Asymmetric chromatin accessibility underlies anterior-posterior axis specification in moth fly embryos

Establishing the anterior-posterior (AP) body axis is a fundamental process during embryogenesis, and the fruit fly, Drosophila melanogaster, provides one of the best-known case studies. But for unknown reasons, different species of flies (Diptera) establish the AP axis through unrelated, structurally distinct anterior determinants. The anterior determinant of Drosophila, Bicoid (Bcd), initiates symmetry-breaking during nuclear cleavage cycles (NCs) when ubiquitous pioneer factors, such as Zelda (Zld), drive zygotic genome activation (ZGA) at the level of chromatin accessibility by nucleosome depletion. While Bcd engages in a concentration-dependent competition with nucleosomes at the loci of a small set of transcription factor (TF) genes that are expressed in the anterior embryo, it remains unknown whether unrelated anterior determinants of other fly species function in the same way and target homologous genes. We have examined the symmetry-breaking mechanism of a moth fly, Clogmia albipunctata, in which a maternally expressed transcript isoform of the pair-rule segmentation gene odd-paired serves as an anterior determinant. We provide a de novo assembly and annotation of the Clogmia genome, report changes in chromatin accessibility during the nuclear cleavage cycles (NCs) of consecutive blastoderm stages, and describe how Clogmia’s orthologs of zelda (Cal-zld) and odd-paired (Cal-opa) affect chromatin accessibility and gene expression. We document extensive opening and closing of chromatin regions during cleavage cycles of blastoderm, important roles of Cal-zld in opening chromatin and driving zygotic gene expression, and show that maternal Cal-opa activity initiates zygotic symmetry-breaking along the AP axis by driving chromatin accessibility and expression at Clogmia’s homeobrain and sloppy-paired loci. These genes are not known as key targets of Bcd but may serve a more widely conserved role in the initiation of anterior pattern formation, given their early anterior expression and function in head development in insects.