Conservation of transgene-induced post-transcriptional gene silencing in plants and fungi Conservation of transgene-induced post-transcriptional gene silencing in plants and fungi Current perspectives on mRNA stability in plants: multiple levels and mechanism of control Gutirrez RA, MacIntosh GC, Green PJ. Current perspectives on mRNA stability in plants: multiple levels and mechanisms of control. Trends Plant Sci. 1999 Nov; 4 (11): 429-438. The control of mRNA stability plays a fundamental role in the regulation of gene expression in plants and other eukaryotes. This control can be influenced by the basal mRNA decay machinery, sequence-specific decay components, and regulatory factors that respond to various stimuli. Important progress has been made towards the identification of some of these elements over the past several years. This is true particularly with respect to cis-acting sequences that control mRNA stability, the identification of which has been the focus of much of the initial work in the field. Characterization of mRNA fragments associated with post-transcriptional gene silencing and two plant transcripts that give rise to detectable decay intermediates have provided insight into the mRNA decay pathways. These, and other studies, are indicative of similarities, as well as of interesting differences between mRNA decay mechanisms in plants and yeast - the system that has been used for most of the pioneering work. Future studies in this area, particularly when enhanced by emerging genetic and genomic approaches, have tremendous potential to provide additional knowledge that is unique to plants or of broad significance. Current perspectives on mRNA stability in plants-multiple levels and mechanism of control Regulation of short-distance transport of RNA and protein Kim JY. Regulation of short-distance transport of RNA and protein. Curr Opin Plant Biol. 2005 Feb; 8 (1): 45-52. The intercellular trafficking of proteins and RNAs has emerged as a novel mechanism of cell-cell communication in plant development. Plasmodesmata (PD), intercellular cytoplasmic channels, have a central role in cell-cell trafficking of regulatory proteins and RNAs. Recent studies have demonstrated that plants use either a selective or a non-selective PD trafficking pathway for regulatory proteins. Moreover, plants have developed strategies to regulate both selective and non-selective movement. Recent work has focused especially on integrating the recent understanding of the function and mechanisms of intercellular macromolecule movement through PD. Regulation of short-distance transport of RNA and protein Systemic transport of RNA in plants Systemic transport of RNA in plants The complex language of chromatin regulation during transcription Berger SL. The complex language of chromatin regulation during transcription. Nature. 2007 May 24; 447 (7143): 407-12. An important development in understanding the influence of chromatin on gene regulation has been the finding that DNA methylation and histone post-translational modifications lead to the recruitment of protein complexes that regulate transcription. Early interpretations of this phenomenon involved gene regulation reflecting predictive activating or repressing types of modification. However, further exploration reveals that transcription occurs against a backdrop of mixtures of complex modifications, which probably have several roles. Although such modifications were initially thought to be a simple code, a more likely model is of a sophisticated, nuanced chromatin 'language' in which different combinations of basic building blocks yield dynamic functional outcomes. The complex language of chromatin regulation during transcription Regulatory mechanism of plant gene transcription by GT-elements and GT-factors Zhou DX. Regulatory mechanism of plant gene transcription by GT-elements and GT-factors. Trends Plant Sci. 1999 Jun; 4 (6): 210-214. GT-elements are regulatory DNA sequences ususally found in tandem repeats in the promoter region of many different plant genes. Depending on promoter structure, GT-elements can have a positive or a negative transcription function. The cognate GT-element binding factors contain one or two trihelix DNA binding motifs, which have so far been identified in plant transcription factors only. GT-factors are ubiquitously expressed; in Arabidopsis they belong to a small family of transcription factors. The functioning of plant GT-elements and GT-factors shows complex regulatory features of plant gene transcription. Regulatory mechanism of plant gene transcription by GT-elements and GT-factors Regulation of translational initiation in plants Kawaguchi R, Bailey-Serres J. Regulation of translational initiation in plants. Curr Opin Plant Biol. 2002 Oct; 5 (5): 460-5. The abundance of cytosolic mRNA does not necessarily correspond to the quantity of polypeptide synthesized in plant cells. The initiation of mRNA translation is regulated at the global and message-specific levels. mRNAs compete for discriminatory initiation factors that couple the 5'-( 7m )GpppN-cap and the 3'-poly(A) tail of the RNA message. The resultant circularization of the mRNA promotes the association of the 43S pre-initiation complex that scans the 5'-leader for the initiation codon of the protein coding sequence. The physiological and developmental regulation of these events governs the level of polypeptide synthesis from endogenous and viral transcripts. Regulation of translational initiation in plants
RNA in control Blencowe BJ, Khanna M. Molecular biology: RNA in control. Nature. 2007 May 24; 447 (7143): 391-3. RNA in control Compartmentalization of the splicing machinery in plant cell nuclei Lorkovi? ZJ, Barta A. Compartmentalization of the splicing machinery in plant cell nuclei. Trends Plant Sci. 2004 Dec; 9 (12): 565-8. The cell nucleus is a membrane-surrounded organelle that contains numerous compartments in addition to chromatin. Compartmentalization of the nucleus is now accepted as an important feature for the organization of nuclear processes and for gene expression. Recent studies on nuclear organization of splicing factors in plant cells provide insights into the compartmentalization of the plant cell nuclei and conservation of nuclear compartments between plants and metazoans. Compartmentalization of the splicing machinery in plant cell nuclei Pre-mRNA splicing in higher plants Lorkovi? ZJ, Wieczorek Kirk DA, Lambermon MH, Filipowicz W. Pre-mRNA splicing in higher plants. Trends Plant Sci. 2000 Apr; 5 (4): 160-7. Most plant mRNAs are synthesized as precursors containing one or more intervening sequences (introns) that are removed during the process of splicing. The basic mechanism of spliceosome assembly and intron excision is similar in all eukaryotes. However, the recognition of introns in plants has some unique features, which distinguishes it from the reactions in vertebrates and yeast. Recent progress has occurred in characterizing the splicing signals in plant pre-mRNAs, in identifying the mutants affected in splicing and in discovering new examples of alternatively spliced mRNAs. In combination with information provided by the Arabidopsis genome-sequencing project, these studies are contributing to a better understanding of the splicing process and its role in the regulation of gene expression in plants. Pre-mRNA splicing in higher plants Plant serine/arginine-rich proteins and their role in pre-mRAN spicing Reddy AS. Plant serine/arginine-rich proteins and their role in pre-mRNA splicing. Trends Plant Sci. 2004 Nov; 9 (11): 541-7. Pre-messenger RNA (pre-mRNA) splicing, a process by which mature mRNAs are generated by excision of introns and ligation of exons, is an important step in the regulation of gene expression in all eukaryotes. Selection of alternative splice sites in a pre-mRNA generates multiple mRNAs from a single gene that encode structurally and functionally distinct proteins. Alternative splicing of pre-mRNAs contributes greatly to the proteomic complexity of plants and animals and increases the coding potential of a genome. However, the mechanisms that regulate constitutive and alternative splicing of pre-mRNA are not understood in plants. A serine/arginine-rich (SR) family of proteins is implicated in constitutive and alternative splicing of pre-mRNAs. Here I review recent progress in elucidating the roles of serine/arginine-rich proteins in pre-mRNA splicing. Plant serine/arginine-rich proteins and their role in pre-mRAN spicing Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged Kazan K. Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged. Trends Plant Sci. 2003 Oct;8(10):468-71. Alternative splicing has recently emerged as one of the most significant generators of functional complexity in several relatively well-studied animal genomes, but little is known about the extent of this phenomenon in higher plants. However, recent computational and experimental studies discussed here suggest that alternative splicing probably plays a far more significant role in the generation of proteome diversity in plants than was previously thought. Alternative splicing and proteome diversity in plants Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms Lapidot M, Pilpel Y. Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms. EMBO Rep. 2006 Dec; 7 (12): 1216-22. Many genomic loci contain transcription units on both strands, therefore two oppositely oriented transcripts can overlap. Often, one strand codes for a protein, whereas the transcript from the other strand is non-encoding. Such natural antisense transcripts (NATs) can negatively regulate the conjugated sense transcript. NATs are highly prevalent in a wide range of species--for example, around 15% of human protein-encoding genes have an associated NAT. The regulatory mechanisms by which NATs act are diverse, as are the means to control their expression. Here, we review the current understanding of NAT function and its mechanistic basis, which has been gathered from both individual gene cases and genome-wide studies. In parallel, we survey findings about the regulation of NAT transcription. Finally, we hypothesize that the regulation of antisense transcription might be tailored to its mode of action. According to this model, the observed relationship between the expression patterns of NATs and their targets might indicate the regulatory mechanism that is in action. Genome-wide natural antisense transcription-coupling its regulation to its different regulatory mechanisms Plant snoRNAs: functional evolution and new models of gene expression Brown JW, Echeverria M, Qu LH. Plant snoRNAs: functional evolution and new modes of gene expression. Trends Plant Sci. 2003 Jan; 8 (1): 42-9. Small nucleolar RNAs (snoRNAs) are a well-characterized family of non-coding RNAs whose main function is rRNA modification. The diversity and complexity of this gene family continues to expand with the discovery of snoRNAs with non-rRNA or unknown targets. Plants contain more snoRNAs than other eukaryotes and have developed novel expression and processing strategies. The increased number of modifications, which will influence ribosome function, and the novel modes of expression might reflect the environmental conditions to which plants are exposed. Polyploidy and chromosomal rearrangements have generated multiple copies of snoRNA genes, allowing the generation of new snoRNAs for selection. The large snoRNA family in plants is an ideal model for investigation of mechanisms of evolution of gene families in plants. MicroRNAs: Genomics, Biogenesis, Mechanism, and Function David P. Bartel. MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell Volume 116, Issue 2, 23 January 2004, Pages 281-297 MicroRNAs (miRNAs) are endogenous 22 nt RNAs that can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes. Let Me Count the Ways: Mechanisms of Gene Regulation by miRNAs and siRNAs Ligang Wu and Joel G. Belasco Let Me Count the Ways: Mechanisms of Gene Regulation by miRNAs and siRNAs. Molecular Cell. Volume 29, Issue 1, 18 January 2008, Pages 1-7 The downregulation of gene expression by miRNAs and siRNAs is a complex process involving both translational repression and accelerated mRNA turnover, each of which appears to occur by multiple mechanisms. Moreover, under certain conditions, miRNAs are also capable of activating translation. A variety of cellular proteins have been implicated in these regulatory mechanisms, yet their exact roles remain largely unresolved. MicroRNAs: Genomics, Biogenesis, Mechanism, and Fu Let Me Count the Ways: Mechanisms of Gene Regulati
the expanding world of small RNAs Grosshans H, Filipowicz W. Molecular biology: the expanding world of small RNAs. Nature. 2008 Jan 24; 451 (7177): 414-6. the expanding world of small RNAs Impact of small RNAs Obernosterer G, Meister G, Poy MN, Kuras A. The impact of small RNAs. Microsymposium on small RNAs. EMBO Rep. 2007 Jan; 8 (1): 23-7. Epub 2006 Dec 15. Impact of small RNAs Small RNAs as big players in plant abiotic stress response and nutrient deprivation Sunkar R, Chinnusamy V, Zhu J, Zhu JK. Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci. 2007 Jul; 12 (7): 301-9. Epub 2007 Jun 18. Abiotic stress is one of the primary causes of crop losses worldwide. Much progress has been made in unraveling the complex stress response mechanisms, particularly in the identification of stress responsive protein-coding genes. In addition to protein coding genes, recently discovered microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) have emerged as important players in plant stress responses. Initial clues suggesting that small RNAs are involved in plant stress responses stem from studies showing stress regulation of miRNAs and endogenous siRNAs, as well as from target predictions for some miRNAs. Subsequent studies have demonstrated an important functional role for these small RNAs in abiotic stress responses. This review focuses on recent advances, with emphasis on integration of small RNAs in stress regulatory networks. Small RNAs as big players in plant abiotic stress response and nutrient deprivation RNA silencing: small RNAs as ubiquitous regulators of gene expression Voinnet O. RNA silencing: small RNAs as ubiquitous regulators of gene expression. Curr Opin Plant Biol. 2002 Oct; 5 (5): 444-51. 'RNA silencing' is the suppression of gene expression through nucleotide sequence-specific interactions that are mediated by RNA. Initially identified as an immune system that is targeted against transposons and viruses, RNA silencing is emerging as a fundamental regulatory process that is likely to affect many layers of endogenous gene expression in most, if not all, eukaryotes. RNA silencing-small RNAs as ubiquitous regulators of gene expression Specialization and evolution of endogenous small RNA pathways Chapman EJ, Carrington JC. Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet. 2007 Nov; 8 (11): 884-96. The specificity of RNA silencing is conferred by small RNA guides that are processed from structured RNA or dsRNA. The core components for small RNA biogenesis and effector functions have proliferated and specialized in eukaryotic lineages, resulting in diversified pathways that control expression of endogenous and exogenous genes, invasive elements and viruses, and repeated sequences. Deployment of small RNA pathways for spatiotemporal regulation of the transcriptome has shaped the evolution of eukaryotic genomes and contributed to the complexity of multicellular organisms. Specialization and evolution of endogenous small RNA pathways Targets of RNA-directed DNA methylation Matzke M, Kanno T, Huettel B, Daxinger L, Matzke AJ. Targets of RNA-directed DNA methylation. Curr Opin Plant Biol. 2007 Oct; 10 (5): 512-9. Epub 2007 Aug 16. RNA-directed DNA methylation contributes substantially to epigenetic regulation of the plant genome. Methylation is guided to homologous DNA target sequences by 24 nt 'heterochromatic' small RNAs produced by nucleolar-localized components of the RNAi machinery and a plant-specific RNA polymerase, Pol IV. Plants contain unusually large and diverse populations of small RNAs, many of which originate from transposons and repeats. These sequences are frequent targets of methylation, and they are able to bring plant genes in their vicinity under small RNA-mediated control. RNA-directed DNA methylation can be removed by enzymatic demethylation, providing plants with a versatile system that facilitates epigenetic plasticity. In addition to subduing transposons, RNA-directed DNA methylation has roles in plant development and, perhaps, stress responses. Targets of RNA-directed DNA methylation Signaling in gene silencing Signaling in gene silencing Nucleolar dominance and silencing of transcription Pikaard CS. Nucleolar dominance and silencing of transcription. Trends Plant Sci. 1999 Dec; 4 (12): 478-483. Nucleolar dominance is a phenomenon in plant and animal hybrids whereby one parental set of ribosomal RNA (rRNA) genes is transcribed, but the hundreds of rRNA genes inherited from the other parent are silent. The phenomenon gets it name because only transcriptionally active rRNA genes give rise to a nucleolus, the site of ribosome assembly. Nucleolar dominance provided the first clear example of DNA methylation and histone deacetylation acting in partnership in a gene-silencing pathway. However, the sites of chromatin modification and the ways in which one set of rRNA genes are targeted for repression remain unclear. Another unresolved question is whether the units of regulation are the individual rRNA genes or the multi-megabase chromosomal domains that encompass the rRNA gene clusters. Nucleolar dominance and silencing of transcription Small RNAs and transposon silencing in plants Hidetaka Ito. Small RNAs and transposon silencing in plants. Develop. Growth Differ., 2011. doi: 10.1111/j.1440-169X.2011.01309.x Transposons are highly conserved in plants and have created a symbiotic relationship with the host genome. An important factor of the successful communication between transposons and host plants is epigenetic modifications including DNA methylation and the modifications of the histone tail. In plants, small interfering RNAs (siRNAs) are responsible for RNA-directed DNA methylation (RdDM) that suppresses transposon activities. Although most transposons are silent in their host plants, certain genomic shocks, such as an environmental stress or a hybridization event, might trigger transposon activation. Further, since transposons can affect the regulation mechanisms of host genes, it is possible that transposons have co-evolved as an important mechanism for plant development and adaptation. Recent new findings reveal that siRNAs control not only transcriptional activation, but also suppress transgenerational transposition of mobile elements making siRNAs critically important towards maintaining genome stability. Together these data suggest host-mediated siRNA regulation of transposons appears to have been adapted for controlling essential systems of plant development, morphogenesis, and reproduction. Small RNAs and transposon silencing in plants.pdf
The silence of genes Hunter P. The silence of genes. Is genomic imprinting the software of evolution or just a battleground for gender conflict? EMBO Rep. 2007 May; 8 (5): 441-3. The silence of genes Return to the RNAi world: rethinking gene expression and evolution Mello CC. Return to the RNAi world: rethinking gene expression and evolution. Cell Death Differ. 2007 Dec; 14 (12): 2013-20. Thanks to the Nobel Foundation for permission to publish this Lecture. Here we report the transcript of the lecture delivered by Professor Craig C Mello at the Nobel Prize ceremony. Professor Mello vividly describes the years of research that led to the discovery of RNA interference and the molecular mechanisms that regulate this fundamental cellular process. The turning point of discoveries and the role played by all his colleagues and collaborators are described, making this a wonderful report of the adventure of research. The lecture explains in simple language the importance of this discovery that has added a great level of complexity to the way cells regulate protein levels; moreover, it points out the beauty and importance of Caenorhabditis elegans as a model organism and how the use of this model has greatly contributed to the advance of science. Finally, Professor Mello leaves us with a number of questions that his research has raised and that will require years of future research to be answered. Return to the RNAi world-rethinking gene expression and evolution RNAi: a defensive RNA-silencing against viruses and transposable elements Buchon N, Vaury C. RNAi: a defensive RNA-silencing against viruses and transposable elements. Heredity. 2006 Feb; 96 (2): 195-202. RNA silencing is a form of nucleic-acid-based immunity, targeting viruses and genomic repeated sequences. First documented in plants and invertebrate animals, this host defence has recently been identified in mammals. RNAi is viewed as a conserved ancient mechanism protecting genomes from nucleic acid invaders. However, these tamed sequences are known to occasionally escape this host surveillance and invade the genome of their host. This response is consistent with the overall idea that parasitic sequences compete with cells to systematically counter host defences. Using examples taken from the current literature, we illustrate the dynamic move-countermove game played between these two protagonists, the host cell and its parasitic sequences, and discuss the consequences of this game on genome stability. RNAi-a defensive RNA-silencing against viruses and transposable elements Chromatin-based silenceing mechanism Bender J. Chromatin-based silencing mechanisms. Curr Opin Plant Biol. 2004 Oct; 7 (5): 521-6. Eukaryotic genomes are organized into regions of transcriptionally active euchromatin and transcriptionally inactive heterochromatin. In plant genomes, heterochromatin is marked by methylation of cytosine and methylation of histone H3 at lysine 9. Heterochromatin formation is targeted to transposons as a means of defending the host genome against the deleterious effects of these sequences. Heterochromatin is directed to transposon sequences by transposon-derived aberrant RNA species and functions to prevent unwanted transcription and movement. Formation of heterochromatin at rRNA-encoding genes and centromere-associated repeats might also involve an RNA-based mechanism that is designed to stabilize these potentially labile structures. Chromatin-based silenceing mechanism Role of histone and DNA methylation in gene regulation Vaillant I, Paszkowski J. Role of histone and DNA methylation in gene regulation. Curr Opin Plant Biol. 2007 Oct; 10 (5): 528-33. Epub 2007 Aug 9. Transcription is known to be regulated by given chromatin states, distinguished as transcriptionally active euchromatin and silent heterochromatin. In plants, silencing in heterochromatin is associated with hypermethylation of DNA and specific covalent modifications of histone H3. Several lines of evidence have suggested that maintenance of DNA methylation patterns at CG sequences is responsible for the formation of stable and thus heritable activity states termed epialleles. By contrast, histone modification and DNA methylation outside CGs confer the flexibility of transcriptional regulation necessary for plant development and adaptive responses to the environment. Recent studies have refined our understanding of the biological significance of and the molecular mechanisms involved in the interplay between DNA and histone H3 methylation. Role of histone and DNA methylation in gene regulation DNA-RNA-protein gang together in silence Stokes T. DNA-RNA-protein gang together in silence. Trends Plant Sci. 2003 Feb; 8 (2): 53-5. Two recent reports demonstrate interdependence between DNA and histone methylation in Arabidopsis. ddm1 (decrease in DNA methylation 1) mutants switch histone methylation from a form associated with inactive chromatin to a form connected to actively transcribed genomic regions. The loss of DNA methylation and shift in histone methylation cause transcriptional derepression of heterochromatic regions. In a related report, small RNAs in Schizosaccharomyces pombe mark histone methylation to form heterochromatin, suggesting that methylation systems work alongside RNA metabolism. DNA-RNA-protein gang together in silence RNA interference against viruses: strike and counterstrike Haasnoot J, Westerhout EM, Berkhout B. RNA interference against viruses: strike and counterstrike. Nat Biotechnol. 2007 Dec; 25 (12): 1435-43. RNA interference (RNAi) is a conserved sequence-specific, gene-silencing mechanism that is induced by double-stranded RNA. RNAi holds great promise as a novel nucleic acid-based therapeutic against a wide variety of diseases, including cancer, infectious diseases and genetic disorders. Antiviral RNAi strategies have received much attention and several compounds are currently being tested in clinical trials. Although induced RNAi is able to trigger profound and specific inhibition of virus replication, it is becoming clear that RNAi therapeutics are not as straightforward as we had initially hoped. Difficulties concerning toxicity and delivery to the right cells that earlier hampered the development of antisense-based therapeutics may also apply to RNAi. In addition, there are indications that viruses have evolved ways to escape from RNAi. Proper consideration of all of these issues will be necessary in the design of RNAi-based therapeutics for successful clinical intervention of human pathogenic viruses. RNA interference against viruses-strike and counterstrike RNA silencing and antiviral defence in plants Wang MB , Metzlaff M. RNA silencing and antiviral defense in plants. Curr Opin Plant Biol. 2005 Apr; 8 (2): 216-22. Much progress has been made recently in identifying the molecular components of RNA silencing in plants, and in understanding their roles in the biogenesis of small interfering RNAs and microRNAs, in RNA-directed DNA methylation, and in RNA-mediated antiviral defense. However, many crucial questions remain unanswered. What are the molecular bases of sense and antisense transgene-mediated silencing? Why does silencing only appear to spread through transgenes? Plant viruses encode silencing suppressors to counteract host RNA silencing, and some of these suppressors affect microRNA accumulation and function and hence normal plant development. Is viral pathogenicity determined, partly or entirely, by their silencing suppressor activity? RNA silencing and antiviral defence in plants RNA silencing bridging the gaps in wheat extracts Voinnet O. RNA silencing bridging the gaps in wheat extracts. Trends Plant Sci. 2003 Jul; 8 (7): 307-9. In plants, RNA silencing plays important roles in antiviral defence, genome integrity and development. This process involves nucleotide sequence-specific interactions that are mediated by small RNA molecules of 21-25 nucleotides. Although the core biochemical reactions of RNA silencing have been well characterized in animals, such information was crucially missing in plants. Recent work now addresses this question and reveals an overall similarity between the plant and animal RNA-silencing pathways, as well as some intriguing plant-specific aspects. RNA silencing bridging the gaps in wheat extracts RNA silencing in plants-defense and counterdefense Vance V, Vaucheret H. RNA silencing in plants--defense and counterdefense. Science. 2001 Jun 22; 292 (5525): 2277-80. RNA silencing is a remarkable type of gene regulation based on sequence-specific targeting and degradation of RNA. The term encompasses related pathways found in a broad range of eukaryotic organisms, including fungi, plants, and animals. In plants, it serves as an antiviral defense, and many plant viruses encode suppressors of silencing. The emerging view is that RNA silencing is part of a sophisticated network of interconnected pathways for cellular defense, RNA surveillance, and development and that it may become a powerful tool to manipulate gene expression experimentally. RNA silencing in plants-defense and counterdefense Strategies for silencing human disease using RNA interference Kim DH, Rossi JJ. Strategies for silencing human disease using RNA interference. Nat Rev Genet. 2007 Mar; 8 (3): 173-84. Since the first description of RNA interference (RNAi) in animals less than a decade ago, there has been rapid progress towards its use as a therapeutic modality against human diseases. Advances in our understanding of the mechanisms of RNAi and studies of RNAi in vivo indicate that RNAi-based therapies might soon provide a powerful new arsenal against pathogens and diseases for which treatment options are currently limited. Recent findings have highlighted both promise and challenges in using RNAi for therapeutic applications. Design and delivery strategies for RNAi effector molecules must be carefully considered to address safety concerns and to ensure effective, successful treatment of human diseases. Strategies for silencing human disease using RNA interference Role of short RNAs in gene silencing Waterhouse PM, Wang MB, Finnegan EJ. Role of short RNAs in gene silencing. Trends Plant Sci. 2001 Jul; 6 (7): 297-301. Recent research has revealed the existence of an elegant defence mechanism in plants and lower eukaryotes. The mechanism, known in plants as post-transcriptional gene silencing, works through sequence-specific degradation of RNA. It appears to be directed by double-stranded RNA, associated with the production of short 21-25 nt RNAs, and spread through the plant by a diffusible signal. The short RNAs are implicated as the guides for both a nuclease complex that degrades the mRNA and a methyltransferase complex that methylates the DNA of silenced genes. It has also been suggested that these short RNAs might be the mobile silencing signal, a suggestion that has been challenged recently. Role of short RNAs in gene silencing
Functions of microRNAs and the related small RNAs in plants Mallory AC, Vaucheret H. Functions of microRNAs and related small RNAs in plants. Nat Genet. 2006 Jun;38 Suppl: S31-6. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs), 20- to 27-nt in length, are essential regulatory molecules that act as sequence-specific guides in several processes in most eukaryotes (with the notable exception of the yeast Saccharomyces cerevisiae). These processes include DNA elimination, heterochromatin assembly, mRNA cleavage and translational repression. This review focuses on the regulatory roles of plant miRNAs during development, in the adaptive response to stresses and in the miRNA pathway itself. This review also covers the regulatory roles of two classes of endogenous plant siRNAs, ta-siRNAs and nat-siRNAs, which participate in post-transcriptional control of gene expression. Functions of microRNAs and the related small RNAs in plants microRNA regulation of gene expression in plants Dugas DV, Bartel B. MicroRNA regulation of gene expression in plants. Curr Opin Plant Biol. 2004 Oct; 7 (5): 512-20. It has only been a few years since we began to appreciate that microRNAs provide an unanticipated level of gene regulation in both plants and metazoans. The high level of complementarity between plant microRNAs and their target mRNAs has allowed rapid progress towards the elucidation of their varied biological functions. MicroRNAs have been shown to regulate diverse developmental processes, including organ separation, polarity, and identity, and to modulate their own biogenesis and function. Recently, they have also been implicated in some processes outside of plant development. microRNA regulation of gene expression in plants The evolution of gene regulation by transcription factors and microRNAs Chen K, Rajewsky N. The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet. 2007 Feb; 8 (2): 93-103. Changes in the patterns of gene expression are widely believed to underlie many of the phenotypic differences within and between species. Although much emphasis has been placed on changes in transcriptional regulation, gene expression is regulated at many levels, all of which must ultimately be studied together to obtain a complete picture of the evolution of gene expression. Here we compare the evolution of transcriptional regulation and post-transcriptional regulation that is mediated by microRNAs, a large class of small, non-coding RNAs in plants and animals, focusing on the evolution of the individual regulators and their binding sites. As an initial step towards integrating these mechanisms into a unified framework, we propose a simple model that describes the transcriptional regulation of new microRNA genes. The evolution of gene regulation by transcription factors and microRNAs Mechanisms of post-transcriptional regulation by microRNAs: are the answer in sight? Filipowicz W, Bhattacharyya SN, Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet. 2008 Feb; 9 (2): 102-14. MicroRNAs constitute a large family of small, approximately 21-nucleotide-long, non-coding RNAs that have emerged as key post-transcriptional regulators of gene expression in metazoans and plants. In mammals, microRNAs are predicted to control the activity of approximately 30% of all protein-coding genes, and have been shown to participate in the regulation of almost every cellular process investigated so far. By base pairing to mRNAs, microRNAs mediate translational repression or mRNA degradation. This Review summarizes the current understanding of the mechanistic aspects of microRNA-induced repression of translation and discusses some of the controversies regarding different modes of microRNA function. Mechanisms of post-transcriptional regulation by microRNAs MicroRNAs: something important between the genes Mallory AC, Vaucheret H. MicroRNAs: something important between the genes. Curr Opin Plant Biol. 2004 Apr; 7 (2): 120-5. Non-coding small endogenous RNAs, of 21-24 nucleotides in length, have recently emerged as important regulators of gene expression in both plants and animals. At least three categories of small RNAs exist in plants: short interfering RNAs (siRNAs) deriving from viruses or transgenes and mediating virus resistance or transgene silencing via RNA degradation; siRNAs deriving from transposons or transgene promoters and controlling transposon and transgene silencing probably via chromatin changes; and microRNAs (miRNAs) deriving from intergenic regions of the genome and regulating the expression of endogenous genes either by mRNA cleavage or translational repression. The disruption of miRNA-mediated regulation causes developmental abnormalities in plants, demonstrating that miRNAs play an important role in the regulation of developmental decisions. MicroRNAs-something important between the genes MicroRNA biogenesis: coordinated cropping and dicing Kim VN. MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol. 2005 May; 6 (5): 376-85. The recent discovery of microRNAs (miRNAs) took many by surprise because of their unorthodox features and widespread functions. These tiny, approximately 22-nucleotide, RNAs control several pathways including developmental timing, haematopoiesis, organogenesis, apoptosis, cell proliferation and possibly even tumorigenesis. Among the most pressing questions regarding this unusual class of regulatory miRNA-encoding genes is how miRNAs are produced in cells and how the genes themselves are controlled by various regulatory networks. MicroRNA biogenesis-coordinated cropping and dicing Prediction of plant microRNA targets Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. Prediction of plant microRNA targets. Cell. 2002 Aug 23;110(4):513-20. We predict regulatory targets for 14 Arabidopsis microRNAs (miRNAs) by identifying mRNAs with near complementarity. Complementary sites within predicted targets are conserved in rice. Of the 49 predicted targets, 34 are members of transcription factor gene families involved in developmental patterning or cell differentiation. The near-perfect complementarity between plant miRNAs and their targets suggests that many plant miRNAs act similarly to small interfering RNAs and direct mRNA cleavage. The targeting of developmental transcription factors suggests that many plant miRNAs function during cellular differentiation to clear key regulatory transcripts from daughter cell lineages. Prediction of plant microRNA targets Developmental role of microRNA in plants Kidner CA , Martienssen RA. The developmental role of microRNA in plants. Curr Opin Plant Biol. 2005 Feb; 8 (1): 38-44. MicroRNAs (miRNAs) are single-stranded RNA molecules of around 22 nucleotides (nt) in length that are associated with the RNA-induced silencing complex (RISC). They play an important role in plant development, either by targeting mRNA for cleavage or by inhibiting translation. Over the past year, the list of known miRNAs, confirmed targets and developmental effects has expanded, as has the realization that they are conserved during evolution and that small RNAs can play a direct role in cell-cell signaling. Developmental role of microRNA in plants Encountering microRNAs in cell fate signalling Karp X, Ambros V. Developmental biology. Encountering microRNAs in cell fate signaling. Science. 2005 Nov 25; 310 (5752): 1288-9. Encountering microRNAs in cell fate signalling
Perceptions of epigenetics Bird A. Perceptions of epigenetics. Nature. 2007 May 24; 447 (7143): 396-8. Geneticists study the gene; however, for epigeneticists, there is no obvious 'epigene'. Nevertheless, during the past year, more than 2,500 articles, numerous scientific meetings and a new journal were devoted to the subject of epigenetics. It encompasses some of the most exciting contemporary biology and is portrayed by the popular press as a revolutionary new science--an antidote to the idea that we are hard-wired by our genes. So what is epigenetics? Perceptions of epigenetics Epigenetic inheritance in plants Henderson IR, Jacobsen SE. Epigenetic inheritance in plants. Nature. 2007 May 24; 447 (7143): 418-24. The function of plant genomes depends on chromatin marks such as the methylation of DNA and the post-translational modification of histones. Techniques for studying model plants such as Arabidopsis thaliana have enabled researchers to begin to uncover the pathways that establish and maintain chromatin modifications, and genomic studies are allowing the mapping of modifications such as DNA methylation on a genome-wide scale. Small RNAs seem to be important in determining the distribution of chromatin modifications, and RNA might also underlie the complex epigenetic interactions that occur between homologous sequences. Plants use these epigenetic silencing mechanisms extensively to control development and parent-of-origin imprinted gene expression. Epigenetic inheritance in plants Passing the message on: inheritance of epigenetic traits Bond DM, Finnegan EJ. Passing the message on: inheritance of epigenetic traits. Trends Plant Sci. 2007 May; 12 (5): 211-6. Epub 2007 Apr 16. Epigenetic modifiers play an important role in genome organization, stability and the control of gene expression. Three research groups that are exploring the transfer of epigenetic information between generations have recently published papers. Mary Alleman et al. have shown that RNA-directed chromatin changes mediate paramutation in maize, and Minoo Rassoulzadegan et al. have demonstrated that RNA also plays a role in paramutation in mice. A new aspect of epigenetic regulation has been revealed by Jean Molinier et al. - they have demonstrated that the memory of exposure to stress is transferred through several generations. Passing the message on-inheritance of epigenetic traits Epigenetics: regulation through repression Wolffe AP, Matzke MA. Epigenetics: regulation through repression. Science. 1999 Oct 15; 286 (5439): 481-6. Epigenetics is the study of heritable changes in gene expression that occur without a change in DNA sequence. Epigenetic phenomena have major economic and medical relevance, and several, such as imprinting and paramutation, violate Mendelian principles. Recent discoveries link the recognition of nucleic acid sequence homology to the targeting of DNA methylation, chromosome remodeling, and RNA turnover. Although epigenetic mechanisms help to protect cells from parasitic elements, this defense can complicate the genetic manipulation of plants and animals. Essential for normal development, epigenetic controls become misdirected in cancer cells and other human disease syndromes. Epigenetics-regulation through repression Inherited epigenetic variation: revisting soft inheritance Richards EJ. Inherited epigenetic variation--revisiting soft inheritance. Nat Rev Genet. 2006 May; 7 (5): 395-401 Phenotypic variation is traditionally parsed into components that are directed by genetic and environmental variation. The line between these two components is blurred by inherited epigenetic variation, which is potentially sensitive to environmental inputs. Chromatin and DNA methylation-based mechanisms mediate a semi-independent epigenetic inheritance system at the interface between genetic control and the environment. Should the existence of inherited epigenetic variation alter our thinking about evolutionary change? Inherited epigenetic variation-revisting soft inheritance Nucleosome destabilization in the epigenetic regulation of gene expression Henikoff S. Nucleosome destabilization in the epigenetic regulation of gene expression. Nat Rev Genet. 2008 Jan; 9 (1): 15-26. Assembly, mobilization and disassembly of nucleosomes can influence the regulation of gene expression and other processes that act on eukaryotic DNA. Distinct nucleosome-assembly pathways deposit dimeric subunits behind the replication fork or at sites of active processes that mobilize pre-existing nucleosomes. Replication-coupled nucleosome assembly appears to be the default process that maintains silent chromatin, counteracted by active processes that destabilize nucleosomes. Nucleosome stability is regulated by the combined effects of nucleosome-positioning sequences, histone chaperones, ATP-dependent nucleosome remodellers, post-translational modifications and histone variants. Recent studies suggest that histone turnover helps to maintain continuous access to sequence-specific DNA-binding proteins that regulate epigenetic inheritance, providing a dynamic alternative to histone-marking models for the propagation of active chromatin. Nucleosome destabilization in the epigenetic regulation of gene expression Arabidopsis epigenetics: when RNA meets chromatin Gendrel A, Colot V. Arabidopsis epigenetics: when RNA meets chromatin. Curr Opin Plant Biol. 2005 Apr; 8 (2): 142-7. Recent work in plants and other eukaryotes has uncovered a major role for RNA interference in silent chromatin formation. The heritability of the silent state through multiple cell division cycles and, in some instances, through meiosis is assured by epigenetic marks. In plants, transposable elements and transgenes provide striking examples of the stable inheritance of repressed states, and are characterized by dense DNA methylation and heterochromatin histone modifications. Arabidopsis is a useful higher eukaryotes model with which to explore the crossroads between silent chromatin and RNA interference both during development and in the genome-wide control of repeat elements. Arabidopsis epigenetics-when RNA meets chromatin Transposable elements and the epigenetic regulation of the genome Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet. 2007 Apr; 8 (4): 272-85. Overlapping epigenetic mechanisms have evolved in eukaryotic cells to silence the expression and mobility of transposable elements (TEs). Owing to their ability to recruit the silencing machinery, TEs have served as building blocks for epigenetic phenomena, both at the level of single genes and across larger chromosomal regions. Important progress has been made recently in understanding these silencing mechanisms. In addition, new insights have been gained into how this silencing has been co-opted to serve essential functions in 'host' cells, highlighting the importance of TEs in the epigenetic regulation of the genome. Transposable elements and the epigenetic regulation of the genome Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation Zemach A, Grafi G. Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation. Trends Plant Sci. 2007 Feb; 12 (2): 80-5. Epub 2007 Jan 8. The effect of DNA methylation on various aspects of plant cellular and developmental processes has been well documented over the past 35 years. However, the underlying molecular mechanism interpreting the methylation signal has only recently been explored with the isolation and characterization of the Arabidopsis methyl-CpG-binding domain (MBD) proteins. In this review, we highlight recent advances and present new models concerning Arabidopsis MBD proteins and their possible role in controlling chromatin structure mediated by CpG methylation. Methyl-CpG-binding domain proteins in plants-interpreters of DNA methylation Imprinting-a green variation Berger F. Plant sciences. Imprinting--a green variation. Science. 2004 Jan 23; 303 (5657): 483-5. Imprinting-a green variation
生物学和遗传学的革命 单核苷酸多态性（ SNP ）取代基因（ gene ）成为遗传单位 《新闻周刊》发表文章《奇迹之年》（ The Year of Miracles ）指出，对人类自身进行探索的基因研究成为全球的科研热点，正是基因研究的奇迹之年 2007 年，有关致病基因的一系列新发现颠覆了人类对于基因和遗传的传统认知，单核苷酸多态性（ SNP ）取代基因（ gene ）成为遗传单位。 The Year of Miracles By Lee Silver | NEWSWEEK ， Oct 15, 2007 Issue Variations in these particular letterscalled snips, or SNPs, for single nucleotide polymorphismshave replaced genes as the unit of heredity. The year 1905 was an annus mirabilis, or miracle yearA rare historical moment in which key flashes of insight suddenly made the field of physics take off in new directions. That was the year Albert Einstein presented four papers that turned the conventional wisdom about how the universe works, from the infinitesimal realm of atoms to the vast reaches of the cosmos, upside down. During the next several decades, Einstein and a handful of other brilliant physicists went on to shape the 20th century and lay the foundation for all its technological accomplishments. A century later, the year 2007 is shaping up to be another annus mirabilis. This time biology is the field in transition, and the ideas being shattered are old notions of genes and inheritance. Ever since 1900, when Gregor Mendel's work on peas and inheritance was rediscovered, scientists have regarded the gene as the fundamental unit of heredity (just as the atom was regarded as the bedrock of pre-Einsteinian physics). Crick and Watson's discovery of the DNA double helix as the carrier of hereditary information did little to disturb the status quo. In recent months, however, a perfect storm of new technology and research has blown apart 20th-century dogma. The notion of the Mendelian gene as a unit of heredity, scientists now realize, is a fiction. What's taking its place? Many scientists now believe that heredity is the result of an incredibly complex interplay among the basic components of the genome, scattered among many different genes and even the vast stretches of junk DNA once thought to serve no purpose. Biology has been building up to this insight for years, but some big puzzle pieces have now fallen into place. Once scientists abandoned their preconceived notions of genes and looked instead at individual DNA letters in the genome the four bases A, C, T and Gthey immediately began to see cause-and-effect connections to myriad diseases and human traits. The result of this seemingly modest conceptual breakthrough has been a torrent of new discoveries. In five months, from April through August, geneticists at the Harvard/MIT Broad Institute, founded by Eric Lander; at deCODE Genetics in Iceland , founded by Kari Stefansson, and several other institutions have published papers suggesting that the key to a deeper understanding of the human genome may finally be in hand. These scientists have identified specific alterations in the sequence of DNA that play causative roles in a broad range of common diseases, including type 1 and type 2 diabetes; schizophrenia; bipolar disorder; glaucoma; inflammatory bowel disease; rheumatoid arthritis; hypertension; restless legs syndrome; susceptibility to gallstone formation; lupus; multiple sclerosis; coronary heart disease; colorectal, prostate and breast cancer, and the pace at which HIV infection causes full-blown AIDS. Unlike so many previous disease gene discoveries, these findings are being replicated and validated. The race to discover disease-linked genes reaches fever pitch, declared the leading British science journal, Nature. Its American counterparts at Science chimed in: After years of chasing false leads, gene hunters feel that they have finally cornered their prey. They are experiencing a rush this spring as they find, time after time, that a new strategy is enabling them to identify genetic variations that likely lie behind common diseases. That the world's top two scientific journals still use the old language of genes to describe these discoveries shows how new the new thinking really is. These findings are just a prelude to what's shaping up as a true conceptual and technological revolution. Just as physics shocked the world in the 20th century, it is now clear that the life sciences will shake up the world in the 21st. In a handful of years, your doctor may be able to run a computer analysis of your personal genome to get a detailed profile of your health prospects. This goes well beyond merely making predictions. A new technology called RNA interference may also allow doctors to control how your DNA is expressed, helping you circumvent potential health risks. Many common diseases that have preyed on humans for eonsdevastating neurological conditions such as Alzheimer's, Parkinson's, cancer and heart diseasecould be eradicated. If this sounds outrageously optimistic, so did the promise of eliminating smallpox and polio to previous generations. Why is all this happening now? What has changed between this year and last? To answer these questions, we need to trace the story of how mainstream biomedical scientists tried to link the cause of diseases to single genes and, despite early success, hit a brick wall. Meanwhile, a handful of renegade scientists, pursuing their own pet projects, happened to develop exactly the intellectual tools needed to break through that wall. These biologists are now the leaders of the new revolution in biomedical science. The seeds of our new understanding were first sown in the 1960s, when molecular biologists figured out how genetic information is organized, regulated and reproduced inside single-cell bacteria. In bacteria, a gene is a discrete segment of DNA that contains the code that tells the cell how to make a particular type of protein. Bacterial genes are arranged along a single DNA molecule, one after the other, with only tiny gaps in between. Since all organisms have DNA and work by essentially the same biochemistry, scientists assumed that a human genome would look like a larger version of a bacterium's. Clues that something was amiss came quickly with the development of DNA-sequencing methods in the 1970s. The first surprising result was that genes accounted for only 2 percent of the human genomethe rest of the DNA didn't seem to have any purpose at all. Biologists Phillip Sharp and Richard Roberts made things worse with a discovery that won them a Nobel Prize in 1993. If the gene were the basic unit of heredity, the DNA required to make any particular protein should be contained in its corresponding gene. But Sharp and Roberts found that DNA that codes for individual proteins is often split and scattered throughout the genome. Scientists could ignore these signs largely because they seemed to be making progress. By combining new DNA-sequencing tools with studies of inherited diseases in large families, medical geneticists identified the genetic culprits responsible for cystic fibrosis, Huntington's disease, Duchenne muscular dystrophy and a host of other diseases. Each of these all or none diseases is caused by a mutation in a single protein-coding region of the DNA. Few diseases, unfortunately, work so neatly. In particular, the search for genetic bases of common diseases that affect large numbers of aging people came up empty. During this lull, a visionary physician-scientist named Leroy Hood, now at the Institute for Systems Biology in Seattle , was growing impatient. Genetics, he recognized, was still a cottage industry of government-funded university professors, who each directed a small group of students and technicians to study an isolated gene. At the pace research was progressing, it would have required 100,000 worker-years of concerted effort to decipher just one complete human genome. Hood thought it was absurd that genetic scientists spent nearly all their lab time performing tedious and repetitive mechanical and chemical procedures. At the same time, he grasped the far-reaching implications of a fundamental fact: while even the simplest organism is immensely complicated, the primary structures of its most complicated partsDNA and proteinsare very simple. The alphabet of DNA contains only the four chemical letters (or bases) A, C, G and T, and proteins are made from just 21 amino acids. Hood saw that this simplicity would make it possible for robots and computers to read and write DNA and proteins more quickly, accurately and cheaply than human beings. The rest of the biomedical community refused to believe that robots could analyze something as complex as a living system. And in any case, no practicing geneticist had the capacity to design such machines. Unable to obtain government grants, Hood secured private funding to bring together dozens of scientists, engineers and computer programmers (far larger and more diverse than any other genetics team). They proceeded to invent the first generation of molecular-biology machines. Two read and recorded information from DNA and proteins respectively (a process known as sequencing), and two others worked backward, converting digital electronic information into newly written sequences of DNA or protein. Hood completely transformed the biomedical enterprise. DNA-writing machines give genetic engineers an unlimited capacity to create novel genes that can be studied in test tubes or added to the genomes of living organisms. And protein-writing and -reading machines provided drug firms with the ability to create a new generation of protein-based drugs. The DNA-reading machines suddenly made it conceivable to crack the 3 billion-base sequence of an entire human genome. In 1990 the U.S. government embarked on a 15-year, $3 billion project to do just that. Eight years later, however, the projectparceled out to many U.S. scientistswas still less than 10 percent complete. Now it was biotech entrepreneur Craig Venter who was frustrated. Convinced that government-funded workers were the problem rather than the solution, Venter enlisted private funding of $200 million to build an enormous lab filled with hundreds of automated machines, working 24/7, overseen by a handful of technicians. Within three years, the first reading of a human genome was essentially complete. Armed with data from the genome project, scientists figured they'd surely be able to crack the really hard diseases, like cancer and heart disease. But a funny thing happened when they began to look closely at this vast storehouse of genetic information. Geneticists Andrew Fire and Craig Melo galvanized the field by discovering a key mechanism that had been completely overlookedthe cellular process of RNA interference. (They shared a Nobel Prize in 2006 for the work.) Finding evidence of extraterrestrial life couldn't have come as a bigger shock. Geneticists had taken for granted that the machinery of cells involved genes directing the production of proteins, and proteins doing the work of the cell. Here was a process that didn't involve proteins at all. Instead, tens of thousands of hitherto mysterious regions of the human genomepart of the so-called junk DNAdirected the production of specific molecules called microRNAs (consisting of bits of RNA, a well-known component of cells). These microRNAs then oversaw a whole new process, called RNA interference (RNAi), that served to modulate the expression of DNA. The good news was that RNAi could open up a whole new approach to biomedical therapy (more on that later). But RNAi also made it clear that the fundamental unit of heredity and genetic function is not the gene but the position of each individual DNA letter. To make it all harder to fathom, each bit of DNA is susceptible to mutation and variation among individuals. Of the 3 billion DNA bases in the human genome, geneticists identified about one tenth of one percent (millions) that differ from one person to another. Variations in these particular letterscalled snips, or SNPs, for single nucleotide polymorphismshave replaced genes as the unit of heredity. Many scientists responded to this devastating realization by going into a funk. It will be difficult, if not impossible, to find the genes involved or develop useful and reliable predictive tests for them, Dr. Neil Holtzman, director of genetics and public policy at Johns Hopkins University , said in 2001. Fortunately, another visionary scientist, Kari Stefansson of Iceland , was already blazing a trail out of this thicket. If the genome was far more complex than scientists had thought, they would need to test for many more variables, and to do that they would need more test subjects. To find the cause of diseases would now require the participation of very large groups of genetically related people. Like Hood and Venter, Stefansson was originally motivated by frustration with the pace of research. In the United States , where most of the disease-gene-discovery projects were being conducted, most people cannot trace their ancestors back more than a few generations, and the largest families consist of a few hundred living subjects at most. Subject panels of this size failed to provide sufficient data to identify the genetic bases for complicated and variable common diseases. Stefansson decided to solve this problem by taking aim at the largest well-documented extended family that he knewhis own. Nearly all the 300,000 citizens of Iceland can trace their ancestors back, through detailed, public genealogical records, to the Vikings who settled this desolate European island more than 1,000 years ago. Stefansson gave up his faculty position at Harvard Medical School to return to Iceland , where he founded the company deCODE Genetics in 1996. He persuaded the Icelandic government to provide deCODE with exclusive access to the health records of its citizens in return for bringing investment capital and high-tech jobs to the capital, Reykjavik . So far, more than 100,000 Icelandic volunteers have donated their DNA to deCODE. Stefansson's project was roundly criticized by international bioethicists and other geneticists for violating the privacy of Icelanders (even though 90 percent of the population approved). Nevertheless, he persevered, placing the genealogy of the entire nation on a computer database, together with the health and DNA records of still-living individuals. The power of large numbers was soon apparent. In a study of obesity, he directed his software to look for SNPs associated with subsets of the population who were either extremely overweight or very thin. Within just a few hours, it began finding evidence that variations among particular DNA letters indeed played a causative role, confirming SNPs as the new unit of inheritance. As of September, deCODE has made progress in identifying SNPs that may play a role in 28 common diseases, including glaucoma, schizophrenia, diabetes, heart disease, prostate cancer, hypertension and stroke. In some cases, such as glaucoma and prostate cancer, deCODE's findings could lead to diagnostic tests for identifying people at risk of developing the disease. In other instances, such as schizophrenia, links to particular proteins have led to insight about the cause of the disease, which could lead to therapies. Buoyed by Stefansson's success, other geneticists were eager to perform large-scale family studies, yet few had similar access to ancient genealogical records. But serendipity would deliver an epiphany: it's possible to study the entire human population as a single extended family, provided scientists collect enormous amounts of data. Eric Lander, an MIT professor and the intellectual leader of the U.S. government effort to sequence the first human genome, realized scaling up would require a new approach. In 2004, Lander persuaded MIT and Harvard to combine their enormous resources toward the creation of the Broad Institute. Backed by $200 million from billionaire philanthropists Eli and Edythe Broad, the institute is driving the development of ever more advanced genetic technologies. One technology, based on computer-chip fabrication, can identify DNA base letters present at 500,000 SNPs in the genomes of 40,000 or more people. Think of this as a spreadsheet with 500,000 columns (each representing a specific SNP) and 40,000 rows (one for each person). To hunt for a genetic basis for, say, bipolar disease, the computer searches rows of people who have the disorder, checking column by column for an unusually high frequency of particular letters in comparison with people without the disease. As it turns out, a collaboration of American and German researchers has done this workand found that variations of DNA letters in 20 different positions are influential in bipolar disease. Incredibly, most disease-causing variants are the most common ones present in the human population: the strongest-acting one, for instance, exists in 80 percent of people without bipolar disease and 85 percent of people with the disease. The implication is that these variants are beneficial in some way, and cause problems only when their number exceeds a threshold. To make sense of this complexity, scientists would like ultimately to build a vast international database that contains the complete sequence of DNA bases in the genomes of hundreds of millions of people. Ideally, such a database would be available for analysis by all biomedical researchers and would provide the foundation for understanding the genetic components of all human traits. That sounds like a lot of datathink of a spreadsheet with 3 billion columns and 100 million rowsbut computing power is getting cheaper by the year. Within a decade, the cost of obtaining a sequence of all 3 billion DNA letters in an individual's genome will drop from $2 million now to $1,000. It will be a routine part of a person's health record, enabling physicians to prescribe genome-specific preventions and treatments. The discovery of RNAi, meanwhile, suggests a completely new personalized form of disease therapy. Whereas drugs act on proteins, RNAi therapy would act on the expression of DNA itself, potentially preventing or reversing diseases such as Alzheimer's, Parkinson's, Huntington's, bipolar disorder, schizophrenia and others. Old-school pharmaceutical firms have taken notice. The largest ones are betting heavily on the gene-targeted RNAi therapeutic approach to fill product pipelines, as the discovery of traditional chemical drugs becomes more elusive. Novartis and Roche have both signed nonexclusive licensing deals with the biotech firm Alnylam (founded by Phillip Sharp) for new therapeutic techniques that are valued at up to $700 million and $1 billion respectively; Merck paid $1.1 billion to buy another biotech company outright, solely to obtain its contested portfolio of RNAi intellectual property, and the London-based drug firm AstraZeneca has a $405 million licensing deal with Alnylam's competitor Silence Therapeutics. The explosion of genetic discoveries shows no sign of letting up any time soon. New diseases are being added to the list every month, and biologists are rapidly parlaying gene- and SNP-disease links into a deeper understanding of how proteins and other molecules can misbehave to cause different medical problems in different people. And other scientists are working to advance the biology revolution (accompanying interviews). As a result of their efforts, many children born this year could very well be alive and healthy at the dawn of the next century, when they may look back in awe at the annus mirabilis of biomedical genetics in 2007. Silver is a professor of molecular biology at Princeton . He is the author of Challenging Nature. He has no financial ties to any biotech or drug firm. Silver is a professor of molecular biology at Princeton . He is the author of Challenging Nature. He has no financial ties to any biotech or drug firm. Newsweek, Inc.
Genetics: what is a gene? Nature . 2006 May 25;441(7092):469-74. The idea of genes as beads on a DNA string is fast fading. Protein-coding sequences have no clear beginning or end and RNAi is a key part of information package, reports Helen Pearson Genetics: what is a gene? - Genetic information: codes and enigmas. Nature . 2006 Nov 16;444(7117):259-61. Theres more than one way to read a stretch of DNA, finds Helen Pearson - and we need to understand them all. Genetic information: codes and enigmas. . Between the cross and the sword: the crisis of the gene concept Charbel Nio El-Hani.Between the cross and the sword: the crisis of the gene concept. Genet. Mol. Biol. 2007vol.30no.2 So Paulo Mar. Challenges to the gene concept have shown the difficulty of preserving the classical molecular concept, according to which a gene is a stretch of DNA encoding a functional product (polypeptide or RNA). The main difficulties are related to the overlaying of the Mendelian idea of the gene as a unit: the interpretation of genes as structural and/or functional units in the genome is challenged by evidence showing the complexity and diversity of genomic organization. This paper discusses the difficulties faced by the classical molecular concept and addresses alternatives to it. Among the alternatives, it considers distinctions between different gene concepts, such as that between the molecular and the evolutionary gene, or between gene-P (the gene as determinant of phenotypic differences) and gene-D (the gene as developmental resource). It also addresses the process molecular gene concept, according to which genes are understood as the whole molecular process underlying the capacity to express a particular product, rather than as entities in bare DNA; a treatment of genes as sets of domains (exons, introns, promoters, enhancers, etc.) in DNA; and a systemic understanding of genes as combinations of nucleic acid sequences corresponding to a product specified or demarcated by the cellular system. In all these cases, possible contributions to the advancement of our understanding of the architecture and dynamics of the genetic material are emphasized. Between the cross and the sword-the crisis of the . Origin of phenotypes: genes and transcripts. Gingeras TR. Origin of phenotypes: genes and transcripts. Genome Res., 2007 Jun;17(6):682-90. While the concept of a gene has been helpful in defining the relationship of a portion of a genome to a phenotype, this traditional term may not be as useful as it once was. Currently, gene has come to refer principally to a genomic region producing a polyadenylated mRNA that encodes a protein. However, the recent emergence of a large collection of unannotated transcripts with apparently little protein coding capacity, collectively called transcripts of unknown function (TUFs), has begun to blur the physical boundaries and genomic organization of genic regions with noncoding transcripts often overlapping protein-coding genes on the same (sense) and opposite strand (antisense). Moreover, they are often located in intergenic regions, making the genic portions of the human genome an interleaved network of both annotated polyadenylated and nonpolyadenylated transcripts, including splice variants with novel 5' ends extending hundreds of kilobases. This complex transcriptional organization and other recently observed features of genomes argue for the reconsideration of the term gene and suggests that transcripts may be used to define the operational unit of a genome. Origin of phenotypes-genes and transcripts . What is a gene, post ENCODE? History and updated definition Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. What is a gene, post ENCODE? History and updated definition. Genome Res., 2007 Jun; 17 (6): 669-81. While sequencing of the human genome surprised us with how many protein-coding genes there are, it did not fundamentally change our perspective on what a gene is. In contrast, the complex patterns of dispersed regulation and pervasive transcription uncovered by the ENCODE project, together with non-genic conservation and the abundance of noncoding RNA genes, have challenged the notion of the gene. To illustrate this, we review the evolution of operational definitions of a gene over the past century--from the abstract elements of heredity of Mendel and Morgan to the present-day ORFs enumerated in the sequence databanks. We then summarize the current ENCODE findings and provide a computational metaphor for the complexity. Finally, we propose a tentative update to the definition of a gene: A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products. Our definition side-steps the complexities of regulation and transcription by removing the former altogether from the definition and arguing that final, functional gene products (rather than intermediate transcripts) should be used to group together entities associated with a single gene. It also manifests how integral the concept of biological function is in defining genes. What is a gene, post ENCODE
这是一个关于关于体育社会学和体质人类学的综述，涉及到体育、种族、文化和基因、兴奋剂的多个方面，共20000余字，将分4-5部分。引用的文献资料列于文后的拓展阅读部分，基本上按照在文中出现的顺序排列，但因为作者对资料数据有所编排，故未注明标号。作者已经确保所有引述的资料来源可靠，如有疏漏，敬请谅解并指出 天赋体能？ ――体育文化基因的是与非（3) 444444444444444444444444444 Black or White 当我们用平均数来表示数据总体情况时，个性也随之消弥殆尽。而很多时候，被平均数丢弃的个性，往往具有更多的意义。平均重量相等的两箱苹果，整齐划一的那箱售价高昂，而参差不齐者只能送往罐头厂。人类基因组的成果告诉我们，决定种族差异的肤色只占据整个基因组的万分之一，更多的个人特质应该归因于种族内部的个体差异，有人说是85%－－另一些人认为更高。 基因是细胞核内DNA上的小片断，由数量庞大的核苷酸以一定的顺序排列而成。虽然只有区区四种核苷酸，却足以使每个人的基因永不雷同。基因内部的核苷酸顺序就是个人的先天蓝图，每三个核苷酸对应着某个氨基酸，在译码员的帮助下翻译为多肽链，从而控制着人体的先天性状。这个过程和莫尔斯码的原理如出一辙。 继承自祖辈的基因决定了我们作为人本质，同时让我们独具特色，无可替代。基因把我们每个人都雕刻成了独一无二的橡皮图章，肤色也是图章的重要部分，不幸的是，这些特征被作为了种族分类的依据，哪怕它们只是人体所有特征的沧海一粟。 虽然在人种划分的问题上众说纷纭，但无一例外地，肤色都被作为区分种族的重要指标之一。早在三四千年前，古埃及画家就尝试用不同的色彩标示各色族人。发展到上世纪初，欧洲逐渐形成了如下的分类法：尼格罗人种（黑种人）；高加索人种（白种人）和蒙古人种（黄种人）。这种分类法因为其简洁直观而广为流传。 作为一种分类尝试，人种这一概念本身并不具备任何破坏性。问题在于，趾高气昂的殖民者把种族与智力道德水平相联系，藉此对各地文化品头论足，以满足白人贵族那高眉骨下的仁厚心智。蒙古人种的浅黄皮肤和内眦赘皮表明他们狡猾而刻板（这对反义词用得堪绝）；尼格罗人种的黑皮肤和厚嘴唇是更接近猿类的证明，而对黑猩猩的白皙皮肤和薄嘴唇这一事实置若罔闻。无论如何，这时的理论为后来的种族主义打下了理论基础，臭名昭著的纳粹和三K党成了人类最痛苦的集体记忆，其后遗症至今尚未完全消除。 出人意料的是，这个把人类历史搅得风声水起的名词，却立足于一块摇摇欲坠的基石。作为同一个物种，各人种的皮肤结构完全一致，所谓的肤色差别只是集中在厚度小于一毫米的表皮层中。表皮中黑色素密度越高，皮肤就越黑，和其它所有性状一样，影响黑色素浓度的原因来自于两个方面：基因和环境。这两者决定了在白黑之间存在一系列的过渡肤色，而不是像双眼皮一样全或无。 现在我们知道，有四对基因（共8个等位基因）插手了黑色素任务。简单说来，白人有8个使其具有浅肤色的b基因，黑人有8个相反效应的n基因，所有中间肤色都有x个b基因和8-x个n基因，b基因越多，肤色就越白。从其他血型系统得到的证据表明美国黑人大概有1/4的欧洲白人基因，也就是说决定肤色的8个等位基因都有1/4的可能是b基因，因此在2000万美国黑人中大概有几百人具有白色肌肤；同理，大概有20万人具有非洲创建者的纯粹黑色n基因。这是一个好消息，当我们发现子女肤色与父母大相径庭时，不用再满地找下巴了。 基因使得人体的天然肤色表现出至少八个等级，环境更是将肤色打造成为无级连续性状，就像身高等体质性状一般。肤色之所以在后天有如此之大的改变，是因为黑色素肩负着一项防护性的生理功能：紫外线光盾。在紫外线照射下，皮肤会合成更多的黑色素，以作防御。黑色素缺乏症患者对光线高度敏感，只能躲避一切光亮，所以荷兰人给他们起绰号叫Hakkerlaken，意即蟑螂－－虽然刻薄恶毒，却也道出了怕光的本质。同等光照下，肤色较浅的高加索人患皮肤癌的比例比黑人高50倍，比日本人高4-12倍。 在椰子油和防晒乳广泛应用之前，人类祖先们只好以黑色肌肤来抵御强烈紫外线。生活在卡拉哈里沙漠深处的布须曼人提示了人类始祖的肤色。作为人类始祖的最可能的嫡系后裔，布须曼人呈现非常广阔的肤色范围，从一个小型的布须曼人群体中，我们就足以发现三大人种的肤色倾向。正如安德烈朗加奈在《种族之间不可调和的问题》一文中写道，如果选取南非人和布须曼人作为中间人，最白的北欧人可以直接过度到最黑的萨拉人。 但是，高密度的黑色素既是紫外线之盾，也是维生素D的克星，在抵御紫外线的入侵的同时，也阻挡了后者的合成之路。维生素D是人体必需的维生素之一，在钙质代谢中起着重要作用，但却无法从食物中获得，只在阳光的照射下由胆固醇转变而来。过深的肤色阻碍了维生素D的转化，从而影响钙质吸收，甚至因此导致佝偻病－－有数据表明低日照地区的黑人儿童更容易罹患维生素D缺乏症。 因此，当10万年前的气候变迁迫使人祖走向迁徙之路时，肤色这一生死攸关而且适应性极强的表层性状逐渐发生了缓慢但醒目的改变。随着光照的减少，皮肤较浅（即b等位基因较多）者更有优势，就有更多机会生育强健后代，进而增加整个群体的b基因的频率，最终使得整个群体的肤色较浅。高加索人种和蒙古人种的浅色肌肤就是由此而来。 肤色无论深浅都是适应自然的产物，其分离不过千代。虽说肤色是最明显，最容易比较的性状，但它极不稳定，而且充其量只占人体基因组的四千分之一，似乎与任何重要的生物性状都没有关联。一个简单的例子来自于对最黑皮肤的认识。赤道附近的美拉尼西亚群岛、印度半岛和撒哈拉以南非洲等地的居民有着最深的肤色，但无论如何难以将他们归入同一种族，因为他们除了肤色这一表观现象，其他分子学证据（如血型系统）都无法指向同一群体分支。 既然肤色如此肤浅，显然，任何只以肤色为标准的种族划分都不具有生物学意义。如果说以乳糖酶的持久性作为分类标准尚且有利于选择合适牛奶的话；以显而易见的肤色差异作为特征来区分种族，又给我们带来了什么？肤色判定是如此的简便易行，然而我们是否有必要将职位、爱情、能力、智商、甚至喝茶的邀请都和对方肤色挂钩？ 虽然现在的人类学家们早已不再这么做，但这一标准在人们心中却已根深蒂固。人种的概念起源于生物学的分类尝试，在最终被证明无功而返时，却早已在社会上留下了不可磨灭的印痕。面对这些，我们唯有说 I m Not Going To Spend My Life Being A Color 。（我这辈子绝不为某种肤色而活，出自迈克杰克逊歌曲《black or white》） 55555555555555555555555555555555 镀金的基因 作为科学名词的种族和人种已经危机重重，是时候让它么回归纯粹社会学阵营了。我们一方面认同各族群文化在人类文明中的独特地位，同时也应该更坦然地面对体质上可能存在的客观差异，虽然这种体质差异极可能和体育优势无关。正如范可所言，对人群多样性的关注，应该达到对独立个体的尊重,而不是助长业已存在的不同群体人与人之间的互不信任。 无论如何，对于运动员个人而言， 种族优势 毫无意义。一个很简单的道理，哪怕周遭都是金灿灿的红富士，一只瘪三苹果仍然难逃作为有机肥的命运。竞技体育真正关心的，是如何将个人推上荣誉的最高峰，同时把国家集体（以及曾经的种族）荣誉附加其上。在这方面，运动员的个人天赋，远比种族的所谓平均体质特征更有价值。 难怪瓦里纳说：人种、肤色都没有关系，重要的是一个运动员的天赋。刘翔和我一样，都有着惊人的天赋，只要我们努力训练，就可以取得优秀的成绩。运动科学家竭力使后天训练更有效率，遗传学家们则想尽办法如何把地基打好－－天赋才是他们的专注主题。 遗传学家们用基因还原了种族的社会学之身，同时也赋予了天赋全新的含义。双眼皮、AB血型、男性、黄皮肤、189厘米的身高这些天赋决定了刘翔之为刘翔，而更多人关心的是，刘翔的成功有多少源于天赋？ 与其说天赋由上天注定，毋宁说是基因和环境的拉锯战；遗传度这个概念被用来描述基因对性状的控制程度。双眼皮、血型和性别等因素几乎完全由基因决定；而肤色、身高等数量性状则在很大程度上受到环境的影响，日光浴和牛奶所起的作用可能比基因还大。通过对比相同环境下个人对训练的应答程度，人们发现了难以用环境解释的差异，由此可知基因必定在体能上插了一脚。让人更感兴趣的是，哪些基因蹈了体能这趟浑水？ 遗传学家们只好又一次搬出相关性这一武器，虽然它射程极短而且准度难料，总归聊胜于无。以大腿力量为例，两人之间运动成绩的相关性随着亲缘关系接近而迅速升高。无关亲族几乎毫不相关（相关系数0.08），收养关系因为环境相同有着0.12的相关性，亲子关系、异卵双生的相关系数更高，同卵双生（基因完全相同）则高达0.76。很显然，共享基因的增多为成绩相关性作出了重大贡献。这个结论提示我们，如果你的立定跳远不达标，千万不要找自己的双胞胎兄弟顶替――对于裁判员这可真是个好消息。 双胞胎在运动方面的相似性也有着众多的直观证据。李小双兄弟可能是我们最熟悉的孪生兄弟，在雅典奥运会上，美国体操队的哈姆兄弟为团体夺银立下汗马功劳，新西兰的双胞胎斯文戴尔姐妹更是一举拿下女子赛艇双人双桨冠军。实在有必要在他们的金牌上刻上一副双螺旋。 更多类似研究铺垫了体能基因的红地毯。在有氧运动能力上，同卵双胞胎比异卵双胞胎有着更多的相似性。另一项关于肌肉运动能力的研究似乎开启了时空之门，让我们重回30多年前：24位大学男生的助跑跳远成绩与大学时的父亲高度相关。姚明能成为NBA现役最高球员，除了要感谢布拉德利（他在2006年退役，把这个高帽送给了姚明），其父母基因也功不可没－－这对亚洲最高夫妻中的一员更曾是国家女篮队长。这些证据都暗示着，有运动基因在家族间流动。所以，如果可以的话，我更愿意在起跑之前查查对手的家谱，对于下面这位天才，翻查家谱更是必要。 芬兰越野滑雪运动员门蒂兰塔Eero Mantyranta的成功首次投射出运动基因的清晰背影。1937年出生的Mantyranta在六十年代所有滑雪赛事中出尽风头，在三届奥运会和两届世锦赛上共获得了十枚奖牌，其中包括5枚金牌。不说别的，这些奖牌的光总重量就超过二千克。如此惊人的成绩很自然地引起了很多人的怀疑，他们认为Mantyranta体内比常人多出的20%红细胞是兴奋剂所致。 三十年后，家族系谱调查才彻底洗脱了Mantyranta的嫌疑，14名与其有血缘关系的同辈表亲中，另有8人的红细胞数量同样超出常人。研究表明这种天赋来源于EPOR（促红细胞生成素受体）基因的变异，该变异导致了过多促红细胞生成素EPO的合成，进而促进机体合成更多的红细胞。不过对于其他表亲来说，这多出的红细胞并无实际意义，反倒增加了阻塞血管的风险。幸而该突变的频率极低。 Mantyranta体内的红细胞倒是多得其所。越野、长跑等耐力项目都依靠肌肉的有氧呼吸来提供能量，而氧气从肺部到肌肉的过程，正是由红细胞来完成的，这些过多的红细胞偶然间成了制胜之道。
标签: 基因
