Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_ChIP). Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_ChIP)

Polyploidization events are known to trigger extensive epigenetic and transcriptional alteration of the duplicated or merged genomes, accompanied by small- and large-scale conformational changes. The genome of modern hexaploid wheat (Triticum aestivum L.; 2n = 6x = 42) is the product of two rounds of interspecific hybridization between three closely related diploid species, resulting in the presence of distinct but highly syntenic sub-genomes (AA, BB and DD). We examined the large-scale chromatin architecture of the nucleus of wheat using Hi-C, a genome-wide chromatin conformation capture (3C) method and GISH, (genomic in situ hybridization). We found evidence that physical interactions occur with significantly higher frequency within sub genomes (A with A, B with B or D with D) than between sub genomes (A with B or D, etc. ...), defining sub-nuclear “genomic territories”. In addition, we observed a polarized distribution of facultative and constitutive heterochromatin that suggests a functional compartmentalization within the nucleus. On a local scale, we found that genes tend to interact mainly with other genes over long-distance “loops” that are especially established between genes presenting similar expression levels and bearing the same histone marks. Moreover, gene pairs in spatial proximity show similar changes in expression levels between shoots and roots. Consistently, we found that physical contact between genes is mediated by RNA polymerase II (RNAPII). Immunofluorescence assays with anti RNAP2 antibodies revealed the presence of “transcription factories” in which multiple interacting genes are co-transcribed. This indicates that local-scale topology is an important factor for transcriptional regulation as it determines the micro-compartimentalization of active genes within the nucleus.Our results provide a framework for understanding the physical organization of wheat genome and highlight the interplay between chromosome conformation and gene expression in wheat. Overall design: 1 ChIP-seq library was sequenced

多倍化（polyploidization）事件已知会引发重复或融合基因组的广泛表观遗传与转录组改变，并伴随小尺度及大尺度的构象变化。现代六倍体小麦（Triticum aestivum L.; 2n = 6x = 42）的基因组是三个近缘二倍体物种历经两轮种间杂交的产物，由此形成了三个虽彼此独立但高度共线性的亚基因组（AA、BB与DD）。我们采用Hi-C——一种全基因组染色质构象捕获（3C, Chromatin Conformation Capture）技术——以及基因组原位杂交（GISH, Genomic In Situ Hybridization），解析了小麦细胞核的大尺度染色质构象。我们发现，亚基因组内部（如A与A、B与B或D与D）的物理互作频率显著高于亚基因组之间（如A与B或A与D等），由此界定了细胞核内"基因组领地"。此外，我们观察到兼性异染色质与组成型异染色质的极化分布，这暗示细胞核内存在功能区室化。在局部尺度上，我们发现基因主要通过长距离"环"与其他基因发生互作，这类环尤其易在表达水平相似且携带相同组蛋白修饰的基因之间形成。此外，空间上邻近的基因对在地上部与根系之间的表达变化模式相似。与之相符的是，我们发现基因间的物理接触由RNA聚合酶II（RNAPII）介导。采用抗RNAP2抗体的免疫荧光实验证实，存在"转录工厂"结构，多个互作基因可在此处被共同转录。这表明局部尺度的染色质拓扑结构是转录调控的重要影响因素，因其决定了细胞核内活跃基因的微区室化分布。本研究结果为解析小麦基因组的物理组织模式提供了研究框架，并揭示了小麦中染色体构象与基因表达之间的互作关系。整体实验设计：对1个染色质免疫共沉淀测序（ChIP-seq, Chromatin Immunoprecipitation Sequencing）文库进行了测序。