Epigenomic analysis reveals prevalent contribution of transposable elements to cis -regulatory elements, tissue-specific expression, and alternative promoters in zebrafish.

Autor:	Lee HJ; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA., Hou Y; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA., Maeng JH; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA., Shah NM; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA., Chen Y; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA., Lawson HA; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA., Yang H; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA., Yue F; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA.; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois 60611, USA., Wang T; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA.
Jazyk:	angličtina
Zdroj:	Genome research [Genome Res] 2022 Jul; Vol. 32 (7), pp. 1424-1436. Date of Electronic Publication: 2022 Jun 01.
DOI:	10.1101/gr.276052.121
Abstrakt:	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. (© 2022 Lee et al.; Published by Cold Spring Harbor Laboratory Press.)
Databáze:	MEDLINE
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