Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms

Arshinoff, Bradley I.; Cary, Gregory A.; Karimi, Kamran; Foley, Saoirse; Agalakov, Sergei; Delgado, Francisco; Lotay, Vaneet; Ku, Carolyn J; Pells, Troy J.; Beatman, Thomas R; Kim, Eugene; Cameron, R. Andrew; Vize, Peter D.; Telmer, Cheryl A.; Croce, Jenifer C.; Ettensohn, Charles A.

doi:10.1093/nar/gkab1005

Cited by 70 publications

(88 citation statements)

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“…CREs with mutations of putative transcription factor binding sites and putative CREs from echinoderm species were synthesized as gBlock gene fragments with flanking restriction sites by Integrated DNA Technologies (Coralville, IA, USA). Sequences of putative CREs from echinoderm species (other than sea urchins) were located directly upstream of the kirrelL gene translational start sites (see Figure 6 source data 2) (Arshinoff et al, 2021;Long et al, 2016).…”

Section: Materials and Methods Animalsmentioning

confidence: 99%

“…There was a total of 463 positions in the final dataset. Evolutionary analyses were conducted in MEGA X (Kumar et al, 2018;Stecher et al, 2020) Figure 6 source data 1: Sequence coordinates for echinoderm kirrelL CREs tested (Arshinoff et al, 2021;Long et al, 2016).…”

Section: Figure Legendsmentioning

confidence: 99%

“…Figure 2source data 1: Quantification of GFP expression patterns in embryos injected with reporter constructs. Figure 5source data 1: Summary of NanoString analysis.Figure 5source data 2: Raw NanoString data for BAC-injected embryos.Figure 5source data 3: NanoString analysis probe target sequences.Figure6source data 1: Sequence coordinates for echinoderm kirrelL CREs tested(Arshinoff et al, 2021;Long et al, 2016).Figure 6source data 2: DNA sequences for CREs validated in this study from Eucidaris tribuloides (Et-kirrelL), Parastichopus parvimensis (Pp-kirrelL), Patiria miniata (Pm-kirrelL), Acanthaster planci (Aplc-kirrelL), Ophionereis fasciata (Of-kirrelL), and Anneissia japonica (Aj-kirrelL).Figure 6source data 3: Echinoderm PMC-specific Ig-domain protein sequences from Strongylocentrotus purpuratus (Sp), Lytechinus variegatus (Lv), Eucidaris tribuloides (Et), Parastichopus parvimensis (Pp), Patiria miniata (Pm), Acanthaster planci (Aplc), Ophionereis fasciata (Of), and Anneissia japonica (Aj) used for tree construction.…”

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confidence: 99%

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Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene

Khor

Ettensohn

2022

eLife

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The gene regulatory network (GRN) that underlies echinoderm skeletogenesis is a prominent model of GRN architecture and evolution. KirrelL is an essential downstream effector gene in this network and encodes an Ig-superfamily protein required for the fusion of skeletogenic cells and the formation of the skeleton. In this study, we dissected the transcriptional control region of the kirrelL gene of the purple sea urchin, Strongylocentrotus purpuratus. Using plasmid- and BAC-based transgenic reporter assays, we identified key cis-regulatory elements (CREs) and transcription factor inputs that regulate Sp-kirrelL, including direct, positive inputs from two key transcription factors in the skeletogenic GRN, Alx1 and Ets1. We next identified kirrelL cis-regulatory regions from seven other echinoderm species that together represent all classes within the phylum. By introducing these heterologous regulatory regions into developing sea urchin embryos we provide evidence of their remarkable conservation across ~500 million years of evolution. We dissected in detail the kirrelL regulatory region of the sea star, Patiria miniata, and demonstrated that it also receives direct inputs from Alx1 and Ets1. Our findings identify kirrelL as a component of the ancestral echinoderm skeletogenic GRN. They support the view that GRN sub-circuits, including specific transcription factor-CRE interactions, can remain stable over vast periods of evolutionary history. Lastly, our analysis of kirrelL establishes direct linkages between a developmental GRN and an effector gene that controls a key morphogenetic cell behavior, cell-cell fusion, providing a paradigm for extending the explanatory power of GRNs.

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Section: Materials and Methods Animalsmentioning

confidence: 99%

Section: Figure Legendsmentioning

confidence: 99%

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confidence: 99%

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Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene

Khor

Ettensohn

2022

eLife

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“…Protein sequences of 15 metazoan species (A. planci, S. purpuratus, Lytechinus variegatus, A. japonicus, Anneissia japonica, Saccoglossus kawalevskii, Branchiostoma floridae, Ciona intestinalis, Danio rerio, Gallus gallus, H. robusta, Mus musculus, Pelodiscus sinensis, Petromyzon marinus, and Xenopus laevis) proteins were downloaded from NCBI. Protein sequences of Parastichopus parvimensis were downloaded from Echinobase 12 . OrthoMCL (v2.0.9) 82 was applied to determine and cluster gene families among these 16 metazoan species and C. heheva.…”

Section: Capitella Teleta Homo Sapiens P In C Ta D a Fu C A Tamentioning

confidence: 99%

“…The deposit-feeding lifestyle of holothurians conferred a selective advantage during the primary productivity collapse of the Permian-Triassic massextinction 9 . As the genomes of only two shallow-water holothurians (Apostichopus japonicus and Parastichopus parvimensis) have been assembled and analyzed [10][11][12] , it is critical to study the genomes of more holothurians to dissect their special morphological characteristics and evolutionary history.…”

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The genome of an apodid holothuroid (Chiridota heheva) provides insights into its adaptation to a deep-sea reducing environment

et al. 2022

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Cold seeps and hydrothermal vents are deep-sea reducing environments that are characterized by lacking oxygen and photosynthesis-derived nutrients. Most animals acquire nutrition in cold seeps or hydrothermal vents by maintaining epi- or endosymbiotic relationship with chemoautotrophic microorganisms. Although several seep- and vent-dwelling animals hosting symbiotic microbes have been well-studied, the genomic basis of adaptation to deep-sea reducing environment in nonsymbiotic animals is still lacking. Here, we report a high-quality genome of Chiridota heheva Pawson & Vance, 2004, which thrives by extracting organic components from sediment detritus and suspended material, as a reference for nonsymbiotic animal’s adaptation to deep-sea reducing environments. The expansion of the aerolysin-like protein family in C. heheva compared with other echinoderms might be involved in the disintegration of microbes during digestion. Moreover, several hypoxia-related genes (Pyruvate Kinase M2, PKM2; Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase, LHPP; Poly(A)-specific Ribonuclease Subunit PAN2, PAN2; and Ribosomal RNA Processing 9, RRP9) were subject to positive selection in the genome of C. heheva, which contributes to their adaptation to hypoxic environments.

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Distinct regulatory states control the elongation of individual skeletal rods in the sea urchin embryo

Tarsis

Gildor

Morgulis

et al. 2022

Developmental Dynamics

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Background: Understanding how gene regulatory networks (GRNs) control developmental progression is a key to the mechanistic understanding of morphogenesis. The sea urchin larval skeletogenesis provides an excellent platform to tackle this question. In the early stages of sea urchin skeletogenesis, skeletogenic genes are uniformly expressed in the skeletogenic lineage. Yet, during skeletal elongation, skeletogenic genes are expressed in distinct spatial sub-domains. The regulation of differential gene expression during late skeletogenesis is not well understood.Results: Here we reveal the dynamic expression of the skeletogenic regulatory genes that define a specific regulatory state for each pair of skeletal rods, in the sea urchin Paracentrotus lividus. The vascular endothelial growth factor (VEGF) signaling, essential for skeleton formation, specifically controls the migration of cells that form the postoral and distal anterolateral skeletogenic rods. VEGF signaling also controls the expression of regulatory genes in cells

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Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms

Cited by 70 publications

References 31 publications

Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene

Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene

The genome of an apodid holothuroid (Chiridota heheva) provides insights into its adaptation to a deep-sea reducing environment

Distinct regulatory states control the elongation of individual skeletal rods in the sea urchin embryo

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