Enhancers and silencers: an integrated and simple model for their function

[1]  F. Grosveld,et al.  Enhancers and silencers: an integrated and simple model for their function , 2012, Epigenetics & Chromatin.

[2]  Ian M. Carr,et al.  The proteomes of transcription factories containing RNA polymerases I, II or III , 2011, Nature Methods.

[3]  Ryan K. Dale,et al.  RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. , 2011, Genes & development.

[4]  P. Scacheri,et al.  Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. , 2011, Genome research.

[5]  Douglas R Higgs,et al.  Polycomb eviction as a new distant enhancer function. , 2011, Genes & development.

[6]  W. V. van IJcken,et al.  The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. , 2011, Genes & development.

[7]  Howard Y. Chang,et al.  A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression , 2011, Nature.

[8]  R. Maeda,et al.  Gene expression in time and space: additive vs hierarchical organization of cis-regulatory regions. , 2011, Current opinion in genetics & development.

[9]  R. Shiekhattar,et al.  Long non-coding RNAs and enhancers. , 2011, Current opinion in genetics & development.

[10]  V. Corces,et al.  Enhancer function: new insights into the regulation of tissue-specific gene expression , 2011, Nature Reviews Genetics.

[11]  Scott T. Younger,et al.  Transcriptional gene silencing in mammalian cells by miRNA mimics that target gene promoters , 2011, Nucleic acids research.

[12]  C. Glass,et al.  Reprogramming Transcription via Distinct Classes of Enhancers Functionally Defined by eRNA , 2011, Nature.

[13]  Li M. Li,et al.  Long- and Short-Range Transcriptional Repressors Induce Distinct Chromatin States on Repressed Genes , 2011, Current Biology.

[14]  Daryl M. Gohl,et al.  Mechanism of Chromosomal Boundary Action: Roadblock, Sink, or Loop? , 2011, Genetics.

[15]  Giacomo Cavalli,et al.  A chromatin insulator driving three-dimensional Polycomb response element (PRE) contacts and Polycomb association with the chromatin fiber , 2011, Proceedings of the National Academy of Sciences.

[16]  J. Lawrence,et al.  The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules , 2011, Nature Structural &Molecular Biology.

[17]  V. Corces,et al.  Chromatin insulators: a role in nuclear organization and gene expression. , 2011, Advances in cancer research.

[18]  Mark Groudine,et al.  Functional and Mechanistic Diversity of Distal Transcription Enhancers , 2011, Cell.

[19]  D. Corey,et al.  Minireview: Switching on progesterone receptor expression with duplex RNA. , 2010, Molecular endocrinology.

[20]  Sohail Malik,et al.  The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation , 2010, Nature Reviews Genetics.

[21]  T. Derrien,et al.  Long Noncoding RNAs with Enhancer-like Function in Human Cells , 2010, Cell.

[22]  Peter Fraser,et al.  Organization of transcription. , 2010, Cold Spring Harbor perspectives in biology.

[23]  Yoshihiro Ohta,et al.  Active RNA Polymerases: Mobile or Immobile Molecular Machines? , 2010, PLoS biology.

[24]  Richard A Young,et al.  Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. , 2010, Molecular cell.

[25]  Peter R Cook,et al.  Genome architecture and the role of transcription , 2010, Current opinion in cell biology.

[26]  Jesse R. Raab,et al.  Insulators and promoters: closer than we think , 2010, Nature Reviews Genetics.

[27]  Hui Zhou,et al.  Deep Sequencing of Human Nuclear and Cytoplasmic Small RNAs Reveals an Unexpectedly Complex Subcellular Distribution of miRNAs and tRNA 3′ Trailers , 2010, PloS one.

[28]  J. Ragoussis,et al.  A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers , 2010, PLoS biology.

[29]  G. Kreiman,et al.  Widespread transcription at neuronal activity-regulated enhancers , 2010, Nature.

[30]  A. Agarwal,et al.  Sp1 Regulates Chromatin Looping between an Intronic Enhancer and Distal Promoter of the Human Heme Oxygenase-1 Gene in Renal Cells* , 2010, The Journal of Biological Chemistry.

[31]  Clifford A. Meyer,et al.  Nucleosome Dynamics Define Transcriptional Enhancers , 2010, Nature Genetics.

[32]  Christine Steinhoff,et al.  The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation. , 2010, Genes & development.

[33]  Peter R Cook,et al.  A model for all genomes: the role of transcription factories. , 2010, Journal of molecular biology.

[34]  Christopher D. Brown,et al.  A Comprehensive Map of Insulator Elements for the Drosophila Genome , 2010, PLoS genetics.

[35]  Jennifer A. Mitchell,et al.  Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells , 2010, Nature Genetics.

[36]  C. Verrijzer,et al.  EZH2-dependent chromatin looping controls INK4a and INK4b, but not ARF, during human progenitor cell differentiation and cellular senescence , 2009, Epigenetics & Chromatin.

[37]  Christel Krueger,et al.  Cohesin Is Required for Higher-Order Chromatin Conformation at the Imprinted IGF2-H19 Locus , 2009, PLoS genetics.

[38]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[39]  J. Rinn,et al.  Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression , 2009, Proceedings of the National Academy of Sciences.

[40]  Jessica Cande,et al.  Stalled Hox promoters as chromosomal boundaries. , 2009, Genes & development.

[41]  Wendy A. Bickmore,et al.  Transcription factories: gene expression in unions? , 2009, Nature Reviews Genetics.

[42]  Tobias A. Knoch,et al.  Fine-structured multi-scaling long-range correlations in completely sequenced genomes—features, origin, and classification , 2009, European Biophysics Journal.

[43]  Nathaniel D. Heintzman,et al.  Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.

[44]  D. Bartel.  MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[45]  F. Calero-Nieto,et al.  A Conserved Insulator That Recruits CTCF and Cohesin Exists between the Closely Related but Divergently Regulated Interleukin-3 and Granulocyte-Macrophage Colony-Stimulating Factor Genes , 2009, Molecular and Cellular Biology.

[46]  Peter R Cook,et al.  The role of specialized transcription factories in chromosome pairing. , 2008, Biochimica et biophysica acta.

[47]  Jeannie T. Lee,et al.  Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome , 2008, Science.

[48]  Xiyou Zhou,et al.  Dysregulated human renin expression in transgenic mice carrying truncated genomic constructs: evidence supporting the presence of insulators at the renin locus. , 2008, American journal of physiology. Renal physiology.

[49]  Christopher M. Vockley,et al.  Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus. , 2008, Genome research.

[50]  J. Steitz,et al.  Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production , 2008, The Journal of cell biology.

[51]  D. Thanos,et al.  Virus Infection Induces NF-κB-Dependent Interchromosomal Associations Mediating Monoallelic IFN-β Gene Expression , 2008, Cell.

[52]  P. Walker,et al.  Epigenetic modifications of SOX2 enhancers, SRR1 and SRR2, correlate with in vitro neural differentiation , 2008, Journal of neuroscience research.

[53]  Venky N. Iyer,et al.  Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation , 2008, PLoS genetics.

[54]  Tobias A. Knoch,et al.  The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions , 2008, Cell.

[55]  B. Chadwick,et al.  The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions , 2008, The Journal of experimental medicine.

[56]  H. Aburatani,et al.  Cohesin mediates transcriptional insulation by CCCTC-binding factor , 2008, Nature.

[57]  Stephan Sauer,et al.  Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms , 2008, Cell.

[58]  G. Blobel,et al.  Exchange of GATA factors mediates transitions in looped chromatin organization at a developmentally regulated gene locus. , 2008, Molecular cell.

[59]  Thomas Cremer,et al.  Light optical precision measurements of the active and inactive Prader-Willi syndrome imprinted regions in human cell nuclei. , 2008, Differentiation; research in biological diversity.

[60]  W. D. Laat,et al.  An evaluation of 3C-based methods to capture DNA interactions , 2007, Nature Methods.

[61]  T. Ono,et al.  Chromatin fine structure of the c-MYC insulator element/DNase I-hypersensitive site I is not preserved during mitosis , 2007, Proceedings of the National Academy of Sciences.

[62]  Howard Y. Chang,et al.  Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.

[63]  A. Feinberg.  Phenotypic plasticity and the epigenetics of human disease , 2007, Nature.

[64]  T. Cremer,et al.  Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions , 2007, Nature Reviews Genetics.

[65]  B. Steensel,et al.  Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C) , 2006, Nature Genetics.

[66]  G. Felsenfeld,et al.  Insulators: exploiting transcriptional and epigenetic mechanisms , 2006, Nature Reviews Genetics.

[67]  Wouter de Laat,et al.  CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. , 2006, Genes & development.

[68]  Richard Axel,et al.  Interchromosomal Interactions and Olfactory Receptor Choice , 2006, Cell.

[69]  P. Cook,et al.  A conserved organization of transcription during embryonic stem cell differentiation and in cells with high C value. , 2006, Molecular biology of the cell.

[70]  C. Allis,et al.  Mouse Polycomb Proteins Bind Differentially to Methylated Histone H3 and RNA and Are Enriched in Facultative Heterochromatin , 2006, Molecular and Cellular Biology.

[71]  R. Kamakaka,et al.  Chromatin insulators. , 2006, Annual review of genetics.

[72]  Michael M. Resch,et al.  High performance computing in science and engineering , 2005, 17th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD'05).

[73]  D. Corey,et al.  Inhibiting gene expression at transcription start sites in chromosomal DNA with antigene RNAs , 2005, Nature chemical biology.

[74]  D. Tuan,et al.  The HS2 enhancer of the beta-globin locus control region initiates synthesis of non-coding, polyadenylated RNAs independent of a cis-linked globin promoter. , 2005, Journal of molecular biology.

[75]  M. Groudine,et al.  Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. , 2005, Molecular cell.

[76]  D. Tuan,et al.  HS2 Enhancer Function Is Blocked by a Transcriptional Terminator Inserted between the Enhancer and the Promoter*[boxs] , 2004, Journal of Biological Chemistry.

[77]  F. Grosveld,et al.  The active spatial organization of the beta-globin locus requires the transcription factor EKLF. , 2004, Genes & development.

[78]  Cameron S. Osborne,et al.  Active genes dynamically colocalize to shared sites of ongoing transcription , 2004, Nature Genetics.

[79]  Richard A Flavell,et al.  Long-range intrachromosomal interactions in the T helper type 2 cytokine locus , 2004, Nature Immunology.

[80]  K. Morris,et al.  Small Interfering RNA-Induced Transcriptional Gene Silencing in Human Cells , 2004, Science.

[81]  F. Recillas-Targa,et al.  CTCF‐dependent enhancer blockers at the upstream region of the chicken α‐globin gene domain , 2004 .

[82]  Frank Grosveld,et al.  Spatial organization of gene expression: the active chromatin hub , 2003, Chromosome Research.

[83]  P. Cook.  Nongenic transcription, gene regulation and action at a distance , 2003, Journal of Cell Science.

[84]  Tobias A. Knoch,et al.  Towards a Holistic Understanding of the Human Genome by Determination and Integration of its Sequential and Three-Dimensional Organization , 2003 .

[85]  S. Tilghman,et al.  CTCF maintains differential methylation at the Igf2/H19 locus , 2003, Nature Genetics.

[86]  Erik Splinter,et al.  Looping and interaction between hypersensitive sites in the active beta-globin locus. , 2002, Molecular cell.

[87]  Cameron S. Osborne,et al.  Long-range chromatin regulatory interactions in vivo , 2002, Nature Genetics.

[88]  E. Geiduschek,et al.  The mechanism of transcriptional activation by the topologically DNA-linked sliding clamp of bacteriophage T4. , 2002, Journal of molecular biology.

[89]  Tobias Knoch,et al.  Approaching the three-dimensional organization of the human genome: structural-, scaling- and dynamic properties in the simulation of interphase chromosomes and cell nuclei, long-range correlations in complete genomes, in vivo quantification of the chromat , 2002 .

[90]  S. Tapscott,et al.  CTCF-binding sites flank CTG/CAG repeats and form a methylation-sensitive insulator at the DM1 locus , 2001, Nature Genetics.

[91]  R. Fournier,et al.  The 5' boundary of the human apolipoprotein B chromatin domain in intestinal cells. , 2001, Biochemistry.

[92]  T. Cremer,et al.  Chromosome territories, nuclear architecture and gene regulation in mammalian cells , 2001, Nature Reviews Genetics.

[93]  Shirley M. Tilghman,et al.  CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus , 2000, Nature.

[94]  J. Langowski,et al.  Three-Dimensional Organization of Chromosome Territories and the Human Cell Nucleus , 2000 .

[95]  M. Groudine,et al.  Looping versus linking: toward a model for long-distance gene activation. , 1999, Genes & development.

[96]  D. Jackson,et al.  Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III , 1999, The EMBO journal.

[97]  A. Pombo,et al.  Bridging the Resolution Gap: Imaging the Same Transcription Factories in Cryosections by Light and Electron Microscopy , 1999, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[98]  Jörg Langowski,et al.  Three-Dimensional Organization of Chromosome Territories and the Human Interphase Nucleus , 1998 .

[99]  A. Pombo,et al.  Regional and temporal specialization in the nucleus: a transcriptionally‐active nuclear domain rich in PTF, Oct1 and PIKA antigens associates with specific chromosomes early in the cell cycle , 1998, The EMBO journal.

[100]  M. Ptashne,et al.  Transcriptional activation by recruitment , 1997, Nature.

[101]  D. Jackson,et al.  The topology of transcription by immobilized polymerases. , 1996, Experimental cell research.

[102]  G. Felsenfeld,et al.  A 5′ element of the chicken β-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila , 1993, Cell.

[103]  J. Banerji,et al.  Expression of a β-globin gene is enhanced by remote SV40 DNA sequences , 1981, Cell.