Activator-blocker model of transcriptional regulation by pioneer-like factors

Aileen Julia Riesle, Meijiang Gao, Marcus Rosenblatt, Jacques Hermes, Helge Hass, Anna Gebhard, Marina Veil, Björn Grüning, Jens Timmer () and Daria Onichtchouk ()
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Aileen Julia Riesle: Albert-Ludwigs-University of Freiburg
Meijiang Gao: Albert-Ludwigs-University of Freiburg
Marcus Rosenblatt: Albert-Ludwigs-University of Freiburg
Jacques Hermes: Albert-Ludwigs-University of Freiburg
Helge Hass: Albert-Ludwigs-University of Freiburg
Anna Gebhard: Albert-Ludwigs-University of Freiburg
Marina Veil: Albert-Ludwigs-University of Freiburg
Björn Grüning: University of Freiburg
Jens Timmer: Signalling Research centers BIOSS and CIBSS
Daria Onichtchouk: Albert-Ludwigs-University of Freiburg

Nature Communications, 2023, vol. 14, issue 1, 1-18

Abstract: Abstract Zygotic genome activation (ZGA) in the development of flies, fish, frogs and mammals depends on pioneer-like transcription factors (TFs). Those TFs create open chromatin regions, promote histone acetylation on enhancers, and activate transcription. Here, we use the panel of single, double and triple mutants for zebrafish genome activators Pou5f3, Sox19b and Nanog, multi-omics and mathematical modeling to investigate the combinatorial mechanisms of genome activation. We show that Pou5f3 and Nanog act differently on synergistic and antagonistic enhancer types. Pou5f3 and Nanog both bind as pioneer-like TFs on synergistic enhancers, promote histone acetylation and activate transcription. Antagonistic enhancers are activated by binding of one of these factors. The other TF binds as non-pioneer-like TF, competes with the activator and blocks all its effects, partially or completely. This activator-blocker mechanism mutually restricts widespread transcriptional activation by Pou5f3 and Nanog and prevents premature expression of late developmental regulators in the early embryo.

Date: 2023
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DOI: 10.1038/s41467-023-41507-z

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