AUTHOR=Das Jutan , Kumar Baibhav , Saha Bibek , Jaiswal Sarika , Iquebal Mir Asif , Angadi U. B. , Kumar Dinesh 

TITLE=Genome-wide identification and characterization of tissue specific long non-coding RNAs and circular RNAs in common carp (Cyprinus carpio L.)

JOURNAL=Frontiers in Genetics

VOLUME=Volume 14 - 2023

YEAR=2023

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1239434

DOI=10.3389/fgene.2023.1239434

ISSN=1664-8021

ABSTRACT=Cyprinus carpio is regarded as a substitute vertebrate fish model for zebrafish. A varied category of non-coding RNAs is comprised of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). These ncRNAs were once considered non-functional “junk DNA” but research now shows they play important roles in gene expression regulation, chromatin modification, and epigenetic regulation. The systemic tissue-specific research of the lncRNAs and circRNAs of C. carpio is yet unexplored. In this study, a total of 33,990 lncRNAs were identified and characterized from 468 RNA-Seq data retrieved from 28 different tissues of common carp. The results of this study revealed 9 miRNAs having 19 unique lncRNAs acting as their precursors. Additionally, 2,837 miRNAs were found to target 4,782 distinct lncRNAs in the lncRNA-miRNA-mRNA interaction network analysis, which resulted in the involvement of 3,718 mRNAs in common carp. The tissue-wise identification of circRNAs revealed a total of 22,854 circRNAs identified across all the 28 tissues. Moreover, the examination of the circRNA-miRNA-mRNA interaction network revealed that 15,731 circRNAs were targeted by 5,906 distinct miRNAs, which in turn targeted 4,524 mRNAs in common carp. Significant signaling pathways like necroptosis, NOD-like receptor signaling pathway, hypertrophic cardiomyopathy, small cell lung cancer, MAPK signaling pathway etc. were identified through the analysis of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The web resource of ncRNAs, CCncRNAdb, available at http://backlin.cabgrid.res.in/ccncrnadb/ give a comprehensive information about common carp lncRNAs, circRNAs, and ceRNAs interactions, which can aid in investigating the functional roles of ncRNAs in common carp for its management.