ABSTRACT

Regulation of gene expression starts from the transcription initiation. Regulated transcription initiation is critical for generating correct transcripts with proper abundance. The impact of epigenetic control, such as histone modifications and chromatin remodelling, on gene regulation has been extensively investigated, but their specific role in regulating transcription initiation is far from well understood. Here we aimed to better understand the roles of genes involved in histone H3 methylations and chromatin remodelling on the regulation of transcription initiation at a genome-scale using the budding yeast as a study system. We obtained and compared maps of transcription start site (TSS) at single-nucleotide resolution by nAnT-iCAGE for a strain with depletion of MINC (Mot1-Ino80C-Nc2) by Mot1p and Ino80p anchor-away (Mot1&Ino80AA) and a strain with loss of histone methylation (set1Δset2Δdot1Δ) to their wild-type controls. Our study showed that the depletion of MINC stimulated transcription initiation from many new sites flanking the dominant TSS of genes, while the loss of histone methylation generates more TSSs in the coding region. Moreover, the depletion of MINC led to less confined boundaries of TSS clusters (TCs) and resulted in broader core promoters, and such patterns are not present in the ssdΔ mutant. Our data also exhibits that the MINC has distinctive impacts on TATA-containing and TATA-less promoters. In conclusion, our study shows that MINC is required for accurate identification of bona fide TSSs, particularly in TATA-containing promoters, and histone methylation contributes to the repression of transcription initiation in coding regions.

摘要

基因表达的调节从转录起始开始。受调控的转录起始对于生成具有适当丰度的正确转录本至关重要。表观遗传控制（如组蛋白修饰和染色质重塑）对基因调控的影响已被广泛研究，但它们在调节转录起始中的具体作用远未得到充分了解。在这里，我们旨在使用出芽酵母作为研究系统，更好地了解参与组蛋白 H3 甲基化和染色质重塑的基因在基因组规模上对转录起始调控的作用。我们通过 nAnT-iCAGE 获得并比较了通过 Mot1p 和 Ino80p 锚定去除 MINC (Mot1-Ino80C-Nc2) 的菌株在单核苷酸分辨率下的转录起始位点 (TSS) 图谱。Mot1&Ino80AA ) 和组蛋白甲基化缺失 ( set1Δset2Δdot1Δ ) 的菌株与其野生型对照相比。我们的研究表明，MINC 的消耗刺激了基因主要 TSS 两侧的许多新位点的转录起始，而组蛋白甲基化的丧失在编码区产生了更多的 TSS。此外，MINC 的消耗导致 TSS 簇 (TC) 的边界不那么受限，并导致更广泛的核心启动子，而这种模式在ssdΔ中不存在突变体。我们的数据还表明，MINC 对含 TATA 和不含 TATA 的启动子具有独特的影响。总之，我们的研究表明，准确识别真正的 TSS 需要 MINC，特别是在含有 TATA 的启动子中，组蛋白甲基化有助于抑制编码区的转录起始。