scholarly journals From genome to anatomy: The architecture and evolution of the skeletogenic gene regulatory network of sea urchins and other echinoderms

genesis ◽  
2018 ◽  
Vol 56 (10) ◽  
pp. e23253 ◽  
Author(s):  
Tanvi Shashikant ◽  
Jian Ming Khor ◽  
Charles A. Ettensohn
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Sea Urchins ◽  
Gene Regulatory

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

2017 ◽  
Author(s):  
David Dylus ◽  
Liisa M. Blowes ◽  
Anna Czarkwiani ◽  
Maurice R. Elphick ◽  
Paola Oliveri
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
De Novo ◽  
Sea Urchins ◽  
Brittle Star ◽  
Stages Of Development ◽  
Sequence Alignments ◽  
Amphiura Filiformis ◽  
Gene Regulatory ◽  
Network Rewiring

ABSTRACTAmongst 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.Data DepositionsAll sequence reads are available at Genbank SRR4436669 - SRR4436674. Any sequence alignments used are available by the corresponding author upon request.

scholarly journals Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins

Development ◽  
2014 ◽  
Vol 141 (12) ◽  
pp. 2542-2542 ◽  
Author(s):  
K. Rafiq ◽  
T. Shashikant ◽  
C. J. McManus ◽  
C. A. Ettensohn
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Sea Urchins ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Gene Regulatory

scholarly journals Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins

Development ◽  
2014 ◽  
Vol 141 (4) ◽  
pp. 950-961 ◽  
Author(s):  
K. Rafiq ◽  
T. Shashikant ◽  
C. J. McManus ◽  
C. A. Ettensohn
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Sea Urchins ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Gene Regulatory

scholarly journals Developmental gene regulatory networks in sea urchins and what we can learn from them

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 203 ◽  
Author(s):  
Megan L. Martik ◽  
Deirdre C. Lyons ◽  
David R. McClay
Keyword(s):  
Transcription Factors ◽  
Gene Regulatory Network ◽  
Sea Urchin ◽  
Network Model ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Sea Urchins ◽  
Cell Types ◽  
Zygotic Transcription ◽  
Gene Regulatory

Sea urchin embryos begin zygotic transcription shortly after the egg is fertilized.  Throughout the cleavage stages a series of transcription factors are activated and, along with signaling through a number of pathways, at least 15 different cell types are specified by the beginning of gastrulation.  Experimentally, perturbation of contributing transcription factors, signals and receptors and their molecular consequences enabled the assembly of an extensive gene regulatory network model.  That effort, pioneered and led by Eric Davidson and his laboratory, with many additional insights provided by other laboratories, provided the sea urchin community with a valuable resource.  Here we describe the approaches used to enable the assembly of an advanced gene regulatory network model describing molecular diversification during early development.  We then provide examples to show how a relatively advanced authenticated network can be used as a tool for discovery of how diverse developmental mechanisms are controlled and work.

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