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.
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This study was supported by the USDA ARS Cooperative Agreement No. 58-1930-0-059. It is published with the approval of the director of the West Virginia Agricultural and Forestry Experiment Station as scientific paper No. 3268.
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Supplemental file 1
Primers used for validation of expression of 10 selected lincRNAs. (XLSX 9 kb)
Supplemental file 2
Total transcript counts in each step of lincRNA prediction pipeline. (XLSX 10 kb)
Supplemental file 3
Catalog of 9764 transcribed lincRNAs in rainbow trout. (XLSX 2309 kb)
Supplemental file 4
Venn diagram representing rainbow trout lincRNAs across different tissues. (A) Overlapping expression profiles of lincRNAs across testis (blue-Te), oocyte (yellow-Oo), pineal (orange-Pi), brain (green-Br), and liver (pink-Li). (B) Overlapping expression profiles of lincRNAs across white muscle (blue-Wm), red muscle (yellow-Rm), skin (orange-Sk), fat (green-Fa) and head kidney (pink-Hk). (JPG 142 kb)
Supplemental file 5
Hierarchical clustering dendrogram of lincRNAs together with protein coding genes. (JPG 50 kb)
Supplemental file 6
Genes and their memberships to each module. MM stands for module membership, which is the correlation between a gene and a module. PMM is the p-value of MM. (XLSX 170 kb)
Supplemental file 7
GO analysis of modules. GO terms enriched in specific modules were tested by Fisher’s exact test. (XLSX 170 kb)
Supplemental file 8
KEGG pathway analysis and network of hub gene of blue module. (A) and (B) Hub gene network. (C) mTOR signaling pathway. (D) T cell receptor signaling pathway. (E) PI3K-AKT signaling pathway. (JPG 709 kb)
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Wang, J., Fu, L., Koganti, P.P. et al. Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss). Mar Biotechnol 18, 271–282 (2016). https://doi.org/10.1007/s10126-016-9689-5
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DOI: https://doi.org/10.1007/s10126-016-9689-5