Bat accelerated regions identify a bat forelimb specific enhancer in the HoxD locus

dc.contributor.authorBooker, Betty Men_ZA
dc.contributor.authorFriedrich, Taraen_ZA
dc.contributor.authorMason, Mandy Ken_ZA
dc.contributor.authorVanderMeer, Julia Een_ZA
dc.contributor.authorZhao, Jingjingen_ZA
dc.contributor.authorEckalbar, Walter Len_ZA
dc.contributor.authorLogan, Malcolmen_ZA
dc.contributor.authorIlling, Nicolaen_ZA
dc.contributor.authorPollard, Katherine Sen_ZA
dc.contributor.authorAhituv, Nadaven_ZA
dc.date.accessioned2016-04-13T12:37:15Z
dc.date.available2016-04-13T12:37:15Z
dc.date.issued2016en_ZA
dc.description.abstractAuthor Summary: The limb is a classic example of vertebrate homology and is represented by a large range of morphological structures such as fins, legs and wings. The evolution of these structures could be driven by alterations in gene regulatory elements that have critical roles during development. To identify elements that may contribute to bat wing development, we characterized sequences that are conserved between vertebrates, but changed significantly in the bat lineage. We then overlapped these sequences with predicted developing limb enhancers as determined by ChIP-seq, finding 166 bat accelerated sequences (BARs). Five BARs that were tested for enhancer activity in mice all drove expression in the limb. Testing the mouse orthologous sequence showed that three had differences in their limb enhancer activity as compared to the bat sequence. Of these, BAR116 was of particular interest as it is located near the HoxD locus, an essential gene complex required for proper spatiotemporal patterning of the developing limb. The bat BAR116 sequence drove robust forelimb expression but the mouse BAR116 sequence did not show enhancer activity. These experiments correspond to analyses of HoxD gene expressions in developing bat limbs, which had strong forelimb versus weak hindlimb expression for Hoxd10 - 11 . Combined, our studies highlight specific genomic regions that could be important in shaping the morphological differences that led to the development of the bat wing.en_ZA
dc.identifier.apacitationBooker, B. M., Friedrich, T., Mason, M. K., VanderMeer, J. E., Zhao, J., Eckalbar, W. L., ... Ahituv, N. (2016). Bat accelerated regions identify a bat forelimb specific enhancer in the HoxD locus. <i>PLOS Genetics</i>, http://hdl.handle.net/11427/18857en_ZA
dc.identifier.chicagocitationBooker, Betty M, Tara Friedrich, Mandy K Mason, Julia E VanderMeer, Jingjing Zhao, Walter L Eckalbar, Malcolm Logan, Nicola Illing, Katherine S Pollard, and Nadav Ahituv "Bat accelerated regions identify a bat forelimb specific enhancer in the HoxD locus." <i>PLOS Genetics</i> (2016) http://hdl.handle.net/11427/18857en_ZA
dc.identifier.citationBooker, B. M., Friedrich, T., Mason, M. K., VanderMeer, J. E., Zhao, J., Eckalbar, W. L., ... & Ahituv, N. (2015). Bat accelerated regions identify a bat forelimb specific enhancer in the HoxD locus. bioRxiv, 034017. doi:10.1371/journal.pgen.1005738en_ZA
dc.identifier.ris TY - Journal Article AU - Booker, Betty M AU - Friedrich, Tara AU - Mason, Mandy K AU - VanderMeer, Julia E AU - Zhao, Jingjing AU - Eckalbar, Walter L AU - Logan, Malcolm AU - Illing, Nicola AU - Pollard, Katherine S AU - Ahituv, Nadav AB - Author Summary: The limb is a classic example of vertebrate homology and is represented by a large range of morphological structures such as fins, legs and wings. The evolution of these structures could be driven by alterations in gene regulatory elements that have critical roles during development. To identify elements that may contribute to bat wing development, we characterized sequences that are conserved between vertebrates, but changed significantly in the bat lineage. We then overlapped these sequences with predicted developing limb enhancers as determined by ChIP-seq, finding 166 bat accelerated sequences (BARs). Five BARs that were tested for enhancer activity in mice all drove expression in the limb. Testing the mouse orthologous sequence showed that three had differences in their limb enhancer activity as compared to the bat sequence. Of these, BAR116 was of particular interest as it is located near the HoxD locus, an essential gene complex required for proper spatiotemporal patterning of the developing limb. The bat BAR116 sequence drove robust forelimb expression but the mouse BAR116 sequence did not show enhancer activity. These experiments correspond to analyses of HoxD gene expressions in developing bat limbs, which had strong forelimb versus weak hindlimb expression for Hoxd10 - 11 . Combined, our studies highlight specific genomic regions that could be important in shaping the morphological differences that led to the development of the bat wing. DA - 2016 DB - OpenUCT DO - 10.1371/journal.pgen.1005738 DP - University of Cape Town J1 - PLOS Genetics LK - https://open.uct.ac.za PB - University of Cape Town PY - 2016 T1 - Bat accelerated regions identify a bat forelimb specific enhancer in the HoxD locus TI - Bat accelerated regions identify a bat forelimb specific enhancer in the HoxD locus UR - http://hdl.handle.net/11427/18857 ER - en_ZA
dc.identifier.urihttp://dx.doi.org/10.1371/journal.pgen.1005738en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/18857
dc.identifier.vancouvercitationBooker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, et al. Bat accelerated regions identify a bat forelimb specific enhancer in the HoxD locus. PLOS Genetics. 2016; http://hdl.handle.net/11427/18857.en_ZA
dc.language.isoengen_ZA
dc.publisherPublic Library of Scienceen_ZA
dc.publisher.departmentDepartment of Molecular and Cell Biologyen_ZA
dc.publisher.facultyFaculty of Scienceen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_ZA
dc.rights.holder© 2016 Booker et alen_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/4.0en_ZA
dc.sourcePLOS Geneticsen_ZA
dc.source.urihttp://journals.plos.org/plosgeneticsen_ZA
dc.subject.otherMultiple alignment calculationen_ZA
dc.subject.otherSequence motif analysisen_ZA
dc.subject.otherSequence alignmenten_ZA
dc.subject.otherEmbryosen_ZA
dc.subject.otherBatsen_ZA
dc.subject.otherMammalian genomicsen_ZA
dc.subject.otherSequence analysisen_ZA
dc.subject.otherVertebratesen_ZA
dc.titleBat accelerated regions identify a bat forelimb specific enhancer in the HoxD locusen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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