Wang Congmao, Liu Chang, Roqueiro Damian, Grimm Dominik, Schwab Rebecca, Becker Claude, Lanz Christa, Weigel Detlef
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
Machine Learning and Computational Biology Research Group, Max Planck Institute for Developmental Biology and Max Planck Institute for Intelligent Systems, 72076 Tübingen, Germany.
Genome Res. 2015 Feb;25(2):246-56. doi: 10.1101/gr.170332.113. Epub 2014 Nov 3.
The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intrachromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1, and H3.3. We also identify more than 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found more than 1000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome.
间期染色体在细胞核内的空间排列对于动植物的基因表达和基因组功能至关重要。最近开发的Hi-C技术是一种研究基因组组装的有效方法。在此，我们展示了植物拟南芥三维基因组组织的详细Hi-C图谱。我们发现，局部染色质组装不同于动物中的模式，存在千碱基对大小的片段，其染色体内相互作用率比相邻区域高得多，这代表了拟南芥基因组构象的主要局部结构特征。这些区域在染色质相互作用的二维表示中呈现为正条带，富含表观遗传标记H3K27me3、H3.1和H3.3。我们还鉴定出400多个类似绝缘子的区域。此外，尽管在动物中突出的拓扑相关结构域（TADs）不是拟南芥基因组组装的明显特征，但我们发现了1000多个具有TAD边界特性的区域，以及数量相近的类似于TAD内部的区域。类似绝缘子的区域、类似TAD边界的区域和类似TAD内部的区域各自富含不同的表观遗传标记，并且各自与不同的基因表达水平相关。我们得出结论，表观遗传修饰、基因密度和转录活性共同塑造了拟南芥核基因组的局部组装。
