The ground-state and evolution of promoter directionality revealed by a functional evolutionary approach

Although the RNA polymerase (Pol) II machinery inherently initiates transcription in one direction, promoter regions are often “bidirectional” in vivo, giving rise to divergent RNA transcripts, many of which are non-coding and highly unstable. Here, we use a functional evolutionary approach to address whether bidirectional promoter regions are a mechanistic consequence of Pol II transcription or serve an evolved biological function. This involves nascent transcript mapping in S. cerevisiae strains containing large segments of foreign, and hence evolutionarily irrelevant, yeast DNA. Promoter regions in foreign species environments lose the directionality they have in their native species, indicating that DNA sequences and proteins co-evolve to promote directional transcription. Furthermore, fortuitous promoters emerge frequently in foreign DNA, and these produce equal transcription in both directions. Thus, without evolutionary pressure, the transcriptional ground state of promoter regions is intrinsically bidirectional. Interestingly, promoter regions of newly evolved genes tend to promote bidirectional transcription, and when fortuitous promoters arise in evolution, transcription factor binding sites are either purged through mutation or retained to enable new functionality. These results indicate that promoter regions are intrinsically bidirectional and are shaped by evolution to bias transcription of coding transcripts while suppressing non-coding transcriptional noise. We transferred artificial chromosomes made of DNA extracted from K. lactis and D. hansenii to S. cerevisiae and performed NET-Seq

尽管RNA聚合酶（Pol II）系统本质上仅能单向起始转录，但启动子区域在体内往往呈现"双向性"，可产生双向RNA转录本，其中多数为非编码且高度不稳定的转录本。本研究采用功能进化研究方法，旨在探究双向启动子区域究竟是RNA聚合酶II转录的机制性产物，还是进化而来的生物学功能载体。本研究通过对携带大片段外源（进化上无关联）酵母DNA的酿酒酵母（S. cerevisiae）菌株进行新生转录本定位分析展开相关研究。外源物种环境中的启动子区域会丧失其在原物种中所具备的方向性，这表明DNA序列与蛋白质协同进化，以促成定向转录。此外，外源DNA中频繁出现偶然启动子，此类启动子可在两个方向产生等量的转录产物。因此，在无进化压力的情况下，启动子区域的转录基础状态本质上是双向的。值得注意的是，新进化基因的启动子区域往往倾向于促成双向转录；当进化过程中出现偶然启动子时，转录因子结合位点要么通过突变被清除，要么被保留以实现新的功能。上述结果表明，启动子区域本质上是双向的，并经由进化塑造，以偏向编码转录本的转录，同时抑制非编码转录噪声。我们将从乳酸克鲁维酵母（K. lactis）与汉逊德巴利酵母（D. hansenii）中提取的DNA构建的人工染色体转入酿酒酵母（S. cerevisiae），并完成了NET-Seq。