Biology subjects

Czarkwiani, A.

Publications and source records attributed to Czarkwiani, A..

4 recordsLinked to original sources

bioRxiv2023

The brittle star genome illuminates the genetic basis of animal appendage regeneration

Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars are a species-rich class of echinoderms with outstanding regenerative abilities, but investigations into the genetic bases of regeneration in this group have been hindered by the limited genomic resources. Here, we report a chromosome-scale genome assembly for the brittle star Amphiura filiformis. We show that the brittle star genome is the most rearranged amongst echinoderms sequenced to date, featuring a reorganised Hox cluster reminiscent of the rearrangements observed in sea urchins. In addition, we performed an extensive profiling of gene expression during brittle star adult arm regeneration and identified sequential waves of gene expression governing wound healing, proliferation and differentiation. We conducted comparative transcriptomic analyses with other invertebrate and vertebrate models for appendage regeneration and uncovered hundreds of genes with conserved expression dynamics, particularly during the proliferative phase of regeneration. Our findings emphasise the crucial importance of echinoderms to detect long-range expression conservation between vertebrates and classical invertebrate regeneration model systems.

evolutionary biology↗

bioRxiv2023

Conserved enhancer logic controls the notochord expression of vertebrate Brachyury

The cell type-specific expression of key transcription factors is central to development. Brachyury/T/TBXT is a major transcription factor for gastrulation, tailbud patterning, and notochord formation; however, how its expression is controlled in the mammalian notochord has remained elusive. Here, we identify the complement of notochord-specific enhancers in the mammalian Brachyury/T/TBXT gene. Using transgenic assays in zebrafish, axolotl, and mouse, we discover three Brachyury-controlling notochord enhancers T3, C, and I in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers, deletion of all three enhancers in mouse abolishes Brachyury/T expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. Sequence and functional conservation of Brachyury-driving notochord enhancers with the brachyury/tbxtb loci from diverse lineages of fishes dates their origin to the last common ancestor of jawed vertebrates. Our data define the enhancers for Brachyury/T/TBXTB notochord expression as ancient mechanism in axis development.

genetics↗

bioRxiv2019

FGF signalling plays similar roles in development and regeneration of the skeleton in the brittle star Amphiura filiformis

Regeneration is an adult developmental process considered to be an epiphenomenon of embryonic development. Although several studies have shown that various embryonic genes are expressed during regeneration, there have been no large-scale, direct and functional comparative studies between the development and regeneration of a specific structure in one animal. Here, we use the brittle star Amphiura filiformis to characterise the role of the FGF signalling pathway during skeletal development and regeneration. In both processes, we find the ligands expressed in ectodermal cells flanking underlying mesodermal cells, and the receptors expressed specifically by these skeletogenic cells. Perturbation of FGF but not VEGF signalling during skeletogenesis completely inhibited skeleton formation in both embryogenesis and regeneration, without affecting other key developmental processes like cell migration or proliferation. Transcriptome-wide differential analysis identified a highly similar cohort of skeletogenic differentiation genes downstream of the FGF signalling pathway, whereas upstream transcription factors involved in the initial specification of the skeletogenic lineage where unaffected. Comparison to the sea urchin indicated that many of the affected genes are associated with differentiation. Moreover, several genes showed no homology to a cohort from other species, leading to the discovery of brittle star specific, downstream skeletogenic genes. In conclusion, our results show that the FGF pathway is crucial for skeletogenesis in the brittle star, as it is in other deuterostomes, and for the first time provide evidence for the re-deployment of a gene regulatory module during both regeneration and development.

developmental biology↗

bioRxiv2017

Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution

Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance, developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm - the sea urchin Strongyloncentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/. With a focus on skeleton development, we have identified highly conserved genes associated with the development of a biomineralized skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring in the evolution of echinoderm larval development.\n\nData DepositionsAll sequence reads are available at Genbank SRR4436669 - SRR4436674. Any sequence alignments used are available by the corresponding author upon request.

evolutionary biology↗