Establishment of developmental gene silencing by ordered polycomb complex recruitment in early zebrafish embryos
- Howard Hughes Medical Institute, University of Utah School of Medicine, United States
Abstract
Vertebrate embryos achieve developmental competency during zygotic genome activation (ZGA) by establishing chromatin states that silence yet poise developmental genes for subsequent lineage-specific activation. Here, we reveal the order of chromatin states in establishing developmental gene poising in preZGA zebrafish embryos. Poising is established at promoters and enhancers that initially contain open/permissive chromatin with 'Placeholder' nucleosomes (bearing H2A.Z, H3K4me1, and H3K27ac), and DNA hypomethylation. Silencing is initiated by the recruitment of Polycomb Repressive Complex 1 (PRC1), and H2Aub1 deposition by catalytic Rnf2 during preZGA and ZGA stages. During postZGA, H2Aub1 enables Aebp2-containing PRC2 recruitment and H3K27me3 deposition. Notably, preventing H2Aub1 (via Rnf2 inhibition) eliminates recruitment of Aebp2-PRC2 and H3K27me3, and elicits transcriptional upregulation of certain developmental genes during ZGA. However, upregulation is independent of H3K27me3 - establishing H2Aub1 as the critical silencing modification at ZGA. Taken together, we reveal the logic and mechanism for establishing poised/silent developmental genes in early vertebrate embryos.
Data availability
Sequencing data have been deposited in GEO under accession code GSE168362.
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Zebrafish Polycomb ZGANCBI Gene Expression Omnibus, GSE168362.
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'Placeholder' nucleosomes underlie germline-to-embryo DNA methylation reprogrammingGene Expression Omnibus, GSE95033.
Article and author information
Author details
Funding
Howard Hughes Medical Institute (Cairns)
- Bradley R Cairns
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: All of our work on zebrafish is authorized and overseen by our institutional animal care and use committee (IACUC). This work is authorized by the current IACUC Protocol #IACUC protocol 20-04011 'Germ Cell Epigenetics in Zebrafish'. We have no surgical procedures, and followed AVMA Guidelines involving a 2-step euthanasia for embryos and larvae which includes rapid chilling followed by immersion in a dilute sodium hypochlorite solution (discussed on page 89 of the 2020 Guidelines).
Copyright
© 2022, Hickey et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Establishment of developmental gene silencing by ordered polycomb complex recruitment in early zebrafish embryos
eLife 11:e67738.
https://doi.org/10.7554/eLife.67738
Further reading
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