The regulatory potential of transposable elements in maize.

Autor:	Bubb KL; Department of Genome Sciences, University of Washington, Seattle, USA., Hamm MO; Department of Genome Sciences, University of Washington, Seattle, USA., Min JK; Department of Genome Sciences, University of Washington, Seattle, USA., Ramirez-Corona B; Department of Genome Sciences, University of Washington, Seattle, USA., Mueth NA; Department of Genome Sciences, University of Washington, Seattle, USA., Ranchalis J; Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA., Vollger MR; Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA., Trapnell C; Department of Genome Sciences, University of Washington, Seattle, USA.; Molecular & Cellular Biology Program, University of Washington, Seattle, USA.; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, USA., Cuperus JT; Department of Genome Sciences, University of Washington, Seattle, USA., Queitsch C; Department of Genome Sciences, University of Washington, Seattle, USA.; Molecular & Cellular Biology Program, University of Washington, Seattle, USA.; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, USA., Stergachis AB; Department of Genome Sciences, University of Washington, Seattle, USA.; Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA.; Molecular & Cellular Biology Program, University of Washington, Seattle, USA.; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, USA.
Jazyk:	angličtina
Zdroj:	BioRxiv : the preprint server for biology [bioRxiv] 2024 Jul 14. Date of Electronic Publication: 2024 Jul 14.
DOI:	10.1101/2024.07.10.602892
Abstrakt:	Since their initial discovery in maize, transposable elements (TEs) have emerged as being integral to the evolution of maize, accounting for 80% of its genome. However, the repetitive nature of TEs has hindered our understanding of their regulatory potential. Here, we demonstrate that long-read chromatin fiber sequencing (Fiber-seq) permits the comprehensive annotation of the regulatory potential of maize TEs. We uncover that only 94 LTR retrotransposons contain the functional epigenetic architecture required for mobilization within maize leaves. This epigenetic architecture degenerates with evolutionary age, resulting in solo TE enhancers being preferentially marked by simultaneous hyper-CpG methylation and chromatin accessibility, an architecture markedly divergent from canonical enhancers. We find that TEs shape maize gene regulation by creating novel promoters within the TE itself as well as through TE-mediated gene amplification. Lastly, we uncover a pervasive epigenetic code directing TEs to specific loci, including that locus that sparked McClintock's discovery of TEs. Competing Interests: Competing interests. A.B.S. is a co-inventor on a patent relating to the Fiber-seq method (US17/995,058).
Databáze:	MEDLINE
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