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RMzyme:regulations of RNA-modifying enzymes in humans 认领 引用
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作者 Ruihan Luo Haixia Xu +12 位作者 Qingbo Zhou Shanli Ding Min Qiang Jianguo Wen Pora Kim Xiaojuan Yang Yunshi Cai Kunlin Xie Jiang Zhu Yungang Xu Tian Lan Xiaobo Zhou Hong Wu 《Signal Transduction and Targeted Therapy》 SCIE CSCD 2026年第3期1575-1591,共17页
RNA modifications represent a dynamic layer of gene expression regulation,RNA stability,and translation with profound implications for cellular function and disease.However,the critical regulation and functions of RNA... RNA modifications represent a dynamic layer of gene expression regulation,RNA stability,and translation with profound implications for cellular function and disease.However,the critical regulation and functions of RNA-modifying proteins(RMPs)remain poorly understood.Here,we present a large-scale characterization of RMPs through 378 multiomics datasets encompassing genomics,bulk and single-cell transcriptomics,epitranscriptomics,proteomics,and posttranslational modifications(PTMs)across 63 human tissues.Our analysis of experimental perturbations of RMPs revealed dynamic differential modification peaks and expressed genes.We applied nonnegative matrix factorization to annotate RMP-mediated cell types in single-cell transcriptomes.Functional annotations in acute myeloid leukemia(AML)revealed RMPs such as ALKBH5 as critical mediators of m6A dynamics,influencing pathways involved in translation initiation,immune regulation,and tumorigenesis.We revealed cell type-specific modification patterns,including those in ALKBH5-enriched AML stem cells with special ligand‒receptor interactions and genetic variations modulated by m6A.We integrated proteogenomic data to uncover PTM-associated regulatory,mutation,and protein‒protein interaction networks linked to RMPs.We developed RMzyme,a platform that consolidates our findings and provides insights into RMPs and their downstream effects.This resource is expected to facilitate biomedical research into the molecular mechanisms of human diseases through the lens of RNA modifications and multiomics data integration. 展开更多
关键词 multiomics posttranslational modifications ptms across RNA stability rna modifications multiomics datasets RNA modifying enzymes gene expression regulation translation
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The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers 认领 引用 被引量：1
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作者 Sijia Wu Zhiwei Fan +2 位作者 Pora Kim Liyu Huang Xiaobo Zhou 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2023年第3期619-631,共13页
Adenosine-to-inosine(A-to-I)RNA editing,constituting nearly 90%of all RNA editing events in humans,has been reported to contribute to the tumorigenesis in diverse cancers.However,the comprehensive map for functional A... Adenosine-to-inosine(A-to-I)RNA editing,constituting nearly 90%of all RNA editing events in humans,has been reported to contribute to the tumorigenesis in diverse cancers.However,the comprehensive map for functional A-to-I RNA editing events in cancers is still insufficient.To fill this gap,we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events in samples across 33 cancer types from The Cancer Genome Atlas.For individual candidate among1,500,000 quantified RNA editing events,we performed diverse types of downstream functional annotations.Finally,we identified 24,236 potentially functional A-to-I RNA editing events,including the cases in APOL1,IGFBP3,GRIA2,BLCAP,and miR-589-3p.These events might play crucial roles in the scenarios of tumorigenesis,due to their tumor-related editing frequencies or probable effects on altered expression profiles,protein functions,splicing patterns,and microRNA regulations of tumor genes.Our functional A-to-I RNA editing events(http://gffzz53f2f6c9ddf14a6bsf59pkuvvuo5v6uo6.ffgz.tsg.suse.edu.cn/CAeditome/)will help better understand the cancer pathology from the A-to-I RNA editing aspect. 展开更多
关键词 A-to-I RNA editing Cancer Protein recoding Alternative splicing MicroRNA regulation
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