Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance.
Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance.
复制标题
DOI：
10.1111/tpj.12963
复制
发表时间：
2015-10
期刊：
影响因子：
--
通讯作者：
Flavell AJ
中科院分区：
文献类型：
--
作者：
Baker K;Dhillon T;Colas I;Cook N;Milne I;Milne L;Bayer M;Flavell AJ
携带不同共价修饰的组蛋白的组合是表观遗传变异的主要组成部分。我们通过染色质免疫沉淀下一代测序（ChIP‐seq）在大麦幼苗表观基因组中绘制了9个修饰的组蛋白。修饰的染色体分布将它们分为四个不同的类别，并且给定类别的成员也倾向于在局部DNA水平上一致，这表明全球分布模式反映了局部表观遗传环境。我们使用这种峰共享来定义10个染色质状态，代表大麦基因组中的局部表观遗传环境。五种状态主要映射到基因，五种映射到基因间区域。涉及H3 K36 me 3的两种基因状态优先与组成型基因表达相关，而含有H3 K27 me 3的基因状态与差异表达基因相关。这10个州显示出惊人的分布模式，将大麦染色体分为三个不同的全球环境。首先，端粒近端区域包含高密度的H3 K27 me 3，覆盖基因和基因间DNA，以及非常低水平的抑制性H3 K27 me 1修饰。在这些区域的两侧是富含基因的内部区域，这些区域富含活性染色质状态，并且H3 K27 me 3的水平大大降低，H3 K27 me 1和H3 K9 me 2的量增加。最后，H3 K27 me 3耗尽的近着丝粒区域包含具有活性染色质状态的基因岛，这些基因岛被广泛的富含反转录转座子的区域分开，这些区域与丰富的H3 K27 me 1和H3 K9 me 2修饰相关。我们提出了大麦的表观基因组框架，其中基因间H3 K27 me 3指定端粒近端区域的兼性异染色质，H3 K27 me 1诊断大麦基因组中其他地方的组成型异染色质。小麦族谷物是世界上最重要的作物之一，但其表观基因组学在很大程度上尚未研究。在这里，我们使用ChIP-Seq来探索大麦的表观基因组，在基因和基因组水平上鉴定和绘制9种修饰组蛋白的染色质状态。
Combinations of histones carrying different covalent modifications are a major component of epigenetic variation. We have mapped nine modified histones in the barley seedling epigenome by chromatin immunoprecipitation next‐generation sequencing (ChIP‐seq). The chromosomal distributions of the modifications group them into four different classes, and members of a given class also tend to coincide at the local DNA level, suggesting that global distribution patterns reflect local epigenetic environments. We used this peak sharing to define 10 chromatin states representing local epigenetic environments in the barley genome. Five states map mainly to genes and five to intergenic regions. Two genic states involving H3K36me3 are preferentially associated with constitutive gene expression, while an H3K27me3‐containing genic state is associated with differentially expressed genes. The 10 states display striking distribution patterns that divide barley chromosomes into three distinct global environments. First, telomere‐proximal regions contain high densities of H3K27me3 covering both genes and intergenic DNA, together with very low levels of the repressive H3K27me1 modification. Flanking these are gene‐rich interior regions that are rich in active chromatin states and have greatly decreased levels of H3K27me3 and increasing amounts of H3K27me1 and H3K9me2. Lastly, H3K27me3‐depleted pericentromeric regions contain gene islands with active chromatin states separated by extensive retrotransposon‐rich regions that are associated with abundant H3K27me1 and H3K9me2 modifications. We propose an epigenomic framework for barley whereby intergenic H3K27me3 specifies facultative heterochromatin in the telomere‐proximal regions and H3K27me1 is diagnostic for constitutive heterochromatin elsewhere in the barley genome. Triticeae cereals are among the most important crops worldwide yet their epigenomics are largely unstudied. Here we have used ChIP‐Seq to explore the epigenome of barley, identifying and mapping chromatin states of nine modified histones at both gene and genome levels.