Broad chromosomal domains of histone modification patterns in C. elegans
Broad chromosomal domains of histone modification patterns in C. elegans
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DOI：
10.1101/gr.115519.110
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发表时间：
2011-02-01
期刊：
影响因子：
7
通讯作者：
Liu, X. Shirley
中科院分区：
文献类型：
--
作者：
Liu, Tao;Rechtsteiner, Andreas;Liu, X. Shirley
染色质免疫沉淀鉴定了基因组DNA和蛋白质之间的特定相互作用，促进了我们对基因水平和染色体水平调控的理解。基于验证抗体的染色质免疫沉淀实验，我们确定了19个组蛋白修饰、一个组蛋白变体和8个染色质相关蛋白在秀丽线虫胚胎和L3幼虫中的全基因组分布。聚类分析确定了五组具有共同特征的染色质标记：两组与基因抑制相关，两组与基因激活相关，一组与X染色体相关。X染色体显示出许多独特的性质，包括富含单甲基化的H4K20和H3K27，这与分别在体细胞组织和生殖细胞中工作的不同抑制机制有关。数据还显示，常染色体之间以及染色体臂和中心之间的染色质组成存在显著差异。与染色体II、IV，特别是V相比，染色体I和III整体上丰富了活性基因的标记，与包含更高表达的基因一致。与细胞学上的异染色质的缺失和线虫染色体的全丝粒性质一致，异染色质的标记，如H3K9甲基化，并不集中在每条染色体上的单个区域。相反，H3K9甲基化在染色体臂上丰富，与减数分裂重组升高的区域重合。染色体臂和染色体中心的活性基因具有非常相似的组蛋白标记分布，这表明臂中的活性区域点缀着异染色质样结构。这些数据证实并扩展了先前的研究，使人们能够深入分析线虫基因组在发育过程中的组织和部署。
Chromatin immunoprecipitation identifies specific interactions between genomic DNA and proteins, advancing our understanding of gene-level and chromosome-level regulation. Based on chromatin immunoprecipitation experiments using validated antibodies, we define the genome-wide distributions of 19 histone modifications, one histone variant, and eight chromatin-associated proteins in Caenorhabditis elegans embryos and L3 larvae. Cluster analysis identified five groups of chromatin marks with shared features: Two groups correlate with gene repression, two with gene activation, and one with the X chromosome. The X chromosome displays numerous unique properties, including enrichment of monomethylated H4K20 and H3K27, which correlate with the different repressive mechanisms that operate in somatic tissues and germ cells, respectively. The data also revealed striking differences in chromatin composition between the autosomes and between chromosome arms and centers. Chromosomes I and III are globally enriched for marks of active genes, consistent with containing more highly expressed genes, compared to chromosomes II, IV, and especially V. Consistent with the absence of cytological heterochromatin and the holocentric nature of C. elegans chromosomes, markers of heterochromatin such as H3K9 methylation are not concentrated at a single region on each chromosome. Instead, H3K9 methylation is enriched on chromosome arms, coincident with zones of elevated meiotic recombination. Active genes in chromosome arms and centers have very similar histone mark distributions, suggesting that active domains in the arms are interspersed with heterochromatin-like structure. These data, which confirm and extend previous studies, allow for in-depth analysis of the organization and deployment of the C. elegans genome during development.