PUBLICATION
Systematic identification and characterization of cardiac long intergenic noncoding RNAs in zebrafish
- Authors
- Wang, L., Ma, X., Xu, X., Zhang, Y.
- ID
- ZDB-PUB-170430-1
- Date
- 2017
- Source
- Scientific Reports 7: 1250 (Journal)
- Registered Authors
- Ma, Xiao, Xu, Xiaolei
- Keywords
- Cardiovascular genetics, Genome informatics
- Datasets
- GEO:GSE85416
- MeSH Terms
-
- Computational Biology
- Gene Expression Profiling*
- DNA, Intergenic*
- Zebrafish/embryology*
- Zebrafish/growth & development*
- Animals
- RNA, Untranslated/genetics*
- Sequence Analysis, RNA
- Heart/embryology*
- Heart/growth & development*
- PubMed
- 28455512 Full text @ Sci. Rep.
Citation
Wang, L., Ma, X., Xu, X., Zhang, Y. (2017) Systematic identification and characterization of cardiac long intergenic noncoding RNAs in zebrafish. Scientific Reports. 7:1250.
Abstract
Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as potential key regulators of heart development and related diseases, but their identities and functions remain elusive. In this study, we sought to identify and characterize the cardiac lincRNA transcriptome in the experimentally accessible zebrafish model by integrating bioinformatics analysis with experimental validation. By conducting genome-wide RNA sequencing profiling of zebrafish embryonic hearts, adult hearts, and adult muscle, we generated a high-confidence set of 813 cardiac lincRNA transcripts, 423 of which are novel. Among these lincRNAs, 564 are expressed in the embryonic heart, and 730 are expressed in the adult heart, including 2 novel lincRNAs, TCONS_00000891 and TCONS_00028686, which exhibit cardiac-enriched expression patterns in adult heart. Using a method similar to a fetal gene program, we identified 51 lincRNAs with differential expression patterns between embryonic and adult hearts, among which TCONS_00009015 responded to doxorubicin-induced cardiac stress. In summary, our genome-wide systematic identification and characterization of cardiac lincRNAs lays the foundation for future studies in this vertebrate model to elucidate crucial roles for cardiac lincRNAs during heart development and cardiac diseases.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping