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ENCODE计划中enhance和promoter的确定-文献辑

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发表于 2016-9-28 20:45:18 | 显示全部楼层 |阅读模式
关于enhance和promoter到底在人类的全基因组是如何分布的,具体坐标是多少,有多少个,是不是有时空特异性?个体和细胞系差异性多大?这是个很复杂的知识点,ENCODE计划中大量的公共数据可以支持它们的确定。我先放一些文献:
增强子的作用同增强子的取向(5’一3’或3’一5’)无关,甚至远离靶基因达几千kb也仍有增强作用。它们一般坐落于基因组的非编码区域。Several histone marks (H3K4me1, H3K4me2, H3K9Ac, H3K14Ac, H3K27Ac) and nucleosome-depleted regions 这些区域一般被认为是有增强子活性的。
nucleosome-depleted regions can be visualized by DNaseI-sensitivity and/or Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE)

有细胞系的特异性:
用H3K4me1 and H3K4me3 peaks来定义promoters and enhancers:
H3K4me3 peaks not overlapping with H3K4me1 peaks and close to a TSS (±5 kb) were defined as promoters, as NA otherwise;
H3K4me1 peaks not overlapping with H3K4me3 peaks were defined as enhancers;
regions with the co-presence of H3K4me1 and H3K4me3 peaks 需要用IGV仔细看看,再根据信号情况和距离TSS的距离判定
Finally, promoters or enhancers were defined as active if overlapping with H3K27ac peaks.


paper:2016-Data integration for identification of important transcription factors of STAT6-mediated cell fate decisions. :http://www.funpecrp.com.br/gmr/year2016/vol15-2/pdf/gmr8493.pdf
paper:2014-Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells :
http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-331
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49651 (MDAMB231 )
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46074 (HMEC )
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29611 (HMEC )

paper:2014-review-Enhancer RNAs and regulated transcriptional programs.: http://www.cell.com/trends/biochemical-sciences/abstract/S0968-0004(14)00032-2
paper:2015-review-The selection and function of cell type-specific enhancers:http://www.nature.com/nrm/journal/v16/n3/full/nrm3949.html
paper:2013-review-Modification of Enhancer Chromatin: What, How, and Why? : http://www.sciencedirect.com/science/article/pii/S1097276513001020
paper:2014- Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth
http://www.nature.com/ncb/journal/v17/n9/full/ncb3216.html
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66081


DNA binding site motif database
http://groups.csail.mit.edu/cgs/gem/
http://nar.oxfordjournals.org/content/32/suppl_2/W199.full
http://meme-suite.org/doc/download.html?man_type=web





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发表于 2016-10-31 18:16:53 | 显示全部楼层
好资源,谢谢
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