Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss)
| Autor: | Jacqelyn M. Hand, Jianbo Yao, Jian Wang, Liyuan Fu, Prasanthi P. Koganti, Hao Ma, Lei Wang |
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| Rok vydání: | 2015 |
| Předmět: |
0301 basic medicine
endocrine system animal structures animal diseases ved/biology.organism_classification_rank.species Computational biology Biology Bioinformatics Applied Microbiology and Biotechnology Genome 03 medical and health sciences Exon Intergenic region Animals Model organism Gene ved/biology Sequence Analysis RNA Gene Expression Profiling Gene Expression Regulation Developmental 030104 developmental biology Organ Specificity Oncorhynchus mykiss Rainbow trout Identification (biology) DNA Intergenic RNA Long Noncoding Transcriptome Neural development Metabolic Networks and Pathways |
| Zdroj: | Marine biotechnology (New York, N.Y.). 18(2) |
| ISSN: | 1436-2236 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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