A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation

Nature Genetics
Rafael D AcemelJosé Luis Gómez-Skarmeta

Abstract

The HoxA and HoxD gene clusters of jawed vertebrates are organized into bipartite three-dimensional chromatin structures that separate long-range regulatory inputs coming from the anterior and posterior Hox-neighboring regions. This architecture is instrumental in allowing vertebrate Hox genes to pattern disparate parts of the body, including limbs. Almost nothing is known about how these three-dimensional topologies originated. Here we perform extensive 4C-seq profiling of the Hox cluster in embryos of amphioxus, an invertebrate chordate. We find that, in contrast to the architecture in vertebrates, the amphioxus Hox cluster is organized into a single chromatin interaction domain that includes long-range contacts mostly from the anterior side, bringing distant cis-regulatory elements into contact with Hox genes. We infer that the vertebrate Hox bipartite regulatory system is an evolutionary novelty generated by combining ancient long-range regulatory contacts from DNA in the anterior Hox neighborhood with new regulatory inputs from the posterior side.

References

Feb 16, 2002·Science·Job DekkerNancy Kleckner
Mar 5, 2003·BioTechniques·A I SaeedJ Quackenbush
Dec 19, 2003·Nucleic Acids Research·Karsten Suhre, Jean-Michel Claverie
Jun 25, 2004·Nucleic Acids Research·Kelly A FrazerInna Dubchak
Aug 3, 2004·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Michael FuentesHector Escriva
Feb 17, 2005·BMC Bioinformatics·Guy St C Slater, Ewan Birney
Sep 1, 2005·PLoS Biology·Paramvir Dehal, Jeffrey L Boore
Jul 18, 2006·Nucleic Acids Research·Mario StankeBurkhard Morgenstern
Apr 24, 2007·Developmental Biology·Federico GonzalezFrançois Spitz
May 24, 2007·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Michael FuentesHector Escriva
Jul 21, 2007·Nature Protocols·Hélène HagègeThierry Forné
Aug 5, 2009·Developmental Dynamics : an Official Publication of the American Association of Anatomists·José BessaJosé Luis Gómez-Skarmeta
Dec 7, 2010·Nature Structural & Molecular Biology·Davide BaùMarc A Marti-Renom
Sep 10, 2011·Bioinformatics·Tanja Magoč, Steven L Salzberg
Oct 15, 2011·Science·Daan NoordermeerDenis Duboule
Oct 27, 2011·Development·Stephanie Bertrand, Hector Escriva
Nov 29, 2011·Cell·Thomas MontavonDenis Duboule
Mar 24, 2012·Briefings in Functional Genomics·Jordi PapsSebastian M Shimeld
May 23, 2012·Methods : a Companion to Methods in Enzymology·Erik SplinterWouter de Laat
Dec 4, 2012·EvoDevo·Juan Pascual-AnayaJordi Garcia-Fernàndez
Mar 1, 2012·Wiley Interdisciplinary Reviews. Developmental Biology·Linda Z Holland, Takayuki Onai
Sep 21, 2013·Development·Moisés Mallo, Claudio R Alonso
Jun 26, 2014·Circulation Research·Jan Hendrik van WeerdVincent M Christoffels
Sep 15, 2014·Trends in Cell Biology·Elena Gómez-Díaz, Victor G Corces
Oct 5, 2014·Journal of Molecular Biology·Filippo Ciabrelli, Giacomo Cavalli
Nov 14, 2014·Genesis : the Journal of Genetics and Development·Kenneth W BaughmanEiichi Shoguchi
Dec 24, 2014·Proceedings of the National Academy of Sciences of the United States of America·Andrew R GehrkeNeil H Shubin

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Citations

Dec 21, 2016·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Aditya SaxenaKimberly L Cooper
Dec 21, 2016·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Patrick Tschopp, Clifford J Tabin
Feb 7, 2017·Nature Reviews. Genetics·Florence PetitNadav Ahituv
Mar 3, 2017·Wiley Interdisciplinary Reviews. Developmental Biology·Rafael D AcemelJosé Luis Gómez-Skarmeta
Nov 15, 2016·Current Opinion in Genetics & Development·Ignacio MaesoJosé Luis Gómez-Skarmeta
Mar 10, 2018·PLoS Computational Biology·Ibai Irastorza-AzcarateDamien P Devos
Aug 12, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Xiaofeng ShenShilin Chen
Jan 27, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Shuai GuoXiaogai Hou
Mar 21, 2018·Nature Genetics·Joaquín LetelierJosé Luis Gómez-Skarmeta
Oct 18, 2018·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Hector Escriva
Nov 23, 2018·Nature·Ferdinand MarlétazManuel Irimia
Jul 3, 2019·Nature Ecology & Evolution·Daniel AldeaHector Escriva
Jun 3, 2018·Molecular Systems Biology·Alvaro Rada-IglesiasArgyris Papantonis
May 19, 2020·Molecular Biology and Evolution·María Touceda-SuárezManuel Irimia
Jul 15, 2016·Genome Biology and Evolution·Jia-Xing YueLinda Z Holland
Sep 2, 2017·Genes & Development·Jacqueline Deschamps, Denis Duboule
Aug 23, 2019·International Journal of Molecular Sciences·Yingxian CuiHui Yao
Jul 11, 2019·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Brigid Leung, Sebastian M Shimeld
Aug 9, 2017·Genome Biology·Pierre J FabreDenis Duboule
Apr 4, 2018·Proceedings of the National Academy of Sciences of the United States of America·Joaquín LetelierCristina Pujades
Dec 10, 2019·Annual Review of Animal Biosciences·Caroline B Albertin, Oleg Simakov
Feb 23, 2020·Chinese Medicine·Xianmei YinShilin Chen
Feb 26, 2016·Nature Genetics·Jacqueline Deschamps
Jul 12, 2017·Scientific Reports·Mitsutaka KadotaShigehiro Kuraku
Sep 27, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Xiaofeng ShenGuangwei Zhu
Dec 29, 2020·Mitochondrial DNA. Part B, Resources·Shuai WangHongwei Wang
May 14, 2021·Frontiers in Cell and Developmental Biology·Stephanie BertrandHector Escrivá
Jun 8, 2021·Frontiers in Cell and Developmental Biology·João E CarvalhoMichael Schubert
May 21, 2016·Genes & Development·Leonardo BeccariDenis Duboule
May 26, 2016·Genes & Development·Marian A Ros

❮ Previous
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