Genome-wide Analysis of Core Promoter Structures in <i>Schizosaccharomyces pombe</i> with DeepCAGE

The core promoter, which immediately flanks the transcription start site (TSS), plays a critical role in transcriptional regulation of eukaryotes. Recent studies on higher eukaryotes have revealed an unprecedented complexity of core promoter structures that underscores diverse regulatory mechanisms of gene expression. For unicellular eukaryotes, however, the structures of core promoters have not been investigated in detail. As an important model organism, <i>Schizosaccharomyces pombe</i> still lacks the precise annotation for TSSs, thus hampering the analysis of core promoter structures and their relationship to higher eukaryotes. Here we used a deep sequencing-based approach (DeepCAGE) to generate 16 million uniquely mapped tags, corresponding to 93,736 positions in the <i>S. pombe</i> genome. The high-resolution TSS landscape enabled identification of over 8,000 core promoters, characterization of four promoter classes and observation of widespread alternative promoters. The landscape also allowed precise determination of the representative TSSs within core promoters, thus redefining the 5' UTR for 82.8% of <i>S. pombe</i> genes. We further identified the consensus initiator (Inr) sequence – PyPyPuN(A/C)(C/A), the TATA-enriched region (between position -25 and -37) and an Inr immediate downstream motif – CC(T/A)(T/C)(T/C/A)(A/G)CCA(A/T/C), all of which were associated with highly expressed promoters. In conclusion, the detailed analysis of core promoters not only significantly improves the genome annotation of <i>S. pombe</i>, but also reveals that this unicellular eukaryote shares a highly similar organization in the core promoters as higher eukaryotes. These findings lend additional evidence for the power of this model system in delineating complex regulatory processes in multicellular organisms, despite its perceived simplicity.

核心启动子（core promoter）紧邻转录起始位点（Transcription Start Site, TSS），在真核生物的转录调控中发挥关键作用。针对高等真核生物的近期研究揭示了核心启动子结构前所未有的复杂性，这凸显了基因表达调控机制的多样性。然而，对于单细胞真核生物，其核心启动子的结构尚未得到细致研究。作为重要的模式生物，粟酒裂殖酵母（Schizosaccharomyces pombe）的转录起始位点仍缺乏精准注释，这阻碍了对核心启动子结构及其与高等真核生物关联的分析。本研究采用基于深度测序的方法（DeepCAGE），生成了1600万个唯一比对标签，对应粟酒裂殖酵母（S. pombe）基因组中的93736个位点。该高分辨率的TSS图谱帮助我们鉴定了超过8000个核心启动子，表征了四类启动子类别，并观察到广泛存在的可变启动子现象。该图谱还实现了对核心启动子内代表性TSS的精准确定，从而为82.8%的S. pombe基因重新定义了5'非翻译区（5' UTR）。我们进一步鉴定了保守的起始子（Initiator, Inr）序列：PyPyPuN(A/C)(C/A)、富集TATA的区域（位于-25至-37位之间），以及紧邻Inr下游的基序：CC(T/A)(T/C)(T/C/A)(A/G)CCA(A/T/C)，所有这些元件均与高表达启动子相关。综上，对核心启动子的细致分析不仅显著完善了粟酒裂殖酵母的基因组注释，还揭示出这种单细胞真核生物的核心启动子组织模式与高等真核生物高度相似。尽管粟酒裂殖酵母常被认为结构简单，但本研究结果为该模式系统在解析多细胞生物复杂调控过程中的应用价值提供了新的佐证。