Verma Paras, Thakur Deeksha, Awasthi Deepanshi, Pandit Shashi Bhushan
Bioinformatics Center, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector-81, SAS Nagar 140306, India.
Bioinformatics Center, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector-81, SAS Nagar 140306, India
Genome Res. 2025 Jun 2;35(6):1440-1455. doi: 10.1101/gr.279878.124.
Isoform diversity is known to enhance a gene's functional repertoire by producing protein variants with distinct functional implications. Despite numerous studies on transcriptome diversifying processes (alternative splicing/transcription), understanding their extent and correlated impact on proteome diversity remains limited owing to dearth of subsequent proteogenomic consequences. To coalesce the genomic information embedded in exons with isoform sequences, we present an innovative framework, "Exon Nomenclature And Classification of Transcripts" (ENACT). This centralizes exonic loci such that protein sequence information is integrated (onto the available/annotated or new transcripts) while enabling tracking and assessing splice-site variability through unique yielded descriptors. The resulting annotation from the ENACT framework enables exon features to be tractable, facilitating a systematic analysis of isoform diversity. Our findings and case studies unveil systemic exon inclusion roles in regulating diversity in coding region. Correspondingly, annotation of protein-coding genes and associated transcripts from , , , , and are publicly accessible in a dedicated resource.
已知异构体多样性可通过产生具有不同功能影响的蛋白质变体来增强基因的功能库。尽管对转录组多样化过程(可变剪接/转录)进行了大量研究,但由于缺乏后续蛋白质基因组学后果,对其程度及其对蛋白质组多样性的相关影响的了解仍然有限。为了将外显子中嵌入的基因组信息与异构体序列合并,我们提出了一个创新框架“外显子命名和转录本分类”(ENACT)。这集中了外显子位点,以便整合蛋白质序列信息(到可用的/注释的或新的转录本上),同时通过独特生成的描述符能够跟踪和评估剪接位点变异性。ENACT框架产生的注释使外显子特征易于处理,有助于对异构体多样性进行系统分析。我们的研究结果和案例研究揭示了系统性外显子包含在调节编码区多样性中的作用。相应地,来自[具体物种1]、[具体物种2]、[具体物种3]、[具体物种4]和[具体物种5]的蛋白质编码基因和相关转录本的注释可在一个专用资源中公开获取。