Characterizing higher order structures of chromatin in human cells
Characterizing higher order structures of chromatin in human cells
复制标题
DOI：
10.1101/267856
复制
发表时间：
2018-02
期刊：
影响因子：
--
通讯作者：
U. Schwartz;A. Németh;Sarah D. Diermeier;Josef H. Exler;Stefan Hansch;Rodrigo Maldonado;Leonhard Heizinger;R. Merkl;Gernot Läengst
中科院分区：
文献类型：
--
作者：
U. Schwartz;A. Németh;Sarah D. Diermeier;Josef H. Exler;Stefan Hansch;Rodrigo Maldonado;Leonhard Heizinger;R. Merkl;Gernot Läengst
将DNA包装到染色质中调节DNA可及性，并因此调节所有DNA依赖性过程，例如转录、重组、修复和复制。核小体是DNA形成阵列的基本包装单位，生物化学研究表明，核小体可以分层折叠成染色质的有序高阶结构。最近，使用显微镜技术对染色质的这种定义的组织提出了质疑，提出了一种相当不规则的结构。为了更深入地了解染色质组织的原理，我们应用了原位差异MNase-seq策略，并通过计算机分析了人类染色质的完全和部分双链化的结果。我们研究了细胞中是否存在不同水平的染色质包装。因此，我们利用统计数据分析和计算机建模，评估了不同结构域的kb到Mb基因组区域内的染色质的可访问性。我们发现，在常染色质和异染色质的结构域之间或染色质的其他序列和表观基因组特征之间的压实程度没有差异。因此，我们的数据表明，染色质的高阶结构的差异压实域的情况下。此外，我们只发现了局部结构变化，单个超可接近的核小体围绕调节元件，如增强子和转录起始位点。调节位点本身被结构改变的核小体占据，表现出增加的MNase敏感性。我们的研究结果提供了支持大规模染色质组织的不规则模型的生化证据。
Packaging of DNA into chromatin regulates DNA accessibility and, consequently, all DNA-dependent processes, such as transcription, recombination, repair, and replication. The nucleosome is the basic packaging unit of DNA forming arrays that are suggested, by biochemical studies, to fold hierarchically into ordered higher-order structures of chromatin. This defined organization of chromatin has been recently questioned using microscopy techniques, proposing a rather irregular structure. To gain more insight into the principles of chromatin organization, we applied an in situ differential MNase-seq strategy and analyzed in silico the results of complete and partial digestions of human chromatin. We investigated whether different levels of chromatin packaging exist in the cell. Thus, we assessed the accessibility of chromatin within distinct domains of kb to Mb genomic regions by utilizing statistical data analyses and computer modelling. We found no difference in the degree of compaction between domains of euchromatin and heterochromatin or between other sequence and epigenomic features of chromatin. Thus, our data suggests the absence of differentially compacted domains of higher-order structures of chromatin. Moreover, we identified only local structural changes, with individual hyper-accessible nucleosomes surrounding regulatory elements, such as enhancers and transcription start sites. The regulatory sites per se are occupied with structurally altered nucleosomes, exhibiting increased MNase sensitivity. Our findings provide biochemical evidence that supports an irregular model of large-scale chromatin organization.