The Regulatory Genome and Cistrome (调控基因组与顺式作用元件组) The cistrome refers to the set of cis-acting targets of a trans-acting factor on a genome-wide scale, also known as the in vivo genome-wide location of or histone modifications. The term cistrome is a portmanteau of cistr (from cistron) + ome (from genome). The term cistrome was coined by investigators at the Dana-Farber Cancer Institute and Harvard Medical School. Technologies such as chromatin immunoprecipitation combined with microarray analysis ChIP-on-chip or with massively parallel DNA sequencing ChIP-Seq have greatly facilitated the definition of the cistrome of transcription factors and other chromatin associated proteins. The Regulatory Genome beautifully explains the control of animal development in terms of structure/function relations of inherited regulatory DNA sequence, and the emergent properties of the gene regulatory networks composed of these sequences. The sequencing of the whole genome of multiple species provides us with the instruction book of how to build an organism and make it work, plus a detailed history of how diversity was generated during evolution. Unfortunately, we still understand only a small fraction, which is locating where genes are and deciphering the proteins they code for. The next step is to understand how the correct amount of gene products are produced in space and time to obtain a fully functioning organism, from the egg to the adult. This is what is known as the regulatory genome, a term coined by Eric H. Davidson. References and Further Reading: http://en.wikipedia.org/wiki/Cistrome http://www.cistrome.org/Cistrome/Cistrome_Project.html http://www.sciencemag.org/content/339/6123/1009.13.full http://www.sciencedirect.com/science/book/9780120885633 http://www.ncbi.nlm.nih.gov/pubmed/19247937 http://www.ndsu.edu/pubweb/~mcclean/plsc731/cis-trans/cis-trans6.htm ( cis-acting elements and trans-acting factors ) http://en.wikipedia.org/wiki/Cis-regulatory_element http://en.wikipedia.org/wiki/Trans-acting_factor http://en.wikipedia.org/wiki/Trans-regulatory_element
An interlinked regulatory networks responsible for selecting cell fates between cell cycle commitment and mating arrest in budding yeast. cell cycle 以及信号级联网络都是生物学很热门的网络，和武大数学系合作基本完成了这个网络的建模和分析，跟实验吻合得不错。有机会跟各位专家好好交流：）
1. Zhang Shumei, Chen Sumei, Chen Fadi*, Liu Zhaolei, Fang Weimin . The regulatory role of the auxin in the creeping chrysanthemum habit. Russian Journal of Plant Physiology. 2012,59(3):364~371 2. Zhao Min, Liu Zhaolei, Chen Sumei, Chen Fadi*, Jiang Jiafu, Song Aiping. PCR primers targeting cis _acting promoter elements in plants. Russian Journal of Plant Physiology, 2012,59(3):413~418 3. Jiang Beibei, Chen Sumei, Jiang Jiafu, Zhang Shumei, Chen Fadi*, Fang Weimin* . Changes of endogenous hormones in lateral buds of chrysanthemum during their outgrowth. Russian Journal of Plant Physiology. 2012,59(3):356~363 4. Deng Yanming, Chen Sumei, Chang Qingshan, Wang Haibin, Chen Fadi*. The chrysanthemum × Artemisia vulgaris intergeneric hybrid has better rooting ability and higher resistance to alternaria leaf spot than its chrysanthemum parent. Scientia Horticulturae. 2012,134:185~190 5. Tang Fangping, Wang Haibin, Chen Sumei, Chen Fadi*, Liu Zhaolei, Fang Weiming. Intergeneric hybridization between Dendranthema nankingense and Tanacetum vulgare. Scientia Horticulturae. doi:10.1016/j.scienta.2011.10.003 email:1004769836@qq.com
1. Zhang Shumei, Chen Sumei, Chen Fadi*, Liu Zhaolei, Fang Weimin . The regulatory role of the auxin in the creeping chrysanthemum habit. Russian Journal of Plant Physiology. 2012,59(3):364~371 2. Zhao Min, Liu Zhaolei, Chen Sumei, Chen Fadi*, Jiang Jiafu, Song Aiping. PCR primers targeting cis _acting promoter elements in plants. Russian Journal of Plant Physiology, 2012,59(3):413~418 3. Jiang Beibei, Chen Sumei, Jiang Jiafu, Zhang Shumei, Chen Fadi*, Fang Weimin* . Changes of endogenous hormones in lateral buds of chrysanthemum during their outgrowth. Russian Journal of Plant Physiology. 2012,59(3):356~363 qq 1004769836
Today I present a Physics Review Letter paper named Cell fate as a high-dimensional attractor of a complex gene regulatory network in the journal club of our group. To my surprise, the response is quite polarized. For some people, they take for granted that cell types are attractors in gene network (maybe because that we are in the physics institute for complex system anyhow). They think that it is nothing more than just rewriting the biological facts in the physics language ( I dont know how many biologists actually accept this hypothesis. It is more widely accepted that cell types arise from turning on the type-specific Transcription Factors). They also complained that the 2-gene cross-inhibition example is too simple to demonstrate the effects of high-dimensional gene regulation space. They demanded a clear mathematical formula for cell reprogramming in the gene network. However, other people quickly recognized the importance of the paper and began to embrace this idea enthusiastically. We even begin to discuss how to build such a network. One guy even suggest the possibility to invite the author here for giving a talk by himself. Maybe a good journal club presentation is not to get the consensus of everybody. Rather it can arise the true interests of the people.
标签: regulatory
