Blar i Bergen Open Research Archive på forfatter "Lenhard, Boris"
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Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans
Nepal, Chirag; Taranta, Andrzej; Hadzhiev, Yavor; Pundhir, Sachin; Mydel, Piotr Mateusz; Lenhard, Boris; Müller, Ferenc; Andersen, Jesper B. (Journal article; Peer reviewed, 2020-04)HOTAIR was proposed to regulate either HoxD cluster genes in trans or HoxC cluster genes in cis, a mechanism that remains unclear. We have identified a 32-nucleotide conserved noncoding element (CNE) as HOTAIR ancient ... -
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. ... -
Chromatin jets define the properties of cohesin-driven in vivo loop extrusion
Guo, Ya; Al-Jibury, Ediem; Garcia-Millan, Rosalba; Ntagiantas, Konstantinos; King, James W.D.; Nash, Alex J.; Galjart, Niels; Lenhard, Boris; Rueckert, Daniel; Fisher, Amanda G.; Pruessner, Gunnar; Merkenschlager, Matthias (Journal article; Peer reviewed, 2022)Complex genomes show intricate organization in three-dimensional (3D) nuclear space. Current models posit that cohesin extrudes loops to form self-interacting domains delimited by the DNA binding protein CTCF. Here, we ... -
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, ... -
Conservative route to genome compaction in a miniature annelid
Martin-Duran, José M.; Vellutini, Bruno Cossermelli; Marletaz, Ferdinand; Cetrangolo, Viviana; Cvetesic, Nevena; Thiel, Daniel; Henriet, Simon; Grau-Bové, Xavier; Carrillo-Baltodano, Allan M.; Gu, Wenjia; Kerbl, Alexandra; Marquez, Yamile; Bekkouche, Nicolas; Chourrout, Daniel; Gómez-Skarmeta, José Luis; Irimia, Manuel; Lenhard, Boris; Worsaae, Katrine; Hejnol, Andreas (Journal article; Peer reviewed, 2021)The causes and consequences of genome reduction in animals are unclear because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact ... -
A deep learning method for replicate-based analysis of chromosome conformation contacts using Siamese neural networks
Al-jibury, Ediem; King, James W. D.; Guo, Ya; Lenhard, Boris; Fisher, Amanda G.; Merkenschlager, Matthias; Rueckert, Daniel (Journal article; Peer reviewed, 2023)The organisation of the genome in nuclear space is an important frontier of biology. Chromosome conformation capture methods such as Hi-C and Micro-C produce genome-wide chromatin contact maps that provide rich data ... -
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) ... -
Functional annotation of human long noncoding RNAs via molecular phenotyping
Ramilowski, Jordan; Yip, Chiu Wai Mickey; Agrawal, Saumya; Chang, Jen-Chien; Ciani, Yari; Kulakovskiy, Ivan; Mendez, Mickaël; Ching Ooi, Jasmine Li; Ouyang, John F; Parkinson, Nick; Kasukawa, Takeya; Kauppinen, Sakari; Kere, Juha; Lenhard, Boris; Schneider, Claudio; Suzuki, Harukazu; Yagi, Ken; De Hoon, Michiel J L; Shin, Jay W; Piero, Carninci (Journal article; Peer reviewed, 2020)Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression ... -
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, 2010)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 ...