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dc.contributor.authorTena, JJ
dc.contributor.authorGonzalez-Aguilera, C
dc.contributor.authorFernandez-Minan, A
dc.contributor.authorVazquez-Marin, J
dc.contributor.authorParra-Acero, H
dc.contributor.authorCross, JW
dc.contributor.authorRigby, PWJ
dc.contributor.authorCarvajal, JJ
dc.contributor.authorWittbrodt, J
dc.contributor.authorGomez-Skarmeta, JL
dc.contributor.authorMartinez-Morales, JR
dc.date.accessioned2018-08-03T11:23:51Z
dc.date.issued2014-07
dc.identifier7
dc.identifier.citationGENOME RESEARCH, 2014, 24 pp. 1075 - 1085
dc.identifier.issn1088-9051
dc.identifier.urihttps://repository.icr.ac.uk/handle/internal/2257
dc.identifier.eissn1549-5469
dc.identifier.doi10.1101/gr.163915.113
dc.description.abstractThe complex relationship between ontogeny and phylogeny has been the subject of attention and controversy since von Baer’s formulations in the 19th century. The classic concept that embryogenesis progresses from clade general features to species-specific characters has often been revisited. It has become accepted that embryos from a clade show maximum morphological similarity at the so-called phylotypic period (i.e., during mid-embryogenesis). According to the hourglass model, body plan conservation would depend on constrained molecular mechanisms operating at this period. More recently, comparative transcriptomic analyses have provided conclusive evidence that such molecular constraints exist. Examining cis-regulatory architecture during the phylotypic period is essential to understand the evolutionary source of body plan stability. Here we compare transcriptomes and key epigenetic marks (H3K4me3 and H3K27ac) from medaka (Oryzias latipes) and zebrafish (Danio rerio), two distantly related teleosts separated by an evolutionary distance of 115-200 Myr. We show that comparison of transcriptome profiles correlates with anatomical similarities and heterochronies observed at the phylotypic stage. Through comparative epigenomics, we uncover a pool of conserved regulatory regions (approximate to 700), which are active during the vertebrate phylotypic period in both species. Moreover, we show that their neighboring genes encode mainly transcription factors with fundamental roles in tissue specification. We postulate that these regulatory regions, active in both teleost genomes, represent key constrained nodes of the gene networks that sustain the vertebrate body plan.
dc.format.extent1075 - 1085
dc.languageeng
dc.language.isoeng
dc.publisherCOLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
dc.rights.urihttps://www.rioxx.net/licenses/all-rights-reserved
dc.titleComparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period
dc.typeJournal Article
rioxxterms.versionofrecord10.1101/gr.163915.113
rioxxterms.licenseref.urihttps://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.licenseref.startdate2014-07
rioxxterms.typeJournal Article/Review
dc.relation.isPartOfGENOME RESEARCH
pubs.notesaffiliation: Gomez-Skarmeta, JL (Reprint Author), CSIC, UPO JA, Ctr Andaluz Biol Desarrollo, Seville 41013, Spain. Tena, Juan J.; Gonzalez-Aguilera, Cristina; Fernandez-Minan, Ana; Vazquez-Marin, Javier; Parra-Acero, Helena; Carvajal, Jaime J.; Gomez-Skarmeta, Jose L.; Martinez-Morales, Juan R., CSIC, UPO JA, Ctr Andaluz Biol Desarrollo, Seville 41013, Spain. Cross, Joe W.; Rigby, Peter W. J.; Carvajal, Jaime J., Inst Canc Res, Div Canc Biol, London SW3 6JB, England. Wittbrodt, Joachim, Heidelberg Univ, COS, D-69120 Heidelberg, Germany. keywords-plus: TRANSCRIPTION FACTOR-BINDING; HUMAN GENOME; GENE-EXPRESSION; CHIP-SEQ; RNA-SEQ; EVOLUTIONARY CONSERVATION; HISTONE MODIFICATIONS; ENHANCER CHROMATIN; NONCODING ELEMENTS; PROVIDES EVIDENCE research-areas: Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity web-of-science-categories: Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity author-email: [email protected] [email protected] researcherid-numbers: Tena, Juan/M-2265-2014 Carvajal, Jaime/O-3681-2014 Wittbrodt, Joachim/D-4735-2014 orcid-numbers: Tena, Juan/0000-0001-8165-7984 Carvajal, Jaime/0000-0002-7277-0317 Wittbrodt, Joachim/0000-0001-8550-7377 Gomez-Skarmeta, Jose Luis/0000-0001-5125-4332 Martinez-Morales, Juan R./0000-0002-4650-4293 Vazquez-Marin, Javier/0000-0002-5832-1363 Gonzalez- Aguilera, Cristina/0000-0003-4845-5744 funding-acknowledgement: Andalusian government; Institute of Cancer Research; Spanish government [BFU2010-14839, CSD2007-00008, P08-CVI-3488, BFU2011-22916, P11-CVI-7256]; Andalusian government [BFU2010-14839, CSD2007-00008, P08-CVI-3488, BFU2011-22916, P11-CVI-7256] funding-text: We thank Gert-Jan Veenstra and Simon van Heeringen for their critical input, Rocio Polvillo and Maria Nicolas-Perez for their excellent technical help, and Iwanka Kozarewa and Lina Chen for their help on the mouse RNA-seq. The Andalusian government (JA) supported A.F-.M. as scientific manager of the Aquatic Vertebrates Platform at CABD. J.W.C. was supported by a studentship from The Institute of Cancer Research. Spanish and Andalusian government grants BFU2010-14839, CSD2007-00008, and P08-CVI-3488 to J.L.G-.S.; and BFU2011-22916 and P11-CVI-7256 to J.R.M-.M. supported this work. number-of-cited-references: 80 times-cited: 19 usage-count-last-180-days: 0 usage-count-since-2013: 25 journal-iso: Genome Res. doc-delivery-number: AK1OS unique-id: ISI:000338185000003 oa: gold_or_bronze da: 2018-08-03
pubs.notesNot known
pubs.organisational-group/ICR
pubs.organisational-group/ICR/Primary Group
pubs.organisational-group/ICR/Primary Group/ICR Divisions
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Closed research teams
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Closed research teams/Molecular Embryology
pubs.organisational-group/ICR
pubs.organisational-group/ICR/Primary Group
pubs.organisational-group/ICR/Primary Group/ICR Divisions
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Closed research teams
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Closed research teams/Molecular Embryology
pubs.volume24
pubs.embargo.termsNot known
icr.researchteamMolecular Embryologyen_US
dc.contributor.icrauthorRigby, Peter William Jacken


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