title: Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout.
abstract: The ENCODE project revealed that ~70% of the human genome is transcribed. While only 1-2% of the RNAs encode for proteins, the rest are non-coding RNAs. Long non-coding RNAs (lncRNAs) form a diverse class of non-coding RNAs that are longer than 200 nt. Emerging evidence indicates that lncRNAs play critical roles in various cellular processes including regulation of gene expression. LncRNAs show low levels of gene expression and sequence conservation, which make their computational identification in genomes difficult. In this study, more than two billion Illumina sequence reads were mapped to the genome reference using the TopHat and Cufflinks software. Transcripts shorter than 200 nt, with more than 83-100 amino acids ORF, or with significant homologies to the NCBI nr-protein database were removed. In addition, a computational pipeline was used to filter the remaining transcripts based on a protein-coding-score test. Depending on the filtering stringency conditions, between 31,195 and 54,503 lncRNAs were identified, with only 421 matching known lncRNAs in other species. A digital gene expression atlas revealed 2,935 tissue-specific and 3,269 ubiquitously-expressed lncRNAs. This study annotates the lncRNA rainbow trout genome and provides a valuable resource for functional genomics research in salmonids.
authors.affiliation: Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States of America.
authors.forename: Rafet
authors.initials: R
authors.lastname: Al-Tobasei
authors.affiliation: Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States of America.
authors.forename: Bam
authors.initials: B
authors.lastname: Paneru
authors.affiliation: Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States of America.|Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States of America.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Salem
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D016678:Genome; D055106:Genome-Wide Association Study; D023281:Genomics; D017686:Oncorhynchus mykiss / Q000235:genetics*; D016366:Open Reading Frames; D009928:Organ Specificity / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger