Mapping the Early Zebrafish Regulatory Landscape Using CUT&RUN

Utilizing the low-input ChIP-Seq method CUT&RUN, we have characterized active regulatory sequence relevant to zygotic genome activation and transcriptional regulation during early embryogenesis. CUT&RUN was carried out at both 3HPF (1000c stage) and 3.7hpf(oblong) with 40,000 cells per experiment, along with no antibody controls. This data was compared against and analyzed in conjunction with published 4.3hpf (dome stage) ChIP-Seq (Bogdanovic et al 2012). The set of promoter adjacent (+/- 1000 bp from the TSS) and distal regulatory elements across all three experiments was analyzed using deeptools to show enrichment. Further analysis will be carried out to determine enhancer dynamics across developmental time and to look for signatures of maternal transcription factors relevant to zygotic genome activation