Coordinated Gene Expression and Chromatin Regulation during Hydra Head Regeneration

Abstract

The cnidarian model organism Hydra has long been studied for its remarkable ability to regenerate its head, which is controlled by a head organizer located near the hypostome. The canonical Wnt pathway plays a central role in head organizer function during regeneration and during bud formation, which is the asexual mode of reproduction in Hydra. However, it is unclear how shared the developmental programs of head organizer genesis are in budding and regeneration. Time-series analysis of gene expression changes during head regeneration and budding revealed a set of 298 differentially expressed genes during the 48-h head regeneration and 72-h budding time courses. In order to understand the regulatory elements controlling Hydra head regeneration, we first identified 27,137 open-chromatin elements that are open in one or more sections of the organism body or regenerating tissue. We used histone modification ChIP-seq to identify 9,998 candidate proximal promoter and 3,018 candidate enhancer-like regions respectively. We show that a subset of these regulatory elements is dynamically remodeled during head regeneration and identify a set of transcription factor motifs that are enriched in the enhancer regions activated during head regeneration. Our results show that Hydra displays complex gene regulatory structures of developmentally dynamic enhancers, which suggests that the evolution of complex developmental enhancers predates the split of cnidarians and bilaterians.

Integrative analysis ofHydrahead regeneration reveals actions of conserved signaling pathways and transposable elements

“…Taken together, these results suggest PaxC has a role in patterning during head regeneration. Supporting this is the enrichment of Pax5 and Pax6 binding motifs for dynamic accessibility during Hydra head regeneration (Murad et al, 2021). These binding motifs are annotated for known vertebrate motifs, so the Hydra binding factor remains to be confirmed.…”

“…We found binding motifs in the promoter for homeodomain, C2H2 zinc finger, basic helix-loop-helix (bHLH), and Highmobility group (HMG) domain factors that match TFs such as including Sox11 and Six3/6 (or Optix) (Table S5). Using only hypostome data that we previously generated (Murad et al, 2021), we found transcription factor binding motifs in the Wnt3 promoter for the Sox family (Sox2, Sox11, Sox13, Sox17, Sox18), and Six3/6 (Table S5).…”

“…Raw read ATAC-seq data for the Hydra hypostome (2 replicates) were obtained from GEO GSE127277 (Murad et al, 2021). Reads were trimmed using Trimmomatic v. 0.39 (Bolger et al, 2014) then mapped to the genome using bwa v. 0.7.17 (Li and Durbin, 2009).…”

“…Bulk RNA-seq data of the Hydra hypostome tissue and head regeneration time points (0, 2, 4, 6, 12, 24, and 48 hours) were obtained from GEO accession GSE127279 (Murad et al, 2021).…”

“…Genes associated with regeneration after injury included FoxM1 , Fos , and Sox2 (Cazet et al, 2021). Another study used RNA-Seq, ATAC-Seq and ChIP-Seq to identify changes in gene expression and chromatin accessibility during regeneration (Murad et al, 2021). This study identified genes upregulated in the adult Hydra hypostome and during regeneration including Wnt genes, KS1 , aristaless related homeobox (HyAlx ), Brachyury (Bra ), COUP - TF , and orthodenticle homeobox ( Otx ).…”