Biology subjects

Sun, D. A.

Publications and source records attributed to Sun, D. A..

4 recordsLinked to original sources

bioRxiv2022

Distinct regulation of Hox genes by Polycomb Group genes in a crustacean

Non-insect crustaceans exhibit tremendous body plan diversity. The evolution of diverse patterns of Hox gene expression has been implicated as a primary driver of body plan evolution between crustacean groups, but the mechanisms underlying Hox regulatory evolution remain unknown. We identify Polycomb and Trithorax Group proteins, crucial for proper Hox regulation across bilaterians, in the genome of the amphipod crustacean Parhyale hawaiensis, and demonstrate their essential functions in crustacean Hox regulation and embryonic development using CRISPR-Cas9 mutagenesis. Examination of Hox misexpression patterns between individual Hox genes with respect to timing, tissue, and PcG mutant gene in mutant embryos reveals that each crustacean Hox gene follows its own idiosyncratic regulatory mechanism. These results suggest a distinct regulation of Hox genes that may have enabled crustacean body plan evolution. Primary Findings- The genome of the amphipod crustacean Parhyale hawaiensis contains all core Polycomb Group (PcG) and Trithorax Group (TrxG) proteins - CRISPR-Cas9 mutagenesis of PcG proteins induces homeotic transformations and misexpression of Hox genes that differ from similar experiments in insects - PcG knockout embryos show proper initiation of Hox expression boundaries at early developmental stages - Each of the three posterior Hox genes in Parhyale displays distinct patterns of misexpression in response to PcG knockout - Hox regulation appears to occur via different mechanisms in the nervous system vs. limbs - PcG phenotypes reveal the potential for distinct layers of Hox regulation in crustaceans O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/485719v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@7508a7org.highwire.dtl.DTLVardef@18b0c2dorg.highwire.dtl.DTLVardef@1cc602corg.highwire.dtl.DTLVardef@bdf7fc_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2022

Combinatorial interactions of Hox genes establish appendage diversity of the amphipod crustacean Parhyale hawaiensis

Hox genes establish regional identity along the anterior-posterior axis in diverse animals. Changes in Hox expression can induce striking homeotic transformations, where one region of the body is transformed into another. Previous work in Drosophila has demonstrated that Hox cross-regulatory interactions are crucial for maintaining proper Hox expression. One major mechanism is the phenomenon of "posterior prevalence", wherein anterior Hox genes are repressed by more posterior Hox genes. Loss of posterior Hox expression under this model would predict posterior-to-anterior transformations, as is frequently observed in Drosophila. While posterior prevalence is thought to occur in many animals, studies of such Hox cross-regulation have focused on a limited number of organisms. In this paper, we examine the cross-regulatory interactions of three Hox genes, Ultrabithorax (Ubx), abdominal-A (abd-A), and Abdominal-B (Abd-B) in patterning thoracic and abdominal appendages in the amphipod crustacean Parhyale hawaiensis. Studies of Hox function in Parhyale have previously revealed two striking phenotypes which differed markedly from what a "posterior prevalence" model would predict, including non-contiguous and anterior-to-posterior transformations. We probe the logic of Parhyale Hox cross-regulation by using CRISPR/Cas9 to systematically examine all combinations of Ubx, abd-A, and Abd-B loss of function in Parhyale. By analyzing homeotic phenotypes and examining the expression of additional Hox genes, we reveal Hox cross-regulatory interactions in Parhyale. From these data, we also demonstrate that some Parhyale Hox genes function combinatorially to specify posterior limb identity, rather than abiding by a posterior prevalence mechanism. These results provide evidence that combinatorial Hox interactions may be responsible for the tremendous body plan diversity of crustaceans. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC="FIGDIR/small/485717v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@16bfc85org.highwire.dtl.DTLVardef@8f859eorg.highwire.dtl.DTLVardef@8d7892org.highwire.dtl.DTLVardef@1e6c9f0_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2021

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

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

developmental biology↗

bioRxiv2019

Developmental transcriptomic analysis of the cave-dwelling crustacean, Asellus aquaticus

Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ in many characteristics, including eye size, pigmentation and antennal length. Existing resources for this species include a linkage map, mapped regions responsible for eye and pigmentation traits, sequenced adult transcriptomes, and comparative embryological descriptions of the surface and cave forms. Our ultimate goal is to identify genes and mutations responsible for the differences between the cave and surface forms. To advance this goal, we decided to use a transcriptomic approach. Because many of these changes first appear during embryonic development, we sequenced embryonic transcriptomes of cave, surface, and hybrid individuals at the stage when eyes and pigment become evident in the surface form. We generated a cave, a surface, a hybrid, and an integrated transcriptome to identify differentially expressed genes in the cave and surface forms. Additionally, we identified genes with allele-specific expression in hybrid individuals. These embryonic transcriptomes are an important resource to assist in our ultimate goal of determining the genetic underpinnings of the divergence between the cave and surface forms.

genetics↗