Regulation of chromatin accessibility in early embryos of the common house spider Parasteatoda tepidariorum

We identified a lineage-specific GATA-like gene named fuchi nashi (fuchi) as a gene required for establishing a germ disc in the early embryo of the common house spider Parasteatoda tepidariorum. To investigate possible involvement of the early fuchi activity in regulation of chromatin accessibility, we used an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Whole embryos at stage 3 that were untreated (wild-type) or treated for fuchi or hedgehog (hh) parental RNAi (pRNAi), as well as wild-type whole embryos at stages 1 and 2, were analyzed by ATAC-seq. We found that chromatin accesibilities were specifically altered by fuchi pRNAi at many regions of the genome, whereas chromatin accessibilities were little affected by Pt-hh pRNAi, which served as negative control. Overall design: We analyzed by ATAC-seq the nuclei that were extracted from wild-type whole embryos at stage 1 (st1, 9 h after egg laying [AEL]), stage 2 (st2, 12 h AEL), and stage 3 (st3, 18 h AEL) and from fuchi and Pt-hh pRNAi whole embryos at stage 3 (st3, 18 h AEL). Two biological replicates were obtained for each sample type. The tagmented genomic DNAs were amplified to produce indexed libraries, which were paired-end sequenced using the Illumina HiSeq X Ten system (2 x 151 bp reads) . Differential accessibilities between the wild-type and fuchi or Pt-hh pRNAi stage 3 samples were statistically evaluated.