The generation of distinct messenger RNA isoforms through alternative RNA processing modulates the expression and function of genes, often in a cell-type-specific manner. Here, we assess the regulatory relationships between transcription initiation, alternative splicing, and 3′ end site selection. Applying long-read sequencing to accurately represent even the longest transcripts from end to end, we quantify mRNA isoforms in Drosophila tissues, including the transcriptionally complex nervous system. We find that in Drosophila heads, as well as in human cerebral organoids, 3′ end site choice is globally influenced by the site of transcription initiation (TSS). “Dominant promoters,” characterized by specific epigenetic signatures including p300/CBP binding, impose a transcriptional constraint to define splice and polyadenylation variants. In vivo deletion or overexpression of dominant promoters as well as p300/CBP loss disrupted the 3′ end expression landscape. Our study demonstrates the crucial impact of TSS choice on the regulation of transcript diversity and tissue identity.

通过替代 RNA 加工产生不同的信使 RNA 亚型，通常以细胞类型特异性的方式调节基因的表达和功能。在这里，我们评估转录起始、选择性剪接和 3' 末端位点选择之间的调控关系。通过应用长读长测序来准确地表示从头到尾最长的转录本，我们量化了果蝇组织中的 mRNA 同工型，包括转录复杂的神经系统。我们发现，在果蝇头部以及人类大脑类器官中，3'末端位点的选择总体上受到转录起始位点（TSS）的影响。“显性启动子”的特征是特定的表观遗传特征，包括 p300/CBP 结合，施加转录限制来定义剪接和多腺苷酸化变体。体内显性启动子的缺失或过度表达以及 p300/CBP 的丢失破坏了 3' 端表达景观。我们的研究证明了 TSS 选择对转录多样性和组织身份调节的关键影响。