PUBLICATION
Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish
- Authors
- Chen, W., Zhang, X., Li, J., Huang, S., Xiang, S., Hu, X., Liu, C.
- ID
- ZDB-PUB-180517-1
- Date
- 2018
- Source
- BMC Genomics 19: 112 (Journal)
- Registered Authors
- Keywords
- Co-expression network, Conservation, Gene ontology, KEGG, LncRNA, Zebrafish
- MeSH Terms
-
- Gene Ontology
- Animals
- RNA, Long Noncoding/genetics*
- Zebrafish/genetics*
- Base Sequence
- Conserved Sequence
- Computational Biology/methods
- Zebrafish Proteins/genetics
- Databases, Genetic
- Sequence Analysis, RNA/methods*
- Gene Regulatory Networks*
- PubMed
- 29764394 Full text @ BMC Genomics
Citation
Chen, W., Zhang, X., Li, J., Huang, S., Xiang, S., Hu, X., Liu, C. (2018) Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish. BMC Genomics. 19:112.
Abstract
Background 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.
Results 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 sequential and functional conservation, with their mammalian counterparts.
Conclusions By integrative data analysis and construction of coding-lncRNA gene co-expression network, we gained the most comprehensive dataset of zebrafish lncRNAs up to present, as well as their systematic annotations and comprehensive analyses on function and conservation. Our study provides a reliable zebrafish-based platform to deeply explore lncRNA function and mechanism, as well as the lncRNA commonality between zebrafish and human.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping