Opa is a late-acting, pioneer factor that coordinates with Zelda to broadly regulate gene expression in early embryos (ChIP-seq, ATAC-seq)

Pioneer factors such as Zelda initiate zygotic transcription within Drosophila early embryos, but whether other factors also support this dynamic patterning process is unclear. Odd-paired (Opa) is a zinc-finger transcription factor expressed during cellularization, shown to act as timing factor to control pair-rule to segmental patterning transition along the anterior-posterior (AP) axis. We found Opa regulates expression through an enhancer active along the dorso-ventral axis (sog_Distal), specifically, to support its late embryonic expression. Opa chromatin immunoprecipitation identified occupancy at this enhancer sequence as well widespread binding throughout the genome, comparable to Zelda. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zelda, influences accessibility and has both common as well as distinct target sequences. opa mutants also exhibit DV and AP patterning changes suggesting Opa acts broadly. This study suggests Opa is a late-acting, pioneer factor whose action follows Zelda to herald in a second wave of zygotic gene expression. NIH Grants R35GM118146 and R03HD097535 to A.S. Genome binding and accessibility profiling by high throughput sequencing: 1. Genome-wide mapping of Opa in 3h and 4h collections of wild-type Drosophila melanogaster embryos, cycles 13-14early and cycle 14mid-gastrulation, respectively. 2. Genome-wide data from mid nc14 Drosophila single-embryo Assay for Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) provide insight into wt versus Opa (sh opa) and Zld (sh zld) dynamics. The raw fastq data (50bp single-end) for Opa ChIP-seq libraries, and for wt, Zld-mutant and Opa-mutant ATAC-seq libraries were generated from the Illumina HiSeq2500 platform.