Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighbouring genes

Transcription can be quite disruptive for chromatin so cells have evolved mechanisms to preserve chromatin integrity during transcription, hence preventing the emergence of cryptic transcript from spurious promoter sequences. How these transcripts are regulated and processed by cells remains poorly characterized. Notably, very little is known about the termination of cryptic transcription. Here we used RNA-Seq to identify and characterize cryptic transcripts in Spt6 mutant cells (spt6-1004) in Saccharomyces cerevisiae. We found polyadenylated cryptic transcripts running both sense and anti-sense relative to genes in this mutant. Cryptic promoters were enriched for TATA boxes, suggesting that the underlying DNA sequence defines the location of cryptic promoters. While intragenic sense cryptic transcripts terminate at the terminator of the genes that host them, we found that anti-sense cryptic transcripts preferentially terminate at the 3’-end of upstream genes. These findings led us to demonstrate that most terminators in yeast are bidirectional, leading to termination and polyadenylation of transcripts coming from either direction. We propose that S. cerevisiae has evolved this mechanism in order to prevent spurious transcription from invading neighbouring genes, a feature particularly critical for organisms with small compact genomes.转录过程会对染色质造成显著干扰，因此细胞演化出了一套机制以在转录期间维持染色质完整性，进而阻止由虚假启动子序列产生的隐秘转录本（cryptic transcript）。细胞如何调控并加工这类转录本，目前仍未得到充分阐明。值得注意的是，学界对隐秘转录的终止机制仍知之甚少。本研究通过RNA测序（RNA-Seq）技术，在酿酒酵母（Saccharomyces cerevisiae）的Spt6突变细胞（spt6-1004）中鉴定并表征了隐秘转录本。研究发现，该突变株中存在相对于基因有义链与反义链方向的聚腺苷酸化隐秘转录本。隐秘启动子中TATA框（TATA box）富集，这表明底层DNA序列决定了隐秘启动子的位置。尽管基因内有义链隐秘转录本会在其所在基因的终止子处终止，但反义链隐秘转录本则优先在上游基因的3'端完成终止。基于上述发现，本研究证实酵母中的大多数终止子具有双向活性，可介导来自任一方向的转录本完成终止与聚腺苷酸化过程。我们推测，酿酒酵母（S. cerevisiae）演化出该机制，旨在阻止虚假转录入侵邻近基因，这一特征对于基因组紧凑小巧的生物体而言尤为关键。