Now showing items 1-17 of 17

  • Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes 

    Engström, Pär G.; Fredman, David; Lenhard, Boris (BioMed Central, 2008-02-12)
    Metazoan genomes contain arrays of highly conserved noncoding elements (HCNEs) that span developmental regulatory genes and define regulatory domains. We describe Ancora http:// ancora.genereg.net, a web resource that ...
  • A cohesin-independent role for NIPBL at promoters provides insights in CdLS 

    Zuin, Jessica; Franke, Vedran; van Ijcken, Wilfred F.J.; van der Sloot, Antoine A.J.; Krantz, Ian D.; van der Reijden, Michael I.J.A.; Nakato, Ryuichiro; Lenhard, Boris; Wendt, Kerstin S. (Public Library of Science, 2014-02-13)
    The cohesin complex is crucial for chromosome segregation during mitosis and has recently also been implicated in transcriptional regulation and chromatin architecture. The NIPBL protein is required for the loading of ...
  • Complex Loci in Human and Mouse Genomes 

    Engström, Pär G.; Suzuki, Harukazu; Ninomiya, Norika; Akalin, Altuna; Sessa, Luca; Lavorgna, Giovanni; Brozzi, Alessandro; Luzi, Lucilla; Lam Tan, Sin; Yang, Liang; Kunarso, Galih; Lian-Chong, Edwin Ng; Batalov, Serge; Wahlestedt, Claes; Kai, Chikatoshi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Wells, Christine; Bajic, Vladimir B.; Orlando, Valerio; Reid, James F.; Lenhard, Boris; Lipovich, Leonard (PLoS, 2006-04-28)
    Mammalian genomes harbor a larger than expected number of complex loci, in which multiple genes are coupled by shared transcribed regions in antisense orientation and/or by bidirectional core promoters. To determine the ...
  • Computational characterization of modes of transcriptional regulation of nuclear receptor genes 

    Sharma, Yogita; Chilamakuri, Chandra Sekhar Reddy; Bakke, Marit; Lenhard, Boris (PLoS, 2014-02-13)
    Background: Nuclear receptors are a large structural class of transcription factors that act with their co-regulators and repressors to maintain a variety of biological and physiological processes such as metabolism, ...
  • Dissecting the Transcriptional Regulatory Properties of Human Chromosome 16 Highly Conserved Non-Coding Regions 

    Royo, José Luis; Hidalgo, Carmen; Roncero, Yolanda; Seda, María Angeles; Akalin, Altuna; Lenhard, Boris; Casares, Fernando; Gómez-Skarmeta, José Luis (Public Library of Science, 2011-09-13)
    Non-coding DNA conservation across species has been often used as a predictor for transcriptional enhancer activity. However, only a few systematic analyses of the function of these highly conserved non-coding regions ...
  • Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis 

    Nepal, Chirag; Hadzhiev, Yavor; Previti, A. Christopher; Haberle, Vanja; Li, Nan; Takahashi, Hazuki; Suzuki, Ana Maria; Sheng, Ying; Abdelhamid, Rehab; Anand, Santosh; Gehrig, Jochen; Akalin, Altuna; Kockx, Christel E.M.; van der Sloot, Antoine A.J.; van Ijcken, Wilfred F.J.; Armant, Olivier; Rastegar, Sepand; Watson, Craig; Strähle, Uwe; Stupka, Elia; Carninci, Piero; Lenhard, Boris; Müller, Ferenc (Cold Spring Harbor Laboratory Press, 2013)
    Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in ...
  • Genome-wide DNA methylation profiling of non-small cell lung carcinomas 

    Carvalho, Rejane Hughes; Haberle, Vanja; Hou, Jun; van Gent, Teus; Thongjuea, Supat; van Ijcken, Wilfred F.J.; Kockx, Christel; Brouwer, Rutger; Rijkers, Erikjan; Sieuwerts, Anieta; Foekens, John; van Vroonhoven, Mirjam; Aerts, Joachim; Grosveld, Frank; Lenhard, Boris; Philipsen, Sjaak (BioMed Central, 2012-06-22)
    Background: Non-small cell lung carcinoma (NSCLC) is a complex malignancy that owing to its heterogeneity and poor prognosis poses many challenges to diagnosis, prognosis and patient treatment. DNA methylation is an important ...
  • The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation 

    Soler, Eric; Andrieu-Soler, Charlotte; Boer, Ernie de; Bryne, Jan Christian; Thongjuea, Supat; Stadhouders, Ralph; Palstra, Robert-Jan; Stevens, Mary; Kockx, Christel; IJcken, Wilfred van; Hou, Jun; Steinhoff, Christine; Rijkers, Erikjan; Lenhard, Boris; Grosveld, Frank (Cold Spring Harbor Laboratory Press, 2009)
    One of the complexes formed by the hematopoietic transcription factor Gata1 is a complex with the Ldb1 (LIM domain-binding protein 1) and Tal1 proteins. It is known to be important for the development and differentiation ...
  • 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. (Cold Spring Harbor Laboratory Press, 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 (Cold Spring Harbor Laboratory Press, 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 ...
  • In Silico Detection of Sequence Variations Modifying Transcriptional Regulation 

    Andersen, Malin C.; Engström, Pär G.; Lithwick, Stuart; Lithwick, David; Eriksson, Per; Lenhard, Boris; Wasserman, Wyeth W.; Odeberg, Jacob (PLoS, 2008-01-18)
    Identification of functional genetic variation associated with increased susceptibility to complex diseases can elucidate genes and underlying biochemical mechanisms linked to disease onset and progression. For genes linked ...
  • JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles 

    Portales-Casamar, Elodie; Thongjuea, Supat; Kwon, Andrew T.; Arenillas, David; Zhao, Xiaobei; Valen, Eivind; Yusuf, Dimas; Lenhard, Boris; Wasserman, Wyeth W.; Sandelin, Albin (Oxford University Press, 2010)
    JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific ...
  • The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner 

    Sleutels, Frank; Soochit, Widia; Bartkuhn, Marek; Heath, Helen; Dienstbach, Sven; Bergmaier, Philipp; Franke, Vedran; Rosa-Garrido, Manuel; van de Nobelen, Suzanne; Caesar, Lisa; van der Reijden, Michael I.J.A.; Bryne, Jan Christian; van Ijcken, Wilfred F.J.; Grootegoed, J. Anton; Delgado, M. Dolores; Lenhard, Boris; Renkawitz, Rainer; Grosveld, Frank; Galjart, Niels (BioMed Central, 2012-06-18)
    Background: CTCF is a highly conserved and essential zinc finger protein expressed in virtually all cell types. In conjunction with cohesin, it organizes chromatin into loops, thereby regulating gene expression and epigenetic ...
  • r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data 

    Thongjuea, Supat; Stadhouders, Ralph; Grosveld, Frank; Soler, Eric; Lenhard, Boris (Oxford University Press, 2013)
    The coupling of chromosome conformation capture (3C) with next-generation sequencing technologies enables the high-throughput detection of longrange genomic interactions, via the generation of ligation products between ...
  • 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. (BioMed Central, 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 ...
  • Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes 

    Dong, Xianjun; Fredman, David; Lenhard, Boris (BioMed Central, 2009-08-21)
    Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into ...
  • Translog, a web browser for studying the expression divergence of homologous genes 

    Dong, Xianjun; Akalin, Altuna; Sharma, Yogita; Lenhard, Boris (BioMed Central, 2010-01-18)
    Background: Increasing amount of data from comparative genomics, and newly developed technologies producing accurate gene expression data facilitate the study of the expression divergence of homologous genes. Previous ...