Chromatin architecture underpinning transcription elongation

References

• Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EE. Enhancer loops appear stable during development and are associated with paused polymerase. Nature 2014; 512:96-100; PMID:25043061
   PubMed Web of Science ®Google Scholar
• Ong CT, Corces VG. Enhancer function: New insights into the regulation of tissue-specific gene expression. Nat Rev Genet 2011; 12:283-93; PMID:21358745; http://dx.doi.org/10.1038/nrg2957
   PubMed Web of Science ®Google Scholar
• Mifsud B, Tavares-Cadete F, Young AN, Sugar R, Schoenfelder S, Ferreira L, Wingett SW, Andrews S, Grey W, Ewels PA, et al. Mapping long-range promoter contacts in human cells with high-resolution capture hi-C. Nat Genet 2015; 47:598-606; PMID:25938943; http://dx.doi.org/10.1038/ng.3286
   PubMed Web of Science ®Google Scholar
• Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature 2012; 489:109-13; PMID:22955621; http://dx.doi.org/10.1038/nature11279
   PubMed Web of Science ®Google Scholar
• Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 2013; 503:290-4; PMID:24141950
   PubMed Web of Science ®Google Scholar
• Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science 2002; 295:1306-11; PMID:11847345; http://dx.doi.org/10.1126/science.1067799
   PubMed Web of Science ®Google Scholar
• Cullen KE, Kladde MP, Seyfred MA. Interaction between transcription regulatory regions of prolactin chromatin. Science 1993; 261:203-6; PMID:8327891; http://dx.doi.org/10.1126/science.8327891
   PubMed Web of Science ®Google Scholar
• Hampsey M, Singh BN, Ansari A, Laine JP, Krishnamurthy S. Control of eukaryotic gene expression: Gene loops and transcriptional memory. Adv Enzyme Regul 2011; 51:118-25; PMID:21036187; http://dx.doi.org/10.1016/j.advenzreg.2010.10.001
   PubMedGoogle Scholar
• Tan-Wong SM, Zaugg JB, Camblong J, Xu Z, Zhang DW, Mischo HE, Ansari AZ, Luscombe NM, Steinmetz LM, Proudfoot NJ. Gene loops enhance transcriptional directionality. Science 2012; 338:671-5; PMID:23019609; http://dx.doi.org/10.1126/science.1224350
   PubMed Web of Science ®Google Scholar
• Casolari JM, Brown CR, Komili S, West J, Hieronymus H, Silver PA. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 2004; 117:427-39; PMID:15137937; http://dx.doi.org/10.1016/S0092-8674(04)00448-9
   PubMed Web of Science ®Google Scholar
• Brickner JH, Walter P. Gene recruitment of the activated INO1 locus to the nuclear membrane. PLoS Biol 2004; 2:e342; PMID:15455074; http://dx.doi.org/10.1371/journal.pbio.0020342
   PubMed Web of Science ®Google Scholar
• Taddei A, Van Houwe G, Hediger F, Kalck V, Cubizolles F, Schober H, Gasser SM. Nuclear pore association confers optimal expression levels for an inducible yeast gene. Nature 2006; 441:774-8; PMID:16760983; http://dx.doi.org/10.1038/nature04845
   PubMed Web of Science ®Google Scholar
• Schones DE, Zhao K. Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 2008; 9:179-91; PMID:18250624; http://dx.doi.org/10.1038/nrg2270
   PubMed Web of Science ®Google Scholar
• Shlyueva D, Stampfel G, Stark A. Transcriptional enhancers: From properties to genome-wide predictions. Nat Rev Genet 2014; 15:272-86; PMID:24614317; http://dx.doi.org/10.1038/nrg3682
   PubMed Web of Science ®Google Scholar
• Kim TK, Shiekhattar R. Architectural and functional commonalities between enhancers and promoters. Cell 2015; 162:948-59; PMID:26317464; http://dx.doi.org/10.1016/j.cell.2015.08.008
   PubMed Web of Science ®Google Scholar
• Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 2013; 503:290-4; PMID:24141950
   PubMed Web of Science ®Google Scholar
• Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 2014; 159:1665-80; PMID:25497547; http://dx.doi.org/10.1016/j.cell.2014.11.021
   PubMed Web of Science ®Google Scholar
• Mitchell JA, Fraser P. Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev 2008; 22:20-5; PMID:18172162; http://dx.doi.org/10.1101/gad.454008
   PubMed Web of Science ®Google Scholar
• Palstra RJ, Simonis M, Klous P, Brasset E, Eijkelkamp B, de Laat W. Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription. PLoS One 2008; 3(2):e1661; PMID:18286208
   PubMedGoogle Scholar
• Lee K, Hsiung CC, Huang P, Raj A, Blobel GA. Dynamic enhancer-gene body contacts during transcription elongation. Genes Dev 2015; 29:1992-7; PMID:26443845; http://dx.doi.org/10.1101/gad.255265.114
   PubMed Web of Science ®Google Scholar
• Larkin JD, Cook PR, Papantonis A. Dynamic reconfiguration of long human genes during one transcription cycle. Mol Cell Biol 2012; 32:2738-47; PMID:22586273; http://dx.doi.org/10.1128/MCB.00179-12
   PubMed Web of Science ®Google Scholar
• Carter D, Chakalova L, Osborne CS, Dai YF, Fraser P. Long-range chromatin regulatory interactions in vivo. Nat Genet 2002; 32:623-6; PMID:12426570; http://dx.doi.org/10.1038/ng1051
   PubMed Web of Science ®Google Scholar
• Tolhuis B, Palstra RJ, Splinter E, Grosveld F, de Laat W. Looping and interaction between hypersensitive sites in the active β-globin locus. Mol Cell 2002; 10:1453-65; PMID:12504019; http://dx.doi.org/10.1016/S1097-2765(02)00781-5
   PubMed Web of Science ®Google Scholar
• Jing H, Vakoc CR, Ying L, Mandat S, Wang H, Zheng X, Blobel GA. Exchange of GATA factors mediates transitions in looped chromatin organization at a developmentally regulated gene locus. Mol Cell 2008; 29:232-42; PMID:18243117; http://dx.doi.org/10.1016/j.molcel.2007.11.020
   PubMed Web of Science ®Google Scholar
• Cook PR. The organization of replication and transcription. Science 1999; 284:1790-5; PMID:10364545; http://dx.doi.org/10.1126/science.284.5421.1790
   PubMed Web of Science ®Google Scholar
• Papantonis A, Cook PR. Transcription factories: Genome organization and gene regulation. Chem Rev 2013; 113:8683-705; PMID:23597155; http://dx.doi.org/10.1021/cr300513p
   PubMed Web of Science ®Google Scholar
• Sutherland H, Bickmore WA. Transcription factories: Gene expression in unions? Nat Rev Genet 2009; 10:457-66; PMID:19506577; http://dx.doi.org/10.1038/nrg2592
   PubMed Web of Science ®Google Scholar
• Cisse II, Izeddin I, Causse SZ, Boudarene L, Senecal A, Muresan L, Dugast-Darzacq C, Hajj B, Dahan M, Darzacq X. Real-time dynamics of RNA polymerase II clustering in live human cells. Science 2013; 341:664-7; PMID:23828889; http://dx.doi.org/10.1126/science.1239053
   PubMed Web of Science ®Google Scholar
• Ghamari A, vande Corput MP, Thongjuea S, van Cappellen WA, van Ijcken W, van Haren J, Soler E, Eick D, Lenhard B, Grosveld FG. In vivo live imaging of RNA polymerase II transcription factories in primary cells. Genes Dev 2013; 27:767-77; PMID:23592796; http://dx.doi.org/10.1101/gad.216200.113
   PubMed Web of Science ®Google Scholar
• Larkin JD, Papantonis A, Cook PR, Marenduzzo D. Space exploration by the promoter of a long human gene during one transcription cycle. Nucleic Acids Res 2013; 41:2216-27; PMID:23303786; http://dx.doi.org/10.1093/nar/gks1441
   PubMed Web of Science ®Google Scholar
• Papantonis A, Larkin JD, Wada Y, Ohta Y, Ihara S, Kodama T, Cook PR. Active RNA polymerases: Mobile or immobile molecular machines? PLoS Biol 2010; 8:e1000419; PMID:20644712; http://dx.doi.org/10.1371/journal.pbio.1000419
   PubMed Web of Science ®Google Scholar
• Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS, et al. DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nat Genet 2013; 45:852-9; PMID:23793028; http://dx.doi.org/10.1038/ng.2677
   PubMed Web of Science ®Google Scholar
• Nagarajan S, Hossan T, Alawi M, Najafova Z, Indenbirken D, Bedi U, Taipaleenmaki H, Ben-Batalla I, Scheller M, Loges S, et al. Bromodomain protein BRD4 is required for estrogen receptor-dependent enhancer activation and gene transcription. Cell Rep 2014; 8:460-9; PMID:25017071; http://dx.doi.org/10.1016/j.celrep.2014.06.016
   PubMed Web of Science ®Google Scholar
• Kanno T, Kanno Y, LeRoy G, Campos E, Sun HW, Brooks SR, Vahedi G, Heightman TD, Garcia BA, Reinberg D, et al. BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones. Nat Struct Mol Biol 2014; 21:1047-57; PMID:25383670; http://dx.doi.org/10.1038/nsmb.2912
   PubMed Web of Science ®Google Scholar
• Wu T, Pinto HB, Kamikawa YF, Donohoe ME. The BET family member BRD4 interacts with OCT4 and regulates pluripotency gene expression. Stem Cell Reports 2015; 4:390-403; PMID:25684227; http://dx.doi.org/10.1016/j.stemcr.2015.01.012
   PubMed Web of Science ®Google Scholar
• Zippo A, Serafini R, Rocchigiani M, Pennacchini S, Krepelova A, Oliviero S. Histone crosstalk between H3S10ph and H4K16ac generates a histone code that mediates transcription elongation. Cell 2009; 138:1122-36; PMID:19766566; http://dx.doi.org/10.1016/j.cell.2009.07.031
   PubMed Web of Science ®Google Scholar
• Zhang W, Prakash C, Sum C, Gong Y, Li Y, Kwok JJ, Thiessen N, Pettersson S, Jones SJ, Knapp S, et al. Bromodomain-containing protein 4 (BRD4) regulates RNA polymerase II serine 2 phosphorylation in human CD4+ T cells. J Biol Chem 2012; 287:43137-55; PMID:23086925; http://dx.doi.org/10.1074/jbc.M112.413047
   PubMed Web of Science ®Google Scholar
• Song SH, Kim A, Ragoczy T, Bender MA, Groudine M, Dean A. Multiple functions of Ldb1 required for β-globin activation during erythroid differentiation. Blood 2010; 116:2356-64; PMID:20570862; http://dx.doi.org/10.1182/blood-2010-03-272252
   PubMed Web of Science ®Google Scholar
• De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei CL, Natoli G. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 2010; 8:e1000384; PMID:20485488; http://dx.doi.org/10.1371/journal.pbio.1000384
   PubMed Web of Science ®Google Scholar
• Schaaf CA, Kwak H, Koenig A, Misulovin Z, Gohara DW, Watson A, Zhou Y, Lis JT, Dorsett D. Genome-wide control of RNA polymerase II activity by cohesin. PLoS Genet 2013; 9:e1003382; PMID:23555293; http://dx.doi.org/10.1371/journal.pgen.1003382
   PubMed Web of Science ®Google Scholar
• Kellner WA, Van Bortle K, Li L, Ramos E, Takenaka N, Corces VG. Distinct isoforms of the drosophila Brd4 homologue are present at enhancers, promoters and insulator sites. Nucleic Acids Res 2013; 41:9274-83; PMID:23945939; http://dx.doi.org/10.1093/nar/gkt722
   PubMed Web of Science ®Google Scholar
• Lai F, Gardini A, Zhang A, Shiekhattar R. Integrator mediates the biogenesis of enhancer RNAs. Nature 2015; 525:399-403; PMID:26308897; http://dx.doi.org/10.1038/nature14906
   PubMed Web of Science ®Google Scholar
• Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, de la Chapelle AL, Heidemann M, Hintermair C, et al. Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol 2011; 18:956-63; PMID:21765417; http://dx.doi.org/10.1038/nsmb.2085
   PubMed Web of Science ®Google Scholar
• Szutorisz H, Dillon N, Tora L. The role of enhancers as centres for general transcription factor recruitment. Trends Biochem Sci 2005; 30:593-9; PMID:16126390; http://dx.doi.org/10.1016/j.tibs.2005.08.006
   PubMed Web of Science ®Google Scholar
• Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 2010; 465:182-7; PMID:20393465; http://dx.doi.org/10.1038/nature09033
   PubMed Web of Science ®Google Scholar
• Deng W, Lee J, Wang H, Miller J, Reik A, Gregory PD, Dean A, Blobel GA. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 2012; 149:1233-44; PMID:22682246; http://dx.doi.org/10.1016/j.cell.2012.03.051
   PubMed Web of Science ®Google Scholar
• Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong CT, Hookway TA, Guo C, Sun Y, et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 2013; 153:1281-95; PMID:23706625; http://dx.doi.org/10.1016/j.cell.2013.04.053
   PubMed Web of Science ®Google Scholar
• Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 2010; 467:430-5; PMID:20720539; http://dx.doi.org/10.1038/nature09380
   PubMed Web of Science ®Google Scholar
• Seitan VC, Hao B, Tachibana-Konwalski K, Lavagnolli T, Mira-Bontenbal H, Brown KE, Teng G, Carroll T, Terry A, Horan K, et al. A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation. Nature 2011; 476:467-71; PMID:21832993; http://dx.doi.org/10.1038/nature10312
   PubMed Web of Science ®Google Scholar
• Takahashi H, Parmely TJ, Sato S, Tomomori-Sato C, Banks CA, Kong SE, Szutorisz H, Swanson SK, Martin-Brown S, Washburn MP, et al. Human mediator subunit MED26 functions as a docking site for transcription elongation factors. Cell 2011; 146:92-104; PMID:21729782; http://dx.doi.org/10.1016/j.cell.2011.06.005
   PubMed Web of Science ®Google Scholar
• Allen BL, Taatjes DJ. The mediator complex: A central integrator of transcription. Nat Rev Mol Cell Biol 2015; 16:155-66; PMID:25693131; http://dx.doi.org/10.1038/nrm3951
   PubMed Web of Science ®Google Scholar
• Alipour E, Marko JF. Self-organization of domain structures by DNA-loop-extruding enzymes. Nucleic Acids Res 2012; 40:11202-12; PMID:23074191; http://dx.doi.org/10.1093/nar/gks925
   PubMed Web of Science ®Google Scholar
• Nasmyth K. Disseminating the genome: Joining, resolving, and separating sister chromatids during mitosis and meiosis. Annu Rev Genet 2001; 35:673-745; PMID:11700297; http://dx.doi.org/10.1146/annurev.genet.35.102401.091334
   PubMed Web of Science ®Google Scholar
• Sanborn AL, Rao SS, Huang SC, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Li J, et al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc Natl Acad Sci U S A 2015; 112:E6456-65; PMID:26499245; http://dx.doi.org/10.1073/pnas.1518552112
   PubMed Web of Science ®Google Scholar
• Dekker J, Mirny L. The 3D genome as moderator of chromosomal communication. Cell 2016; 164:1110-21; PMID:26967279; http://dx.doi.org/10.1016/j.cell.2016.02.007
   PubMed Web of Science ®Google Scholar
• Kim Y, Geiger JH, Hahn S, Sigler PB. Crystal structure of a yeast TBP/TATA-box complex. Nature 1993; 365:512-20; PMID:8413604; http://dx.doi.org/10.1038/365512a0
   PubMed Web of Science ®Google Scholar
• Yao J, Ardehali MB, Fecko CJ, Webb WW, Lis JT. Intranuclear distribution and local dynamics of RNA polymerase II during transcription activation. Mol Cell 2007; 28:978-90; PMID:18158896; http://dx.doi.org/10.1016/j.molcel.2007.10.017
   PubMed Web of Science ®Google Scholar