Transcriptome analysis of Drrp6 and Drrp6, sen1DNIM by RNAseq

Pervasive transcription is a widespread phenomenon leading to the production of a plethora of non-coding RNAs (ncRNAs) without apparent function. Pervasive transcription poses a risk that needs to be controlled to prevent the perturbation of gene expression. In yeast, the highly conserved helicase Sen1 restricts pervasive transcription by inducing termination of non-coding transcription. However, the mechanisms underlying the specific function of Sen1 at ncRNAs are poorly understood. Here we identify a motif in an intrinsically disordered region of Sen1 that mimics the phosphorylated carboxy terminal domain (CTD) of RNA polymerase II and characterize structurally its recognition by the CTD-interacting domain of Nrd1, an RNA-binding protein that binds specific sequences in ncRNAs. In addition, we show that Sen1-dependent termination strictly requires the recognition of the Ser5-phosphorylated form of the CTD by the N-terminal domain of Sen1. Furthermore, we find that the N-terminal and the C-terminal domains of Sen1 can mediate intra-molecular interactions. Our results shed light onto the network of protein-protein interactions that control termination of non-coding transcription by Sen1.广泛转录是一种普遍存在的生物学现象，可产生大量无明确功能的非编码RNA（non-coding RNAs，ncRNAs）。广泛转录会带来潜在风险，需对其加以调控以避免基因表达受到扰动。在酵母中，高度保守的解旋酶Sen1可通过诱导非编码转录的终止来抑制广泛转录过程。然而，学界对Sen1在ncRNAs上发挥特异性功能的分子机制仍知之甚少。本研究中，我们在Sen1的内在无序区域中鉴定出一段模体，该模体可模拟RNA聚合酶II的磷酸化羧基末端结构域（carboxy terminal domain，CTD）；同时我们还解析了RNA结合蛋白（RNA-binding protein）Nrd1的CTD相互作用结构域对该模体的识别结构，Nrd1是一种可结合ncRNAs特定序列的蛋白。此外，我们证实依赖Sen1的转录终止过程严格需要Sen1的N端结构域识别CTD的Ser5磷酸化形式。进一步研究发现，Sen1的N端结构域与C端结构域可介导分子内相互作用。本研究结果为解析调控Sen1介导的非编码转录终止的蛋白质-蛋白质相互作用网络提供了新的见解。