Chromatin profiling data indicate regulatory mechanisms for differentiation during development in the acoel Hofstenia miamia

Abstract

Chromatin profiling data can corroborate and generate hypotheses for regulatory events that underlie the control of gene expression in any biological process. Here, we applied the Assay for Transposase Accessible Chromatin (ATAC) sequencing to build a catalog of putative regulatory DNA during the process of embryonic development in an acoel. Acoels represent an enigmatic phylum-level lineage of animals, the Xenacoelomorpha, which is placed either as a sister-group to all other animals with bilateral symmetry or as an early-diverging ambulacrarian, two alternative phylogenetic placements that both position acoels equally well to inform the evolution of developmental mechanisms. We focused on the acoel Hofstenia miamia, a.k.a. the three-banded panther worm, which has emerged as a new laboratory research organism for whole-body regeneration that also enables the study of development from zygote to hatching. We profiled chromatin landscapes over a time course encompassing many major morphological events, including gastrulation, axial patterning, and differentiation of tissues such as epidermis and muscle. Broad patterns of chromatin accessibility and predicted binding of various transcription factor (TF) motifs identified major biological processes and their putative regulators, and we noted that differential accessibility tended to precede major developmental transitions in embryogenesis. Focused analysis of TF binding combined with single-cell RNA-seq data provided regulatory linkages for genes in a previously hypothesized differentiation trajectory for epidermis and generated new hypotheses for gene regulatory networks associated with the formation of muscle. This work provides a platform for the identification of developmental mechanisms in Hofstenia and enables comparisons of embryogenesis in acoels to other animals as well as comparisons of embryogenesis to regeneration.