Chromatin loop anchors contain core structural components of the gene expression machinery in maize.
Chromatin loop anchors contain core structural components of the gene expression machinery in maize.
复制标题
DOI：
10.1186/s12864-020-07324-0
复制
发表时间：
2021-01-06
期刊：
影响因子：
4.4
通讯作者：
May GD
中科院分区：
文献类型：
--
作者：
Deschamps S;Crow JA;Chaidir N;Peterson-Burch B;Kumar S;Lin H;Zastrow-Hayes G;May GD
三维染色质环结构将调控元件连接到锚定区域的靶基因上。在复杂的植物基因组中，如玉米，已经提出环跨越异染色质区域，以较高的重复序列含量为标志，但对其空间组织和全基因组发生与转录活性的关系知之甚少。本研究将玉米B73叶片组织的超深Hi-C测序与基因表达和开放染色质测序相结合，以发现染色质环，并与分层拓扑相关结构域（TADs）和转录活性相关。大多数锚点在以前公开的玉米高分辨率相互作用数据集的多个循环之间共享，这表明一个高度动态的环境，在多个相互作用网络中涉及一组保守的锚点。染色质环内部的重复内容比它们两侧的锚点高。一小部分高分辨率相互作用锚点完全嵌入较大的染色质环中，与活性基因和假定的蛋白质结合位点共定位。组合分析表明，这里研究的所有锚点与至少81.5%的表达基因和74%的开放染色质区域共定位。大约38%的Hi-C染色质环完全嵌入分层的类tad结构域，而其余的染色质环与结构域边界或与不同的结构域共享锚点。这些不同的环类型表现出开放染色质区域和表达基因的特定重叠模式，但没有明显的基因表达模式。此外，来自先前公开的玉米eQTL数据集的所有独特变体中，多达63%与Hi-C环锚点重叠。锚点注释表明，这里检测到的所有环中有不到7%可能缺乏任何基因或调控元件。玉米基因组中染色质环锚点的整体组织表明，一个环建模系统假设类似于重复序列丰富区域的相分离。一组保守的染色质环锚点映射到层次结构域，包含玉米基因表达机制的核心结构成分。本文提供的数据将为进一步研究它们在玉米基因组中转录复合物的形成和转录活性调控方面的功能提供有用的参考。在线版本包含补充材料，可在10.1186/s12864-020-07324-0获得。
Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with hierarchical topologically-associating domains (TADs) and transcriptional activity. A majority of all anchors are shared between multiple loops from previous public maize high-resolution interactome datasets, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analyses indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Approximately 38% of all Hi-C chromatin loops are fully embedded within hierarchical TAD-like domains, while the remaining ones share anchors with domain boundaries or with distinct domains. Those various loop types exhibit specific patterns of overlap for open chromatin regions and expressed genes, but no apparent pattern of gene expression. In addition, up to 63% of all unique variants derived from a prior public maize eQTL dataset overlap with Hi-C loop anchors. Anchor annotation suggests that < 7% of all loops detected here are potentially devoid of any genes or regulatory elements. The overall organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. Sets of conserved chromatin loop anchors mapping to hierarchical domains contains core structural components of the gene expression machinery in maize. The data presented here will be a useful reference to further investigate their function in regard to the formation of transcriptional complexes and the regulation of transcriptional activity in the maize genome. The online version contains supplementary material available at 10.1186/s12864-020-07324-0.
登录
查看更多内容
DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
染色质相互作用图揭示了玉米数量性状的遗传调控
影响因子：
16.6
作者：
Peng, Yong;Xiong, Dan;Li, Xingwang
通讯作者：
Li, Xingwang
由局部 A/B 区室确定的大型植物基因组的 3D 染色质结构。
影响因子：
27.5
作者：
Dong, Pengfei;Tu, Xiaoyu;Zhong, Silin
通讯作者：
Zhong, Silin
影响因子：
9.3
作者：
Durand NC;Shamim MS;Machol I;Rao SS;Huntley MH;Lander ES;Aiden EL
通讯作者：
Aiden EL
影响因子：
9.3
作者：
Robinson, James T.;Turner, Douglass;Aiden, Erez Lieberman
通讯作者：
Aiden, Erez Lieberman