Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis

Abstract

Emerging research organisms enable the study of biology that cannot be addressed using classical "model" organisms. The development of new data resources can accelerate research in such animals. Here, we present new functional genomic resources for the amphipod crustacean Parhyale hawaiensis, facilitating the exploration of gene regulatory evolution using this emerging research organism. We use Omni-ATAC-Seq, an improved form of the Assay for Transposase-Accessible Chromatin coupled with next-generation sequencing (ATAC-Seq), to identify accessible chromatin genome-wide across a broad time course of Parhyale embryonic development. This time course encompasses many major morphological events, including segmentation, body regionalization, gut morphogenesis, and limb development. In addition, we use short- and long-read RNA-Seq to generate an improved Parhyale genome annotation, enabling deeper classification of identified regulatory elements. We discover differential accessibility, predict nucleosome positioning, infer transcription factor binding, cluster peaks based on accessibility dynamics, classify biological functions, and correlate gene expression with accessibility. Using a Minos transposase reporter system, we demonstrate the potential to identify novel regulatory elements using this approach, including distal regulatory elements. This work provides a platform for the identification of novel developmental regulatory elements in Parhyale, and offers a framework for performing such experiments in other emerging research organisms. Primary Findings- Omni-ATAC-Seq identifies cis-regulatory elements genome-wide during crustacean embryogenesis - Combined short- and long-read RNA-Seq improves the Parhyale genome annotation - ImpulseDE2 analysis identifies dynamically regulated candidate regulatory elements - NucleoATAC and HINT-ATAC enable inference of nucleosome occupancy and transcription factor binding - Fuzzy clustering reveals peaks with distinct accessibility and chromatin dynamics - Integration of accessibility and gene expression reveals possible enhancers and repressors - Omni-ATAC can identify known and novel regulatory elements O_FIG O_LINKSMALLFIG WIDTH=196 HEIGHT=200 SRC="FIGDIR/small/460328v2_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1f849b6org.highwire.dtl.DTLVardef@1af655borg.highwire.dtl.DTLVardef@274baaorg.highwire.dtl.DTLVardef@1d8af02_HPS_FORMAT_FIGEXP M_FIG C_FIG