PUBLICATION
Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Authors
- Lee, H.J., Hou, Y., Maeng, J.H., Shah, N.M., Chen, Y., Lawson, H.A., Yang, H., Yue, F., Wang, T.
- ID
- ZDB-PUB-220602-18
- Date
- 2022
- Source
- Genome research 32(7): 1424-1436 (Journal)
- Registered Authors
- Chen, Yujie, Hou, Yiran, Wang, Ting
- Keywords
- alternative promoters, cis-regulatory elements, epigenomics, transposable elements, zebrafish
- Datasets
- GEO:GSE134055
- MeSH Terms
-
- Animals
- DNA Transposable Elements*/genetics
- Epigenomics*
- Promoter Regions, Genetic
- Regulatory Sequences, Nucleic Acid
- Zebrafish/genetics
- PubMed
- 35649578 Full text @ Genome Res.
Citation
Lee, H.J., Hou, Y., Maeng, J.H., Shah, N.M., Chen, Y., Lawson, H.A., Yang, H., Yue, F., Wang, T. (2022) Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish. Genome research. 32(7):1424-1436.
Abstract
Transposable elements (TEs) encode regulatory elements that impact gene expression in multiple species, yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here, we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE-derived transcriptional units expressed across tissues. Finally, we show that novel TE-derived promoters can initiate tissue-specific transcription of alternate gene isoforms. This work provides a comprehensive profile of TE activity across normal zebrafish tissues, shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping