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

作　　者：Sitao Zhu Shu Yuan Ruixia Niu Yulu Zhou Zhao Wang Guoyong Xu 

机构地区：[1]State Key Laboratory of Hybrid Rice,Institute for Advanced Studies(IAS),Wuhan University,Wuhan,Hubei 430072,China [2]Hubei Hongshan Laboratory,Wuhan,Hubei 430070,China

出　　处：《Journal of Genetics and Genomics》2024年第6期652-664,共13页遗传学报（英文版）

基　　金：supported by grants from the National Key R&D Program of China(2023ZD04073);the Major Project of Hubei Hongshan Laboratory(2022hszd016);the Key Research and Development Program of Hubei Province(2022BFE003);the National Natural Science Foundation of China(32070284)to G.Xu.

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'leaderP 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.

关 键 词：5'-leader Transcript isoforms RNA regulatory elements UORF Deep learning Synthetic biology Translational control 

分 类 号：Q786[生物学—分子生物学]