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Experimental and computation approaches reveal mechanisms of evolution of gene regulatory networks underlying echinoderm skeletogenesis

Dylus, DV; (2015) Experimental and computation approaches reveal mechanisms of evolution of gene regulatory networks underlying echinoderm skeletogenesis. Doctoral thesis , UCL (University College London). Green open access

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Abstract

The evolutionary mechanisms in distantly related animals involved in shaping complex gene regulatory networks (GRN) that encode morphologically similar structures remain elusive. In this context, echinoderm larval skeletons found only in brittle stars and sea urchins out of the five classes provide an ideal system. Here, we characterise for the first time the development of the larval skeleton in the poorly described class of echinoderms, the ophiuroid Amphiura filiformis, and we compare it systematically with the well-established sea urchin. In the first part of this study, we show that ophiuroids and euechinoids, that split at least 480 Million years ago (Mya), have remarkable similarities in tempo and mode of skeletal development. Despite morphological and ontological similarities, our high-resolution study of the dynamics of regulatory states using 24 sea urchin candidates highlights that gene duplication, protein function diversification and cis-regulatory element evolution all contributed to shape the regulatory program for larval skeletogenesis in different branches of echinoderms. Our data allows to comment on the independent or homologous evolution of the larval skeleton in light of the recently established phylogeny of echinoderm classes. In the second part of this study, we employ mRNA sequencing to establish a transcriptome and analyse its content quantitatively and qualitatively. We identify a core set of skeletogenic genes that is highly conserved using various comparative genomic analyses including other three classes of echinoderms. Additionally, from a differential screen on samples with inhibited skeleton we obtain a list of candidates specific for brittle star skeleton development and analyse their expression using experimental techniques. Finally, we provide access to all transcriptomic and expression data via a customised web interface. In conclusion, we establish the brittle star A. filiformis as new developmental model system and provide novel insights into evolution of GRNs.

Type: Thesis (Doctoral)
Title: Experimental and computation approaches reveal mechanisms of evolution of gene regulatory networks underlying echinoderm skeletogenesis
Open access status: An open access version is available from UCL Discovery
Language: English
Keywords: Brittle Star, GRN, Evolution, Development, Amphiura filiformis
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
URI: https://discovery.ucl.ac.uk/id/eprint/1470330
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