Binding to RNA regulates Set1 function [ChIP-seq]. Binding to RNA regulates Set1 function [ChIP-seq]

The Set1 family of histone H3 lysine 4 (H3K4) methyltransferases is highly conserved from yeast to humans. Here we show that the Set1 complex (Set1C) directly binds RNA in vitro through the regions that comprise the double RNA recognition motifs (dRRM) and N-SET domain within Set1 and its subunit Spp1. To investigate the functional relevance of RNA binding, we performed UV RNA cross-linking (CRAC) for Set1 and RNA polymerase II in parallel with ChIP-seq experiments. Set1 binds nascent transcripts through its dRRM. RNA binding is important to define the appropriate topology of Set1C distribution along transcription units and correlates with the efficient deposition of the H3K4me3 mark. In addition, we uncovered that Set1 binds to different classes of RNAs to levels that largely exceed the levels of binding to the general population of transcripts, suggesting the Set1 persists on these RNAs after transcription. This class includes RNAs derived from SET1, Ty1 retrotransposons, specific transcription factors genes and snRNAs. We propose that Set1 modulates adaptive responses, as exemplified by the posttranscriptional inhibition of Ty1 retrotransposition. Overall design: Investigation of the functional relevance of RNA binding in yeast using RNA cross-linking (CRAC) for Set1 and RNA polymerase II and ChIP-seq experiments.

组蛋白H3赖氨酸4（H3K4）甲基转移酶的Set1家族在从酵母到人类的物种间高度保守。本研究证实，Set1复合物（Set1C）可通过Set1及其亚基Spp1内包含双RNA识别基序（double RNA recognition motifs, dRRM）与N-SET结构域的区域，在体外直接结合RNA。为探究RNA结合的功能相关性，本研究并行开展了针对Set1与RNA聚合酶II（RNA polymerase II）的紫外RNA交联（UV RNA cross-linking, CRAC）实验以及染色质免疫沉淀测序（chromatin immunoprecipitation sequencing, ChIP-seq）实验。Set1可通过其双RNA识别基序结合新生转录本。RNA结合对于确定Set1复合物在转录单元上的适宜分布拓扑结构至关重要，且与H3K4me3（组蛋白H3赖氨酸4三甲基化）修饰的高效沉积密切相关。此外，本研究发现Set1对不同类别RNA的结合水平远高于其对普通转录本群体的结合水平，提示Set1可在转录结束后仍结合于这些RNA上。该类RNA包括源自SET1、Ty1反转录转座子（Ty1 retrotransposons）、特定转录因子基因以及小核RNA（snRNAs）的转录产物。本研究提出，Set1可调控适应性应答，这一结论可通过Ty1反转录转座的转录后抑制得到佐证。实验整体设计：通过针对Set1与RNA聚合酶II的紫外RNA交联实验及染色质免疫沉淀测序实验，探究酵母中RNA结合的功能相关性。