title: Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss).
abstract: Long noncoding RNAs (lncRNAs) have been recognized in recent years as key regulators of diverse cellular processes. Genome-wide large-scale projects have uncovered thousands of lncRNAs in many model organisms. Large intergenic noncoding RNAs (lincRNAs) are lncRNAs that are transcribed from intergenic regions of genomes. To date, no lincRNAs in non-model teleost fish have been reported. In this report, we present the first reference catalog of 9674 rainbow trout lincRNAs based on analysis of RNA-Seq data from 15 tissues. Systematic analysis revealed that lincRNAs in rainbow trout share many characteristics with those in other mammalian species. They are shorter and lower in exon number and expression level compared with protein-coding genes. They show tissue-specific expression pattern and are typically co-expressed with their neighboring genes. Co-expression network analysis suggested that many lincRNAs are associated with immune response, muscle differentiation, and neural development. The study provides an opportunity for future experimental and computational studies to uncover the functions of lincRNAs in rainbow trout.
authors: Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506-6108, USA.
authors: Jian
authors: J
authors: Wang
authors: Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506-6108, USA.
authors: Liyuan
authors: L
authors: Fu
authors: Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506-6108, USA.
authors: Prasanthi P
authors: PP
authors: Koganti
authors: Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506-6108, USA.
authors: Lei
authors: L
authors: Wang
authors: Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506-6108, USA.
authors: Jacqelyn M
authors: JM
authors: Hand
authors: USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, 25430, USA.
authors: Hao
authors: H
authors: Ma
authors: Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506-6108, USA. jianbo.yao@mail.wvu.edu.
authors: Jianbo
authors: J
authors: Yao
mesh_terms: D000818:Animals; D021901:DNA, Intergenic; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D053858:Metabolic Networks and Pathways / Q000235:genetics; D017686:Oncorhynchus mykiss / Q000235:genetics* / Q000254:growth & development; D009928:Organ Specificity; D062085:RNA, Long Noncoding; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D021901:DNA, Intergenic; D062085:RNA, Long Noncoding
keywords: Co-expression network; LincRNA; LncRNA; Rainbow trout