Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
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DOI：
10.1101/gr.110098.110
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发表时间：
2011-02-01
期刊：
影响因子：
7
通讯作者：
Karpen, Gary H.
中科院分区：
文献类型：
--
作者：
Riddle, Nicole C.;Minoda, Aki;Karpen, Gary H.
真核生物的基因组有两种基本形式，常染色质和异染色质。我们研究了果蝇异染色质的组成和组织在不同的细胞类型，使用ChIP阵列分析组蛋白修饰和染色体蛋白。如预期的，臂间异染色质和4号染色体平均富集“沉默”标记H3 K9 me 2、H3 K9 me 3、HP 1a和SU（VAR）3-9，并且通常耗尽与活性转录相关的标记。通过这些标记识别的常染色质-异染色质边界的位置在动物组织和大多数细胞系中是相似的，尽管异染色质的量在一些细胞系中是可变的。染色质模式的组合分析揭示了不同的配置文件常染色质，臂间异染色质，和第4染色体。异染色质中沉默和活性蛋白编码基因都显示出染色体蛋白和组蛋白修饰的复杂模式;大多数活性基因都表现出“激活”标记（例如，例如，在一个实施例中，H3 K4 me 3和H3 K36 me 3）和“沉默”标记（e.例如，在一个实施例中，H3 K9 me 2和HP 1a）。异染色质结构域中活性基因的标志似乎是转录起始位点处H3 K9甲基化的丧失。我们还观察到复杂的表观基因组图谱的基因间区域，重复转座因子（TE）序列，并在异染色质的延伸基因。常染色质染色体臂中出乎意料的大部分序列表现出异染色质特征，其在大小、位置和对细胞类型之间的基因表达的影响方面不同。我们的结论是，异染色质/常染色质包装模式显示出更大的复杂性和可塑性比预期的。这种全面的分析为将来研究受异染色质影响或依赖于异染色质的基因活性和染色体功能提供了基础。
Eukaryotic genomes are packaged in two basic forms, euchromatin and heterochromatin. We have examined the composition and organization of Drosophila melanogaster heterochromatin in different cell types using ChIP-array analysis of histone modifications and chromosomal proteins. As anticipated, the pericentric heterochromatin and chromosome 4 are on average enriched for the "silencing" marks H3K9me2, H3K9me3, HP1a, and SU(VAR)3-9, and are generally depleted for marks associated with active transcription. The locations of the euchromatin-heterochromatin borders identified by these marks are similar in animal tissues and most cell lines, although the amount of heterochromatin is variable in some cell lines. Combinatorial analysis of chromatin patterns reveals distinct profiles for euchromatin, pericentric heterochromatin, and the 4th chromosome. Both silent and active protein-coding genes in heterochromatin display complex patterns of chromosomal proteins and histone modifications; a majority of the active genes exhibit both "activation" marks (e. g., H3K4me3 and H3K36me3) and "silencing" marks (e. g., H3K9me2 and HP1a). The hallmark of active genes in heterochromatic domains appears to be a loss of H3K9 methylation at the transcription start site. We also observe complex epigenomic profiles of intergenic regions, repeated transposable element (TE) sequences, and genes in the heterochromatic extensions. An unexpectedly large fraction of sequences in the euchromatic chromosome arms exhibits a heterochromatic chromatin signature, which differs in size, position, and impact on gene expression among cell types. We conclude that patterns of heterochromatin/euchromatin packaging show greater complexity and plasticity than anticipated. This comprehensive analysis provides a foundation for future studies of gene activity and chromosomal functions that are influenced by or dependent upon heterochromatin.