Functional and Mechanistic Diversity of Distal Transcription Enhancers
Open accessAbstract
Biological differences among metazoans and between cell types in a given organism arise in large part due to differences in gene expression patterns. Gene-distal enhancers are key contributors to these expression patterns, exhibiting both sequence diversity and cell type specificity. Studies of long-range interactions indicate that enhancers are often important determinants of nuclear organization, contributing to a general model for enhancer function that involves direct enhancer-promoter contact. However, mechanisms for enhancer function are emerging that do not fit solely within such a model, suggesting that enhancers as a class of DNA regulatory element may be functionally and mechanistically diverse.
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Active and primed enhancers are marked by H3K4me1 in a cell type-specific manner.
“In mammalian cells, active and primed enhancers are marked by monomethylation of histone 3 (H3) at lysine 4 (K4) (H3K4me1) in a cell type-specific manner.”
From HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements (2024) · cites this paper as [29]
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References 128 · Cited by 803
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- Andrulis ED Neiman AM Zappulla DC Sternglanz R 1998 Perinuclear localization of chromatin facilitates transcriptional silencing Nature 394 592 595 9707122
- Banerji J Rusconi S Schaffner W 1981 Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences Cell 27 299 308 6277502
- Banerji J Olson L Schaffner W 1983 A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes Cell 33 729 740 6409418
- Blackwood EM Kadonaga JT 1998 Going the distance: a current view of enhancer action Science 281 60 63 9679020
- Blow MJ McCulley DJ Li Z Zhang T Akiyama JA Holt A Plajzer-Frick I Shoukry M Wright C Chen F Afzal V Bristow J Ren B Black BL Rubin EM Visel A Pennacchio LA 2010 ChIP-Seq identification of weakly conserved heart enhancers Nat Genet 42 806 810 20729851 PMC3138496
- Branco MR Pombo A 2007 Chromosome organization: new facts, new models Curr Biol 17 127 134 17197184
- Brown JM Green J das Neves RP Wallace HA Smith AJ Hughes J Gray N Taylor S Wood WG Higgs DR Iborra FJ Buckle VJ 2008 Association between active genes occurs at nuclear speckles and is modulated by chromatin environment J Cell Biol 182 1083 1097 18809724 PMC2542471
- Bulger M Groudine M 1999 Looping versus linking: toward a model for longdistance gene activation Genes Dev 13 2465 2477 10521391
- Butler JE Kadonaga JT 2001 Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs Genes Dev 15 2515 2519 11581157 PMC312797
- Cai S Han HJ Kohwi-Shigematsu T 2003 Tissue-specific nuclear architecture and gene expression regulated by SATB1 Nat Genet 34 42 51 12692553
- Cai S Lee CC Kohwi-Shigematsu T 2006 SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes Nat Genet 38 1278 1288 17057718
- Calhoun VC Levine M 2003 Long-range enhancer-promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex Proc Natl Acad Sci USA 100 9878 9883 12909726 PMC187872
- Calhoun VC Stathopoulos A Levine M 2002 Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex Proc Natl Acad Sci USA 99 9243 9247 12093913 PMC123125
- Chan YF Marks ME Jones FC Villarreal G Jr Shapiro MD Brady SD Southwick AM Absher DM Grimwood J Schmutz J Myers RM Petrov D Jónsson B Schluter D Bell MA Kingsley DM 2010 Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer Science 327 302 305 20007865 PMC3109066
- Chaturvedi CP Hosey AM Palii C Perez-Iratxeta C Nakatani Y Ranish JA Dilworth FJ Brand M Dual role for the methyltransferase G9a in the maintenance of beta-globin gene transcription in adult erythroid cells Proc Natl Acad Sci USA 106 18303 18308 19822740 PMC2775297
- Cosma MP Tanaka T Nasmyth K 1999 Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter Cell 97 299 311 10319811
- Cremer T Cremer M 2010 Chromosome territories Cold Spring Harbor Perspect Bio 2 a003889 PMC2829961 20300217
- Crawford GE Davis S Scacheri PC Renaud G Halawi MJ Erdos MR Green R Meltzer PS Wolfsberg TG Collins FS 2006 DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays Nat Methods 3 503 509 16791207 PMC2698431
- Creyghton MP Cheng AW Welstead GG Kooistra T Carey BW Steine EJ Hanna J Lodato MA Frampton GM Sharp PA Boyer LA Young RA Jaenisch R 2010 Histone H3K27ac separates active from poised enhancers and predicts developmental state Proc Natl Acad Sci USA 107 21931 21936 21106759 PMC3003124
- Cullen KE Kladde MP Seyfred MA 1993 Interaction between transcription regulatory regions of prolactin chromatin Science 261 203 206 8327891
- de Bruin D Zaman Z Liberatore RA Ptashne M 2001 Telomere looping permits gene activation by a downstream UAS in yeast Nature 409 109 113 11343124
- Dekker J Rippe K Dekker M Kleckner N 2002 Capturing chromosome conformation Science 295 1306 1311 11847345
- de Kok YJ Vossenaar ER Cremers CW Dahl N Laporte J Hu LJ Lacombe D Fischel-Ghodsian N Friedman RA Parnes LS Thorpe P Bitner-Glindzicz M Pander HJ Heilbronner H Graveline J den Dunnen JT Brunner HG Ropers HH Cremers FP 1996 Identification of a hot spot for microdeletions in patients with X-linked deafness type 3 (DFN3) 900 kb proximal to the DFN3 gene POU3F4 Hum Mol Genet 5 1229 1235 8872461
- de Laat W Klous P Kooren J Noordermeer D Palstra RJ Simonis M Splinter E Grosveld F 2008 Three-dimensional organization of gene expression in erythroid cells Curr, Top, Dev, Biol 82 117 139 18282519
- Demers C Chaturvedi CP Ranish JA Juban G Lai P Morle F Aebersold R Dilworth FJ Groudine M Brand M 2007 Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus Mol Cell 27 573 584 17707229 PMC2034342
- Dobi KC Winston F 2007 Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae Mol Cell Biol 27 5575 5586 17526727 PMC1952096
- Dorsett D 1999 Distant liaisons: long-range enhancer-promoter interactions in Drosophila Curr Opin Genet Dev 9 505 514 10508687
- Dostie J Richmond TA Arnaout RA Selzer RR Lee WL Honan TA Rubio ED Krumm A Lamb J Nusbaum C Green RD Dekker J 2006 Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements Genome Res 16 1299 1309 16954542 PMC1581439
- Drissen R Palstra RJ Gillemans N Splinter E Grosveld F Philipsen S de Laat W 2004 The active spatial organization of the beta-globin locus requires the transcription factor EKLF Genes Dev 18 2485 2490 15489291 PMC529536
- Elgin SC 1988 The formation and function of DNaseI hypersensitive sites in the process of gene activation J Biol Chem 263 19259 19262 3198625
- Emison ES McCallion AS Kashuk CS Bush RT Grice E Lin S Portnoy ME Cutler DJ Green ED Chakravarti A 2005 A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk Nature 434 857 863 15829955
- ENCODE Project Consortium 2007 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 447 799 816 17571346 PMC2212820
- Ferrai C de Castro IJ Lavitas L Chotalia M Pombo A Gene positioning Cold Spring Harbor Perspect Biol 2 a000588 PMC2869523 20484389
- Finlan LE Sproul D Thomson I Boyle S Kerr E Perry P Ylstra B Chubb JR Bickmore WA 2008 Recruitment to the nuclear periphery can alter expression of genes in human cells PLoS Genet 4 e1000039 18369458 PMC2265557
- Francastel C Walters MC Groudine M Martin DI 1999 A functional enhancer suppresses silencing of a transgene and prevents its localization close to centrometric heterochromatin Cell 29 259 969 10555142
- Gillies SD Morrison SL Oi VT Tonegawa S 1983 A tissue-specific transcription enhancer element is located in the major intron of a rearranged immunoglobulin heavy chain gene Cell 33 717 728 6409417
- Gross DS Garrard WT 1988 Nuclease hypersensitive sites in chromatin Annu Rev Biochem 57 159 197 3052270
- Grosveld F van Assendelft GB Greaves DR Kollias G 1987 Position-independent, high-level expression of the human beta-globin gene in transgenic mice Cell 51 975 985 3690667
- Hardison R Slightom JL Gumucio DL Goodman M Stojanovic N Miller W 1997 Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights Gene 205 73 94 9461381
- Hare EE Peterson BK Iyer VN Meier R Eisen MB 2008 Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation PLoS Genet 4 e1000106 18584029 PMC2430619
- Ho Y Elefant F Cooke N Liebhaber S 2002 A defined locus control region determinant links chromatin domain acetylation with long-range gene activation Mol Cell 9 291 302 11864603
- Ho Y Elefant F Liebhaber SA Cooke NE Locus control region transcription plays an active role in long-range gene activation Mol Cell 23 365 375 16885026
- Holmes SG Broach JR 1996 Silencers are required for inheritance of the repressed state in yeast Genes Dev 10 1021 1032 8608937
- Hou C Dale R Dean A 2010 Cell type specificity of chromatin organization mediated by CTCF and cohesin Proc Natl Acad Sci USA 107 3651 3656 20133600 PMC2840441
- Iborra FJ Pombo A Jackson DA Cook PR 1996 Active RNA polymerases are localized within discrete transcription “factories” in human nuclei J Cell Sci 109 1427 1436 8799830
- Juven-Gershon R Hsu JY Kadonaga JT 2008 Caudal, a key developmental regulator, is a DPE-specific transcriptional factor Genes Dev 22 2823 2830 18923080 PMC2569877
- Kim A Zhao H Ifrim I Dean A 2007 Beta-globin intergenic transcription and histone acetylation dependent on an enhancer Mol Cell Biol 27 2980 2986 17283048 PMC1899946
- Kim E Magen A Ast G 2006 Different levels of alternative splicing among eukaryotes Nucl Acids Res 35 125 131 17158149 PMC1802581
- Kleinjan DA van Heyningen V 2005 Long-range control of gene expression: emerging mechanisms and disruption in disease Am J Hum Genet 76 8 32 15549674 PMC1196435
- Koch CM Andrews RM Flicek P Dillon SC Karaöz U Clelland GK Wilcox S Beare DM Fowler JC Couttet P James KD Lefebvre GC Bruce AW Dovey OM Ellis PD Dhami P Langford CF Weng Z Birney E Carter NP Vetrie D Dunham I 2007 The landscape of histone modifications across 1% of the human genome in five human cell lines Genome Res 17 691 707 17567990 PMC1891331
- Koch F Jourquin F Ferrier P Andrau JC 2008 Genome-wide RNA polymerase II: not genes only! Trends Biochem Sci 33 265 273 18467100
- Krebs JE Kuo MH Allis CD Peterson CL 1999 Cell cycle-regulated histone acetylation required for expression of the yeast HO gene Genes Dev 13 1412 1421 10364158 PMC316758
- Kurukuti S Tiwari VK Tavoosidana G Pugacheva E Murrell A Zhao Z Lobanenkov V Reik W Ohlsson R 2006 CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2 Proc Natl Acad Sci USA 103 10684 10689 16815976 PMC1484419
- Leach KM Nightingale K Igarashi K Levings PP Engel JD Becker PB Bungert J 2001 Reconstitution of human beta-globin locus control region hypersensitive sites in the absence of chromatin assembly Mol Cell Biol 21 2629 2640 11283243 PMC86894
- Levine M 2010 Transcriptional enhancers in animal development and evolution Curr Biol 20 R754 R763 20833320 PMC4280268
- Liber D Domaschenz R Holmqvist PH Mazzarella L Georgiou A Leleu M Fisher AG Labosky PA Dillon N 2010 Epigenetic priming of a pre-B cell-specific enhancer through binding of Sox2 and Foxd3 at the ESC stage Cell Stem Cell 7 114 126 20621055
- Lieberman-Aiden E van Berkum NL Williams L Imakaev M Ragoczy T Telling A Amit I Lajoie BR Sabo PJ Dorschner MO Sandstrom R Bernstein B Bender MA Groudine M Gnirke A Stamatoyannopoulos J Mirny LA Lander ES Dekker J 2009 Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 289 93 10 19815776 PMC2858594
- Chromosoma 2008 4 117 2 137 45 Epub 2007 Nov 17994318
- Melnikova L Kostuchenko M Silicheva M Georgiev P 2008 Drosophila gypsy insulator and yellow enhancers regulate activity of yellow promoter through the same regulatory element Chromosoma 117 137 145 17994318
- Miele A Dekker J 2008 Long-range chromosomal interactions and gene regulation Mol Biosyst 4 1046 1057 18931780 PMC2653627
- Miele A Dekker J 2009 Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C) Methods Mol Biol 464 105 121 18951182 PMC3874836
- Moon AM Ley TJ 1990 Conservation of the primary structure, organization, and function of the human and mouse beta-globin locus-activating regions Proc Natl Acad Sci U S A 87 7693 7697 2217202 PMC54814
- McGaughey DM Vinton RM Huynh J Al-Saif A Beer MA McCallion AS 2008 Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b Genome Res 18 252 260 18071029 PMC2203623
- Moen PT Johnson CV Byron M Shopland LS de la Serna IL Imbalzano AN Lawrence JB 2004 Repositioning of muscle-specific genes relative to the periphery of SC-35 domains during skeletal myogenesis Mol Cell Biol 15 197 206 PMC307540 14617810
- Moreau P Hen R Wasylyk B Everett R Gaub MP Chambon P 1981 The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants Nucleic Acids Res 9 6047 6068 6273820 PMC327583
- Morrow BE Johnson SP Warner JR 1993 The rRNA enhancer regulates rRNA transcription in Saccharomyces cerevisiae Mol Cell Biol 13 1283 1289 8423793 PMC359013
- Neigeborn L Warner JR 1990 Expression of yeast 5S RNA is independent of the rDNA enhancer region Nucl Acids Res 18 4179 4184 2198535 PMC331176
- Noonan JP 2009 Regulatory DNAs and the evolution of human development Curr Opin Genet Dev 19 557 564 19913404
- Noonan JP McCallion AS 2010 Genomics of long-range regulatory elements Annu Rev Genomics Hum Genet 11 1 23 20438361
- Noordermeer D Branco MR Splinter E Klous P van Ijcken W Swagemakers S Koutsourakis M van der Spek P Pombo A de Laat W 2008 Transcription and chromatin organization of a housekeeping gene cluster containing an integrated beta-globin locus control region PLoS Genet 4 e1000016 18369441 PMC2265466
- Ohtsuki S Levine M Cai HN 1998 Different core promoters possess distinct regulatory activities in the Drosophila embryo Genes Dev 12 547 556 9472023 PMC316525
- Orom UA Derrien T Beringer M Gumireddy K Gardini A Bussotti G Lai F Zytnicki M Notredame C Huang Q Guigo R Shiekhattar R 2010 Long Noncoding RNAs with Enhancer-like Function in Human Cells Cell 143 46 58 20887892 PMC4108080
- Osborne CS Chakalova L Brown KE Carter D Horton A Debrand E Goyenechea B Mitchell JA Lopes S Reik W Fraser P 2004 Active genes dynamically colocalize to shared sites of ongoing transcription Nat Genet 36 1065 1071 15361872
- Pant V Kurukuti S Pugacheva E Shamsuddin S Mariano P Renkawitz R Klenova E Lobanenkov V Ohlsson R 2004 Mutation of a single CTCF target site within the H19 imprinting control region leads to loss of Igf2 imprinting and complex patterns of de novo methylation upon maternal inheritance Mol Cell Biol 24 3497 3504 15060168 PMC381662
- Petrascheck M Escher D Mahmoudi T Verrijzer CP Schaffner W Barberis A 2005 DNA looping induced by a transcriptional enhancer in vivo Nucl Acids Res 33 3743 3750 16002789 PMC1174898
- Pollard KS Salama SR Lambert N Lambot MA Coppens S Pedersen JS Katzman S King B Onodera C Siepel A Kern AD Dehay C Igel H Ares M Jr Vanderhaeghen P Haussler D 2006 An RNA gene expressed during cortical development evolved rapidly in humans Nature 443 167 172 16915236
- Prabhakar S Noonan JP Pääbo S Rubin E 2006 Accelerated evolution of conserved noncoding sequences in humans Science 314 786 17082449
- Prabhakar S Visel A Akiyama JA Shoukry M Lewis KD Holt A Plajzer-Frick I Morrison H Fitzpatrick DR Afzal V Pennacchio LA Rubin EM Noonan JP 2008 Human-specific gain of function in a developmental enhancer Science 321 1346 1350 18772437 PMC2658639
- Ptashne M 1986 Gene regulation by proteins acting nearby and at a distance Nature 322 697 701 3018583
- Ragoczy T Telling A Sawado T Groudine M Kosak ST 2003 A genetic analysis of chromosome territory looping: diverse roles for distal regulatory elements Chromosome Res 11 513 525 12971726
- Ragoczy T Bender MA Telling A Byron R Groudine M 2006 The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation Genes Dev 20 1447 1457 16705039 PMC1475758
- Rebeiz M Pool JE Kassner VA Aquadro CF Carroll SB 2009 Stepwise modification of a modular enhancer underlies adaptation in a Drosphila population Science 326 1663 1667 20019281 PMC3363996
- Reddy KL Zullo JM Bertolino E Singh H 2008 Transcriptional repression mediated by repositioning of genes to the nuclear lamina Nature 452 243 247 18272965
- Rollins RA Morcillo P Dorsett D 1999 Nipped-B, a Drosophila homologue of chromosomal adherins, participates in activation by remote enhancers in the cut and Ultrabithorax genes Genetics 152 577 593 10353901 PMC1460629
- Rusche LN Kirchmaier AL Rine J 2003 The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae Annu Rev Biochem 72 481 516 12676793
- Sagai T Hosoya M Mizushina Y Tamura M Shiroishi T 2005 Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb Development 132 797 803 15677727
- Sawado T Halow J Bender MA Groudine M 2003 The beta -globin locus control region (LCR) functions primarily by enhancing the transition from transcription initiation to elongation Genes Dev 17 1009 1018 12672691 PMC196035
- Schmidt D Wilson MD Ballester B Schwalie PC Brown GD Marshall A Kutter C Watt S Martinez-Jimenez CP Mackay S Talianidis I Flicek P Odom DT 2010 Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding Science 328 1036 1040 20378774 PMC3008766
- Schoenfelder S Sexton T Chakalova L Cope NF Horton A Andrews S Kurukuti S Mitchell JA Umlauf D Dimitrova DS Eskiw CH Luo Y Wei CL Ruan Y Bieker JJ Fraser P 2010 Preferential associations between coregulated genes reveal a transcriptional interactome in erythroid cells Nat Genet 42 53 61 20010836 PMC3237402
- Simonis M Klous P Splinter E Moshkin Y Willemsen R de Wit E van Steensel B de Laat W 2006 Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C) Nature Genet 38 1348 1354 17033623
- Splinter E Heath H Kooren J Palstra RJ Klous P Grosveld F Galjart N de Laat W 2006 CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus Genes Dev 20 2349 2354 16951251 PMC1560409
- Stamatoyannopoulos JA Goodwin A Joyce T Lowrey CH 1995 NF-E2 and GATA binding motifs are required for the formation of DNase I hypersensitive site 4 of the human beta-globin locus control region EMBO J 14 106 116 7828582 PMC398057
- Sutherland H Bickmore WA 2009 Transcription factories: gene expression in unions? Nature Rev Genet 10 457 466 19506577
- Swanson CI Evans NC Barolo S 2010 Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer Dev Cell 18 359 370 20230745 PMC2847355
- Taddei A 2007 Active genes at the nuclear pore complex Curr Opin Cell Biol 19 305 310 17467257
- Talbert PB Henikoff S 2006 Spreading of silent chromatin: inaction at a distance Nature Rev Genet 7 793 803 16983375
- Vakoc CR Letting DL Gheldof N Sawado T Bender MA Groudine M Weiss MJ Dekker J Blobel GA 2005 Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1 Mol Cell 17 453 462 15694345
- Valenzuela L Dhillon N Dubey RN Gartenberg MR Kamakaka RT 2008 Long-range communication between the silencers of HMR Mol Cell Biol 28 1924 1935 18195043 PMC2268393
- Visel A Blow MJ Li Z Zhang T Akiyama JA Holt A Plajzer-Frick I Shoukry M Wright C Chen F Afzal V Ren B Rubin EM Pennacchio LA 2009 ChIP-seq accurately predicts tissue-specific activity of enhancers Nature 457 854 858 19212405 PMC2745234
- Visel A Rubin EM Pennacchio LA 2009 Genomic views of distant-acting enhancers Nature 461 199 205 19741700 PMC2923221
- Wai H Johzuka K Vu L Eliason K Kobayashi T Horiuchi T Nomura M 2001 Yeast RNA polymerase I enhancer is dispensable for transcription of the chromosomal rRNA gene and cell growth, and its apparent transcription enhancement from ectopic promoters requires Fob1 protein Mol Cell Biol 21 5541 5553 11463836 PMC87276
- Wilson MD Barbosa-Morais NL Schmidt D Conboy CM Vanes L Tybulewicz VLJ Fisher EMC Tavare S Odom DT 2008 Species-specific transcription in mice carrying human chromosome 21 Science 322 434 438 18787134 PMC3717767
- Wu C 1980 The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNaseI Nature 286 854 860 6774262
- Xi H Shulha HP Lin JM Vales TR Fu Y Bodine DM McKay RD Chenoweth JG Tesar PJ Furey TS Ren B Weng Z Crawford GE 2007 Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome PLoS Genet 3 e136 17708682 PMC1950163
- Xu H Hoover TR 2001 Transcriptional regulation at a distance in bacteria Curr Opin Microbiol 4 138 144 11282468
- Xu J Watts JA Pope SD Gadue P Kamps M Plath K Zaret KS Smale ST 2009 Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells Genes Dev 23 2824 2838 20008934 PMC2800090
- Xu M Cook PR 2008 Similar active genes cluster in specialized transcription factories J Cell Biol 181 615 623 18490511 PMC2386102
- Yusufzai TM Tagami H Nakatani Y Felsenfeld G 2004 CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species Mol Cell 13 291 298 14759373
- Zhao Z Tavoosidana G Sjölinder M Göndör A Mariano P Wang S Kanduri C Lezcano M Sandhu KS Singh U Pant V Tiwari V Kurukuti S Ohlsson R 2006 Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions Nature Genet 38 1341 1347 17033624
- Zhu X Ling J Zhang L Pi W Wu M Tuan D 2007 A facilitated tracking and transcription mechanism of long-range enhancer function Nucl Acids Res 35 5532 5544 17704132 PMC2018613
- Authors
- Bulger, M., & Groudine, M.
- Affiliations
- University of Rochester Medicine (US)
- University of Washington (US)
- Corresponding author
- Bulger, Michael
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2011-02
- Volume
- 144
- Issue
- 3
- Pages
- 327-339
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3742076
- OpenAlex
- W2036619779
- Cited by
- 803
- References
- 128
- Citations by year
- 2026: 25 · 2025: 33 · 2024: 39 · 2023: 41 · 2022: 40 · 2021: 50 · 2020: 43 · 2019: 47 · 2018: 54 · 2017: 49 · 2016: 62 · 2015: 86 · 2014: 74 · 2013: 75 · 2012: 57
- FWCI
- 6.82
- Type
- journal article
- Language
- en
- Update notices
- erratum (2011-03-04)
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Heart, Lung, and Blood Institute (R01HL065440)
- National Institute of Diabetes and Digestive and Kidney Diseases (R37DK044746, R01DK070687)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- distal enhancers, gene expression regulation, enhancer-promoter interactions, long-range chromatin interactions, nuclear organization, cell type specificity, animal evolution, DNA regulatory elements
- MeSH terms
- Animals, Chromatin, Enhancer Elements, Genetic, Gene Expression Regulation, Humans, Promoter Regions, Genetic, Transcription Factors, Transcription, Genetic
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