title: LNCediting: a database for functional effects of RNA editing in lncRNAs.
abstract: RNA editing is a widespread post-transcriptional mechanism that can make a single base change on specific nucleotide sequence in an RNA transcript. RNA editing events can result in missense codon changes and modulation of alternative splicing in mRNA, and modification of regulatory RNAs and their binding sites in noncoding RNAs. Recent computational studies accurately detected more than 2 million A-to-I RNA editing sites from next-generation sequencing (NGS). However, the vast majority of these RNA editing sites have unknown functions and are in noncoding regions of the genome. To provide a useful resource for the functional effects of RNA editing in long noncoding RNAs (lncRNAs), we systematically analyzed the A-to-I editing sites in lncRNAs across human, rhesus, mouse, and fly, and observed an appreciable number of RNA editing sites which can significantly impact the secondary structures of lncRNAs and lncRNA-miRNA interactions. All the data were compiled into LNCediting, a user-friendly database (http://bioinfo.life.hust.edu.cn/LNCediting/). LNCediting provides customized tools to predict functional effects of novel editing sites in lncRNAs. We hope that it will become an important resource for exploring functions of RNA editing sites in lncRNAs.
authors.affiliation: Department of Bioinformatics and Systems Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China.|Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA.|Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China.
authors.forename: Jing
authors.initials: J
authors.lastname: Gong
authors.affiliation: Department of Bioinformatics and Systems Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China.|Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA.
authors.forename: Chunjie
authors.initials: C
authors.lastname: Liu
authors.affiliation: Department of Bioinformatics and Systems Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China.
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.affiliation: Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Xiang
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
authors.forename: Lixia
authors.initials: L
authors.lastname: Diao
authors.affiliation: Department of Bioinformatics and Systems Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China guoay@mail.hust.edu.cn.
authors.forename: An-Yuan
authors.initials: AY
authors.lastname: Guo
authors.affiliation: Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA Leng.Han@uth.tmc.edu.
authors.forename: Leng
authors.initials: L
authors.lastname: Han
mesh_terms: D000241:Adenosine / Q000378:metabolism; D000818:Animals; D030561:Databases, Nucleic Acid; D004331:Drosophila melanogaster / Q000235:genetics; D006801:Humans; D007288:Inosine / Q000378:metabolism; D008253:Macaca mulatta; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism; D009690:Nucleic Acid Conformation; D017393:RNA Editing; D062085:RNA, Long Noncoding / Q000737:chemistry* / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding; D007288:Inosine; D000241:Adenosine