Mick Steven T, Carroll Christine L, Uriostegui-Arcos Maritere, Fiszbein Ana
Biology Department, Boston University, 24 Cummington Ave., Boston, 02215, USA.
Computing & Data Sciences, Boston University, 665 Commonwealth Ave., Boston, 02215, USA.
Nucleic Acids Res. 2025 Jan 24;53(3). doi: 10.1093/nar/gkae1251.
Exons within transcripts are traditionally classified as first, internal or last exons, each governed by different regulatory mechanisms. We recently described the widespread usage of 'hybrid' exons that serve as terminal or internal exons in different transcripts. Here, we employ an interpretable deep learning pipeline to dissect the sequence features governing the co-regulation of transcription initiation and splicing in hybrid exons. Using ENCODE data from human tissues, we identified 80 000 hybrid first-internal exons. These exons often possess a relaxed chromatin state, allowing transcription initiation within the gene body. Interestingly, transcription start sites of hybrid exons are typically centered at the 3' splice site, suggesting tight coupling between splicing and transcription initiation. We identified two subcategories of hybrid exons: the majority resemble internal exons, maintaining strong 3' splice sites, while a minority show enrichment in promoter elements, resembling first exons. Diving into the evolution of their sequences, we found that human hybrid exons with orthologous first exons in other species usually gained 3' splice sites or whole exons upstream, while those with orthologous internal exons often gained promoter elements. Overall, our findings unveil the intricate regulatory landscape of hybrid exons and reveal stronger connections between transcription initiation and RNA splicing than previously acknowledged.
传统上，转录本中的外显子被分类为首个、内部或最后一个外显子，每个外显子都受不同的调控机制支配。我们最近描述了“混合”外显子的广泛使用情况，这些外显子在不同的转录本中充当末端或内部外显子。在这里，我们采用一种可解释的深度学习流程来剖析控制混合外显子中转录起始和剪接共同调控的序列特征。利用来自人类组织的ENCODE数据，我们鉴定出8万个混合首个-内部外显子。这些外显子通常具有松弛的染色质状态，允许在基因体内进行转录起始。有趣的是，混合外显子的转录起始位点通常以3'剪接位点为中心，这表明剪接和转录起始之间存在紧密的耦合。我们确定了混合外显子的两个亚类：大多数类似于内部外显子，保持较强的3'剪接位点，而少数在启动子元件中富集，类似于首个外显子。深入研究它们的序列进化，我们发现与其他物种中直系同源首个外显子相对应的人类混合外显子通常在其上游获得3'剪接位点或整个外显子，而与直系同源内部外显子相对应的混合外显子则通常获得启动子元件。总体而言，我们的研究结果揭示了混合外显子复杂的调控格局，并揭示了转录起始与RNA剪接之间比以前所认识到的更强的联系。
