The Francis Crick Institute, London, UK.
Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore.
Genome Biol. 2021 Jan 14;22(1):34. doi: 10.1186/s13059-020-02245-3.
The start and end sites of messenger RNAs (TSSs and TESs) are highly regulated, often in a cell-type-specific manner. Yet the contribution of transcript diversity in regulating gene expression remains largely elusive. We perform an integrative analysis of multiple highly synchronized cell-fate transitions and quantitative genomic techniques in Saccharomyces cerevisiae to identify regulatory functions associated with transcribing alternative isoforms.
Cell-fate transitions feature widespread elevated expression of alternative TSS and, to a lesser degree, TES usage. These dynamically regulated alternative TSSs are located mostly upstream of canonical TSSs, but also within gene bodies possibly encoding for protein isoforms. Increased upstream alternative TSS usage is linked to various effects on canonical TSS levels, which range from co-activation to repression. We identified two key features linked to these outcomes: an interplay between alternative and canonical promoter strengths, and distance between alternative and canonical TSSs. These two regulatory properties give a plausible explanation of how locally transcribed alternative TSSs control gene transcription. Additionally, we find that specific chromatin modifiers Set2, Set3, and FACT play an important role in mediating gene repression via alternative TSSs, further supporting that the act of upstream transcription drives the local changes in gene transcription.
The integrative analysis of multiple cell-fate transitions suggests the presence of a regulatory control system of alternative TSSs that is important for dynamic tuning of gene expression. Our work provides a framework for understanding how TSS heterogeneity governs eukaryotic gene expression, particularly during cell-fate changes.
信使 RNA（TSS 和 TES）的起始和结束位点受到高度调控，通常以细胞类型特异性的方式进行调控。然而，转录本多样性在调节基因表达中的作用在很大程度上仍未被揭示。我们在酿酒酵母中进行了多次高度同步的细胞命运转变和定量基因组技术的综合分析，以确定与转录替代异构体相关的调节功能。
细胞命运转变的特征是广泛上调替代 TSS 的表达，在较小程度上也上调 TES 的使用。这些动态调节的替代 TSS 主要位于典型 TSS 的上游，但也位于基因体中，可能编码蛋白质异构体。上游替代 TSS 使用的增加与典型 TSS 水平的各种影响有关，从共激活到抑制。我们确定了与这些结果相关的两个关键特征：替代和典型启动子强度之间的相互作用，以及替代和典型 TSS 之间的距离。这两个调节特性为局部转录的替代 TSS 如何控制基因转录提供了一个合理的解释。此外，我们发现特定的染色质修饰物 Set2、Set3 和 FACT 通过替代 TSS 在介导基因抑制中发挥重要作用，进一步支持了上游转录的作用驱动了基因转录的局部变化。
对多个细胞命运转变的综合分析表明，存在替代 TSS 的调节控制系统，这对于动态调节基因表达很重要。我们的工作为理解 TSS 异质性如何控制真核生物基因表达，特别是在细胞命运转变期间提供了一个框架。
