bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/544049

Integrative analysis of Hydra head regeneration reveals activation of distal enhancer-like elements

Murad, R.·Macias-Munoz, A.·Wong, A.·Ma, X.·Mortazavi, A.
View original source ↗Export metadata ↓

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. Cnidarians and bilaterians diverged about 600 millions years ago but the gene contents of species of both phyla are surprisingly similar despite divergent morphologies and functions. While little is known about the role of cis-regulatory elements in cnidarians, understanding gene regulatory mechanisms in cnidarians can potentially shed light on metazoan evolution. 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-hour head regeneration and 72-hour 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 organism. We used histone modification ChIP-seq to identify 9998 candidate proximal promoter and 3018 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.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Murad, R., Macias-Munoz, A., Wong, A., Ma, X., Mortazavi, A.. 2019-02-07. Integrative analysis of Hydra head regeneration reveals activation of distal enhancer-like elements. https://doi.org/10.1101/544049

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Genome-wide chromatin accessibility during early embryogenesis in a generalist cichlid fish

Background Lake Malawi's haplochromine cichlids are one of the most rapid and species-rich vertebrate adaptive radiations known, generating hundreds of species within < 1 million years, yet how regulatory regions shape their embryonic development remains poorly understood. Astatotilapia calliptera, a generalist riverine lineage and proxy for the ancestral stock that seeded this radiation, offers a developmental chromatin baseline against which regulatory divergence in specialised lineages can be compared. Results We generated genome-wide ATAC-seq profiles of A. calliptera embryos across three developmental stages (3, 7 and 12 days post-fertilisation, dpf), identifying 550,876-701,889 accessible chromatin peaks per stage. Accessible chromatin was enriched at gene promoters and at both highly conserved and accelerated conserved noncoding elements at every stage. The functional repertoire of accessible-promoter genes shifted across development, from early patterning at 3 dpf to the broadest regulatory repertoire at 7 dpf, and an increasingly neural- and locomotory-behaviour-enriched repertoire by 12 dpf, coinciding with post-hatching motor maturation. Differential accessibility showed that chromatin opening, rather than closing, dominates the earliest transitions (3 vs 7 and 3 vs 12 dpf), driven mostly by general metabolic genes, whereas the smaller, later 7 vs 12 dpf transition combined targeted gains at tissue-remodelling and apoptosis genes with losses at genes governing early neural and retinal patterning; almost all of these losses (96%) were at promoters that had opened between 3 and 7 dpf, indicating transient rather than sustained opening. Transcription factor (TF) footprinting identified stage-specific regulatory activity among developmentally important TFs, while the broader TF-promoter network remained topologically stable across all three stages, built around conserved hub regulators of core neural and sensory patterning genes e.g., SOX2, FOXG1, PTF1A, SOX10. This suggests that wiring is established early and largely maintained, following the hourglass model, with developmental progression driven by changes in activity of this conserved programme. Conclusions Together, these findings establish the first embryonic epigenomic resource for A. calliptera, revealing a developmental chromatin landscape of broad early opening and progressive functional specialisation, and providing a comparative framework for understanding how regulatory evolution has shaped Lake Malawi cichlid diversification.

genomics↗
bioRxiv2026

Salinity adaptation in date palm (Phoenix dactylifera): evidence for selective sweeps at Salt Overly Sensitive (SOS) genes

The date palm is a high salinity tolerant fruit tree grown mainly in the region spanning from North Africa to parts of South Asia. Climate change models of this region indicate the possibility of increasing salinity in the future. The Salt Overly Sensitive (SOS) pathway is crucial for salinity tolerance in plants, serving as a primary defense mechanism by facilitating sodium exclusion. To better understand date palms' salt tolerance, we analyzed variation in SOS pathway genes in a set of 197 date palm genomes collected from across the range of cultivation. Here, we show evidence for selective sweeps in multiple SOS pathway genes. A single major pdSOS1 haplotype is at very high frequency in Eastern and Western subpopulations, with a minor, likely ancestral haplotype still present in both geographical locations. Allele-specific gene expression analysis showed differences in salt-treated roots between swept and ancestral haplotypes. Interestingly, sequence-based analysis of the pdSOS1 haplotype suggested a second, much earlier introgression event between P. theophrasti and date palm, though direction is unclear. This event happened before both the selective sweep and the previously reported recent introgression to date palm. We identified a MITE transposable element inserted into a pdSOS1 intron on the swept haplotype, and a similar insertion was found in an intron of the SOS2 paralog pdCIPK8. Both insertions are unique to date palm among Phoenix species. The pdCIPK8 haplotype containing the MITE is also at high frequency in both populations. Further analysis showed evidence for a selective sweep spanning the pdSOS3 region in the western population that shares similarity to an Eastern haplotype spanning the promoter region only. Slower extended haplotype homozygosity decay surrounding the genes in the western population suggests that the swept haplotype originated in the East and spread to the West in all cases. Altogether, our data provide evidence of selective sweeps in the date palm SOS pathway and may go to explaining how this species has developed such high salinity tolerance.

genomics↗
bioRxiv2026

Genome evolution and glycosyltransferase diversification shape asperosaponin biosynthesis in Dipsacus asperoides

Deciphering the genomic and enzymatic features associated with high-abundance specialized metabolism is important for understanding and engineering bioactive natural product biosynthesis. Asperosaponin , a hederagenin-based saponin, accumulates at exceptionally high levels in Dipsacus asperoides roots and is by far the predominant triterpenoid saponin. Here, by integrating a chromosome-level genome assembly with comparative genomics, transcriptomics, metabolite profiling, and biochemical characterization, we reconstructed a major biosynthetic route to asperosaponin and identified diversification of triterpenoid-associated gene families. Functional analyses revealed an ordered glycosylation sequence in which DaUGT73GZ2 preferentially accepts C-3-glycosylated substrates retaining a free C-28 carboxyl group, thereby establishing a C-3-before-C-28 glycosylation order during asperosaponin biosynthesis. Phylogenetic and biochemical analyses further uncovered functional differentiation among UGT85CA enzymes involved in C-3 arabinosylation, while genomic and expression analyses revealed lineage-specific patterns of pathway gene duplication and transcriptional regulation. Together, these findings identify genomic, enzymatic, and transcriptional features associated with the distinctive, high-abundance triterpenoid saponin profile of D. asperoides roots and provide a framework for understanding and engineering triterpenoid saponin biosynthesis.

genomics↗