Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish

BMC Genomics
Wen ChenChangning Liu

Abstract

Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs' function and conservation is really intriguing. We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures. As a result, we obtained by far the most complete dataset of zebrafish lncRNAs, containing 13,604 lncRNA genes (21,128 transcripts) in total. Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA. Meanwhile, we made a conservation analysis on zebrafish lncRNA, identifying 1828 conserved zebrafish lncRNA genes (1890 transcripts) that have their putative mammalian orthologs. We also found that zebrafish lncRNAs play important roles in regulation of the development and function of nervous system; these conserved lncRNAs present a significant sequ...Continue Reading

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Citations

Apr 17, 2020·Disease Models & Mechanisms·Alon DayaDavid Karasik
Oct 20, 2018·Database : the Journal of Biological Databases and Curation·Xiang HuChangning Liu
Mar 24, 2021·Briefings in Functional Genomics·Gyan RanjanSridhar Sivasubbu
Sep 23, 2020·Non-coding RNA Research·He Chen, Ge Shan
Jun 15, 2021·Frontiers in Oncology·Cecilia ZampedriJorge Melendez-Zajgla

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Methods Mentioned

BETA
RNA-Seq
transgenic

Software Mentioned

NONCODE
SRA
BLAST
Ensembl
Trimmomatic
BLASTN
zflncRNApedia
house
CPC
goatools

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