PUBLICATION

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

Authors
Pálfy, M., Schulze, G., Valen, E., Vastenhouw, N.L.
ID
ZDB-PUB-200116-10
Date
2020
Source
PLoS Genetics   16: e1008546 (Journal)
Registered Authors
Vastenhouw, Nadine
Keywords
none
Datasets
GEO:GSE130944
MeSH Terms
  • Animals
  • Chromatin/genetics
  • Chromatin Assembly and Disassembly*
  • Embryo, Nonmammalian/metabolism
  • Gene Expression Regulation, Developmental*
  • Genomic Imprinting
  • Nanog Homeobox Protein/metabolism*
  • Octamer Transcription Factor-3/metabolism*
  • SOX Transcription Factors/metabolism*
  • Zebrafish
  • Zebrafish Proteins/metabolism*
(all 11)
PubMed
31940339 Full text @ PLoS Genet.
Abstract
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.
Genes / Markers
Marker Marker Type Name
apoebGENEapolipoprotein Eb
cxcr4aGENEchemokine (C-X-C motif) receptor 4a
eif4g2aGENEeukaryotic translation initiation factor 4, gamma 2a
eomesaGENEeomesodermin homolog a
fbxw4GENEF-box and WD repeat domain containing 4
foxh1GENEforkhead box H1
gata6GENEGATA binding protein 6
id1GENEinhibitor of DNA binding 1, HLH protein
inka1aGENEinka box actin regulator 1a
mxtx2GENEmix-type homeobox gene 2
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Figures
Figure Gallery (5 images)
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Expression
Phenotype
Fish Conditions Stage Phenotype Figure
nanogm1435/m1435standard conditionsOblong
pou5f3zf3267/zf3267standard conditionsOblong
sox19bzf3268/zf3268standard conditionsOblong
1 - 3 of 3
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Mutations / Transgenics
Allele Construct Type Affected Genomic Region
m1435
    		Small Deletion
    zf3267
      		Small Deletion
      zf3268
        		Small Deletion
        1 - 3 of 3
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        Human Disease / Model
        No data available
        Sequence Targeting Reagents
        Target Reagent Reagent Type
        pou5f3CRISPR2-pou5f3CRISPR
        pou5f3CRISPR3-pou5f3CRISPR
        sox19bCRISPR2-sox19bCRISPR
        sox19bCRISPR3-sox19bCRISPR
        1 - 4 of 4
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        Fish
        Fish
        nanogm1435/m1435
        pou5f3zf3267/zf3267
        sox19bzf3268/zf3268
        1 - 3 of 3
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        Antibodies
        No data available
        Orthology
        No data available
        Engineered Foreign Genes
        No data available
        Mapping
        No data available
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        Citation
        Pálfy, M., Schulze, G., Valen, E., Vastenhouw, N.L. (2020) Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation. PLoS Genetics. 16:e1008546.