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 11 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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1424-1436 |
| Number of pages | 13 |
| Journal | Genome research |
| Volume | 32 |
| Issue number | 8 |
| DOIs | |
| State | Published - Jul 2022 |
Funding
We thank all the Ting Wang laboratory members for the insightful discussion. T.W. is supported by National Institutes of Health (NIH) grants R01HG007175, U24ES026699, U01CA200060, U01HG009391, and U41HG010972. F.Y. is supported by NIH grants R35GM124820, R01HG009906, R24DK106766, and U01CA200060.
ASJC Scopus subject areas
- Genetics(clinical)
- Genetics