A phase separated active subnuclear compartment safeguards repressive chromatin domains [iCLIP]. A phase separated active subnuclear compartment safeguards repressive chromatin domains [iCLIP]

The nucleus is composed of membrane-less subnuclear compartments, containing intrinsically disordered proteins and RNAs that phase separate (PS) and contribute to specific nuclear reactions. However, whether and how different subnuclear compartments can intercommunicate remains elusive. Here we identified nuclear bodies with PS features composed of BAZ2A, a factor associating with active chromatin. BAZ2A-bodies depend on active transcription, RNAs, and the non-disordered BAZ2A RNA-binding TAM domain. Although BAZ2A and H3K27me3 occupancies anticorrelate in the linear genome, in the nuclear space BAZ2A-bodies contact H3K27me3-bodies. Disruption of BAZ2A-bodies promotes BAZ2A invasion into H3K27me3-domains, causing H3K27me3-bodies loss, H3K27me3 decrease, and gene upregulation. BAZ2A-bodies formation is negatively regulated by the nuclear-speckles associated lncRNA Malat1 that interacts with BAZ2A and mediates BAZ2A association to chromatin at nuclear speckles, which do not contact BAZ2A-bodies. The results unravel how active compartments protect repressive compartments using PS mechanisms that are promoted or impaired according to the type of RNA interactions with RNA-binding proteins. Overall design: iCLIP in mouse ESCs.

细胞核由无膜亚核区室组成，这类区室包含固有无序蛋白（intrinsically disordered proteins）以及可发生相分离（phase separation, PS）的核糖核酸，参与特定核反应过程。然而，不同亚核区室是否能够相互通讯、以及其具体的通讯机制，目前仍尚不明确。
本研究鉴定出一类具有相分离特征的核体，其组成为BAZ2A——一种与活性染色质相关的因子。BAZ2A核体的形成依赖于活性转录、核糖核酸以及无无序结构的BAZ2A RNA结合TAM结构域。尽管在线性基因组中，BAZ2A的结合富集与H3K27me3（组蛋白H3赖氨酸27三甲基化）的分布呈负相关，但在核空间内，BAZ2A核体可与H3K27me3核体发生相互接触。
破坏BAZ2A核体可促进BAZ2A侵入H3K27me3结构域，进而导致H3K27me3核体丢失、H3K27me3水平降低以及基因上调。BAZ2A核体的形成受到核斑相关长链非编码RNA（long non-coding RNA, lncRNA）Malat1的负调控。该lncRNA可与BAZ2A结合，并介导BAZ2A与核斑处的染色质结合，而此类染色质区域并不与BAZ2A核体发生接触。
本研究结果揭示了活性区室如何通过相分离机制保护抑制性区室：此类相分离过程会根据RNA与RNA结合蛋白的相互作用类型被促进或削弱。
整体实验设计：小鼠胚胎干细胞（mouse embryonic stem cells, ESCs）中的紫外交联免疫沉淀测序（iCLIP）实验。