Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss)

Authors: WANG, JIAN - West Virginia University; FU, LIYUAN - West Virginia University; KOGANTI, PRASANTHI - West Virginia University; WANG, LEI - West Virginia University; HAND, JACQULYN - West Virginia University; Ma, Hao; YAO, JIANBO - West Virginia University

Submitted to: Marine Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/30/2015
Publication Date: 2/11/2016
Publication URL: http://handle.nal.usda.gov/10113/63163
Citation: Wang, J., Fu, L., Koganti, P.P., Wang, L., Hand, J.M., Ma, H., Yao, J. 2016. Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss). Marine Biotechnology. doi 10.1007/s10126-016-9689-5.

Interpretive Summary: Thousands of long noncoding RNA (lncRNAs) have been discovered to regulate many cellular processes in model organisms in recent years. Large intergenic noncoding RNAs (lincRNAs) belong to lncRNA which are produced from a stretch of DNA sequences located between genes. To date, lincRNAs have not been reported in teleost fish. In this report, we present a list of 9,674 rainbow trout lincRNAs based on analysis of RNA sequencing data from 15 tissues. The expression of the identified lincRNAs varied greatly among different tissues and many characteristics are similar to mammalian species. Our analysis revealed that many of the identified lincRNAs are related to immune response, muscle differentiation, and neural development. The results can be used as a starting point to study the functions of the lincRNAs in rainbow trout.

Technical 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.