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第一作者:Ezgi Süheyla Karaaslan
第一单位:德国图宾根大学
通讯作者:Chang Liu
Abstract
背景回顾:Information in the genome is not only encoded within sequence or epigenetic modifications, but is also found in how it folds in three-dimensional space. The formation of self-interacting genomic regions, named topologically associated domains (TADs), is known as a key feature of genome organization beyond the nucleosomal level.
提出问题:However, our understanding of the formation and function of TADs in plants is extremely limited. 主要研究:Here we show that the genome of Marchantia polymorpha, a member of a basal land plant lineage, exhibits TADs with epigenetic features similar to those of higher plants. 结果1-表观标记:By analysing various epigenetic marks across Marchantia TADs, we find that these regions generally represent interstitial heterochromatin and their borders are enriched with Marchantia transcription factor TCP1. 结果2-TCP1:We also identify a type of TAD that we name ‘TCP1-rich TAD’, in which genomic regions are highly accessible and are densely bound by TCP1 proteins. 结果3-TCP1靶基因表达:Transcription of TCP1 target genes differs on the basis gene location, and those in TCP1-rich TADs clearly show a lower expression level. 结果4-tcp1突变体:In tcp1 mutant lines, neither TCP1-bound TAD borders nor TCP1-rich TADs display drastically altered chromatin organization patterns, suggesting that, in Marchantia, TCP1 is dispensable for TAD formation. However, we find that in tcp1 mutants, genes residing in TCP1-rich TADs have a greater extent of expression fold change as opposed to genes that do not belong to these TADs. 结论:Our results suggest that, besides standing as spatial chromatin-packing modules, plant TADs function as nuclear microcompartments associated with transcription factor activities.
摘 要
基因组的信息不仅仅局限于序列或者表观修饰,还涉及到其在三维空间上是如何折叠的。拓扑关联结构域TAD是基因组上自我互作的基因组区域,是超越核小体层面的基因组组织关键信息。然而,目前我们对于植物中TADs的形成与功能了解有限。本文中,作者发现基部陆地植物地钱的基因组中,存在与高等植物类似表观特征的TADs。通过分析地钱TADs的多个表观标记,作者发现这些区域通常位于间质异染色质,且其边界序列显著富集TCP1转录因子。作者甚至鉴定到了一类叫做“TCP1-rich”的TAD,其所处的基因组区域高度开放,并且存在多个TCP1结合位点。TCP1靶基因的转录基于基因的位置而有所差异,在TCP1-rich TAD上的TCP1靶基因的表达水平明显更低。在tcp1突变体中,无论是TCP1结合的TAD边界,还是TCP1-rich的TADs,染色质组织模式都发生了剧烈的改变,说明在地钱中TCP1对于TAD的形成是不可或缺的。然而,作者还发现在tcp1突变体中,位于TCP1-rich TADs中的基因具有更高水平的基因表达水平变化,这与其它不属于该类TAD区域上的基因变化趋势相反。本文的研究结果说明,植物的TADs除了是空间染色质包装模块之外,同时还作为核微室,作用于转录因子的活性。
通讯作者
**Chang Liu** 个人简介: 2001-2005年,新加坡国立大学,学士; 2005-2010年,新加坡国立大学,博士。 研究方向: 植物3D染色质结构。
doi: 10.1038/s41477-020-00766-0
Journal: Nature Plants
Published date: September 07, 2020
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