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

Abstract

Chromatin profiling data can generate and corroborate hypotheses for regulatory events that underlie the control of gene expression in biological processes. Here, we have profiled chromatin accessibility to build a catalog of putative regulatory DNA during 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, positioned equally well to inform the evolution of developmental mechanisms. We focused on the acoel Hofstenia miamia, a new research organism for studying whole-body regeneration that also enables investigations of development from zygote to hatching. We profiled chromatin landscapes encompassing major morphological events during development, and combined transcription factor-binding analyses with single-cell RNA-sequencing data to provide regulatory linkages in a hypothesized differentiation trajectory for epidermis, as well as a new gene regulatory network associated with the formation of muscle. This work enables comparisons of chromatin state during embryogenesis between acoels and other animals, as well as comparisons of embryogenesis to regeneration.

Keywords: Acoel; Chromatin; Embryonic development; Evolution; Gene regulation; Regeneration; Regulatory DNA; Transcription factor binding.