Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

In many organisms, early embryonic development is driven by maternally provided factors until the controlled onset of transcription during zygotic genome activation. The regulation of chromatin accessibility and its relationship to gene activity during this transition remain poorly understood. Here,...

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Bibliographic Details
Published in:PLoS genetics 2020-01, Vol.16 (1), p.e1008546-e1008546
Main Authors: Pálfy, Máté, Schulze, Gunnar, Valen, Eivind, Vastenhouw, Nadine L
Format: Article
Language:English
Subjects:
Animal genetics
Animals
Authorship
Biology
Biology and Life Sciences
Chromatin
Chromatin - genetics
Chromatin Assembly and Disassembly
Danio rerio
DNA binding proteins
DNA-directed RNA polymerase
Embryo, Nonmammalian - metabolism
Embryogenesis
Embryonic development
Gene Expression Regulation, Developmental
Gene loci
Gene mapping
Genetic aspects
Genomes
Genomic Imprinting
Genomics
Informatics
Nanog Homeobox Protein - metabolism
Octamer Transcription Factor-3 - metabolism
Regulatory sequences
Research and Analysis Methods
RNA
RNA polymerase
SOX Transcription Factors - metabolism
Transcription (Genetics)
Transcription activation
Transcription factors
Zebrafish
Zebrafish Proteins - metabolism
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Summary:In many organisms, early embryonic development is driven by maternally provided factors until the controlled onset of transcription during zygotic genome activation. The regulation of chromatin accessibility and its relationship to gene activity during this transition remain poorly understood. Here, we generated chromatin accessibility maps with ATAC-seq from genome activation until the onset of lineage specification. During this period, chromatin accessibility increases at regulatory elements. This increase is independent of RNA polymerase II-mediated transcription, with the exception of the hypertranscribed miR-430 locus. Instead, accessibility often precedes the transcription of associated genes. Loss of the maternal transcription factors Pou5f3, Sox19b, and Nanog, which are known to be required for zebrafish genome activation, results in decreased accessibility at regulatory elements. Importantly, the accessibility of regulatory regions, especially when established by Pou5f3, Sox19b and Nanog, is predictive for future transcription. Our results show that the maternally provided transcription factors Pou5f3, Sox19b, and Nanog open up chromatin and prime genes for activity during zygotic genome activation in zebrafish.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1008546