Poster Presentation 40th Annual Lorne Genome Conference 2019

Depletion of Cohesin Factor Rad21 Alters Genome Organisation around Key Transcription Factors During Zygotic Genome Activation (#245)

William Schierding 1 , Amy Dowdle 2 , Michael Meier 2 , Justin M O'Sullivan 1 , Julia A Horsfield 2
  1. Liggins Institute, University of Auckland, Auckland, New Zealand
  2. Department of Pathology, University of Otago, Dunedin, New Zealand

Introduction:

As embryo genomes progress through the maternal-to-zygotic transition the zygotic genome is activated for the first time (zygotic genome activation, ZGA). This process is likely induced through a progression in zygotic chromatin structure with the nuclear architectural protein cohesin ring (including the Rad21 subunit) playing a major role. At ZGA, chromatin reorganisation opens up areas of the genome and activating genes that encode the ‘pioneer’ transcription factors (e.g. Nanog, Pou5f3, Sox2). Therefore, it is reasonable to hypothesize that the opening up of the genome at pioneer factor binding sites is important for ZGA.

Methods:

Here we use ATACseq to explore genome organisation in wildtype versus Rad21-depleted zebrafish embryos at three time points across the ZGA window: 1) pre-ZGA (maternally dominated, 2.5 hours post-fertilization); 2) ZGA transition period (3.3 hourspost-fertilization); and 3) post-ZGA (zygotically dominated, 4.5 and 10.0 hours post-fertilization).

Results:

We determined that Rad21 depletion alters genome organisation around regions co-occupied by pioneer transcription factors. There is wildtype-specific Sox2 binding site enrichment at ATACseq peaks at ZGA. Therefore, Rad21 depletion alters Sox2 accessibility at ZGA. ATACseq peak intensity at pioneer factor binding sites for Nanog and Pou5f3 are enriched both at- and post-ZGA. However, ATACseq peak intensity at Nanog and Pou5f3 sites are enriched within those ATACseq peaks that are lost or gained following Rad21 depletion at ZGA but not at those peaks lost or gained post-ZGA. Therefore, Rad21 depletion is associated with a redistribution ATACseq peaks at ZGA, away from key pioneer factor binding sites.

Discussion:

Genome organisation involves the formation of domains that influence the availability of transcription factor binding sites and enhancers, regulating key aspects of gene expression. The results of this study are consistent with Rad21 depletion delaying the opening of chromatin at important developmental regions, resulting in an overall delay in ZGA timing.