Nascent RNA antagonises the interaction of a set of regulatory proteins with chromatin

A number of regulatory factors are recruited to chromatin by specialised RNAs. Whether RNA has a more general role in regulating the interaction of proteins with chromatin has not been determined. We used proteomics methods to measure the global impact of nascent RNA on chromatin in embryonic stem cells. Surprisingly, we found that nascent RNA primarily antagonised the interaction of chromatin modifiers and transcriptional regulators with chromatin. Transcriptional inhibition and RNA degradation induced recruitment of a set of transcriptional regulators, chromatin modifiers, nucleosome remodelers, and regulators of higher-order structure. RNA directly bound to factors including BAF, NuRD, EHMT1 and INO80 and inhibited their interaction with nucleosomes. The transcriptional elongation factor P-TEFb directly bound pre-mRNA and its recruitment to chromatin upon Pol II inhibition was regulated by the 7SK ribonucleoprotein complex. We postulate that by antagonising the interaction of regulatory proteins with chromatin, nascent RNA links transcriptional output with chromatin composition.

已有研究表明，多种调控因子可通过特异性RNA被招募至染色质（chromatin）。但RNA在调控蛋白质与染色质相互作用中是否具有更广泛的功能，目前尚未明确。本研究借助蛋白质组学方法，检测了胚胎干细胞（embryonic stem cells）中新生RNA（nascent RNA）对染色质的整体影响。令人意外的是，我们发现新生RNA主要会拮抗染色质修饰因子与转录调控因子同染色质的相互作用。转录抑制与RNA降解实验会诱导一系列转录调控因子、染色质修饰因子、核小体重塑因子以及染色质高级结构调控因子的招募。RNA可直接结合包括BAF、NuRD、EHMT1与INO80在内的多种因子，并抑制这些因子与核小体的相互作用。转录延伸因子P-TEFb可直接结合前体mRNA（pre-mRNA），其在RNA聚合酶II（Pol II）抑制条件下向染色质的招募过程受7SK核糖核蛋白复合物调控。我们据此提出假设：新生RNA可通过拮抗调控蛋白与染色质的相互作用，将转录产出与染色质组成关联起来。