Browsing Bergen Open Research Archive by Author "Becker, Thomas S."

Now showing items 1-6 of 6

    • Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons 

      Dong, Xianjun; Navratilova, Pavla; Fredman, David; Drivenes, Øyvind; Becker, Thomas S.; Lenhard, Boris (Journal article; Peer reviewed, 2009-12-06)
      Using a comparative genomics approach to reconstruct the fate of genomic regulatory blocks (GRBs) and identify exonic remnants that have survived the disappearance of their host genes after whole-genome duplication (WGD) ...

    • Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates 

      Kikuta, Hiroshi; Laplante, Mary; Navrátilová, Pavla; Komisarczuk, Anna Zofia; Engström, Pär G.; Fredman, David; Akalin, Altuna; Caccamo, Mario; Sealy, Ian; Howe, Kerstin; Ghislain, Julien; Pezeron, Guillaume; Mourrain, Philippe; Ellingsen, Staale; Oates, Andrew C.; Thisse, Christine; Thisse, Bernard; Foucher, Isabelle; Adolf, Birgit; Geling, Andrea; Lenhard, Boris; Becker, Thomas S. (Peer reviewed; Journal article, 2007-03-06)
      We report evidence for a mechanism for the maintenance of long-range conserved synteny across vertebrate genomes. We found the largest mammal-teleost conserved chromosomal segments to be spanned by highly conserved noncoding ...

    • Genomic regulatory blocks underlie extensive microsynteny conservation in insects 

      Engström, Pär G.; Sui, Shannan J. Ho; Drivenes, Øyvind; Becker, Thomas S.; Lenhard, Boris (Journal article, 2007-11-07)
      Insect genomes contain larger blocks of conserved gene order (microsynteny) than would be expected under a random breakage model of chromosome evolution. We present evidence that microsynteny has been retained to keep large ...

    • Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome 

      Naville, Magali; Ishibashi, Minaka; Ferg, Marco; Bengani, Hemant; Rinkwitz, Silke; Krecsmarik, Monika; Hawkins, Thomas A.; Wilson, Stephen W.; Manning, Elizabeth; Chilamakuri, Chandra Sekhar Reddy; Wilson, David I.; Louis, Alexandra; Raymond, F. Lucy; Rastegar, Sepand; Strähle, Uwe; Lenhard, Boris; Bally-Cuif, Laure; van Heyningen, Veronica; Fitzpatrick, David R.; Becker, Thomas S.; Crollius, Hugues Roest (Peer reviewed; Journal article, 2015-04-24)
      Enhancers can regulate the transcription of genes over long genomic distances. This is thought to lead to selection against genomic rearrangements within such regions that may disrupt this functional linkage. Here we test ...

    • Morphogenesis underlying the development of the everted teleost telencephalon 

      Folgueira, Mónica; Bayley, Philippa; Navrátilová, Pavla; Becker, Thomas S.; Wilson, Stephen W.; Clarke, Jonathan D. W. (Peer reviewed; Journal article, 2012-09-18)
      Background: Although the mechanisms underlying brain patterning and regionalization are very much conserved, the morphology of different brain regions is extraordinarily variable across vertebrate phylogeny. This is ...

    • Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes 

      Kikuta, Hiroshi; Fredman, David; Rinkwitz, Silke; Lenhard, Boris; Becker, Thomas S. (Journal article; Peer reviewed, 2007-10-31)
      A large-scale enhancer detection screen was performed in the zebrafish using a retroviral vector carrying a basal promoter and a fluorescent protein reporter cassette. Analysis of insertional hotspots uncovered areas around ...