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Chromatin accessibility and histone acetylation in the regulation of competence in early development

Melody Esmaeili, Shelby A. Blythe, John W Tobias, Kai Zhang, Jing Yang, Peter S Klein
doi: https://doi.org/10.1101/797183
Melody Esmaeili
1 Perelman School of Medicine at the University of Pennsylvania;
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  • For correspondence: melodye@pennmedicine.upenn.edu
Shelby A. Blythe
2 Northwestern University;
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  • For correspondence: shelby.blythe@northwestern.edu
John W Tobias
1 Perelman School of Medicine at the University of Pennsylvania;
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  • For correspondence: jtobias@pennmedicine.upenn.edu
Kai Zhang
3 University of Illinois at Urbana Champagne;
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  • For correspondence: kaizkaiz@illinois.edu
Jing Yang
3 University of Illinois at Urbana Champagne;
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  • For correspondence: yangj@illinois.edu
Peter S Klein
4 University of Pennsylvania
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  • For correspondence: pklein@pennmedicine.upenn.edu
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Abstract

As development proceeds, inductive cues are interpreted by competent tissues in a spatially and temporally restricted manner. While key inductive signaling pathways within competent cells are well-described at a molecular level, the mechanisms by which tissues lose responsiveness to inductive signals are not well understood. Localized activation of Wnt signaling before zygotic gene activation in Xenopus laevis leads to dorsal development, but competence to induce dorsal genes in response to Wnts is lost by the late blastula stage. We hypothesize that loss of competence is mediated by changes in histone modifications leading to a loss of chromatin accessibility at the promoters of Wnt target genes. We use ATAC-seq to evaluate genome-wide changes in chromatin accessibility across several developmental stages. Based on overlap with p300 binding, we identify thousands of putative cis-regulatory elements at the gastrula stage, including sites that lose accessibility by the end of gastrulation and are enriched for pluripotency factor binding motifs. Dorsal Wnt target gene promoters are not accessible after the loss of competence in the early gastrula while genes involved in mesoderm and neural crest development maintain accessibility at their promoters. Inhibition of histone deacetylases increases acetylation at the promoters of dorsal Wnt target genes and extends competence for dorsal gene induction by Wnt signaling. Histone deacetylase inhibition, however, is not sufficient to extend competence for mesoderm or neural crest induction. These data suggest that chromatin state regulates the loss of competence to inductive signals in a context-dependent manner.

Footnotes

  • Corrected error in Figure 7 (duplicated panels).

  • https://data.mendeley.com/datasets/fbkvhzbyy5/1

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 24, 2020.
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Chromatin accessibility and histone acetylation in the regulation of competence in early development
Melody Esmaeili, Shelby A. Blythe, John W Tobias, Kai Zhang, Jing Yang, Peter S Klein
bioRxiv 797183; doi: https://doi.org/10.1101/797183
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Chromatin accessibility and histone acetylation in the regulation of competence in early development
Melody Esmaeili, Shelby A. Blythe, John W Tobias, Kai Zhang, Jing Yang, Peter S Klein
bioRxiv 797183; doi: https://doi.org/10.1101/797183

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