Annotation of chromatin states in 66 complete mouse epigenomes during development.
Annotation of chromatin states in 66 complete mouse epigenomes during development.
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DOI：
10.1038/s42003-021-01756-4
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发表时间：
2021-02-22
影响因子：
5.9
通讯作者：
Weng Z
中科院分区：
文献类型：
--
作者：
van der Velde A;Fan K;Tsuji J;Moore JE;Purcaro MJ;Pratt HE;Weng Z
多细胞生物体的形态和功能不同的细胞类型由其独特的表观基因组和基因表达程序维持。ENCODE项目的第三阶段分析了从胚胎第11.5天到出生每天间隔的12种组织中的66个小鼠表观基因组。将ChromHMM算法应用于这些表观基因组，我们注释了18个染色质状态的启动子，增强子，转录区，抑制区和静止区的特征。我们的综合分析描绘了这些染色质状态的位点的组织特异性和发育轨迹。每个表观基因组的大约0.3%被分配到二价染色质状态，其具有活性标记和抑制性标记H3 K27 me 3。这些基因座在进化上高度保守，富含多梳抑制复合物蛋白结合的沉默子，以及其沉默靶基因的转录起始位点。这些染色质状态分配的集合为研究哺乳动物的发育提供了有用的资源。货车der Velde等人提供了一种了解小鼠产前发育过程中染色质状态变化的资源。作者对来自ENCODE项目III期的ATAC-seq、全基因组亚硫酸氢盐测序和ChIP-seq数据进行了注释，发现二价区域对于沉默谱系特异性基因（包括主转录因子）尤其重要。
The morphologically and functionally distinct cell types of a multicellular organism are maintained by their unique epigenomes and gene expression programs. Phase III of the ENCODE Project profiled 66 mouse epigenomes across twelve tissues at daily intervals from embryonic day 11.5 to birth. Applying the ChromHMM algorithm to these epigenomes, we annotated eighteen chromatin states with characteristics of promoters, enhancers, transcribed regions, repressed regions, and quiescent regions. Our integrative analyses delineate the tissue specificity and developmental trajectory of the loci in these chromatin states. Approximately 0.3% of each epigenome is assigned to a bivalent chromatin state, which harbors both active marks and the repressive mark H3K27me3. Highly evolutionarily conserved, these loci are enriched in silencers bound by polycomb repressive complex proteins, and the transcription start sites of their silenced target genes. This collection of chromatin state assignments provides a useful resource for studying mammalian development. van der Velde et al. present a resource for understanding changes in chromatin states during mouse prenatal development. The authors annotate ATAC-seq, whole-genome bisulfite sequencing, and ChIP-seq of data from Phase III of the ENCODE Project and find that bivalent regions are especially important for silencing lineage-specific genes, including master transcription factors.
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影响因子：
64.8
作者：
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
通讯作者：
Bernstein, Bradley E.
影响因子：
64.8
作者：
Heintzman, Nathaniel D.;Hon, Gary C.;Hawkins, R. David;Kheradpour, Pouya;Stark, Alexander;Harp, Lindsey F.;Ye, Zhen;Lee, Leonard K.;Stuart, Rhona K.;Ching, Christina W.;Ching, Keith A.;Antosiewicz-Bourget, Jessica E.;Liu, Hui;Zhang, Xinmin;Green, Roland D.;Lobanenkov, Victor V.;Stewart, Ron;Thomson, James A.;Crawford, Gregory E.;Kellis, Manolis;Ren, Bing
通讯作者：
Ren, Bing
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
46.9
作者：
Becht, Etienne;McInnes, Leland;Newell, Evan W.
通讯作者：
Newell, Evan W.