Staged embryos were homogenized on ice with Dounce homogenizer. Tagged nuclei were isolated by antibody pull-down with Dynabeads protein G (ThermoFisher: 10009D) adsorbed to monoclonal anti-FLAG M2 antibody (Sigma-Aldrich: F1804). Fragmentation and amplification of ATAC-seq libraries were performed according to the standard protocol (Buenrostro et al., Current Protocols in Molecular Biology, 2015). Nuclei pellet corresponding to 340 ng of genomic DNA was resuspended in Nextera Tagment DNA Buffer and combined with 6 μl of Nextera Tn5 transposase (Illumina) to the final volume of 25 μl. After 12 PCR amplification cycles, ATAC-seq libraries were purified with Agencourt AMPure XP beads (Beckman Coulter: A63881), using double size selection (left ratio: 2.0x, right ratio: 0.5x). Whole-embryo control samples were generated according to the same protocol, but with exclusion of the step of antibody pull-down.