Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee1,2,6,7,
- Yiran Hou1,2,6,
- Ju Heon Maeng1,2,6,
- Nakul M. Shah1,2,
- Yujie Chen1,2,
- Heather A. Lawson1,
- Hongbo Yang3,8,
- Feng Yue3,4 and
- Ting Wang1,2,5
- 1Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- 2Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- 3Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA;
- 4Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois 60611, USA;
- 5McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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↵6 These authors contributed equally to this work.
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.276052.121.
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Freely available online through the Genome Research Open Access option.
- Received August 7, 2021.
- Accepted May 27, 2022.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
