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

      Engström, Pär G.; Fredman, David; Lenhard, Boris (Journal article; Peer reviewed, 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 ...
    • CAGEr: Precise TSS data retrieval and high-resolution promoterome mining for integrative analyses 

      Haberle, Vanja; Forrest, Alistair R.R.; Hayashizaki, Yoshihide; Carninci, Piero; Lenhard, Boris (Peer reviewed; Journal article, 2015)
      Cap analysis of gene expression (CAGE) is a high-throughput method for transcriptome analysis that provides a single base-pair resolution map of transcription start sites (TSS) and their relative usage. Despite their high ...
    • Chromatin and epigenetic features of long-range gene regulation 

      Harmston, Nathan; Lenhard, Boris (Peer reviewed; Journal article, 2013-06-13)
      The precise regulation of gene transcription during metazoan development is controlled by a complex system of interactions between transcription factors, histone modifications and modifying enzymes and chromatin conformation. ...
    • CNEr: A toolkit for exploring extreme noncoding conservation 

      Tan, Ge; Polychronopoulos, Dimitris; Lenhard, Boris (Journal article; Peer reviewed, 2019-08-26)
      Conserved Noncoding Elements (CNEs) are elements exhibiting extreme noncoding conservation in Metazoan genomes. They cluster around developmental genes and act as long-range enhancers, yet nothing that we know about their ...
    • 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. (Peer reviewed; Journal article, 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 (Peer reviewed; Journal article, 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 (Peer reviewed; Journal article, 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 (Peer reviewed; Journal article, 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 (Peer reviewed; Journal article, 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 ...
    • 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) ...
    • 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 (Peer reviewed; Journal article, 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 (Peer reviewed; Journal article, 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. (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 ...
    • 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 (Journal article; Peer reviewed, 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 (Peer reviewed; Journal article, 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 ...
    • JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles 

      Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W.; Parcy, François; Worsley-Hunt, Rebecca; Arenillas, David J.; Buchman, Sorana; Chen, Chih-yu; Chou, Alice; Ienasescu, Hans; Lim, Jonathan; Shyr, Casper; Tan, Ge; Zhou, Michelle; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W. (Peer reviewed; Journal article, 2014-01)
      JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly ...
    • JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update 

      Bryne, Jan Christian; Valen, Eivind; Tang, Man-Hung Eric; Marstrand, Troels; Winther, Ole; da Piedade, Isabelle; Krogh, Anders; Lenhard, Boris; Sandelin, Albin (Journal article; Peer reviewed, 2007-11-15)
      JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with ...
    • 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 ...
    • 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 (Peer reviewed; Journal article, 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 ...