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外显子命名与转录本分类(ENACT)提供了一个用于注释外显子属性的系统框架。

Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes.

作者信息

Verma Paras, Thakur Deeksha, Awasthi Deepanshi, Pandit Shashi Bhushan

机构信息

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

出版信息

Genome Res. 2025 Jun 2;35(6):1440-1455. doi: 10.1101/gr.279878.124.

DOI:10.1101/gr.279878.124
PMID:40335152
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12129085/
Abstract

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.

摘要

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。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dddc/12129085/96c328d5d7fd/1440f06.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dddc/12129085/cf3b9462327c/1440f01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dddc/12129085/053aeb609887/1440f02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dddc/12129085/8058f39edacc/1440f03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dddc/12129085/69a6732a7fe3/1440f04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dddc/12129085/d712c1337fb6/1440f05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dddc/12129085/96c328d5d7fd/1440f06.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dddc/12129085/cf3b9462327c/1440f01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dddc/12129085/053aeb609887/1440f02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dddc/12129085/8058f39edacc/1440f03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dddc/12129085/69a6732a7fe3/1440f04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dddc/12129085/d712c1337fb6/1440f05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dddc/12129085/96c328d5d7fd/1440f06.jpg

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本文引用的文献

1
Exon nomenclature and classification of transcripts database (ENACTdb): a resource for analyzing alternative splicing mediated proteome diversity.外显子命名与转录本分类数据库(ENACTdb):一个用于分析可变剪接介导的蛋白质组多样性的资源。
Bioinform Adv. 2024 Oct 29;4(1):vbae157. doi: 10.1093/bioadv/vbae157. eCollection 2024.
2
Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis.罕见病中的剪接缺陷:转录组学和机器学习策略在基因诊断中的应用。
Brief Bioinform. 2023 Sep 20;24(5). doi: 10.1093/bib/bbad284.
3
Not all exons are protein coding: Addressing a common misconception.
并非所有外显子都编码蛋白质:纠正一个常见的误解。
Cell Genom. 2023 Apr 12;3(4):100296. doi: 10.1016/j.xgen.2023.100296.
4
Splicing complexity as a pivotal feature of alternative exons in mammalian species.剪接复杂性作为哺乳动物物种中可变外显子的关键特征。
BMC Genomics. 2023 Apr 12;24(1):198. doi: 10.1186/s12864-023-09247-y.
5
Re-evaluating the impact of alternative RNA splicing on proteomic diversity.重新评估可变RNA剪接对蛋白质组多样性的影响。
Front Genet. 2023 Feb 9;14:1089053. doi: 10.3389/fgene.2023.1089053. eCollection 2023.
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Monitoring the 5'UTR landscape reveals isoform switches to drive translational efficiencies in cancer.监测 5'UTR 景观揭示了异构体转换以驱动癌症中的翻译效率。
Oncogene. 2023 Feb;42(9):638-650. doi: 10.1038/s41388-022-02578-2. Epub 2022 Dec 23.
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The importance of alternative splicing in adaptive evolution.可变剪接在适应性进化中的重要性。
Mol Ecol. 2022 Apr;31(7):1928-1938. doi: 10.1111/mec.16377. Epub 2022 Feb 17.
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Uncovering the impacts of alternative splicing on the proteome with current omics techniques.利用当前组学技术揭示可变剪接对蛋白质组的影响。
Wiley Interdiscip Rev RNA. 2022 Jul;13(4):e1707. doi: 10.1002/wrna.1707. Epub 2022 Jan 3.
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The role of alternative splicing in adaptation and evolution.选择性剪接在适应和进化中的作用。
Trends Ecol Evol. 2022 Apr;37(4):299-308. doi: 10.1016/j.tree.2021.11.010. Epub 2021 Dec 14.
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Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish.可变剪接和基因表达在鲑鱼属鱼类的平行表型进化中发挥相反的作用。
Mol Ecol. 2021 Oct;30(20):4955-4969. doi: 10.1111/mec.15817. Epub 2021 Feb 18.