数字农科院2.0

A comprehensive atlas of pig RNA editome across 23 tissues reveals RNA editing affecting interaction mRNA-miRNAs

文献类型： 外文期刊

作者： Long, Jiajia;Liu, Weiwei;Fan, Xinhao;Yang, Yalan;Yang, Xiaogan;Tang, Zhonglin

作者机构：

关键词： （1-1-3）pig;RNA editing;multiple tissue;skeletal muscle;miRNA

期刊名称： G3-GENES GENOMES GENETICS

ISSN： 2160-1836

年卷期： 2024 年

页码：

收录情况： SCIE（2024版）

摘要： RNA editing is a co-transcriptional/post-transcriptional modification that is mediated by the ADAR enzyme family. Profiling of RNA editing is very limited in pigs. In this study, we collated 3813 RNA-seq data from the public repositories across 23 tissues and carried out comprehensive profiling of RNA editing in pigs. In total, 127,927 A-to-I RNA-editing sites were detected. Our analysis showed that 98.2% of RNA-editing sites were located within repeat regions, primarily within the pig-specific SINE retrotransposon PRE-1/Pre0_SS elements. Subsequently, we focused on analyzing specific RNA-editing sites (SESs) in skeletal muscle tissues. Functional enrichment analyses suggested that they were enriched in signaling pathways associated with muscle cell differentiation, including DMD, MYOD1, and CAV1 genes. Furthermore, we discovered that RNA editing event in the 3 ' UTR of CFLAR mRNA influenced miR-708-5p binding in this region. In this study, the panoramic RNA-editing landscape of different tissues of pigs was systematically mapped, and RNA-editing sites and genes involved in muscle cell differentiation were identified. In summary, we identified modifications to pig RNA-editing sites and provided candidate targets for further validation.

分类号：

  • 相关文献

[1]Genomic Landscape and Regulation of RNA Editing in Pekin Ducks Susceptible to Duck Hepatitis A Virus Genotype 3 Infection. Zhao, Haonao,Wu, Zifang,Wang, Zezhong,Ru, Jinlong,Wang, Shuaiqin,Li, Yang,Hou, Shuisheng,Zhang, Yunsheng,Wang, Xia. 2024

[2]MiR-208b Regulates the Conversion of Skeletal Muscle Fiber Types by Inhibiting Mettl8 Expression. Xiang Li,Hanfang Bi,Shanshan Xie,Wentao Cui. 2022

[3]Recent insertion of a 52-kb mitochondrial DNA segment in the wheat lineage. Kong, Xiuying,Zhang, Juncheng,Jia, Jizeng,Kong, Xiuying,Breen, James.

[4]Kinetic analysis of RNA editing of Newcastle disease virus P gene in the early period of infection. Qiu, X.,Fu, Q.,Meng, C.,Yu, S.,Zhan, Y.,Dong, L.,Ren, T.,Sun, Y.,Tan, L.,Song, C.,Han, X.,Ding, C.,Ding, C..

[5]Identification of RNA editing sites in cotton (Gossypium hirsutum) chloroplasts and editing events that affect secondary and three-dimensional protein structures. Y. Jiang,S.L. Fan,M.Z. Song,J.N. Yu,S.X. Yu. 2012

[6]RNA editing events in mitochondrial genes by ultra-deep sequencing methods: a comparison of cytoplasmic male sterile, fertile and restored genotypes in cotton. Yu, Jiwen,O'Connell, Mary A.,Zhang, Jinfa,Suzuki, Hideaki,Ness, Scott A.,Yu, Jiwen.

[7]Comparative Analysis of Asteraceae Chloroplast Genomes: Structural Organization, RNA Editing and Evolution. Cui, Licao,Feng, Kewei,Deng, Pingchuan,Du, Xianghong,Song Weining,Nie, Xiaojun,Wang, Mengxing,Cui, Licao,Feng, Kewei,Deng, Pingchuan,Du, Xianghong,Song Weining,Nie, Xiaojun,Wan, Fanghao.

[8]Genome-wide detection of RNA editing events during the hair follicles cycle of Tianzhu white yak. Xuelan Zhou,Pengjia Bao,Xiaolan Zhang,Xian Guo,Chunnian Liang,Min Chu,Xiaoyun Wu,Ping Yan. 2022

[9]Genome-Wide Investigation And Functional Analysis O.f Sus Scrofa Rna E diting Sites Across Eleven Tissues. Feng, Xikang,Li, Shuai Cheng,Tang, Zhonglin,Wang, Zishuai. 2019

[10]Characterization of RNA Editome in the Mammary Gland of Yaks during the Lactation and Dry Periods. Xiaoyun Wu,Wondossen Ayalew,Min Chu,Jie Pei,Chunnian Liang,Pengjia Bao,Xian Guo,Ping Yan. 2022

[11]Preliminary identification and analysis of differential RNA editing between higher and lower backfat thickness pigs using DNA-seq and RNA-seq data. Zhang, Yuebo,Liu, Xin,Zhang, Longchao,Wang, Ligang,He, Jun,Ma, Haiming,Wang, Lixian. 2022

[12]Developmental Atlas Of The Rna E.ditome In Sus Scrofa S keletal Muscle. Yang, YL, Zhu, M, Fan, XH, Yao, YL, Yan, JY, Tang, YJ, Liu, SY, Li, K, Tang, ZL. 2019

[13]RNA Editing and Its Roles in Plant Organelles. Wei Hao,Guoxiang Liu,Weipeng Wang,Wei Shen,Yuping Zhao,Jialiang Sun,Qiuyue Yang,Yaxin Zhang,Wenjia Fan,Shuaishuai Pei,Zhuanqing Chen,Dongbei Xu,Tengfei Qin. 2021

[14]Dek504 Encodes a Mitochondrion-Targeted E+-Type Pentatricopeptide Repeat Protein Essential for RNA Editing and Seed Development in Maize. Zheyuan Wang,Weiwei Chen,Song Zhang,Jiawen Lu,Rongrong Chen,Junjie Fu,Riliang Gu,Guoying Wang,Jianhua Wang,Yu Cui. 2022

[15]Rice FLOURY ENDOSPERM22, encoding a pentatricopeptide repeat protein, is involved in both mitochondrial RNA splicing and editing and is crucial for endosperm development. Yang, Hang,Wang, Yunlong,Tian, Yunlu,Teng, Xuan,Lv, Zehui,Lei, Jie,Duan, Erchao,Dong, Hui,Yang, Xue,Zhang, Yuanyan,Sun, Yinglun,Chen, Xiaoli,Bao, Xiuhao,Chen, Rongbo,Gu, Chuanwei,Zhang, Yipeng,Jiang, Xiaokang,Ma, Wenyu,Zhang, Pengcheng. 2023

[16]Comprehensive Analysis of the Complete Mitochondrial Genome of Rehmannia chingii: An Autotrophic Species in the Orobanchaceae Family. Han Y.,Feng Y.-L.,Wang J.,Zhu S.-S.,Jin X.-J.,Wu Z.-Q.,Zhang Y.-H.. 2024

[17]Recent advances and biotechnological applications of RNA metabolism in plant chloroplasts and mitochondria. Ali, Nadia Ahmed,Song, Wenjian,Huang, Jianyan,Wu, Dianxing,Zhao, Xiaobo. 2024

[18]OsPGL3A encodes a DYW-type pentatricopeptide repeat protein involved in chloroplast RNA processing and regulated chloroplast development. Min Xu,Xinying Zhang,Jinzhe Cao,Jiali Liu,Yiyuan He,Qingjie Guan,Xiaojie Tian,Jiaqi Tang,Xiufeng Li,Deyong Ren,Qingyun Bu,Zhenyu Wang. 2024

[19]RAS, a Pentatricopeptide Repeat Protein, Interacts with OsTRX z to Regulate Chloroplast Gene Transcription and RNA Processing. Zhennan Qiu,Shiyong Wen,Peinan Sun,Dongdong Chen,Chunmiao Wang,Xiliang Song,Liying Xiao,Peiliang Zhang,Dongying Zhao,Cuiping Wen,Peiyan Guan,Xuechu Du,Yinghui Sun,Chenshan Xu,Jian Song. 2025

[20]Association Analysis Provides Insights into Plant Mitonuclear Interactions. Lian Q.,Li S.,Kan S.,Liao X.,Huang S.,Sloan D.B.,Wu Z.. 2024

作者其他论文 更多>>
  • The Farm Animal Genotype-Tissue Expression (FarmGTEx) Project

    作者：Fang, Lingzhao;Teng, Jinyan;Lin, Qing;Bai, Zhonghao;Liu, Shuli;Guan, Dailu;Li, Bingjie;Gao, Yahui;Hou, Yali;Gong, Mian;Pan, Zhangyuan;Yu, Ying;Clark, Emily L.;Smith, Jacqueline;Rawlik, Konrad;Xiang, Ruidong;Chamberlain, Amanda J.;Goddard, Michael E.;Littlejohn, Mathew;Larson, Greger;MacHugh, David E.;O'Grady, John F.;Sorensen, Peter;Sahana, Goutam;Lund, Mogens Sando;Jiang, Zhihua;Pan, Xiangchun;Gong, Wentao;Zhang, Haihan;He, Xi;Zhang, Yuebo;Gao, Ning;He, Jun;Yi, Guoqiang;Liu, Yuwen;Tang, Zhonglin;Zhao, Pengju;Zhou, Yang;Fu, Liangliang;Wang, Xiao;Hao, Dan;Liu, Lei;Chen, Siqian;Young, Robert S.;Shen, Xia;Xia, Charley;Cheng, Hao;Ma, Li;Cole, John B.;Baldwin, Ransom L.;Li, Cong-jun;Van Tassell, Curtis P.;Rosen, Benjamin D.;Bhowmik, Nayan;Lunney, Joan;Liu, Wansheng;Guan, Leluo;Zhao, Xin;Ibeagha-Awemu, Eveline M.;Luo, Yonglun;Lin, Lin;Canela-Xandri, Oriol;Derks, Martijn F. L.;Crooijmans, Richard P. M. A.;Godia, Marta;Madsen, Ol

    关键词：

  • Suppressing IGF2R mitigates hypoxia-induced apoptosis by reducing the expression of pro-apoptotic factor BAX

    作者：Guo, Xiaorong;Fan, Xinhao;Xie, Chundi;Afe, Ayoola Ebenezer;Yang, Yalan;Zhou, Rong

    关键词：（0-2-3）Hypoxia;IGF2R;Apoptosis

  • Multiomics analysis reveals signatures of selection and loci associated with complex traits in pigs

    作者：Liu, Lei;Yi, Guoqiang;Yao, Yilong;Liu, Yuwen;Li, Jiang;Yang, Yalan;Liu, Mei;Fang, Lingzhao;Mo, Delin;Zhang, Longchao;Liu, Yonggang;Niu, Yongchao;Wang, Liyuan;Qu, Xiaolu;Pan, Zhangyuan;Wang, Lei;Chen, Muya;Fan, Xinhao;Chen, Yun;Zhang, Yongsheng;Li, Xingzheng;Wang, Zhen;Tang, Yijie;Huang, Hetian;Yuan, Pengxiang;Liao, Yuying;Li, Xinjian;Yin, Zongjun;Liu, Di;Zhang, Dongjie;Zhou, Quanyong;Wu, Wangjun;Jiang, Jicai;Gao, Yahui;Liu, George E.;Wang, Lixian;Chen, Yaosheng;Li, Kui;Groenen, Martien A. M.;Tang, Zhonglin

    关键词：（1-1-1）epigenetics;genomic variation;pan-genome;phenotype differentiation;pig;skeletal muscle development

  • Genomic Insights into Post-Domestication Expansion and Selection of Body Size in Ponies

    作者：Li, Xingzheng;Wang, Zihao;Zhu, Min;Wang, Binhu;Teng, Shaohua;Yan, Jing;Wang, Haoyu;Yuan, Pengxiang;Cao, Shuwei;Qu, Xiaolu;Wang, Zhen;Zhan, Kai;Choudhury, Md. Panir;Yang, Xintong;Bao, Qi;He, Sang;Liu, Lei;Zhao, Pengju;Jiang, Jicai;Xiang, Hai;Fang, Lingzhao;Tang, Zhonglin;Liao, Yuying;Yi, Guoqiang

    关键词：（1-1-1）body size;genome;pony;population genetics;regulatory elements

  • The Spatial-Temporal Alternative Splicing Profile Reveals the Functional Diversity of FXR1 Isoforms in Myogenesis

    作者：Wang, Wei;Fan, Xinhao;Liu, Weiwei;Huang, Yuxin;Zhao, Shuhong;Yang, Yalan;Tang, Zhonglin

    关键词：（1-1-1）alternative splicing;FXR1;myogenesis;muscle regeneration;RBM24

  • DPImpute: A Genotype Imputation Framework for Ultra-Low Coverage Whole-Genome Sequencing and its Application in Genomic Selection

    作者：Zheng, Weigang;Ma, Wenlong;Chen, Zhilong;Wang, Chao;Sun, Tao;Dong, Wenjun;Zhang, Wenjing;Zhang, Song;Tang, Zhonglin;Li, Kui;Zhao, Yunxiang;Liu, Yuwen

    关键词：（1-1-1）breeding models;genetic screening of embryos;genomic selection;genotype imputation;single cell genotype

  • PIGOME: An Integrated and Comprehensive Multi-omics Database for Pig Functional Genomics Studies

    作者：Han, Guohao;Yang, Peng;Zhang, Yongjin;Li, Qiaowei;Fan, Xinhao;Chen, Ruipu;Yan, Chao;Zeng, Mu;Yang, Yalan;Tang, Zhonglin

    关键词：（1-1-2）Pig;Multi-omics;Genome;Gene expression;Epigenetics;Database