RNAirport:a deep neural network-based database characterizing representative gene models in plants

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NSTL
万方数据

外文摘要：A 5'-leader,known initially as the 5'-untranslated region,contains multiple isoforms due to alternative splicing(aS)and alternative transcription start site(aTSS).Therefore,a representative 5'-leader is demanded to examine the embedded RNA regulatory elements in controlling translation efficiency.Here,we develop a ranking algorithm and a deep-learning model to annotate representative 5'-leaders for five plant species.We rank the intra-sample and inter-sample frequency of aS-mediated transcript isoforms using the Kruskal-Wallis test-based algorithm and identify the representative aS-5'-leader.To further assign a representative 5'-end,we train the deep-learning model 5'IeaderP to learn aTSS-mediated 5'-end distribution patterns from cap-analysis gene expression data.The model accurately predicts the 5'-end,confirmed experimentally in Arabidopsis and rice.The representative 5'-leader-contained gene models and 5'leaderP can be accessed at RNAirport(http://www.rnairport.com/leader5P/).The Stage 1 annotation of 5'-leader records 5'-leader diversity and will pave the way to Ribo-Seq open-reading frame annotation,identical to the project recently initiated by human GENCODE.

外文关键词：

5'-leaderTranscript isoformsRNA regulatory elementsuORFDeep learningSynthetic biologyTranslational control

作者：

Sitao Zhu、Shu Yuan、Ruixia Niu、Yulu Zhou、Zhao Wang、Guoyong Xu

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作者单位：

State Key Laboratory of Hybrid Rice,Institute for Advanced Studies(IAS),Wuhan University,Wuhan,Hubei 430072,China

Hubei Hongshan Laboratory,Wuhan,Hubei 430070,China

基金：

National Key R&D Program of ChinaMajor Project of Hubei Hongshan LaboratoryKey Research and Development Program of Hubei ProvinceNational Natural Science Foundation of China

项目编号：

2023ZD040732022hszd0162022BFE00332070284t

出版年：

2024

DOI：

10.1016/j.jgg.2024.03.004

遗传学报

中国遗传学会中国科学院遗传与发育生物学研究所

遗传学报

CSTPCD

影响因子：0.821

ISSN：1673-8527

年,卷(期)：2024.51(6)