一种酿酒酵母中新发现的RNA转录干扰机制研究

Our recent study has demonstrated that, overlapping 3’ untranslated regions of convergent genes (account for over 20% of all ORFs) can mediate mutually transcriptional interference in the budding yeast Saccharomyces cerevisiae genome. The interference is independent of the RNAi pathway, and is determined only by overlapping 3’UTRs and independent of the coding products of genes. These 3’UTRs can regulate expression of the convergent partners both locally and ectopically. The newly discovered regulatory mechanics is quickly highlighted by Nature Reviews Genetics right after its publication. However, much of the 3’-UTR anti-regulation of gene expression remains unknown mechanistically, the project proposed is here designed to fill the gaps through implementing a multi-angle approach that integrates multilayer omics data from chromatin structure, transcriptional process and post-transcription modification, which may be revealed from the next-generation sequencing techniques. In addition, we will further exploit the impacts and extents of the new expression regulatory machinery on cell response upon environmental variation in the model organism. The project will undoubtedly broaden our view on RNA biology, and enrich the knowledge of RNA-molecule-based regulatory pattern. We expect that a mechanistic model would be developed to understand the sophistication of the similar transcrptional interference phenomina in other model organisms such as Drosophila and Arabidopsis and regulatory pattern of lncRNA in higher organisms.

我们最新的研究发现，酿酒酵母基因组中对向基因（占全基因组编码基因的20%以上）3’UTR的重叠会导致相互转录干扰；该干扰现象不依赖于基因编码产物本身，仅决定于重叠的3’UTR；它不仅在原位而且还可以从异位反式起作用，但完全异于RNAi的调控机制。这是一种全新的基因调控模式，刚报道就引起Nature Reviews Genetics期刊的关注。为此，本项目将聚焦这一新发现的转录干扰现象，整合现代分子生物学的精巧和新一代测序数据解析的深度和广度，从染色质结构、转录过程以及转录后调控等多重视角，揭示其内在的遗传调控规律，并阐明其对细胞响应环境变化等生命活动的科学意义。本项目的开展必将进一步拓展人们对RNA生物学的认知，为RNA分子介导的基因调控模式积累新的科学知识；此外，本项目所发展的分子机制对解释果蝇、拟南芥等物种的类似转录干扰现象以及高等生物中lncRNA的调控模式具有潜在的适应性。

高等动植物中广泛存在microRNA分子对基因表达的负调控模式。然而，酿酒酵母中缺乏类似的RNA转录干扰机制，却存在比较原始的转录干扰机制，即：酵母基因组紧凑导致大量的基因存在重叠，转录过程存在转录干扰的可能。我们发现了对向排列基因的转录本3’UTR可以介导对与之重叠基因的转录干扰。本项目通过核小体占位实验和组蛋白的表观遗传修饰水平的检测，发现对向排列基因3’UTR区域染色质结构松散，处于活性状态，易于被其它生物分子结合和调控。此外，借助基因组转录继续实验(Genomic run-on)，进一步揭示了这种转录调控是通过3’UTR介导、抑制了被调控基因转录速率。最后，利用链特异性RNA-seq，对酿酒酵母发酵和非发酵两种培养条件下全转录组进行了比较，发现对向排列基因对之间的相互负调控在碳源代谢的生物学途径上有着协同作用，其中代表基因对包括ALD4和GDH1、TAF12和SWI5以及SCC2和SAS4等 。这进一步证实了对向排列基因的调控机制对于酿酒酵母包括碳源代谢等基本的生理活动具有重要的作用。本项目的开展给我们对生物界中的转录调控模式的理解打开了一个新的视角，也积累了新的科学知识。