Regulatory principles of echinoderm metamorphosis

棘皮动物变态的调控原理

• 批准号: BB/V01109X/1
• 负责人: Ferdinand Marlétaz
• 金额: $ 62.81万
• 依托单位: University College London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2021
• 资助国家: 英国
• 起止时间: 2021 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FV01109X%2F1
• 关键词: Regulatory; principles; echinoderm; metamorphosis

While some animals develop directly from embryos into their adult forms, others present an intermediate larval stage. The metamorphosis of the larva into the adult form can be more or less dramatic, and, in the case of echinoderms, involve a drastic change in body symmetry from a bilateral larva into a pentaradial adult (five-way symmetry). The adult first grows as a set of cells, the 'rudiment' that grows within the larva and finally everts from it. While this process relies on the same development genes as embryonic development, these genes are mobilised by an alternative developmental program encoded in the genome. I want to understand how these two regulatory programs that control development from egg to larva and from larva to pentaradial adult can coexist in the same genome. Genes are controlled by regulatory elements, segments of DNA that are bound by specialised proteins called transcription factors. I want to determine what are the regulatory elements in the genome that control the metamorphosis of the larval into an adult with an alternative body symmetry and which transcription factors play the most important role in mobilising these elements. We will use sequencing-based technologies, such as single-cell transcriptomics and computational analyses to find this out. We will then use transgenic sea urchin larvae carrying a gene encoding for a fluorescent protein under the control of such promoters to monitor where these regulatory elements are active. Echinoderm genomes are quite plastic, which means gene order can change and some have postulated that this could have played a key role in rewiring gene regulation. To test this idea, we will evaluate the genomic changes that took place in different echinoderm lineages. Then, as regulatory elements are embedded in loops of DNA known as three-dimensional chromatin compartments, we will see if these are affected during metamorphosis, and finally build an integrative model of rudiment development. We expect to uncover the new regulatory route that has made possible the evolution of a new body plan in these mesmerising organisms.

虽然有些动物直接从胚胎发育成成年形态，但其他动物则呈现中间幼虫阶段。幼虫向成虫的变态或多或少是戏剧性的，对于棘皮动物来说，涉及身体对称性的巨大变化，从双侧幼虫转变为五径向成虫（五向对称）。成虫首先以一组细胞的形式生长，即在幼虫体内生长的“雏形”，最后从幼虫中脱离出来。虽然这个过程依赖于与胚胎发育相同的发育基因，但这些基因是由基因组中编码的替代发育程序调动的。我想了解这两个控制从卵到幼虫以及从幼虫到五径向成虫发育的调控程序如何在同一基因组中共存。基因由调控元件控制，调控元件是由称为转录因子的特殊蛋白质结合的 DNA 片段。我想确定基因组中控制幼虫变态为具有替代身体对称性的成虫的调控元件是什么，以及哪些转录因子在调动这些元件方面发挥着最重要的作用。我们将使用基于测序的技术，例如单细胞转录组学和计算分析来找出答案。然后，我们将使用携带在此类启动子控制下编码荧光蛋白的基因的转基因海胆幼虫来监测这些调节元件在何处活跃。棘皮动物基因组具有很强的可塑性，这意味着基因顺序可以改变，一些人推测这可能在重新连接基因调控方面发挥了关键作用。为了验证这个想法，我们将评估不同棘皮动物谱系中发生的基因组变化。然后，当调控元件嵌入被称为三维染色质区室的 DNA 环中时，我们将观察这些元件在变态过程中是否受到影响，并最终构建基本发育的综合模型。我们期望发现新的调控途径，使这些令人着迷的生物体的新身体计划的进化成为可能。

项目成果

DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics.

• DOI: 10.1093/gbe/evab179
• 发表时间: 2021-08-03
• 期刊: Genome biology and evolution
• 影响因子: 3.3
• 作者: Finet C;Kassner VA;Carvalho AB;Chung H;Day JP;Day S;Delaney EK;De Ré FC;Dufour HD;Dupim E;Izumitani HF;Gautério TB;Justen J;Katoh T;Kopp A;Koshikawa S;Longdon B;Loreto EL;Nunes MDS;Raja KKB;Rebeiz M;Ritchie MG;Saakyan G;Sneddon T;Teramoto M;Tyukmaeva V;Vanderlinde T;Wey EE;Werner T;Williams TM;Robe LJ;Toda MJ;Marlétaz F
• 通讯作者: Marlétaz F

Annelid functional genomics reveal the origins of bilaterian life cycles.

• DOI: 10.1038/s41586-022-05636-7
• 发表时间: 2023-03
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Martin-Zamora, Francisco M.;Liang, Yan;Guynes, Kero;Carrillo-Baltodano, Allan M.;Davies, Billie E.;Donnellan, Rory D.;Tan, Yongkai;Moggioli, Giacomo;Seudre, Oceane;Tran, Martin;Mortimer, Kate;Luscombe, Nicholas M.;Hejnol, Andreas;Marletaz, Ferdinand;Martin-Duran, Jose M.
• 通讯作者: Martin-Duran, Jose M.

Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes.

• DOI: 10.1016/j.xgen.2023.100295
• 发表时间: 2023-04
• 期刊: Cell genomics
• 作者: Ferdinand Marlétaz;A. Couloux;J. Poulain;K. Labadie;C. da Silva;S. Mangenot;Benjamin Noel;A. Poustka;Philippe Dru;C. Pegueroles;M. Borra;E. Lowe;G. Lhomond;L. Besnardeau;S. Le Gras;Tao Ye;Daria Gavriouchkina;R. Russo;C. Costa;F. Zito;L. Anello;A. Nicosia;M. Ragusa;M. Pascual;M. D. Molina;Aline Chessel;M. Di Carlo;X. Turon;R. Copley;J. Exposito;P. Martinez;V. Cavalieri;Smadar Ben Tabou de Leon;Jenifer C. Croce;P. Oliveri;V. Matranga;M. Di Bernardo;J. Morales;P. Cormier;Anne Genevieve;J. Aury;V. Barbe;P. Wincker;M. Arnone;C. Gache;T. Lepage

Publisher Correction: Conservative route to genome compaction in a miniature annelid.

• DOI: 10.1038/s41559-020-01366-z
• 发表时间: 2021-03
• 期刊: Nature ecology & evolution
• 影响因子: 16.8
• 作者: Martín-Durán JM;Vellutini BC;Marlétaz F;Cetrangolo V;Cvetesic N;Thiel D;Henriet S;Grau-Bové X;Carrillo-Baltodano AM;Gu W;Kerbl A;Marquez Y;Bekkouche N;Chourrout D;Gómez-Skarmeta JL;Irimia M;Lenhard B;Worsaae K;Hejnol A
• 通讯作者: Hejnol A

Conservative route to genome compaction in a miniature annelid.

• DOI: 10.1038/s41559-020-01327-6
• 发表时间: 2021-03
• 期刊: Nature ecology & evolution
• 影响因子: 16.8
• 作者: Martín-Durán JM;Vellutini BC;Marlétaz F;Cetrangolo V;Cvetesic N;Thiel D;Henriet S;Grau-Bové X;Carrillo-Baltodano AM;Gu W;Kerbl A;Marquez Y;Bekkouche N;Chourrout D;Gómez-Skarmeta JL;Irimia M;Lenhard B;Worsaae K;Hejnol A
• 通讯作者: Hejnol A