the rodent lineage. Intron gain resulted from the origin of new splice variants, and both genes have two transcript forms, one with retained intron and one with the intron spliced out. Evolution of these genes, especially RNF113B, has been very dynamic and has been accompanied by several additional events including parental gene loss, secondary retroposition, and exaptation of transposable elements. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Structural insights and ab initio sequencing within the DING proteins family AU- Elias, Mikael AU- Liebschner, Dorothee AU- Gotthard, Guillaume AU- Chabriere, Eric PY- 2011 T2- Journal of Synchrotron Radiation J2- J Synchrotron Radiat UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004253/ VL- 18 IS- Pt 1 SP- 45-49 DO- 10.1107/S0909049510036009 C2- 3004253 N2- DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38?kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- dbDNV: a resource of duplicated gene nucleotide variants in human genome AU- Ho, Meng-Ru AU- Tsai, Kuo-Wang AU- Chen, Chun-Houh AU- Lin, Wen-Chang PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013738/ VL- 39 IS- Database issue SP- D920-D925 DO- 10.1093/nar/gkq1197 C2- 3013738 N2- Gene duplications are scattered widely throughout the human genome. A single-base difference located in nearly identical duplicated segments may be misjudged as a single nucleotide polymorphism (SNP) from individuals. This imperfection is undistinguishable in current genotyping methods. As the next-generation sequencing technologies become more popular for sequence-based association studies, numerous ambiguous SNPs are rapidly accumulated. Thus, analyzing duplication variations in the reference genome to assist in preventing false positive SNPs is imperative. We have identified 10% of human genes associated with duplicated gene loci (DGL). Through meticulous sequence alignments of DGL, we systematically designated 1236956 variations as duplicated gene nucleotide variants (DNVs). The DNV database (dbDNV) () has been established to promote more accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates. This is useful while 58% of exonic SNPs in DGL are DNV-coupled. Because of high accumulation of ambiguous SNPs, we suggest that annotating SNPs with DNVs possibilities should improve association studies of these variants with human diseases. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Database resources of the National Center for Biotechnology Information AU- Sayers, Eric W AU- Barrett, Tanya AU- Benson, Dennis A AU- Bolton, Evan AU- Bryant, Stephen H AU- Canese, Kathi AU- Chetvernin, Vyacheslav AU- Church, Deanna M AU- Dicuccio, Michael AU- Federhen, Scott AU- Feolo, Michael AU- Fingerman, Ian M AU- Geer, Lewis Y AU- Helmberg, Wolfgang AU- Kapustin, Yuri AU- Landsman, David AU- Lipman, David J AU- Lu, Zhiyong AU- Madden, Thomas L AU- Madej, Tom AU- Maglott, Donna R AU- Marchler-Bauer, Aron AU- Miller, Vadim AU- Mizrachi, Ilene AU- Ostell, James AU- Panchenko, Anna AU- Phan, Lon AU- Pruitt, Kim D AU- Schuler, Gregory D AU- Sequeira, Edwin AU- Sherry, Stephen T AU- Shumway, Martin AU- Sirotkin, Karl AU- Slotta, Douglas AU- Souvorov, Alexandre AU- Starchenko, Grigory AU- Tatusova, Tatiana A AU- Wagner, Lukas AU- Wang, Yanli AU- Wilbur, W John AU- Yaschenko, Eugene AU- Ye, Jian PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013733/ VL- 39 IS- Database issue SP- D38-D51 DO- 10.1093/nar/gkq1172 C2- 3013733 N2- In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at . N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Isolation of Specific Clones from Nonarrayed BAC Libraries through Homologous Recombination AU- Nefedov, Mikhail AU- Carbone, Lucia AU- Field, Matthew AU- Schein, Jacquie AU- de Jong, Pieter J PY- 2011 T2- Journal of Biomedicine and Biotechnology J2- J Biomed Biotechnol UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957146/ VL- 2011 DO- 10.1155/2011/560124 C2- 2957146 N2- We have developed a new approach to screen bacterial artificial chromosome (BAC) libraries by recombination selection. To test this method, we constructed an orangutan BAC library using an E. coli strain (DY380) with temperature inducible homologous recombination (HR) capability. We amplified one library segment, induced HR at 42C to make it recombination proficient, and prepared electrocompetent cells for transformation with a kanamycin cassette to target sequences in the orangutan genome through terminal recombineering homologies. Kanamycin-resistant colonies were tested for the presence of BACs containing the targeted genes by the use of a PCR-assay to confirm the presence of the kanamycin insertion. The results indicate that this is an effective approach for screening clones. The advantage of recombination screening is that it avoids the high costs associated with the preparation, screening, and archival storage of arrayed BAC libraries. In addition, the screening can be conceivably combined with genetic engineering to create knockout and reporter constructs for functional studies. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- DBASS3 and DBASS5: databases of aberrant 3- and 5-splice sites AU- Buratti, Emanuele AU- Chivers, Martin AU- Hwang, Gyulin AU- Vorechovsky, Igor PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013770/ VL- 39 IS- Database issue SP- D86-D91 DO- 10.1093/nar/gkq887 C2- 3013770 N2- DBASS3 and DBASS5 provide comprehensive repositories of new exon boundaries that were induced by pathogenic mutations in human disease genes. Aberrant 5- and 3-splice sites were activated either by mutations in the consensus sequences of natural exonintron junctions (cryptic sites) or elsewhere (de novo sites). DBASS3 and DBASS5 currently contain approximately 900 records of cryptic and de novo 3- and 5-splice sites that were produced by over a thousand different mutations in approximately 360 genes. DBASS3 and DBASS5 data can be searched by disease phenotype, gene, mutation, location of aberrant splice sites in introns and exons and their distance from authentic counterparts, by bibliographic references and by the splice-site strength estimated with several prediction algorithms. The user can also retrieve reference sequences of both aberrant and authentic splice sites with the underlying mutation. These data will facilitate identification of introns or exons frequently involved in aberrant splicing, mutation analysis of human disease genes and study of germline or somatic mutations that impair RNA processing. Finally, this resource will be useful for fine-tuning splice-site prediction algorithms, better definition of auxiliary splicing signals and design of new reporter assays. DBASS3 and DBASS5 are freely available at . N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Identification of causal sequence variants of disease in the next generation sequencing era. AU- Kingsley, Christopher B PY- 2011 T2- Methods in molecular biology (Clifton, N.J.) J2- Methods Mol Biol UR- http://www.ncbi.nlm.nih.gov/pubmed/21204025 VL- 700 SP- 37-46 N2- Over the last decade, genetic studies have identified numerous associations between single nucleotide polymorphism (SNP) alleles in the human genome and important human diseases. Unfortunately, extending these initial associative findings to identification of the true causal variants that underlie disease susceptibility is usually not a straightforward task. Causal variant identification typically involves searching through sizable regions of genomic DNA in the vicinity of disease-associated SNPs for sequence variants in functional elements including protein coding, regulatory, and structural sequences. Prioritization of these searches is greatly aided by knowledge of the location of functional sequences in the human genome. This chapter briefly reviews several of the common approaches used to functionally annotate the human genome and discusses how this information can be used in concert with the emerging technology of next generation high-throughput sequencing to identify causal variants of human disease. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Cell-Based Co-transfection Microarrays for Use with HEK293T Cells on a Poly D: -Lysine-Coated Polystyrene Microplate. AU- Soni, Meenal AU- Lai, Fang PY- 2011 T2- Methods in molecular biology (Clifton, N.J.) J2- Methods Mol Biol UR- http://www.ncbi.nlm.nih.gov/pubmed/21104051 VL- 706 SP- 13-25 N2- Analysis of the human genome sequence has identified thousands of putative genes with unknown function; therefore, a new tool allowing for rapid identification of gene functions is needed. Reverse transfection microarray technology, which turns a DNA microarray into a cell-based microarray, has emerged for simultaneously studying the function of many genes. Since the initial demonstration in 2001, many variations have surfaced, making the technology more versatile for a broad range of applications. We have developed a protocol to make ready-to-transfect DNA microarrays in a 96-well microplate for co-transfection of two plasmids into HEK293T cells. This cell-based microarray in a microplate may be used for screening hundreds of analytes against multiple protein targets in parallel, providing a powerful tool for functional genomics and drug discovery. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Bovine Genome Database: integrated tools for genome annotation and discovery AU- Childers, Christopher P AU- Reese, Justin T AU- Sundaram, Jaideep P AU- Vile, Donald C AU- Dickens, C Michael AU- Childs, Kevin L AU- Salih, Hanni AU- Bennett, Anna K AU- Hagen, Darren E AU- Adelson, David L AU- Elsik, Christine G PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013744/ VL- 39 IS- Database issue SP- D830-D834 DO- 10.1093/nar/gkq1235 C2- 3013744 N2- The Bovine Genome Database (BGD; ) strives to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome browsers, available for both scaffold and chromosome coordinate systems, display the bovine Official Gene Set (OGS), RefSeq and Ensembl gene models, non-coding RNA, repeats, pseudogenes, single-nucleotide polymorphism, markers, QTL and alignments to complementary DNAs, ESTs and protein homologs. The Bovine QTL viewer is connected to the BGD Chromosome GBrowse, allowing for the identification of candidate genes underlying QTL. The Apollo Annotation Editor connects directly to the BGD Chado database to provide researchers with remote access to gene evidence in a graphical interface that allows editing and creating new gene models. Researchers may upload their annotations to the BGD server for review and integration into the subsequent release of the OGS. Gene pages display information for individual OGS gene models, including gene structure, transcript variants, functional descriptions, gene symbols, Gene Ontology terms, annotator comments and links to National Center for Biotechnology Information and Ensembl. Each gene page is linked to a wiki page to allow input from the research community. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Characterization of New Otic Enhancers of the Pou3f4 Gene Reveal Distinct Signaling Pathway Regulation and Spatio-Temporal Patterns AU- Robert-Moreno, lex AU- Naranjo, Silvia AU- de la Calle-Mustienes, Elisa AU- Gmez-Skarmeta, Jos Luis AU- Alsina, Berta PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013142/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0015907 C2- 3013142 N2- POU3F4 is a member of the POU-homedomain transcription factor family with a prominent role in inner ear development. Mutations in the human POU3F4 coding unit leads to X-linked deafness type 3 (DFN3), characterized by conductive hearing loss and progressive sensorineural deafness. Microdeletions found 1 Mb 5 upstream of the coding region also displayed the same phenotype, suggesting that cis-regulatory elements might be present in that region. Indeed, we and others have recently identified several enhancers at the 1 Mb 5 upstream interval of the pou3f4 locus. Here we characterize the spatio-temporal patterns of these regulatory elements in zebrafish transgenic lines. We show that the most distal enhancer (HCNR 81675) is activated earlier and drives GFP reporter expression initially to a broad ear domain to progressively restrict to the sensory patches. The proximal enhancer (HCNR 82478) is switched later during development and promotes expression, among in other tissues, in sensory patches from its onset. The third enhancer (HCNR 81728) is also active at later stages in the otic mesenchyme and in the otic epithelium. We also characterize the signaling pathways regulating these enhancers. While HCNR 81675 is regulated by very early signals of retinoic acid, HCNR 82478 is regulated by Fgf activity at a later stage and the HCNR 81728 enhancer is under the control of Hh signaling. Finally, we show that Sox2 and Pax2 transcription factors are bound to HCNR 81675 genomic region during otic development and specific mutations to these transcription factor binding sites abrogates HCNR 81675 enhancer activity. Altogether, our results suggest that pou3f4 expression in inner ear might be under the control of distinct regulatory elements that fine-tune the spatio-temporal activity of this gene and provides novel data on the signaling mechanisms controlling pou3f4 function. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Activation of Pluripotency Genes in Human Fibroblast Cells by a Novel mRNA Based Approach AU- Plews, Jordan R. AU- Li, JianLiang AU- Jones, Mark AU- Moore, Harry D. AU- Mason, Chris AU- Andrews, Peter W. AU- Na, Jie PY- 2010 T2 - PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012685/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0014397 C2- 3012685 N2- Background: Several methods have been used to induce somatic cells to re-enter the pluripotent state. Viral transduction of reprogramming genes yields higher efficiency but involves random insertions of viral sequences into the human genome. Although induced pluripotent stem (iPS) cells can be obtained with the removable PiggyBac transposon system or an episomal system, both approaches still use DNA constructs so that resulting cell lines need to be thoroughly analyzed to confirm they are free of harmful genetic modification. Thus a method to change cell fate without using DNA will be very useful in regenerative medicine. Methodology/Principal Findings: In this study, we synthesized mRNAs encoding OCT4, SOX2, cMYC, KLF4 and SV40 large T (LT) and electroporated them into human fibroblast cells. Upon transfection, fibroblasts expressed these factors at levels comparable to, or higher than those in human embryonic stem (ES) cells. Ectopically expressed OCT4 localized to the cell nucleus within 4 hours after mRNA introduction. Transfecting fibroblasts with a mixture of mRNAs encoding all five factors significantly increased the expression of endogenous OCT4, NANOG, DNMT3, REX1 and SALL4. When such transfected fibroblasts were also exposed to several small molecules (valproic acid, BIX01294 and 5-aza-2-deoxycytidine) and cultured in human embryonic stem cell (ES) medium they formed small aggregates positive for alkaline phosphatase activity and OCT4 protein within 30 days. Conclusion/Significance: Our results demonstrate that mRNA transfection can be a useful approach to precisely control the protein expression level and short-term expression of reprogramming factors is sufficient to activate pluripotency genes in differentiated cells. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence. AU- Trost, Eva AU- Ott, Lisa AU- Schneider, Jessica AU- Schroder, Jasmin AU- Jaenicke, Sebastian AU- Goesmann, Alexander AU- Husemann, Peter AU- Stoye, Jens AU- Alves Dorella, Fernanda AU- Souza Rocha, Flavia AU- de Castro Soares, Siomar AU- D'Afonseca, Vivian AU- Miyoshi, Anderson AU- Ruiz, Jeronimo AU- Silva, Artur AU- Azevedo, Vasco AU- Burkovski, Andreas AU- Guiso, Nicole AU- Join-Lambert, Olivier F AU- Kayal, Samer AU- Tauch, Andreas PY- 2010 T2- BMC genomics J2- BMC Genomics UR- http://www.ncbi.nlm.nih.gov/pubmed/21192786 VL- 11 IS- 1 SP- 728 N2- ABSTRACT: BACKGROUND: Corynebacterium pseudotuberculosis is generally regarded as an important animal pathogen that rarely infects humans. Clinical strains are occasionally recovered from human cases of lymphadenitis, such as C. pseudotuberculosis FRC41 that was isolated from the inguinal lymph node of a 12-year-old girl with necrotizing lymphadenitis. To detect potential virulence factors and corresponding gene-regulatory networks in this human isolate, the genome sequence of C. pseudotuberculosis FCR41 was determined by pyrosequencing and functionally annotated. RESULTS: Sequencing and assembly of the C. pseudotuberculosis FRC41 genome yielded a circular chromosome with a size of 2,337,913 bp and a mean G+C content of 52.2%. Specific gene sets associated with iron and zinc homeostasis were detected among the 2,110 predicted protein-coding regions and integrated into a gene-regulatory network that is linked with both the central metabolism and the oxidative stress response of FRC41. Two gene clusters encode proteins involved in the sortase-mediated polymerization of adhesive pili that can probably mediate the adherence to host tissue to facilitate additional ligand-receptor interactions and the delivery of virulence factors. The prominent virulence factors phospholipase D (Pld) and corynebacterial protease CP40 are encoded in the genome of this human isolate. The genome annotation revealed additional serine proteases, neuraminidase H, nitric oxide reductase, an invasion-associated protein, and acyl-CoA carboxylase subunits involved in mycolic acid biosynthesis as potential virulence factors. The cAMP-sensing transcription regulator GlxR plays a key role in controlling the expression of several genes contributing to virulence. CONCLUSION: The functional data deduced from the genome sequencing and the extended knowledge of virulence factors indicate that the human isolate C. pseudotuberculosis FRC41 is equipped with a distinct gene set promoting its survival under unfavorable environmental conditions encountered in the mammalian host. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Analysis of MicroRNA Expression in the Prepubertal Testis AU- Buchold, Gregory M AU- Coarfa, Cristian AU- Kim, Jong AU- Milosavljevic, Aleksandar AU- Gunaratne, Preethi H AU- Matzuk, Martin M PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012074/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0015317 C2- 3012074 N2- Only thirteen microRNAs are conserved between D. melanogaster and the mouse; however, conditional loss of miRNA function through mutation of Dicer causes defects in proliferation of premeiotic germ cells in both species. This highlights the potentially important, but uncharacterized, role of miRNAs during early spermatogenesis. The goal of this study was to characterize on postnatal day 7, 10, and 14 the content and editing of murine testicular miRNAs, which predominantly arise from spermatogonia and spermatocytes, in contrast to prior descriptions of miRNAs in the adult mouse testis which largely reflects the content of spermatids. Previous studies have shown miRNAs to be abundant in the mouse testis by postnatal day 14; however, through Next Generation Sequencing of testes from a B6;129 background we found abundant earlier expression of miRNAs and describe shifts in the miRNA signature during this period. We detected robust expression of miRNAs encoded on the X chromosome in postnatal day 14 testes, consistent with prior studies showing their resistance to meiotic sex chromosome inactivation. Unexpectedly, we also found a similar positional enrichment for most miRNAs on chromosome 2 at postnatal day 14 and for those on chromosome 12 at postnatal day 7. We quantified in vivo developmental changes in three types of miRNA variation including 5 heterogeneity, editing, and 3 nucleotide addition. We identified eleven putative novel pubertal testis miRNAs whose developmental expression suggests a possible role in early male germ cell development. These studies provide a foundation for interpretation of miRNA changes associated with testicular pathology and identification of novel components of the miRNA editing machinery in the testis. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Primate-specific evolution of noncoding element insertion into PLA2G4C and human preterm birth AU- Plunkett, Jevon AU- Doniger, Scott AU- Morgan, Thomas AU- Haataja, Ritva AU- Hallman, Mikko AU- Puttonen, Hilkka AU- Menon, Ramkumar AU- Kuczynski, Edward AU- Norwitz, Errol AU- Snegovskikh, Victoria AU- Palotie, Aarno AU- Peltonen, Leena AU- Fellman, Vineta AU- Defranco, Emily A AU- Chaudhari, Bimal P AU- Oates, John AU- Boutaud, Olivier AU- McGregor, Tracy L AU- McElroy, Jude J AU- Teramo, Kari AU- Borecki, Ingrid AU- Fay, Justin C AU- Muglia, Louis J PY- 2010 T2- BMC Medical Genomics J2- BMC Medical Genomics UR- http://www.biomedcentral.com/1755-8794/3/62 VL- 3 IS- 1 SP- 62 DO- 10.1186/1755-8794-3-62 N2- Abstract Background: The onset of birth in humans, like other apes, differs from non-primate mammals in its endocrine physiology. We hypothesize that higher primate-specific gene evolution may lead to these differences and target genes involved in human preterm birth, an area of global health significance. Methods: We performed a comparative genomics screen of highly conserved noncoding elements and identified PLA2G4C, a phospholipase A isoform involved in prostaglandin biosynthesis as human accelerated. To examine whether this gene demonstrating primate-specific evolution was associated with birth timing, we genotyped and analyzed 8 common single nucleotide polymorphisms (SNPs) in PLA2G4C in US Hispanic (n = 73 preterm, 292 control), US White (n = 147 preterm, 157 control) and US Black (n = 79 preterm, 166 control) mothers. Results: Detailed structural and phylogenic analysis of PLA2G4C suggested a short genomic element within the gene duplicated from a paralogous highly conserved element on chromosome 1 specifically in primates. SNPs rs8110925 and rs2307276 in US Hispanics and rs11564620 in US Whites were significant after correcting for multiple tests (p 0.006). Additionally, rs11564620 (Thr360Pro) was associated with increased metabolite levels of the prostaglandin thromboxane in healthy individuals (p = 0.02), suggesting this variant may affect PLA2G4C activity. Conclusions: Our findings suggest that variation in PLA2G4C may influence preterm birth risk by increasing levels of prostaglandins, which are known to regulate labor. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Complete genome sequence of the zoonotic pathogen Chlamydophila psittaci. AU- Seth-Smith, Helena M B AU- Harris, Simon R AU- Rance, Richard AU- West, Anthony P AU- Severin, Juliette A AU- Ossewaarde, Jacobus M AU- Cutcliffe, Lesley T AU- Skilton, Rachel J AU- Marsh, Pete AU- Parkhill, Julian AU- Clarke, Ian N AU- Thomson, Nicholas R PY- 2010 T2- Journal of bacteriology J2- J Bacteriol UR- http://www.ncbi.nlm.nih.gov/pubmed/21183672 N2- We present the first genome sequence of Chlamydophila psittaci, an intracellular pathogen of birds, and a human zoonotic pathogen. A comparison with previously sequenced Chlamydophila genomes shows that, like other chlamydiae, most of the genome diversity is restricted to the plasticity zone. The Cp. psittaci plasmid was also sequenced. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Cancer and Neurodegeneration: Between the Devil and the Deep Blue Sea AU- Plun-Favreau, Hlne AU- Lewis, Patrick A AU- Hardy, John AU- Martins, L Miguel AU- Wood, Nicholas W PY- 2010 T2- PLoS Genetics J2- PLoS Genet UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009676/ VL- 6 IS- 12 DO- 10.1371/journal.pgen.1001257 C2- 3009676 N2- Cancer and neurodegeneration are often thought of as disease mechanisms at opposite ends of a spectrum; one due to enhanced resistance to cell death and the other due to premature cell death. There is now accumulating evidence to link these two disparate processes. An increasing number of genetic studies add weight to epidemiological evidence suggesting that sufferers of a neurodegenerative disorder have a reduced incidence for most cancers, but an increased risk for other cancers. Many of the genes associated with either cancer and/or neurodegeneration play a central role in cell cycle control, DNA repair, and kinase signalling. However, the links between these two families of diseases remain to be proven. In this review, we discuss recent and sometimes as yet incomplete genetic discoveries that highlight the overlap of molecular pathways implicated in cancer and neurodegeneration. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- A Novel HMM-Based Method for Detecting Enriched Transcription Factor Binding Sites Reveals RUNX3 as a Potential Target in Pancreatic Cancer Biology AU- Levkovitz, Liron AU- Yosef, Nir AU- Gershengorn, Marvin C AU- Ruppin, Eytan AU- Sharan, Roded AU- Oron, Yoram PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008686/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0014423 C2- 3008686 N2- Background: Pancreatic adenocarcinoma (PAC) is one of the most intractable malignancies. In order to search for potential new therapeutic targets, we relied on computational methods aimed at identifying transcription factor binding sites (TFBSs) over-represented in the promoter regions of genes differentially expressed in PAC. Though many computational methods have been implemented to accomplish this, none has gained overall acceptance or produced proven novel targets in PAC. To this end we have developed DEMON, a novel method for motif detection. Methodology: DEMON relies on a hidden Markov model to score the appearance of sequence motifs, taking into account all potential sites in a promoter of potentially varying binding affinities. We demonstrate DEMON's accuracy on simulated and real data sets. Applying DEMON to PAC-related data sets identifies the RUNX family as highly enriched in PAC-related genes. Using a novel experimental paradigm to distinguish between normal and PAC cells, we find that RUNX3 mRNA (but not RUNX1 or RUNX2 mRNAs) exhibits time-dependent increases in normal but not in PAC cells. These increases are accompanied by changes in mRNA levels of putative RUNX gene targets. Conclusions: The integrated application of DEMON and a novel differentiation system led to the identification of a single family member, RUNX3, which together with four of its putative targets showed a robust response to a differentiation stimulus in healthy cells, whereas this regulatory mechanism was absent in PAC cells, emphasizing RUNX3 as a promising target for further studies. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Nicotinic Receptor Gene CHRNA4 Interacts with Processing Load in Attention AU- Espeseth, Thomas AU- Sneve, Markus Handal AU- Rootwelt, Helge AU- Laeng, Bruno PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008676/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0014407 C2- 3008676 N2- Background: Pharmacological studies suggest that cholinergic neurotransmission mediates increases in attentional effort in response to high processing load during attention demanding tasks . Methodology/Principal Findings: In the present study we tested whether individual variation in CHRNA4, a gene coding for a subcomponent in 42 nicotinic receptors in the human brain, interacted with processing load in multiple-object tracking (MOT) and visual search (VS). We hypothesized that the impact of genotype would increase with greater processing load in the MOT task. Similarly, we predicted that genotype would influence performance under high but not low load in the VS task. Two hundred and two healthy persons (age range?=?39 77, Mean ?=?57.5, SD?=?9.4) performed the MOT task in which twelve identical circular objects moved about the display in an independent and unpredictable manner. Two to six objects were designated as targets and the remaining objects were distracters. The same observers also performed a visual search for a target letter (i.e. X or Z) presented together with five non-targets while ignoring centrally presented distracters (i.e. X, Z, or L). Targets differed from non-targets by a unique feature in the low load condition, whereas they shared features in the high load condition. CHRNA4 genotype interacted with processing load in both tasks. Homozygotes for the T allele (N?=?62) had better tracking capacity in the MOT task and identified targets faster in the high load trials of the VS task. Conclusion: The results support the hypothesis that the cholinergic system modulates attentional effort, and that common genetic variation can be used to study the molecular biology of cognition. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Somatic Mutation Profiles of MSI and MSS Colorectal Cancer Identified by Whole Exome Next Generation Sequencing and Bioinformatics Analysis AU- Timmermann, Bernd AU- Kerick, Martin AU- Roehr, Christina AU- Fischer, Axel AU- Isau, Melanie AU- Boerno, Stefan T AU- Wunderlich, Andrea AU- Barmeyer, Christian AU- Seemann, Petra AU- Koenig, Jana AU- Lappe, Michael AU- Kuss, Andreas W AU- Garshasbi, Masoud AU- Bertram, Lars AU- Trappe, Kathrin AU- Werber, Martin AU- Herrmann, Bernhard G AU- Zatloukal, Kurt AU- Lehrach, Hans AU- Schweiger, Michal R PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008745/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0015661 C2- 3008745 N2- Background: Colorectal cancer (CRC) is with approximately 1 million cases the third most common cancer worldwide. Extensive research is ongoing to decipher the underlying genetic patterns with the hope to improve early cancer diagnosis and treatment. In this direction, the recent progress in next generation sequencing technologies has revolutionized the field of cancer genomics. However, one caveat of these studies remains the large amount of genetic variations identified and their interpretation. Methodology/Principal Findings: Here we present the first work on whole exome NGS of primary colon cancers. We performed 454 whole exome pyrosequencing of tumor as well as adjacent not affected normal colonic tissue from microsatellite stable (MSS) and microsatellite instable (MSI) colon cancer patients and identified more than 50,000 small nucleotide variations for each tissue. According to predictions based on MSS and MSI pathomechanisms we identified eight times more somatic non-synonymous variations in MSI cancers than in MSS and we were able to reproduce the result in four additional CRCs. Our bioinformatics filtering approach narrowed down the rate of most significant mutations to 359 for MSI and 45 for MSS CRCs with predicted altered protein functions. In both CRCs, MSI and MSS, we found somatic mutations in the intracellular kinase domain of bone morphogenetic protein receptor 1A, BMPR1A, a gene where so far germline mutations are associated with juvenile polyposis syndrome, and show that the mutations functionally impair the protein function. Conclusions/Significance: We conclude that with deep sequencing of tumor exomes one may be able to predict the microsatellite status of CRC and in addition identify potentially clinically relevant mutations. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- High-Definition Mapping of Retroviral Integration Sites Defines the Fate of Allogeneic T Cells After Donor Lymphocyte Infusion AU- Cattoglio, Claudia AU- Maruggi, Giulietta AU- Bartholomae, Cynthia AU- Malani, Nirav AU- Pellin, Danilo AU- Cocchiarella, Fabienne AU- Magnani, Zulma AU- Ciceri, Fabio AU- Ambrosi, Alessandro AU- von Kalle, Christof AU- Bushman, Frederic D AU- Bonini, Chiara AU- Schmidt, Manfred AU- Mavilio, Fulvio AU- Recchia, Alessandra PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008730/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0015688 C2- 3008730 N2- The infusion of donor lymphocytes transduced with a retroviral vector expressing the HSV-TK suicide gene in patients undergoing hematopoietic stem cell transplantation for leukemia/lymphoma promotes immune reconstitution and prevents infections and graft-versus-host disease. Analysis of the clonal dynamics of genetically modified lymphocytes in vivo is of crucial importance to understand the potential genotoxic risk of this therapeutic approach. We used linear amplification-mediated PCR and pyrosequencing to build a genome-wide, high-definition map of retroviral integration sites in the genome of peripheral blood T cells from two different donors and used gene expression profiling and bioinformatics to associate integration clusters to transcriptional activity and to genetic and epigenetic features of the T cell genome. Comparison with matched random controls and with integrations obtained from CD34+ hematopoietic stem/progenitor cells showed that integration clusters occur within chromatin regions bearing epigenetic marks associated with active promoters and regulatory elements in a cell-specific fashion. Analysis of integration sites in T cells obtained ex vivo two months after infusion showed no evidence of integration-related clonal expansion or dominance, but rather loss of cells harboring integration events interfering with RNA post-transcriptional processing. The study shows that high-definition maps of retroviral integration sites are a powerful tool to analyze the fate of genetically modified T cells in patients and the biological consequences of retroviral transduction. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- In silico prediction of drug targets in Vibrio cholerae. AU- Katara, Pramod AU- Grover, Atul AU- Kuntal, Himani AU- Sharma, Vinay PY- 2010 T2- Protoplasma J2- Protoplasma UR- http://www.ncbi.nlm.nih.gov/pubmed/21174131 N2- Identification of potential drug targets is the first step in the process of modern drug discovery, subjected to their validation and drug development. Whole genome sequences of a number of organisms allow prediction of potential drug targets using sequence comparison approaches. Here, we present a subtractive approach exploiting the knowledge of global gene expression along with sequence comparisons to predict the potential drug targets more efficiently. Based on the knowledge of 155 known virulence and their coexpressed genes mined from microarray database in the public domain, 357 coexpressed probable virulence genes for Vibrio cholerae were predicted. Based on screening of Database of Essential Genes using blastn, a total of 102 genes out of these 357 were enlisted as vitally essential genes, and hence good putative drug targets. As the effective drug target is a protein which is only present in the pathogen, similarity search of these 102 essential genes against human genome sequence led to subtraction of 66 genes, thus leaving behind a subset of 36 genes whose products have been called as potential drug targets. The gene ontology analysis using Blast2GO of these 36 genes revealed their roles in important metabolic pathways of V. cholerae or on the surface of the pathogen. Thus, we propose that the products of these genes be evaluated as target sites of drugs against V. cholerae in future investigations. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Gene processing control loops suggested by sequencing, splicing, and RNA folding AU- Jeffries, Clark D AU- Perkins, Diana O AU- Guan, Xiaojun PY- 2010 T2- BMC bioinformatics J2- BMC Bioinformatics UR- http://www.biomedcentral.com/1471-2105/11/602 VL- 11 IS- 1 SP- 602 DO- 10.1186/1471-2105-11-602 N2- Abstract Background: Small RNAs are known to regulate diverse gene expression processes including translation, transcription, and splicing. Among small RNAs, the microRNAs (miRNAs) of 17 to 27 nucleotides (nts) undergo biogeneses including primary transcription, RNA excision and folding, nuclear export, cytoplasmic processing, and then bioactivity as regulatory agents. We propose that analogous hairpins from RNA molecules that function as part of the spliceosome might also be the source of small, regulatory RNAs (somewhat smaller than miRNAs). Results: Deep sequencing technology has enabled discovery of a novel 16-nt RNA sequence in total RNA from human brain that we propose is derived from RNU1, an RNA component of spliceosome assembly. Bioinformatic alignments compel inquiring whether the novel 16-nt sequence or its precursor have a regulatory function as well as determining aspects of how processing intersects with the miRNA biogenesis pathway. Specifically, our preliminary in silico investigations reveal the sequence could regulate splicing factor Arg/Ser rich 1 (SFRS1), a gene coding an essential protein component of the spliceosome. All 16-base source sequences in the UCSC Human Genome Browser are within the 14 instances of RNU1 genes listed in wgEncodeGencodeAutoV3. Furthermore, 10 of the 14 instances of the sequence are also within a common 28-nt hairpin-forming subsequence of RNU1. Conclusions: An abundant 16-nt RNA sequence is sourced from a spliceosomal RNA, lies in a stem of a predicted RNA hairpin, and includes reverse complements of subsequences of the 3'UTR of a gene coding for a spliceosome protein. Thus RNU1 could function both as a component of spliceosome assembly and as inhibitor of production of the essential, spliceosome protein coded by SFRS1. Beyond this example, a general procedure is needed for systematic discovery of multiple alignments of sequencing, splicing, and RNA folding data. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Aromatase Is a Direct Target of FOXL2: C134W in Granulosa Cell Tumors via a Single Highly Conserved Binding Site in the Ovarian Specific Promoter AU- Fleming, Nicholas I AU- Knower, Kevin C AU- Lazarus, Kyren A AU- Fuller, Peter J AU- Simpson, Evan R AU- Clyne, Colin D PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004790/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0014389 C2- 3004790 N2- Background: Granulosa cell tumors (GCT) of the ovary often express aromatase and synthesize estrogen, which in turn may influence their progression. Recently a specific point mutation (C134W) in the FOXL2 protein was identified in 94% of adult-type GCT and it is likely to contribute to their development. A number of genes are known to be regulated by FOXL2, including aromatase/CYP19A1, but it is unclear which are direct targets and whether the C134W mutation alters their regulation. Recently, it has been reported that FOXL2 forms a complex with steroidogenic factor 1 (SF-1) which is a known regulator of aromatase in granulosa cells. Methodology/Principal Findings: In this work, the human GCT-derived cell lines KGN and COV434 were heterozygous and wildtype for the FOXL2:C134W mutation, respectively. KGN had abundant FOXL2 mRNA expression but it was not expressed in COV434. Expression of exogenous FOXL2:C134W in COV434 cells induced higher expression of a luciferase reporter for the ovarian specific aromatase promoter, promoter II (PII) (516bp) than expression of wildtype FOXL2, but did not alter induction of a similar reporter for the steroidogenic acute regulatory protein (StAR) promoter (1300bp). Co-immunoprecipitation confirmed that FOXL2 bound SF-1 and that it also bound its homologue, liver receptor homologue 1 (LRH-1), however, the C134W mutation did not alter these interactions or induce a selective binding of the proteins. A highly conserved putative binding site for FOXL2 was identified in PII. FOXL2 was demonstrated to bind the site by electrophoretic mobility shift assays (EMSA) and site-directed mutagenesis of this element blocked its differential induction by wildtype FOXL2 and FOXL2:C134W. Conclusions/Significance: These findings suggest that aromatase is a direct target of FOXL2:C134W in adult-type GCT via a single distinctive and highly conserved binding site in PII and therefore provide insight into the pathogenic mechanism of this mutation. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Evidences showing wide presence of small genomic aberrations in chronic lymphocytic leukemia AU- Kim, Yeong C AU- Jung, Yong-Chul AU- Chen, Jun AU- Alhasan, Ali H AU- Kaewsaard, Parawee AU- Zhang, Yanming AU- Ma, Shuo AU- Rosen, Steve AU- Wang, San Ming PY- 2010 T2- BMC research notes J2- BMC Res Notes UR- http://www.biomedcentral.com/1756-0500/3/341 VL- 3 IS- 1 SP- 341 DO- 10.1186/1756-0500-3-341 C2- 3016268 N2- Abstract Background: Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in the western population. Although genetic factors are considered to contribute to CLL etiology, at present genomic aberrations identified in CLL are limited compared with those identified in other types of leukemia, which raises the question of the degree of genetic influence on CLL. We performed a high-resolution genome scanning study to address this issue. Findings: Using the restriction paired-end-based Ditag Genome Scanning technique, we analyzed three primary CLL samples at a kilobase resolution, and further validated the results in eight primary CLL samples including the two used for ditag collection. From 51,632 paired-end tags commonly detected in the three CLL samples representing 5% of the HindIII restriction fragments in the genomes, we identified 230 paired-end tags that were present in all three CLL genomes but not in multiple normal human genome reference sequences. Mapping the full-length sequences of the fragments detected by these unmapped tags in seven additional CLL samples confirmed that these are the genomic aberrations caused by small insertions and deletions, and base changes spreading across coding and non-coding regions. Conclusions: Our study identified hundreds of loci with insertion, deletion, base change, and restriction site polymorphism present in both coding and non-coding regions in CLL genomes, indicating the wide presence of small genomic aberrations in chronic lymphocytic leukemia. Our study supports the use of a whole genome sequencing approach for comprehensively decoding the CLL genome for better understanding of the genetic defects in CLL. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- A Rare Myelin Protein Zero (MPZ) Variant Alters Enhancer Activity In Vitro and In Vivo AU- Antonellis, Anthony AU- Dennis, Megan Y AU- Burzynski, Grzegorz AU- Huynh, Jimmy AU- Maduro, Valerie AU- Hodonsky, Chani J AU- Khajavi, Mehrdad AU- Szigeti, Kinga AU- Mukkamala, Sandeep AU- Bessling, Seneca L AU- NISC Comparative Sequencing Program AU- Pavan, William J AU- McCallion, Andrew S AU- Lupski, James R AU- Green, Eric D PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002941/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0014346 C2- 3002941 N2- Background: Myelin protein zero (MPZ) is a critical structural component of myelin in the peripheral nervous system. The MPZ gene is regulated, in part, by the transcription factors SOX10 and EGR2. Mutations in MPZ, SOX10, and EGR2 have been implicated in demyelinating peripheral neuropathies, suggesting that components of this transcriptional network are candidates for harboring disease-causing mutations (or otherwise functional variants) that affect MPZ expression. Methodology: We utilized a combination of multi-species sequence comparisons, transcription factor-binding site predictions, targeted human DNA re-sequencing, and in vitro and in vivo enhancer assays to study human non-coding MPZ variants. Principal Findings: Our efforts revealed a variant within the first intron of MPZ that resides within a previously described SOX10 binding site is associated with decreased enhancer activity, and alters binding of nuclear proteins. Additionally, the genomic segment harboring this variant directs tissue-relevant reporter gene expression in zebrafish. Conclusions: This is the first reported MPZ variant within a cis-acting transcriptional regulatory element. While we were unable to implicate this variant in disease onset, our data suggests that similar non-coding sequences should be screened for mutations in patients with neurological disease. Furthermore, our multi-faceted approach for examining the functional significance of non-coding variants can be readily generalized to study other loci important for myelin structure and function. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Recombinant expression, purification and copper-binding characteristics of the amino terminus of a Plasmodium falciparum copper transport protein AU- Choveaux, David AU- Goldring, JP Dean PY- 2010 T2- Malaria journal J2- Malar J UR- http://www.malariajournal.com/content/9/S2/-P62 VL- 9 IS- Suppl 2 SP- P62 DO- 10.1186/1475-2875-9-S2-P62 N2- N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Concurrent genetic alterations in DNA polymerase proofreading and mismatch repair in human colorectal cancer. AU- Yoshida, Rintaro AU- Miyashita, Kaname AU- Inoue, Mayuko AU- Shimamoto, Akiyoshi AU- Yan, Zhao AU- Egashira, Akinori AU- Oki, Eiji AU- Kakeji, Yoshishiro AU- Oda, Shinya AU- Maehara, Yoshihiko PY- 2010 T2- European journal of human genetics : EJHG J2- Eur J Hum Genet UR- http://www.ncbi.nlm.nih.gov/pubmed/21157497 N2- Genomic sequences encoding the 3' exonuclease (proofreading) domains of both replicative DNA polymerases, pol delta and pol epsilon, were explored simultaneously in human colorectal carcinomas including six established cell lines. Three unequivocal sequence alterations, including one previously reported, were found, and all these were considered as dysfunctional mutations in light of the local amino-acid sequences. In particular, the F367S mutation found in the POLE gene encoding the pol epsilon catalytic subunit, which includes the proofreading domain, is the first found in human diseases. Surprisingly, the tumours carrying these proofreading domain mutations were all defective in DNA mismatch repair (MMR). In addition to the two cell lines with acknowledged MMR gene mutations, the third tumour was also demonstrated to harbour a distinct mutation in MLH1, and indeed exhibited a microsatellite-unstable phenotype. These findings suggest that, in concert with MMR deficiency, defective polymerase proofreading may also contribute to the mutator phenotype observed in human colorectal cancer. Our observations may suggest previously unrecognised complexities in the molecular abnormalities underlying the mutator phenotype in human neoplasms.European Journal of Human Genetics advance online publication, 15 December 2010; doi:10.1038/ejhg.2010.216. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Evolution of MicroRNAs and the Diversification of Species. AU- Loh, Yong-Hwee E AU- Yi, Soojin V AU- Streelman, J Todd PY- 2010 T2- Genome Biology and Evolution J2- Genome Biol Evol UR- http://www.ncbi.nlm.nih.gov/pubmed/21169229 N2- MicroRNAs (miRNAs) are ancient, short, non-coding RNA molecules that regulate the transcriptome through post-transcriptional mechanisms. miRNA riboregulation is involved in a diverse range of biological processes and mis-regulation is implicated in disease. It is generally thought that miRNAs function to canalize cellular outputs, for instance as 'fail-safe' repressors of gene mis-expression. Genomic surveys in humans have revealed reduced genetic polymorphism and the signature of negative selection for both miRNAs themselves and the target sequences to which they are predicted to bind. We investigated the evolution of miRNAs and their binding sites across cichlid fishes from Lake Malawi (East Africa), where hundreds of diverse species have evolved in the last million years. Using low-coverage genome sequence data, we identified 100 cichlid miRNA genes with mature regions that are highly conserved in other animal species. We computationally predicted target sites on the 3'-UTRs of cichlid genes to which miRNAs may bind, and found that these sites possessed elevated single nucleotide polymorphism (SNP) densities. Furthermore, polymorphic sites in predicted miRNA targets showed higher minor allele frequencies on average and greater genetic differentiation between Malawi lineages when compared to a neutral expectation and non-target 3' UTR SNPs. Our data suggest that divergent selection on miRNA riboregulation may have contributed to the diversification of cichlid species, and may similarly play a role in rapid phenotypic evolution of other natural systems. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- A unique chromatin signature uncovers early developmental enhancers in humans. AU- Rada-Iglesias, Alvaro AU- Bajpai, Ruchi AU- Swigut, Tomek AU- Brugmann, Samantha A AU- Flynn, Ryan A AU- Wysocka, Joanna PY- 2010 T2- Nature J2- Nature UR- http://www.ncbi.nlm.nih.gov/pubmed/21160473 N2- Cell-fate transitions involve the integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of genomic sequences that control human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, monomethylation of histone H3 at lysine 4 (H3K4me1), and low nucleosomal density. In addition, elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized hESC enhancers, and are located proximally to genes expressed in hESCs and the epiblast. In contrast, elements of the second class, which we term 'poised enhancers', are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3), and are linked to genes inactive in hESCs and instead are involved in orchestrating early steps in embryogenesis, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of poised enhancers acquires a chromatin signature associated with active enhancers. When assayed in zebrafish embryos, poised enhancers are able to direct cell-type and stage-specific expression characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi AU- Subramanian, Sankar AU- Huynen, Leon AU- Millar, Craig D AU- Lambert, David M PY- 2010 T2- BMC evolutionary biology J2- BMC Evol Biol UR- http://www.biomedcentral.com/1471-2148/10/387 VL- 10 IS- 1 SP- 387 DO- 10.1186/1471-2148-10-387 C2- 3009673 N2- Abstract Background: Kiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli) and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. Results: Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. Conclusions: The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Transcriptional Activation of REST by Sp1 in Huntington's Disease Models AU- Ravache, Myriam AU- Weber, Chantal AU- Mrienne, Karine AU- Trottier, Yvon PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001865/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0014311 C2- 3001865 N2- In Huntington's disease (HD), mutant huntingtin (mHtt) disrupts the normal transcriptional program of disease neurons by altering the function of several gene expression regulators such as Sp1. REST (Repressor Element-1 Silencing Transcription Factor), a key regulator of neuronal differentiation, is also aberrantly activated in HD by a mechanism that remains unclear. Here, we show that the level of REST mRNA is increased in HD mice and in NG108 cells differentiated into neuronal-like cells and expressing a toxic mHtt fragment. Using luciferase reporter gene assay, we delimited the REST promoter regions essential for mHtt-mediated REST upregulation and found that they contain Sp factor binding sites. We provide evidence that Sp1 and Sp3 bind REST promoter and interplay to fine-tune REST transcription. In undifferentiated NG108 cells, Sp1 and Sp3 have antagonistic effect, Sp1 acting as an activator and Sp3 as a repressor. Upon neuronal differentiation, we show that the amount and ratio of Sp1/Sp3 proteins decline, as does REST expression, and that the transcriptional role of Sp3 shifts toward a weak activator. Therefore, our results provide new molecular information to the transcriptional regulation of REST during neuronal differentiation. Importantly, specific knockdown of Sp1 abolishes REST upregulation in NG108 neuronal-like cells expressing mHtt. Our data together with earlier reports suggest that mHtt triggers a pathogenic cascade involving Sp1 activation, which leads to REST upregulation and repression of neuronal genes. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Personalized medicine - The promised land are we there yet? AU- Li, Chumei PY- 2010 T2- Clinical genetics J2- Clin Genet UR- http://www.ncbi.nlm.nih.gov/pubmed/21204795 N2- The delivery of personalized genomic medicine (see box1 for a comparison of genomic vs. genetic medicine and box2 for glossary) hinges on obtaining personal genomic data through genome-wide association studies (GWAS) or whole genome sequencing. After the completion of the human genome project (see box 3 for human genome projects and its derivative projects) in 2003, there appeared to be a period of euphoric optimism that as soon as the cost of sequencing the whole human genome could be brought down to an affordable range, the promise of personalized medicine would become a reality. However, inasmuch as the miraculous technological advancements are making whole genome data acquisition an inexpensive reality, we are also starting to appreciate that making sense of the enormous amount of genomic data is a far bigger hurdle. Issues, both scientific and ethico-legal, will have to be addressed as genomic data are been pushed for clinical and direct-to-consumer utilization. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Mining human genome for novel purinergic P2Y receptors: a sequence analysis and molecular modeling approach. AU- Bhatnagar, Sonika AU- Mishra, Shubhi AU- Pathak, Ravi PY- 2010 T2- Journal of receptor and signal transduction research J2- J Recept Signal Transduct Res UR- http://www.ncbi.nlm.nih.gov/pubmed/21142848 N2- The purinergic P2Y receptors are G-protein coupled receptors (GPCRs) that control many physiological processes by mediating cellular responses to purines, pyrimidines and their analogues. They can be used as potential therapeutic targets in a variety of disease conditions. Therefore, it is critical to identify new members of this family of receptors from the human genome and characterize them for their role in health and disease. In the present work, molecular modeling was carried out for the 21 known P2Y receptors. Binding site analysis was done on the basis of docking and site-directed mutagenesis data. Thus, conserved features of P2Y receptors could be formulated. These features can be used to determine the purinergic nature of potential P2Y receptors in the human genome. We applied this knowledge to human genome GPCR sequences found by sensitive sequence search techniques and identified two orphan receptors, namely GPR34 and GP171 that have all the necessary conserved features of P2Y receptors. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER-
《自然》杂志预测2011年科研热点 http://news.sciencenet.cn//htmlnews/2011/1/242378.shtm 基因组测序大爆发 在2011年里，人类基因组测序所需花费无疑将有所下降。下一代基因测序仪器已开始投放市场，这将使得进行全测序的人类基因组数量节节攀升。 New year, new science http://www.nature.com/news/2010/101231/full/469012a.html Genome-sequencing explosion This year should surely see the price of human-genome sequencing dropping to US$1,000 per genome. As next-generation sequencing machines reach the market, the number of fully sequenced human genomes will skyrocket. http://www.gopubmed.org/web/gopubmed/1?WEB01lys5moqoa0ueIvI1I00h001000j100200010 5,874 documents semantically analyzed 1 2 Top Years Publications 2010 801 2009 563 2008 434 2007 412 2005 381 2006 373 2002 328 2004 323 2003 315 2001 315 2000 259 1998 206 1999 176 1997 173 1996 139 1995 120 1994 92 1991 87 1992 84 1993 74 1 2 1 2 3 4 5 Top Countries Publications USA 2,460 United Kingdom 456 Japan 373 Germany 361 China 282 France 234 Canada 172 Italy 106 Australia 103 Sweden 101 Netherlands 76 Spain 71 India 62 South Korea 56 Brazil 56 Denmark 54 Switzerland 46 Singapore 40 Taiwan 37 Israel 33 1 2 3 4 5 1 2 3 ... 36 Top Cities Publications Bethesda 220 Houston 143 Tokyo 112 Cambridge 111 London 100 St. Louis 100 Seattle 94 Baltimore 91 Boston 87 Paris 78 Beijing, China 77 Rockville 77 New York City 75 Los Angeles 73 San Francisco 65 San Diego 61 Shanghai, China 59 Cambridge, USA 57 Berlin, Germany 57 Heidelberg 55 1 2 3 ... 36 1 2 3 ... 67 Top Journals Publications Genome Res 241 Nucleic Acids Res 144 Genomics 136 J Virol 127 Nature 127 P Natl Acad Sci Usa 113 Science 102 Bmc Genomics 92 Gene 81 Plos One 80 Virology 78 Hum Mol Genet 74 J Gen Virol 62 Genome Biol 60 Am J Hum Genet 59 Bioinformatics 57 J Biol Chem 57 Nat Genet 54 Hum Mutat 53 J Clin Microbiol 51 1 2 3 ... 67 1 2 3 ... 893 Top Terms Publications Genome 5,081 Genomics 5,060 Humans 4,640 Genes 3,668 Genome, Human 2,634 DNA 2,573 Base Sequence 2,456 Animals 2,011 Proteins 1,636 Sequence Analysis, DNA 1,500 Polymerase Chain Reaction 1,292 Mutation 1,265 Chromosomes 1,209 Nucleotides 1,032 chromosome 886 Patients 863 Chromosome Mapping 843 Technology 836 Amino Acid Sequence 811 Viruses 785 1 2 3 ... 893 1 2 3 ... 1527 Top Authors Publications Gibbs R 43 Green E 38 Weinstock G 25 Hillier L 24 Eichler E 22 Venter J 22 Waterston R 21 Scherer S 21 Marra M 20 McPherson J 18 Lander E 18 Wilson R 16 Mardis E 16 Adams M 16 Lehrach H 16 NISC Comparative Sequencing Program 15 Metzker M 14 Ohara O 14 Rosenthal A 14 Hayashizaki Y 13 1 2 3 ... 1527
前天，Science在线发表了海洋浮游尾索动物Oikopleura dioica的基因组测序分析论文（重点是分析）。网络科技新闻杂志The Scientist立即就此文章的结果采访了相关领域的几位专家，并做了跟踪报道。我是看到此报道之后，怀着很好奇的心情看完了Science这篇论文。确实值得研究，值得发在Science上。 我们国家总喜欢研究有重大理论和应用价值的物种，这个仅生活4天就死掉的小虫虫有什么意义呢？ 它在海洋水表挺多，系统发育上是脊椎动物的近亲。这可能是此基因组测序的理由。 显然，生物学研究不能太功利，表面上看似有重大研究价值，那个重大价值不一定那么容易被你揭示。比如说大熊猫为什么濒危，测完序离回答问题差得很远，只能说是万里长征走了第一步。法国人带领的这个研究组，测序之前无论如何也不会想到他们的重要发现。甚至我估计，其中一些关键作者，如Scott W. Roy，很可能是在分析数据时临时征召的。这一点也提醒国内的基因组测序带头人，一开始团队不一定很整齐，有什么问题找什么人来做就行了。因为问题是无法预期的，所以预先组织好的团队就不可能是最适于研究你的问题的团队。 这个小虫虫测序到底说明了什么，看他们摘要中的一句话multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura , belonging to the sister group of vertebrates and retaining chordate morphology。什么意思呢？尽管这个小虫虫和脊椎动物一样保留了脊索动物的形态，但是众多基因组特征在在此物种中shattered。shattered的意思有粉碎；砸碎，破坏。说的直观一些就是，这个基因组测序的结果offers unique perspectives on the level of genome plasticity。 要看通俗介绍的网友可以参考The Scientist的报道，简单明了：Who needs structure, anyway? http://www.the-scientist.com/news/display/57814/ ， 研究相关问题的专业网友请参考Science原文 http://www.sciencemag.org/content/early/2010/11/17/science.1194167 ，或 http://www.doi.org/10.1126/science.1194167 （此链接暂时不能用）。
JGI-联合基因组研究中心，美国能源部的一个基因组研究中心，也许是世界上最大的非动物基因组测序研究中心了，预计今年其基因组数据量将到达4-5Tb，这样庞大的数据，他们感到已经难以承受数据的存储、分析所需计算设备的压力了，这促使JGI寻求更专业的计算设备维护和管理中心。 从这点来看，以后，测序中心将不会关注数据存储、分析所需要的计算能力，这样的计算能力可以使用别家的计算中心，比如云计算中心。那么测序中心很重要的一点就是如何快速的把测序获得的数据传输到云计算中心上以进行处理。可以预计，随着测序费用的下降，和基因组测序的广泛应用，测序服务中心和云计算中心的合作将会成为一种趋势！ JGI Consolidates High-Performance Computing Operations into NERCS April 20, 2010 By Alex Philippidis NEW YORK (GenomeWeb News) – The Joint Genome Institute says the torrent of sequencing data it has generated, and plans to generate this year, explains its decision to consolidate its high-performance scientific computing operations into the US Department of Energy's National Energy Research Scientific Computer Center (NERSC). JGI has agreed to transfer to NERSC six Lawrence Berkeley National Laboratory employees specializing in scientific computing, including computer and network security and instrumentation computer systems. JGI's desktop support services will remain under the control of the institute, which is located in Walnut Creek, Calif. The consolidation, announced April 12, follows JGI's expectation this year that it will multiply the quantity of data it expects to generate through its sequencing of plant, microbe, fungal, and metagenomes. That quantity surpassed 1 terabase, or 1 trillion bases, in 2009, an eight-fold increase over 2008 — with "maybe 4 to 5 trillion this year" expected to be sequenced, JGI spokesman David Gilbert told GenomeWeb Daily News. "In that alone, you can tell why we need that computational horsepower that we could handle on our own, but now it's getting to the point where it's just crazy. Why build something in house when we've got a partnership where all the folks who are, in effect, being transferred over to NERSC? They've been Lawrence Berkeley people anyhow, so it's not a major change from their perspective," Gilbert said. The institute's current data center lacks the capacity to store the exponentially higher amount of data projected, and JGI staff did not have the same breadth of experience with running very large-scale systems that staffers at the computer center have, Jeff Broughton, systems department head at NERSC, told GWDN. Under the consolidation, NERSC will be responsible for existing JGI scientific computing equipment and new equipment to be procured, which will be housed about 16 miles southwest of Walnut Creek, at the computer center's Oakland facility. Broughton said the new equipment will include 500 dual-socket, quad-core Nehalem processor nodes from SGI — of which 160 nodes are in place, with the remaining 340 nodes "expected to arrive within the next six weeks, by the end of May" — as well as a 120 nodes from the IBM iDataPlex system already in use at NERSC's "Magellan" cloud computing cluster, part of a joint research effort between NERSC and the Argonne Leadership Computing Facility, funded with $32 million from the $862 billion American Recovery and Reinvestment Act. "In general, genomics is a pretty good fit for cloud computing, and they were able to take advantage of that," Broughton said. "The new sequencers are producing ever-increasing flows of data, and it's important to make sure that the computational infrastructure scales appropriately to match it," he added. He said NERSC runs "in excess of" 50,000 cores for high-performance computing now, a figure expected to quadruple by the end of the year. JGI would account for about 10 percent of NERSC's total computing power, based on core count. By teaming with NERSC, JGI can enjoy access to a dedicated 10 Gbps-per-second link between both institutions on the Science Data Network of the Energy Sciences Network, as well as other benefits, such as redundant cooling systems, an uninterruptible source of power, environmental and energy-use monitoring, and a central help desk.
Nature 463 , 763-768 (11 February 2010) | :10.1038/nature08747 :10.1038/nature08747 ; Received 29 August 2009; Accepted 9 December 2009 Genome sequencing and analysis of the model grass Brachypodium distachyon Science ：科学家绘制出首幅小麦基因组物理图谱 Science ：玉米B73系基因组序列 Nature Reviews Genetics ：解密41000个水稻基因的功能 Nature ：高粱基因组完成测序
标签: 基因组测序
