Transcription regulation by distal enhancers: Who's in the loop?

Transcription

Volumn 3, Issue 4, 2012, Pages

  Stadhouders, Ralph ^a   van den Heuvel, Anita ^a   Kolovos, Petros ^a   Jorna, Ruud ^a   Leslie, Kris ^a   Grosveld, Frank ^a   Soler, Eric ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

Chromatin looping; Chromosome conformation capture; Enhancer; Long range interactions; Myb; Transcription elongation; Transcription regulatory networks

Indexed keywords

BETA GLOBIN; CYCLIN DEPENDENT KINASE 9; PROTEIN LDB1; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GATA 1; TRANSCRIPTION FACTOR GATA 2; TRANSCRIPTION FACTOR RUNX1; TRANSCRIPTION FACTOR TAL1; UNCLASSIFIED DRUG;

BETA THALASSEMIA; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; CTCF GENE; ENHANCER REGION; GENE; GENE EXPRESSION REGULATION; GENE INTERACTION; GENE LOCUS; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; GENOME ANALYSIS; HISTONE MODIFICATION; HUMAN; NONHUMAN; ONCOGENE C KIT; ONCOGENE MYB; PROMOTER REGION; REGULATORY SEQUENCE; REVIEW; RNA TRANSLATION; SEQUENCE ANALYSIS; SICKLE CELL ANEMIA; SINGLE NUCLEOTIDE POLYMORPHISM; TISSUE SPECIFICITY; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION; ANIMAL; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENETIC TRANSCRIPTION; GENOME; TRANSCRIPTION ELONGATION;

ANIMALS; CHROMATIN ASSEMBLY AND DISASSEMBLY; ENHANCER ELEMENTS, GENETIC; GENE EXPRESSION REGULATION; GENOME; HUMANS; TRANSCRIPTION ELONGATION, GENETIC; TRANSCRIPTION, GENETIC;

EID: 84864081597     PISSN: 21541264     EISSN: 21541272     Source Type: Journal    
DOI: 10.4161/trns.20720     Document Type: Review

References (38)

1. Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, et al. H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J 2011; 30:4198-210; PMID:21847099; http://dx.doi.org/10.1038/emboj.2011.295.
2. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 2009; 459:108-12; PMID:19295514; http://dx.doi.org/10.1038/nature07829.
3. Koch F, Andrau JC. Initiating RNA polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity. Transcription 2011; 2:263-8; PMID:22223044; http://dx.doi.org/10.4161/trns.2.6.18747.
4. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 2009; 457:854-8; PMID:19212405; http://dx.doi.org/10.1038/nature07730.
5. Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 2011; 146:1016-28; PMID:21925322; http://dx.doi.org/10.1016/j.cell.2011.08.008.
6. Soler E, Andrieu-Soler C, de Boer E, Bryne JC, Thongjuea S, Stadhouders R, et al. The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation. Genes Dev 2010; 24:277-89; PMID:20123907; http://dx.doi.org/10.1101/gad.551810.
7. Wilson NK, Foster SD, Wang X, Knezevic K, Schütte J, Kaimakis P, et al. Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators. Cell Stem Cell 2010; 7:532-44; PMID:20887958; http://dx.doi.org/10.1016/j.stem.2010.07.016.
8. Snow JW, Trowbridge JJ, Fujiwara T, Emambokus NE, Grass JA, Orkin SH, et al. A single cis element maintains repression of the key developmental regulator Gata2. PLoS Genet 2010; 6; PMID:20838598; http://dx.doi.org/10.1371/journal.pgen.1001103.
9. Stadhouders R, Thongjuea S, Andrieu-Soler C, Palstra RJ, Bryne JC, van den Heuvel A, et al. Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development. EMBO J 2012; 31:986-99; PMID:22157820; http://dx.doi.org/10.1038/emboj.2011.450.
10. Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 2010; 328:1036-40; PMID:20378774; http://dx.doi.org/10.1126/science.1186176.
11. Visel A, Rubin EM, Pennacchio LA. Genomic views of distant-acting enhancers. Nature 2009; 461:199-205; PMID:19741700; http://dx.doi.org/10.1038/nature08451.
12. Thein SL, Menzel S, Lathrop M, Garner C. Control of fetal hemoglobin: new insights emerging from genomics and clinical implications. Hum Mol Genet 2009; 18:216-23; PMID:19808799; http://dx.doi.org/10.1093/hmg/ddp401.
13. Visser M, Kayser M, Palstra RJ. HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter. Genome Res 2012; 22:446-55; PMID:22234890; http://dx.doi.org/10.1101/gr.128652.111.
14. Sagai T, Hosoya M, Mizushina Y, Tamura M, Shiroishi T. Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb. Development 2005; 132:797-803; PMID:15677727; http://dx.doi.org/10.1242/dev.01613.
15. Lettice LA, Heaney SJ, Purdie LA, Li L, de Beer P, Oostra BA, et al. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet 2003; 12:1725-35; PMID:12837695; http://dx.doi.org/10.1093/hmg/ddg180.
16. Montavon T, Soshnikova N, Mascrez B, Joye E, Thevenet L, Splinter E, et al. A regulatory archipelago controls Hox genes transcription in digits. Cell 2011; 147:1132-45; PMID:22118467; http://dx.doi.org/10.1016/j.cell.2011.10.023.
17. Ruf S, Symmons O, Uslu VV, Dolle D, Hot C, Ettwiller L, et al. Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nat Genet 2011; 43:379-86; PMID:21423180; http://dx.doi.org/10.1038/ng.790.
18. 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.
19. de Wit E, de Laat W. A decade of 3C technologies: insights into nuclear organization. Genes Dev 2012; 26:11-24; PMID:22215806; http://dx.doi.org/10.1101/gad.179804.111.
20. Palstra RJ, Tolhuis B, Splinter E, Nijmeijer R, Grosveld F, de Laat W. The beta-globin nuclear compartment in development and erythroid differentiation. Nat Genet 2003; 35:190-4; PMID:14517543; http://dx.doi.org/10.1038/ng1244.
21. Ramsay RG, Gonda TJ. MYB function in normal and cancer cells. Nat Rev Cancer 2008; 8:523-34; PMID:18574464; http://dx.doi.org/10.1038/nrc2439.
22. Jing H, Vakoc CR, Ying L, Mandat S, Wang H, Zheng X, et al. 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.
23. Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, Duboule D. The dynamic architecture of Hox gene clusters. Science 2011; 334:222-5; PMID:21998387; http://dx.doi.org/10.1126/science.1207194.
24. Kolovos P, Knoch TA, Grosveld FG, Cook PR, Papantonis A. Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin 2012; 5:1; PMID:22230046; http://dx.doi.org/10.1186/1756-8935-5-1.
25. 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.
26. Ribeiro de Almeida C, Stadhouders R, de Bruijn MJ, Bergen IM, Thongjuea S, Lenhard B, et al. The DNA-binding protein CTCF limits proximal Vκ recombination and restricts κ enhancer interactions to the immunoglobulin κ light chain locus. Immunity 2011; 35:501-13; PMID:22035845; http://dx.doi.org/10.1016/j.immuni.2011.07.014.
27. Splinter E, Heath H, Kooren J, Palstra RJ, Klous P, Grosveld F, et al. CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev 2006; 20:2349-54; PMID:16951251; http://dx.doi.org/10.1101/gad.399506.
28. Wendt KS, Yoshida K, Itoh T, Bando M, Koch B, Schirghuber E, et al. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 2008; 451:796-801; PMID:18235444; http://dx.doi.org/10.1038/nature06634.
29. Ribeiro de Almeida C, Stadhouders R, Thongjuea S, Soler E, Hendriks RW. DNA-binding factor CTCF and long-range gene interactions in V(D)J recombination and oncogene activation. Blood 2012; PMID:22538856; http://dx.doi.org/10.1182/blood-2012-03-402586.
30. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, 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.
31. Drissen R, Palstra RJ, Gillemans N, Splinter E, Grosveld F, Philipsen S, et al. The active spatial organization of the beta-globin locus requires the transcription factor EKLF. Genes Dev 2004; 18:2485-90; PMID:15489291; http://dx.doi.org/10.1101/gad.317004.
32. Song SH, Hou C, Dean A. A positive role for NLI/Ldb1 in long-range beta-globin locus control region function. Mol Cell 2007; 28:810-22; PMID:18082606; http://dx.doi.org/10.1016/j.molcel.2007.09.025.
33. Vakoc CR, Letting DL, Gheldof N, Sawado T, Bender MA, Groudine M, et al. Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol Cell 2005; 17:453-62; PMID:15694345; http://dx.doi.org/10.1016/j.molcel.2004.12.028.
34. Xu J, Sankaran VG, Ni M, Menne TF, Puram RV, Kim W, et al. Transcriptional silencing of gamma-globin by BCL11A involves long-range interactions and cooperation with SOX6. Genes Dev 2010; 24:783-98; PMID:20395365; http://dx.doi.org/10.1101/gad.1897310.
35. Sawado T, Halow J, Bender MA, Groudine M. The beta-globin locus control region (LCR) functions primarily by enhancing the transition from transcription initiation to elongation. Genes Dev 2003; 17:1009-18; PMID:12672691; http://dx.doi.org/10.1101/gad.1072303.
36. Song SH, Kim A, Ragoczy T, Bender MA, Groudine M, Dean A. Multiple functions of Ldb1 required for beta-globin activation during erythroid differentiation. Blood 2010; 116:2356-64; PMID:20570862; http://dx.doi.org/10.1182/blood-2010-03-272252.
37. Wong P, Hattangadi SM, Cheng AW, Frampton GM, Young RA, Lodish HF. Gene induction and repression during terminal erythropoiesis are mediated by distinct epigenetic changes. Blood 2011; 118:128-38; PMID:21860024; http://dx.doi.org/10.1182/blood-2011-03-341404.
38. Bulger M, Groudine M. Functional and mechanistic diversity of distal transcription enhancers. Cell 2011; 144:327-39; PMID:21295696; http://dx.doi.org/10.1016/j.cell.2011.01.024.