Literature DB >> 18369139

Gene regulation in the third dimension.

Job Dekker1.   

Abstract

Analysis of the spatial organization of chromosomes reveals complex three-dimensional networks of chromosomal interactions. These interactions affect gene expression at multiple levels, including long-range control by distant enhancers and repressors, coordinated expression of genes, and modification of epigenetic states. Major challenges now include deciphering the mechanisms by which loci come together and understanding the functional consequences of these often transient associations.

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Year:  2008        PMID: 18369139      PMCID: PMC2666883          DOI: 10.1126/science.1152850

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  24 in total

1.  Looping and interaction between hypersensitive sites in the active beta-globin locus.

Authors:  Bas Tolhuis; Robert Jan Palstra; Erik Splinter; Frank Grosveld; Wouter de Laat
Journal:  Mol Cell       Date:  2002-12       Impact factor: 17.970

2.  Long-range intrachromosomal interactions in the T helper type 2 cytokine locus.

Authors:  Charalampos G Spilianakis; Richard A Flavell
Journal:  Nat Immunol       Date:  2004-09-19       Impact factor: 25.606

Review 3.  Remote control of gene transcription.

Authors:  Adam G West; Peter Fraser
Journal:  Hum Mol Genet       Date:  2005-04-15       Impact factor: 6.150

4.  The three 'C' s of chromosome conformation capture: controls, controls, controls.

Authors:  Job Dekker
Journal:  Nat Methods       Date:  2006-01       Impact factor: 28.547

5.  Long-range directional movement of an interphase chromosome site.

Authors:  Chien-Hui Chuang; Anne E Carpenter; Beata Fuchsova; Terezina Johnson; Primal de Lanerolle; Andrew S Belmont
Journal:  Curr Biol       Date:  2006-04-18       Impact factor: 10.834

6.  Transient homologous chromosome pairing marks the onset of X inactivation.

Authors:  Na Xu; Chia-Lun Tsai; Jeannie T Lee
Journal:  Science       Date:  2006-01-19       Impact factor: 47.728

7.  Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation.

Authors:  Christian P Bacher; Michèle Guggiari; Benedikt Brors; Sandrine Augui; Philippe Clerc; Philip Avner; Roland Eils; Edith Heard
Journal:  Nat Cell Biol       Date:  2006-01-24       Impact factor: 28.824

8.  Capturing chromosome conformation.

Authors:  Job Dekker; Karsten Rippe; Martijn Dekker; Nancy Kleckner
Journal:  Science       Date:  2002-02-15       Impact factor: 47.728

9.  Interchromosomal associations between alternatively expressed loci.

Authors:  Charalampos G Spilianakis; Maria D Lalioti; Terrence Town; Gap Ryol Lee; Richard A Flavell
Journal:  Nature       Date:  2005-05-08       Impact factor: 49.962

Review 10.  Long-range control of gene expression: emerging mechanisms and disruption in disease.

Authors:  Dirk A Kleinjan; Veronica van Heyningen
Journal:  Am J Hum Genet       Date:  2004-11-17       Impact factor: 11.025

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  128 in total

1.  The fractal globule as a model of chromatin architecture in the cell.

Authors:  Leonid A Mirny
Journal:  Chromosome Res       Date:  2011-01       Impact factor: 5.239

2.  Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization.

Authors:  Iouri Chepelev; Gang Wei; Dara Wangsa; Qingsong Tang; Keji Zhao
Journal:  Cell Res       Date:  2012-01-24       Impact factor: 25.617

3.  Gammaretroviral vector integration occurs overwhelmingly within and near DNase hypersensitive sites.

Authors:  Mingdong Liu; Chang Long Li; George Stamatoyannopoulos; Michael O Dorschner; Richard Humbert; John A Stamatoyannopoulos; David W Emery
Journal:  Hum Gene Ther       Date:  2011-12-14       Impact factor: 5.695

Review 4.  Chromosome territories.

Authors:  Thomas Cremer; Marion Cremer
Journal:  Cold Spring Harb Perspect Biol       Date:  2010-03       Impact factor: 10.005

5.  Looping probabilities in model interphase chromosomes.

Authors:  Angelo Rosa; Nils B Becker; Ralf Everaers
Journal:  Biophys J       Date:  2010-06-02       Impact factor: 4.033

6.  Integrating one-dimensional and three-dimensional maps of genomes.

Authors:  Natalia Naumova; Job Dekker
Journal:  J Cell Sci       Date:  2010-06-15       Impact factor: 5.285

7.  Setdb1 histone methyltransferase regulates mood-related behaviors and expression of the NMDA receptor subunit NR2B.

Authors:  Yan Jiang; Mira Jakovcevski; Rahul Bharadwaj; Caroline Connor; Frederick A Schroeder; Cong L Lin; Juerg Straubhaar; Gilles Martin; Schahram Akbarian
Journal:  J Neurosci       Date:  2010-05-26       Impact factor: 6.167

Review 8.  Long Noncoding RNAs in Host-Pathogen Interactions.

Authors:  Federica Agliano; Vijay A Rathinam; Andrei E Medvedev; Sivapriya Kailasan Vanaja; Anthony T Vella
Journal:  Trends Immunol       Date:  2019-04-30       Impact factor: 16.687

9.  GATA transcription factors directly regulate the Parkinson's disease-linked gene alpha-synuclein.

Authors:  Clemens R Scherzer; Jeffrey A Grass; Zhixiang Liao; Imelda Pepivani; Bin Zheng; Aron C Eklund; Paul A Ney; Juliana Ng; Meghan McGoldrick; Brit Mollenhauer; Emery H Bresnick; Michael G Schlossmacher
Journal:  Proc Natl Acad Sci U S A       Date:  2008-07-31       Impact factor: 11.205

10.  A genome-wide screen for beta-catenin binding sites identifies a downstream enhancer element that controls c-Myc gene expression.

Authors:  Gregory S Yochum; Ryan Cleland; Richard H Goodman
Journal:  Mol Cell Biol       Date:  2008-10-13       Impact factor: 4.272

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