Chromatin-dependent cryptic promoters encode alternative protein isoforms in yeast

Cryptic transcription is widespread and generates a heterogeneous group of RNA molecules of unknown function. To improve our understanding of cryptic transcription, we investigated their transcription start site usage, chromatin organization and post-transcriptional consequences in Saccharomyces cerevisiae. We show that transcription start sites of chromatin-dependent internal cryptic transcripts resemble those of protein coding genes in terms of DNA sequence, directionality and chromatin accessibility. We define the 5’ and 3’ boundaries of cryptic transcripts and show that, contrary to RNA degradation-dependent ones , they often overlap with the end of the gene thereby using the canonical polyadenylation site and associate to polyribosomes. In fact, we show that chromatin-dependent cryptic transcripts can be recognized by ribosomes and may produce truncated polypeptides from downstream, in-frame start codons. Our work suggests that a significant fraction of chromatin-dependent internal cryptic promoters are in fact alternative truncated mRNA isoforms. The expression of these chromatin-dependent isoforms is conserved from yeast to human expanding the functional consequences of cryptic transcription and proteome complexity.隐秘转录（Cryptic transcription）广泛存在，可产生一组功能未知的异质性RNA分子。为深化对隐秘转录的认知，本研究以酿酒酵母（Saccharomyces cerevisiae）为研究对象，探究了其转录起始位点的使用模式、染色质组织特征以及转录后效应。研究发现，染色质依赖型内部隐秘转录本的转录起始位点，在DNA序列、转录方向性与染色质可及性三个维度上，与蛋白编码基因的转录起始位点高度相似。本研究明确了隐秘转录本的5’与3’边界，并发现与依赖RNA降解的转录本不同，这类转录本常与基因末端区域重叠，从而利用经典多聚腺苷酸化位点（polyadenylation site），并可与多聚核糖体（polyribosomes）结合。进一步研究证实，染色质依赖型隐秘转录本可被核糖体识别，并可通过下游可读框内起始密码子（in-frame start codons）翻译产生截短多肽。本研究结果表明，相当一部分染色质依赖型内部隐秘启动子，实际上属于替代型截短型mRNA同工异构体（truncated mRNA isoforms）。这类染色质依赖型转录同工异构体的表达在从酵母到人类的多个物种中均保守存在，这一发现拓展了隐秘转录的功能效应与蛋白质组复杂性。