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Nature Plants:地钱的TCP转录因子活性与三维染色质结构相关

已有 2051 次阅读 2020-9-15 09:31 |个人分类:每日摘要|系统分类:论文交流

Marchantia TCP transcription factor activity correlates with three-dimensional chromatin structure

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-TCP1We 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 MarchantiaTCP1 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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