SWI/SNF Associates with Nascent Pre-mRNPs and Regulates Alternative Pre-mRNA Processing

The SWI/SNF chromatin remodeling complexes regulate the transcription of many genes by remodeling nucleosomes at promoter regions. In Drosophila, SWI/SNF plays an important role in ecdysone-dependent transcription regulation. Studies in human cells suggest that Brahma (Brm), the ATPase subunit of SWI/SNF, regulates alternative pre-mRNA splicing by modulating transcription elongation rates. We describe, here, experiments that study the association of Brm with transcribed genes in Chironomus tentans and Drosophila melanogaster, the purpose of which was to further elucidate the mechanisms by which Brm regulates pre-mRNA processing. We show that Brm becomes incorporated into nascent Balbiani ring pre-mRNPs co-transcriptionally and that the human Brm and Brg1 proteins are associated with RNPs. We have analyzed the expression profiles of D. melanogaster S2 cells in which the levels of individual SWI/SNF subunits have been reduced by RNA interference, and we show that depletion of SWI/SNF core subunits changes the relative abundance of alternative transcripts from a subset of genes. This observation, and the fact that a fraction of Brm is not associated with chromatin but with nascent pre-mRNPs, suggest that SWI/SNF affects pre-mRNA processing by acting at the RNA level. Ontology enrichment tests indicate that the genes that are regulated post-transcriptionally by SWI/SNF are mostly enzymes and transcription factors that regulate postembryonic developmental processes. In summary, the data suggest that SWI/SNF becomes incorporated into nascent pre-mRNPs and acts post-transcriptionally to regulate not only the amount of mRNA synthesized from a given promoter but also the type of alternative transcript produced.SWI/SNF染色质重塑复合物（SWI/SNF chromatin remodeling complexes）通过重塑启动子区域的核小体，调控众多基因的转录进程。在果蝇（Drosophila）中，SWI/SNF复合物在蜕皮激素依赖的转录调控中发挥关键作用。针对人类细胞的研究显示，SWI/SNF的ATP酶亚基Brahma（Brm）可通过调控转录延伸速率，参与前信使RNA（pre-mRNA）的可变剪接调控。 本研究针对摇蚊（Chironomus tentans）与黑腹果蝇（Drosophila melanogaster）中Brm与转录基因的结合情况开展实验，旨在进一步阐明Brm调控前信使RNA加工的分子机制。研究结果表明，Brm可共转录地整合至新生巴尔比亚尼环（Balbiani ring）前信使核糖核蛋白颗粒（pre-mRNPs）中，且人类Brm与Brg1蛋白可与核糖核蛋白颗粒（RNPs）结合。 我们通过RNA干扰（RNA interference）技术下调黑腹果蝇S2细胞中单个SWI/SNF亚基的表达水平，并对其转录组表达谱进行分析，结果发现SWI/SNF核心亚基的敲除会改变部分基因的可变转录本相对丰度。这一观察结果，加之部分Brm并不结合染色质而是与新生前信使核糖核蛋白颗粒结合的事实，提示SWI/SNF可通过作用于RNA层面调控前信使RNA的加工过程。基因本体富集分析（ontology enrichment tests）结果显示，受SWI/SNF转录后调控的基因大多为调控胚胎后发育过程的酶类与转录因子。 综上，本研究数据表明SWI/SNF可整合至新生前信使核糖核蛋白颗粒中，在转录后水平同时调控特定启动子合成的mRNA总量，以及所产生的可变转录本类型。