Identification of non-coding transcripts regulated by the transcription factor Rap1 by RNA-Seq analysis

Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1 regulated gene promoters. Specifically, Rap1 prevents transcription initiation at cryptic promoters near its binding sites, which is uncoupled from transcription regulation in the protein-coding direction. We further provide evidence that Rap1 acts independently of chromatin-based mechanisms to repress cryptic or divergent transcription. Finally, we show that divergent transcription in the absence of Rap1 is elicited by the RSC chromatin remodeller. We propose that a sequence-specific transcription factor limits access of basal transcription machinery to regulatory elements and adjacent sequences that act as divergent cryptic promoters, thereby providing directionality towards productive transcription.许多活性真核基因启动子（eukaryotic gene promoters）会表现出双向非编码转录（divergent noncoding transcription）现象，但限制这类转录本表达的具体机制尚未得到充分阐明。本研究揭示了序列特异性转录因子（sequence-specific transcription factor）如何在酵母高表达基因处抑制双向非编码转录。我们发现，转录因子Rap1的缺失会在其调控的绝大多数基因启动子区域诱导非编码转录。具体而言，Rap1能够阻止其结合位点附近的隐蔽启动子（cryptic promoters）启动转录，这一过程与蛋白编码方向的转录调控相互独立。我们进一步提供证据表明，Rap1可通过不依赖于染色质调控机制（chromatin-based mechanisms）的方式，抑制隐蔽或双向非编码转录。最后我们证实，在Rap1缺失的情况下，双向非编码转录由RSC染色质重塑复合物（RSC chromatin remodeller）所介导。我们提出，序列特异性转录因子可限制基础转录机器（basal transcription machinery）接触调控元件及邻近的、可作为双向隐蔽启动子的序列，从而为功能性转录（productive transcription）赋予方向性。