三维基因组研究快讯（2021.03.24）

1.R-loop resolution promotes co-transcriptional chromatin silencing

RNA-mediated chromatin silencing is central to genome regulation in many organisms.
However, how nascent non-coding transcripts regulate chromatin is poorly understood. Here,
through analysis of Arabidopsis FLC, we show that resolution of a nascent-transcript-induced
R-loop promotes chromatin silencing. Stabilization of an antisense-induced R-loop at the
3′ end of FLC enables an RNA binding protein FCA, with its direct partner FY/WDR33 and
other 3′-end processing factors, to polyadenylate the nascent antisense transcript. This clears
the R-loop and recruits the chromatin modifiers demethylating H3K4me1. FCA immunoprecipitates
with components of the m6A writer complex, and m6A modification affects dynamics of FCA nuclear condensates, and promotes FLC chromatin silencing. This mechanism also targets other loci in the Arabidopsis genome, and consistent with this fca and fy are hypersensitive to a DNA damage-inducing drug. These results show how modulation of R-loop stability by co-transcriptional RNA processing can trigger chromatin silencing.

RNA介导的染色质沉默在许多生物中对于基因组调控至关重要。但是，关于新生的非编码转录本如何调节染色质的了解却很少。通过对拟南芥FLC的分析，我们显示了新生转录本诱导的R环的分解可促进染色质沉默。在FLC的3’端稳定反义诱导的R环，可使RNA结合蛋白FCA及其直接伴侣FY / WDR33和其他3’端加工因子将新生的反义转录物聚腺苷酸化。这样可以清除R环并募集染色质修饰剂使H3K4me1脱甲基。 FCA会与m6A writer复合物的成分发生免疫沉淀，而m6A修饰会影响FCA核冷凝物的动力学，并促进FLC染色质沉默。该机制还靶向拟南芥基因组中的其他基因座，并且与此fca和fy一致，它们对诱导DNA损伤的药物高度敏感。这些结果表明，通过共转录RNA处理对R环稳定性的调节如何触发染色质沉默。

2. Investigating the Genome-Wide Localization of the Xist lncRNA and its Roles in X-Chromosome Dampening and the Formation of the Inactive X-Chromosome Compartment

Despite decades of biochemical, proteomic and genetic characterizations of the Xist long non-coding RNA, the master regulator of X-chromosome inactivation (XCI), the spatiotemporal kinetics of Xist expression and how it coordinates the dynamic recruitment of protein effectors to direct robust gene silencing across the X-chromosome remain unexplored. Furthermore, most studies of Xist are conducted in the mouse system, so its role in mediating X-chromosome dampening (XCD), a unique mode of X-chromosome dosage compensation in humans, is still an open question. Therefore, in this thesis, I sought to plug this lack of understanding by (i) elucidating the molecular mechanism by which the chromosome-wide silencing compartment on the inactive X-chromosome (Xi) is formed and maintained across XCI, (ii) determining if XIST is responsible for XCD in human embryonic development, and (iii) characterizing the link between the genome-wide localization patterns of Xist and its effect on gene silencing.

尽管Xist长非编码RNA具有数十年的生化，蛋白质组学和遗传学特征，X染色体失活（XCI）的主要调节剂，Xist表达的时空动力学及其如何协调蛋白质效应子的动态募集以指导健壮基因 X染色体上的沉默仍未开发。 此外，Xist的大多数研究都是在小鼠系统中进行的，因此它在介导X染色体阻尼（XCD）（人类X染色体剂量补偿的独特模式）中的作用仍然是一个悬而未决的问题。 因此，在本论文中，我试图通过（i）阐明无活性X染色体（Xi）上形成并维持整个XCI的全染色体沉默区隔的分子机制，来填补这种缺乏理解的知识，（ii）确定 如果XIST是负责XCD在人类胚胎发育中的作用；以及（iii）表征Xist的全基因组定位模式与其对基因沉默的影响之间的联系。

3. Molecular and computational approaches to map regulatory elements in 3D chromatin structure

Epigenetic marks do not change the sequence of DNA but affect gene expression in a cell-type specific manner by altering the activities of regulatory elements. Development of new molecular biology assays, sequencing technologies,and computational approaches enables