Zygotic activation of transposable elements during zebrafish early embryogenesis

Bo Li, Ting Li, Dingjie Wang, Ying Yang, Puwen Tan, Yunhao Wang, Yun-Gui Yang (), Shunji Jia () and Kin Fai Au ()
Additional contact information
Bo Li: University of Michigan
Ting Li: Fudan University
Dingjie Wang: University of Michigan
Ying Yang: China National Center for Bioinformation
Puwen Tan: University of Michigan
Yunhao Wang: University of Michigan
Yun-Gui Yang: China National Center for Bioinformation
Shunji Jia: Chinese Academy of Sciences
Kin Fai Au: University of Michigan

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: Abstract Although previous studies have shown that transposable elements (TEs) are conservatively activated to play key roles during early embryonic development, the details of zygotic TE activation (ZTA) remain poorly understood. Here, we employ long-read sequencing to precisely identify that only a small subset of TE loci are activated among numerous copies, allowing us to map their hierarchical transcriptional cascades at the single-locus and single-transcript level. Despite the heterogeneity of ZTA across family, subfamily, locus, and transcript levels, our findings reveal that ZTA follows a markedly different pattern from conventional zygotic gene activation (ZGA): ZTA occurs significantly later than ZGA and shows a pronounced bias for nuclear localization of TE transcripts. This study advances our understanding of TE activation by providing a high-resolution view of TE copies and creating a comprehensive catalog of thousands of previously unannotated transcripts and genes that are activated during early zebrafish embryogenesis. Among these genes, we highlight two that are essential for zebrafish development.

Date: 2025
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-58863-7 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58863-7

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-58863-7

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().