{"id":272261,"date":"2026-01-07T13:45:09","date_gmt":"2026-01-07T13:45:09","guid":{"rendered":"https:\/\/www.europesays.com\/ie\/272261\/"},"modified":"2026-01-07T13:45:09","modified_gmt":"2026-01-07T13:45:09","slug":"deep-conservation-of-cis-regulatory-elements-and-chromatin-organization-in-echinoderms-uncover-ancestral-regulatory-features-of-animal-genomes","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/ie\/272261\/","title":{"rendered":"Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes"},"content":{"rendered":"
  • \n

    Seb\u00e9-Pedr\u00f3s, A. et al. The dynamic regulatory genome of capsaspora and the origin of animal multicellularity. Cell 165<\/b>, 1224\u20131237 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bern\u00e1, L. & Alvarez-Valin, F. Evolutionary genomics of fast evolving tunicates. Genome Biol. Evol. 6<\/b>, 1724\u20131738 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Harmston, N. et al. Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. Nat. Commun. 8<\/b>, 441 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kapusta, A., Suh, A. & Feschotte, C. Dynamics of genome size evolution in birds and mammals. Proc. Natl Acad. Sci. USA 114<\/b>, E1460\u2013E1469 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Moriyama, Y. & Koshiba-Takeuchi, K. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings Funct. Genomics 17<\/b>, 329\u2013338 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mart\u00edn-Dur\u00e1n, J. M. et al. Conservative route to genome compaction in a miniature annelid. Nat. Ecol. Evol. 5<\/b>, 231\u2013242 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Marl\u00e9taz, F. et al. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature 564<\/b>, 64\u201370 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zimmermann, B. et al. Topological structures and syntenic conservation in sea anemone genomes. Nat. Commun. 14<\/b>, 8270 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Schwaiger, M. et al. Evolutionary conservation of the eumetazoan gene regulatory landscape. Genome Res. 24<\/b>, 639\u2013650 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    modENCODE Consortium et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330<\/b>, 1787\u20131797 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mart\u00edn-Zamora, F. M. et al. Annelid functional genomics reveal the origins of bilaterian life cycles. Nature 615<\/b>, 105\u2013110 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    P\u00e9rez-Posada, A. et al. Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes. Nat. Ecol. Evol. https:\/\/doi.org\/10.1038\/s41559-024-02562-x<\/a> (2024).<\/p>\n<\/li>\n

  • \n

    Irimia, M. et al. Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome Res. 22<\/b>, 2356\u20132367 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Acemel, R. D. & Lupi\u00e1\u00f1ez, D. G. Evolution of 3D chromatin organization at different scales. Curr. Opin. Genet. Dev. 78<\/b>, 102019 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Irimia, M. & Maeso, I. in Old Questions and Young Approaches to Animal Evolution (eds Mart\u00edn-Dur\u00e1n, J. M. & Vellutini, B. C.) 175\u2013207 (Springer International Publishing, 2019).<\/p>\n<\/li>\n

  • \n

    Simakov, O. et al. Insights into bilaterian evolution from three spiralian genomes. Nature 493<\/b>, 526\u2013531 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wong, E. S. et al. Deep conservation of the enhancer regulatory code in animals. Science 370<\/b>, eaax8137 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kim, I. V. et al. Chromatin loops are an ancestral hallmark of the animal regulatory genome. Nature https:\/\/doi.org\/10.1038\/s41586-025-08960-w<\/a> (2025).<\/p>\n<\/li>\n

  • \n

    Rao, S. S. P. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159<\/b>, 1665\u20131680 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    de Wit, E. et al. CTCF binding polarity determines chromatin looping. Mol. Cell 60<\/b>, 676\u2013684 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kaaij, L. J. T., Mohn, F., van der Weide, R. H., de Wit, E. & B\u00fchler, M. The ChAHP complex counteracts chromatin looping at CTCF sites that emerged from SINE expansions in mouse. Cell 178<\/b>, 1437\u20131451.e14 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Franke, M. et al. CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression. Nat. Commun. 12<\/b>, 5415 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cavalheiro, G. R. et al. CTCF, BEAF-32, and CP190 are not required for the establishment of TADs in early Drosophila embryos but have locus-specific roles. Sci. Adv. https:\/\/doi.org\/10.1126\/sciadv.ade1085<\/a> (2023).<\/p>\n<\/li>\n

  • \n

    Kaushal, A. et al. CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions. Nat. Commun. 12<\/b>, 1011 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Maeso, I. & Tena, J. J. Favorable genomic environments for cis-regulatory evolution: a novel theoretical framework. Semin. Cell Dev. Biol. 57<\/b>, 2\u201310 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nord, A. S. et al. Rapid and pervasive changes in genome-wide enhancer usage during mammalian development. Cell 155<\/b>, 1521\u20131531 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Paris, M. et al. Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression. PLoS Genet. 9<\/b>, e1003748 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Vierstra, J. et al. Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. Science 346<\/b>, 1007\u20131012 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Villar, D., Flicek, P. & Odom, D. T. Evolution of transcription factor binding in metazoans\u2014mechanisms and functional implications. Nat. Rev. Genet. 15<\/b>, 221\u2013233 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Villar, D. et al. Enhancer evolution across 20 mammalian species. Cell 160<\/b>, 554\u2013566 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Glazov, E. A., Pheasant, M., McGraw, E. A., Bejerano, G. & Mattick, J. S. Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Res. 15<\/b>, 800\u2013808 (2005).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    He, Q. et al. High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat. Genet. 43<\/b>, 414\u2013420 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Tan, G., Polychronopoulos, D. & Lenhard, B. CNEr: a toolkit for exploring extreme noncoding conservation. PLoS Comput. Biol. https:\/\/doi.org\/10.1371\/journal.pcbi.1006940<\/a> (2019).<\/p>\n<\/li>\n

  • \n

    Vavouri, T., Walter, K., Gilks, W. R., Lehner, B. & Elgar, G. Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. Genome Biol. 8<\/b>, R15 (2007).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Royo, J. L. et al. Transphyletic conservation of developmental regulatory state in animal evolution. Proc. Natl Acad. Sci. USA 108<\/b>, 14186\u201314191 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Clarke, S. L. et al. Human developmental enhancers conserved between deuterostomes and protostomes. PLoS Genet. 8<\/b>, e1002852 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Frith, M. C. & Ni, S. DNA conserved in diverse animals since the Precambrian controls genes for embryonic development. Mol. Biol. Evol. https:\/\/doi.org\/10.1093\/molbev\/msad275<\/a> (2023).<\/p>\n<\/li>\n

  • \n

    Harmston, N., Baresic, A. & Lenhard, B. The mystery of extreme non-coding conservation. Philos. Trans. R. Soc. London, Ser. B 368<\/b>, 20130021 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pennacchio, L. A., Bickmore, W., Dean, A., Nobrega, M. A. & Bejerano, G. Enhancers: five essential questions. Nat. Rev. Genet. 14<\/b>, 288\u2013295 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Woolfe, A. et al. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3<\/b>, e7 (2005).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pennacchio, L. A. et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444<\/b>, 499\u2013502 (2006).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wang, J., Lee, A. P., Kodzius, R., Brenner, S. & Venkatesh, B. Large number of ultraconserved elements were already present in the jawed vertebrate ancestor. Mol. Biol. Evol. 26<\/b>, 487\u2013490 (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lee, A. P., Kerk, S. Y., Tan, Y. Y., Brenner, S. & Venkatesh, B. Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes. Mol. Biol. Evol. 28<\/b>, 1205\u20131215 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Thompson, A. W. et al. The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nat. Genet. 53<\/b>, 1373\u20131384 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Najle, S. R. et al. Stepwise emergence of the neuronal gene expression program in early animal evolution. Cell 186<\/b>, 4676\u20134693.e29 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sea Urchin Genome Sequencing Consortium et al. The genome of the sea urchin Strongylocentrotus purpuratus. Science 314<\/b>, 941\u2013952 (2006).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Simakov, O. et al. Hemichordate genomes and deuterostome origins. Nature 527<\/b>, 459\u2013465 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lewin, T. D., Liao, I. J.-Y. & Luo, Y.-J. Conservation of bilaterian genome structure is the exception, not the rule. Genome Biol. 26<\/b>, 247 (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gildor, T., Hinman, V. & Ben-Tabou-De-Leon, S. Regulatory heterochronies and loose temporal scaling between sea star and sea urchin regulatory circuits. Int. J. Dev. Biol. 61<\/b>, 347\u2013356 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Annunziata, R., Andrikou, C., Perillo, M., Cuomo, C. & Arnone, M. I. Development and evolution of gut structures: from molecules to function. Cell Tissue Res 377<\/b>, 445\u2013458 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Voronov, D. et al. Integrative multi-omics increase resolution of the sea urchin posterior gut gene regulatory network at single-cell level. Development https:\/\/doi.org\/10.1242\/dev.202278<\/a> (2024).<\/p>\n<\/li>\n

  • \n

    Marl\u00e9taz, F. et al. Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes. Cell Genomics 3<\/b>, 100295 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Eno, C. C., B\u00f6ttger, S. A. & Walker, C. W. Methods for karyotyping and for localization of developmentally relevant genes on the chromosomes of the purple sea urchin, Strongylocentrotus purpuratus. Biol. Bull. https:\/\/doi.org\/10.1086\/BBLv217n3p306<\/a> (2009).<\/p>\n<\/li>\n

  • \n

    Saotome, K. & Komatsu, M. Chromosomes of Japanese starfishes. Zool. Sci. 19<\/b>, 1095\u20131103 (2002).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Byrne, M. Life history diversity and evolution in the Asterinidae. Integr. Comp. Biol. 46<\/b>, 243\u2013254 (2006).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Colombera, D. & Tagliaferri, F. The male chromosomes of five species of echinoderms together with some technical hints. Caryologia 39<\/b>, 347\u2013352 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Thibaud-Nissen, F. et al. P8008 The NCBI eukaryotic genome annotation pipeline. J. Anim. Sci. 94<\/b>, 184 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485<\/b>, 376\u2013380 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nora, E. P. et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485<\/b>, 381\u2013385 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sexton, T. et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148<\/b>, 458\u2013472 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Schmidbaur, H. et al. Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization. Nat. Commun. 13<\/b>, 2172 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Huang, Z. et al. Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. Proc. Natl Acad. Sci. USA 120<\/b>, e2201504120 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Marl\u00e9taz, F. et al. The little skate genome and the evolutionary emergence of wing-like fins. Nature 616<\/b>, 495\u2013503 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kaaij, L. J. T., van der Weide, R. H., Ketting, R. F. & de Wit, E. Systemic loss and gain of chromatin architecture throughout zebrafish development. Cell Rep. 24<\/b>, 1\u201310.e4 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Vargas-Ch\u00e1vez, C. et al. An episodic burst of massive genomic rearrangements and the origin of non-marine annelids. Nat. Ecol. Evol. 9<\/b>, 1263\u20131279 (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wang, Y. et al. Chromosome-level genome assembly of the northern Pacific seastar Asterias amurensis. Sci. Data https:\/\/doi.org\/10.1038\/s41597-023-02688-w<\/a> (2023).<\/p>\n<\/li>\n

  • \n

    Watanabe, K. et al. The crucial role of CTCF in mitotic progression during early development of sea urchin. Dev. Growth Differ. 65<\/b>, 395\u2013407 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pallar\u00e8s-Albanell, J. et al. Gene regulatory dynamics during the development of a paleopteran insect, the mayfly Cloeon dipterum. Development https:\/\/doi.org\/10.1242\/dev.203017<\/a> (2024).<\/p>\n<\/li>\n

  • \n

    de-Leon, S. B.-T. & Davidson, E. H. Information processing at the foxa node of the sea urchin endomesoderm specification network. Proc. Natl Acad. Sci. USA 107<\/b>, 10103\u201310108 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nam, J., Dong, P., Tarpine, R., Istrail, S. & Davidson, E. H. Functional cis-regulatory genomics for systems biology. Proc. Natl Acad. Sci. USA 107<\/b>, 3930\u20133935 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Oliveri, P., Walton, K. D., Davidson, E. H. & McClay, D. R. Repression of mesodermal fate by foxa, a key endoderm regulator of the sea urchin embryo. Development 133<\/b>, 4173\u20134181 (2006).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hinman, V. F. & Davidson, E. H. Evolutionary plasticity of developmental gene regulatory network architecture. Proc. Natl Acad. Sci. USA 104<\/b>, 19404\u201319409 (2007).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Dylus, D. V. et al. Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks. Evodevo 7<\/b>, 2 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hore, T. A., Deakin, J. E. & Ja, M. G. The evolution of epigenetic regulators CTCF and BORIS\/CTCFL in amniotes. PLoS Genet. https:\/\/doi.org\/10.1371\/journal.pgen.1000169<\/a> (2008).<\/p>\n<\/li>\n

  • \n

    Kadota, M., Yamaguchi, K., Hara, Y. & Kuraku, S. Early vertebrate origin of CTCFL, a CTCF paralog, revealed by proximity-guided shark genome scaffolding. Sci. Rep. 10<\/b>, 14629 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mongiardino Koch, N. et al. Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record. eLife https:\/\/doi.org\/10.7554\/eLife.72460<\/a> (2022).<\/p>\n<\/li>\n

  • \n

    Linchangco, G. V. Jr et al. The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics. Mol. Phylogenet. Evol. 115<\/b>, 161\u2013170 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Villier, L. et al. Superstesaster promissor gen. et sp. nov., a new starfish (Echinodermata, Asteroidea) from the Early Triassic of Utah, USA, filling a major gap in the phylogeny of asteroids. J. Syst. Palaeontol. 16<\/b>, 395\u2013415 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Deline, B. et al. Evolution and development at the origin of a phylum. Curr. Biol. 30<\/b>, 1672\u20131679.e3 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Telford, M. J., Budd, G. E. & Philippe, H. Phylogenomic insights into animal evolution. Curr. Biol. 25<\/b>, R876\u2013R887 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cunningham, J. A., Liu, A. G., Bengtson, S. & Donoghue, P. C. J. The origin of animals: can molecular clocks and the fossil record be reconciled?. Bioessays 39<\/b>, 1\u201312 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Odom, D. T. et al. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat. Genet. 39<\/b>, 730\u2013732 (2007).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Schmidt, D. et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328<\/b>, 1036\u20131040 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ksepka, D. T. et al. The fossil calibration database\u2014a new resource for divergence dating. Syst. Biol. 64<\/b>, 853\u2013859 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Seb\u00e9-Pedr\u00f3s, A. & Ruiz-Trillo, I. Evolution and classification of the T-box transcription factor family. Curr. Top. Dev. Biol. 122<\/b>, 1\u201326 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ben-Tabou de-Leon, S., Su, Y.-H., Lin, K.-T., Li, E. & Davidson, E. H. Gene regulatory control in the sea urchin aboral ectoderm: spatial initiation, signaling inputs, and cell fate lockdown. Dev. Biol. 374<\/b>, 245\u2013254 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gross, J. M., Peterson, R. E., Wu, S.-Y. & McClay, D. R. LvTbx2\/3: a T-box family transcription factor involved in formation of the oral\/aboral axis of the sea urchin embryo. Development 130<\/b>, 1989\u20131999 (2003).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Valencia, J. E., Feuda, R., Mellott, D. O., Burke, R. D. & Peter, I. S. Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation. BMC Biol. 19<\/b>, 257 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Fresques, T. M. & Wessel, G. M. Nodal induces sequential restriction of germ cell factors during primordial germ cell specification. Development https:\/\/doi.org\/10.1242\/dev.155663<\/a> (2018).<\/p>\n<\/li>\n

  • \n

    Paganos, P., Voronov, D., Musser, J. M., Arendt, D. & Arnone, M. I. Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome. eLife https:\/\/doi.org\/10.7554\/eLife.70416<\/a> (2021).<\/p>\n<\/li>\n

  • \n

    Meyer, A., Ku, C., Hatleberg, W. L., Telmer, C. A. & Hinman, V. New hypotheses of cell type diversity and novelty from orthology-driven comparative single cell and nuclei transcriptomics in echinoderms. eLife https:\/\/doi.org\/10.7554\/eLife.80090<\/a> (2023).<\/p>\n<\/li>\n

  • \n

    Nora, E. P. et al. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169<\/b>, 930\u2013944.e22 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rao, S. S. P. et al. Cohesin loss eliminates all loop domains. Cell 171<\/b>, 305\u2013320.e24 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Niu, L. et al. Three-dimensional folding dynamics of the Xenopus tropicalis genome. Nat. Genet. 53<\/b>, 1075\u20131087 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cui, M., Vielmas, E., Davidson, E. H. & Peter, I. S. Sequential response to multiple developmental network circuits encoded in an intronic cis-regulatory module of sea urchin hox11\/13b. Cell Rep. 19<\/b>, 364\u2013374 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Damle, S. & Davidson, E. H. Precise cis-regulatory control of spatial and temporal expression of the alx-1 gene in the skeletogenic lineage of S. purpuratus. Dev. Biol. 357<\/b>, 505\u2013517 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lee, P. Y., Nam, J. & Davidson, E. H. Exclusive developmental functions of gatae cis-regulatory modules in the Strongylocentrorus purpuratus embryo. Dev. Biol. 307<\/b>, 434\u2013445 (2007).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Livi, C. B. & Davidson, E. H. Regulation of spblimp1\/krox1a, an alternatively transcribed isoform expressed in midgut and hindgut of the sea urchin gastrula. Gene Expr. Patterns 7<\/b>, 1\u20137 (2007).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yuh, C.-H. et al. Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin. Dev. Biol. 246<\/b>, 148\u2013161 (2002).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Irie, N. & Kuratani, S. Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis. Nat. Commun. 2<\/b>, 248 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hu, H. et al. Constrained vertebrate evolution by pleiotropic genes. Nat. Ecol. Evol. 1<\/b>, 1722\u20131730 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Duboule, D. Temporal colinearity and the phylotypic progression: a basis for the stability of a vertebrate Bauplan and the evolution of mor\u00ffphologies through heterochrony. Development 1994<\/b>, 135\u2013142 (1994).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bogdanovic, O. et al. Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome Res. 22<\/b>, 2043\u20132053 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Buono, L. et al. Conservation of cis-regulatory syntax underlying deuterostome gastrulation. Cells https:\/\/doi.org\/10.3390\/cells13131121<\/a> (2024).<\/p>\n<\/li>\n

  • \n

    Skvortsova, K. et al. Active DNA demethylation of developmental cis-regulatory regions predates vertebrate origins. Sci. Adv. https:\/\/doi.org\/10.1126\/sciadv.abn2258<\/a> (2022).<\/p>\n<\/li>\n

  • \n

    Gonzalez, P., Hauck, Q. C. & Baxevanis, A. D. Conserved noncoding elements evolve around the same genes throughout metazoan evolution. Genome Biol. Evol. 16<\/b>, evae052 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27<\/b>, 722\u2013736 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sim\u00e3o, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31<\/b>, 3210\u20133212 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25<\/b>, 1754\u20131760 (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Robinson, J. T. et al. Juicebox.js provides a cloud-based visualization system for Hi-C data. Cell Syst. 6<\/b>, 256\u2013258.e1 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Knight, P. A. & Ruiz, D. A fast algorithm for matrix balancing. IMA J. Numer. Anal. 33<\/b>, 1029\u20131047 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kruse, K., Hug, C. B. & Vaquerizas, J. M. FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data. Genome Biol. 21<\/b>, 303 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Crane, E. et al. Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature 523<\/b>, 240\u2013244 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356<\/b>, 92\u201395 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 3<\/b>, 99\u2013101 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215<\/b>, 403\u2013410 (1990).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Katoh, K., Rozewicki, J. & Yamada, K. D. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings Bioinf. 20<\/b>, 1160\u20131166 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Larsson, A. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30<\/b>, 3276\u20133278 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32<\/b>, 268\u2013274 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35<\/b>, 518\u2013522 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Heger, P., Marin, B., Bartkuhn, M., Schierenberg, E. & Wiehe, T. The chromatin insulator CTCF and the emergence of metazoan diversity. Proc. Natl Acad. Sci. USA 109<\/b>, 17507\u201317512 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14<\/b>, 587\u2013589 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Letunic, I. & Bork, P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49<\/b>, W293\u2013W296 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Armstrong, J. et al. Progressive cactus is a multiple-genome aligner for the thousand-genome era. Nature 587<\/b>, 246\u2013251 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Arshinoff, B. I. et al. Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms. Nucleic Acids Res. 50<\/b>, D970\u2013D979 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10<\/b>, 1213\u20131218 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Magri, M. S. et al. Assaying chromatin accessibility using ATAC-Seq in invertebrate chordate embryos. Front Cell Dev. Biol. 7<\/b>, 372 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9<\/b>, 357\u2013359 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Li, H. et al. The sequence alignment\/map format and SAMtools. Bioinformatics 25<\/b>, 2078\u20132079 (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9<\/b>, R137 (2008).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Li, Q., Brown, J. B., Huang, H. & Bickel, P. J. Measuring reproducibility of high-throughput experiments. Ann. Appl. Stat. 5<\/b>, 1752\u20131779 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26<\/b>, 841\u2013842 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15<\/b>, 550 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38<\/b>, 576\u2013589 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ye, T. et al. seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res. 39<\/b>, e35 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ram\u00edrez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44<\/b>, W160\u2013W165 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hickey, G., Paten, B., Earl, D., Zerbino, D. & Haussler, D. HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics 29<\/b>, 1341\u20131342 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20<\/b>, 238 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods https:\/\/doi.org\/10.1038\/nmeth.3176<\/a> (2015).<\/p>\n<\/li>\n

  • \n

    Mart\u00ednez-Redondo, G. I. et al. FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life. Commun. Biol. 8<\/b>, 1227 (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Alexa, A. & Rahnenfuhrer, J. topGO: Enrichment Analysis for Gene Ontology (Bioconductor, 2025); https:\/\/doi.org\/10.18129\/B9.bioc.topGO<\/a><\/p>\n<\/li>\n

  • \n

    Untergasser, A. et al. Primer3\u2014new capabilities and interfaces. Nucleic Acids Res. 40<\/b>, e115 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Xiong, A.-S. et al. PCR-based accurate synthesis of long DNA sequences. Nat. Protoc. 1<\/b>, 791\u2013797 (2006).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Arnone, M. I., Dmochowski, I. J. & Gache, C. in Development of Sea Urchins, Ascidians, and Other Invertebrate Deuterostomes: Experimental Approaches (eds Ettensohn, C. A. et al.) 621\u2013652 (Academic Press, 2004).<\/p>\n<\/li>\n

  • \n

    Perillo, M., Paganos, P., Spurrell, M., Arnone, M. I. & Wessel, G. M. Methodology for whole mount and fluorescent RNA in situ hybridization in echinoderms: single, double, and beyond. Methods Mol. Biol. 2219<\/b>, 195\u2013216 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Paganos, P. et al. FISH for all: a fast and efficient fluorescent hybridization (FISH) protocol for marine embryos and larvae. Front Physiol. 13<\/b>, 878062 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Foley, S. Files for viewing multiple genome alignment of marine invertebrates from \u2018Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes\u2019. figshare https:\/\/doi.org\/10.6084\/m9.figshare.30506378<\/a> (2025).<\/p>\n<\/li>\n

  • \n

    Bras\u00f3-Vives, M. et al. Parallel evolution of amphioxus and vertebrate small-scale gene duplications. Genome Biol. 23<\/b>, 1\u201324 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Saudemont, A. et al. Ancestral regulatory circuits governing ectoderm patterning downstream of Nodal and BMP2\/4 revealed by gene regulatory network analysis in an echinoderm. PLoS Genet. 6<\/b>, e1001259 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n","protected":false},"excerpt":{"rendered":"Seb\u00e9-Pedr\u00f3s, A. et al. The dynamic regulatory genome of capsaspora and the origin of animal multicellularity. Cell 165,…\n","protected":false},"author":2,"featured_media":272262,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[77],"tags":[18886,75137,7266,6130,18,6721,138535,5197,910,138536,19,17,3544,12151,133,18885],"class_list":{"0":"post-272261","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-science","8":"tag-biological-and-physical-anthropology","9":"tag-comparative-genomics","10":"tag-development","11":"tag-ecology","12":"tag-eire","13":"tag-evolutionary-biology","14":"tag-evolutionary-developmental-biology","15":"tag-functional-genomics","16":"tag-general","17":"tag-genome-evolution","18":"tag-ie","19":"tag-ireland","20":"tag-life-sciences","21":"tag-paleontology","22":"tag-science","23":"tag-zoology"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@ie\/115854123083239183","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/272261","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/comments?post=272261"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/272261\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media\/272262"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media?parent=272261"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/categories?post=272261"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/tags?post=272261"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}