GSE130944
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 transcription factors until the controlled onset of transcription during zygotic genome activation (ZGA). The regulation of chromatin accessibility and its relationship to gene activity during this transition remains poorly understood. Here, we generated chromatin accessibility maps for the early stages of zebrafish development spanning genome activation and the onset of lineage specification. We find that during this period, chromatin accessibility increases at regulatory elements. This is independent of RNA pol II-mediated transcription, with the exception of the 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 ZGA, results in decreased accessibility at regulatory elements. Finally, we show that accessibility of regulatory regions, especially when established by Pou5f3, Sox19b and Nanog, is predictive for future transcription. Together, our results suggest that maternally provided transcription factors prime genes for activity during zygotic genome activation. Overall design: Chromatin accessibility profiles (ATAC-seq) for zebrafish whole embryos were generated for 7 WT developmental stages (256-cell, high, oblong, sphere, dome, shield, 80%-epiboly),  maternal-zygotic transcription factor mutants (pou5f3(-/-), sox19b(-/-), nanog(-/-) ) at oblong stage and alpha-amanitin treated embryos at oblong stage. Additionally, a nucleosome-free genomic DNA sample was generated as control. Each stage/condition except for the  control was replicated with duplicates or triplicates  and sequenced on an Illumina HiSeq 2500  instrument or NextSeq550 instrument.