Global view of enhancer-promoter interactome in human cells

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 21, 2014, Pages

  He, Bing ^a   Chen, Changya ^a   Teng, Li ^b   Tan, Kai ^a,b  

^a UNIVERSITY OF IOWA   (United States)

^b UNIVERSITY OF IOWA   (United States)

Author keywords

3C; Bioinformatics; Chromatin interaction; Gene regulation; Genomics

Indexed keywords

COHESIN; TRANSCRIPTION FACTOR;

ARTICLE; CELL COMMUNICATION; CELL INTERACTION; CELL TYPE; CELLULAR PARAMETERS; CHROMATIN; ENHANCER PROMOTER; ENHANCER REGION; GENE CONTROL; GENE EXPRESSION; GENETIC ASSOCIATION; GENOMICS; HISTONE MODIFICATION; HUMAN; HUMAN CELL; HUMAN CELL CULTURE; K562 CELL LINE; MCF 7 CELL LINE; PRIORITY JOURNAL; PROMOTER REGION; TISSUE SPECIFICITY;

3C; BIOINFORMATICS; CHROMATIN INTERACTION; GENE REGULATION; GENOMICS;

CELL CYCLE PROTEINS; CHROMOSOMAL PROTEINS, NON-HISTONE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ENHANCER ELEMENTS, GENETIC; GENE EXPRESSION REGULATION; GENOMICS; HUMANS; MODELS, GENETIC; PROMOTER REGIONS, GENETIC; SIGNAL TRANSDUCTION;

EID: 84901649822     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1320308111     Document Type: Article

References (49)

1. Visel A, Rubin EM, Pennacchio LA (2009) Genomic views of distant-acting enhancers. Nature 461(7261):199-205.
2. Williamson I, Hill RE, Bickmore WA (2011) Enhancers: From developmental genetics to the genetics of common human disease. Dev Cell 21(1):17-19.
3. Gallo SM, et al. (2011) REDfly v3.0: Toward a comprehensive database of transcrip-tional regulatory elements in Drosophila. Nucleic Acids Res 39(Database issue): D118-D123.
4. Sanyal A, Lajoie BR, Jain G, Dekker J (2012) The long-range interaction landscape of gene promoters. Nature 489(7414):109-113.
5. Li G, et al. (2012) Extensive promoter-centered chromatin interactions provide a to-pological basis for transcription regulation. Cell 148(1-2):84-98.
6. Chepelev I, Wei G, Wangsa D, Tang Q, Zhao K (2012) Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res 22(3):490-503.
7. Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295(5558):1306-1311. (Pubitemid 34157624)
8. Simonis M, Kooren J, de Laat W (2007) An evaluation of 3C-based methods to capture DNA interactions. Nat Methods 4(11):895-901. (Pubitemid 350042374)
9. van Steensel B, Dekker J (2010) Genomics tools for unraveling chromosome architecture. Nat Biotechnol 28(10):1089-1095.
10. Horike S, Cai S, Miyano M, Cheng JF, Kohwi-Shigematsu T (2005) Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nat Genet 37(1):31-40. (Pubitemid 40070937)
11. Fullwood MJ, et al. (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462(7269):58-64.
12. DeMare LE, et al. (2013) The genomic landscape of cohesin-associated chromatin interactions. Genome Res 23(8):1224-1234.
13. Heintzman ND, et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459(7243):108-112.
14. Ernst J, et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473(7345):43-49.
15. Corradin O, et al. (2014) Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits. Genome Res 24(1):1-13.
16. Thurman RE, et al. (2012) The accessible chromatin landscape of the human genome. Nature 489(7414):75-82.
17. Firpi HA, Ucar D, Tan K (2010) Discover regulatory DNA elements using chromatin signatures and artificial neural network. Bioinformatics 26(13):1579-1586.
18. Borok MJ, Tran DA, Ho MC, Drewell RA (2010) Dissecting the regulatory switches of development: Lessons from enhancer evolution in Drosophila. Development 137(1): 5-13.
19. Ahituv N, Prabhakar S, Poulin F, Rubin EM, Couronne O (2005) Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny. Hum Mol Genet 14(20):3057-3063. (Pubitemid 41535470)
20. Kikuta H, et al. (2007) Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res 17(5):545-555. (Pubitemid 46715504)
21. Breiman L (2001) Random forests. Mach Learn 45(1):5-32. (Pubitemid 32933532)
22. Rada-Iglesias A, et al. (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470(7333):279-283.
23. Creyghton MP, et al. (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 107(50):21931-21936.
24. Kim TK, et al. (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465(7295):182-187.
25. Visel A, et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457(7231):854-858.
26. Harrow J, et al. (2012) GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res 22(9):1760-1774.
27. Jin F, et al. (2013) A high-resolution map of the three-dimensional chromatin inter-actome in human cells. Nature 503(7475):290-294.
28. Li G, et al. (2010) ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol 11(2):R22.
29. Hong JW, Hendrix DA, Levine MS (2008) Shadow enhancers as a source of evolutionary novelty. Science 321(5894):1314.
30. Perry MW, Boettiger AN, Levine M (2011) Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. Proc Natl Acad Sci USA 108(33): 13570-13575.
31. Li Q, Barkess G, Qian H (2006) Chromatin looping and the probability of transcription. Trends Genet 22(4):197-202.
32. Gibcus JH, Dekker J (2012) The context of gene expression regulation. F1000 Biol Rep 4:8.
33. Handoko L, et al. (2011) CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 43(7):630-638.
34. Dorsett D (2011) Cohesin: Genomic insights into controlling gene transcription and development. Curr Opin Genet Dev 21(2):199-206.
35. Faure AJ, et al. (2012) Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules. Genome Res 22(11):2163-2175.
36. Schmidt D, et al. (2010) A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res 20(5):578-588.
37. Kagey MH, et al. (2010) Mediator and cohesin connect gene expression and chromatin architecture. Nature 467(7314):430-435.
38. Nitzsche A, et al. (2011) RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity. PLoS One 6(5):e19470.
39. van den Berg DL, et al. (2010) An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell 6(4):369-381.
40. Smale ST (2001) Core promoters: Active contributors to combinatorial gene regulation. Genes Dev 15(19):2503-2508. (Pubitemid 32937860)
41. Butler JE, Kadonaga JT (2001) Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev 15(19):2515-2519. (Pubitemid 32937862)
42. 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(14):9243-9247. (Pubitemid 34764598)
43. Calo E, Wysocka J (2013) Modification of enhancer chromatin: What, how, and why? Mol Cell 49(5):825-837.
44. Matys V, et al. (2006) TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34(Database issue):D108-D110.
45. Bryne JC, et al. (2008) JASPAR, the open access database of transcription factor-binding profiles: New content and tools in the 2008 update. Nucleic Acids Res 36(Database issue): D102-D106. (Pubitemid 351149704)
46. Newburger DE, Bulyk ML (2009) UniPROBE: An online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 37(Database issue): D77-D82.
47. Stormo GD, Fields DS (1998) Specificity, free energy and information content in protein-DNA interactions. Trends Biochem Sci 23(3):109-113. (Pubitemid 28175261)
48. Göke J, Schulz MH, Lasserre J, Vingron M (2012) Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinformatics 28(5):656-663.
49. Hagège H, et al. (2007) Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc 2(7):1722-1733.