Systematic identification of protein combinations mediating chromatin looping

Nature Communications

Volumn 7, Issue , 2016, Pages

  Zhang, Kai ^a   Li, Nan ^a,b   Ainsworth, Richard I ^a,b   Wang, Wei ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATING TRANSCRIPTION FACTOR 2; DNA BINDING PROTEIN; INTERFERON REGULATORY FACTOR 4; MYC PROTEIN; OCTAMER TRANSCRIPTION FACTOR 2; PROTEIN BCL 3; TRANSCRIPTION FACTOR GATA 2; TRANSCRIPTION FACTOR JUND; TRANSCRIPTION FACTOR PAX5; TRANSCRIPTION FACTOR TAL1; PROTEIN BINDING;

CELLS AND CELL COMPONENTS; CHEMICAL BINDING; CHROMOSOME; GENE EXPRESSION; GENOME; PROTEIN;

ARTICLE; CHROMATIN; CHROMATIN LOOPING; CONTROLLED STUDY; PROTEIN PROTEIN INTERACTION; REGULATORY MECHANISM; BIOLOGICAL MODEL; CHEMISTRY; CONFORMATION; GENE REGULATORY NETWORK; HUMAN; K-562 CELL LINE; METABOLISM; NORMAL DISTRIBUTION; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; CHROMATIN; DNA-BINDING PROTEINS; GENE REGULATORY NETWORKS; HUMANS; K562 CELLS; MODELS, BIOLOGICAL; NORMAL DISTRIBUTION; NUCLEIC ACID CONFORMATION; PROTEIN BINDING;

EID: 84979935416     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms12249     Document Type: Article

References (70)

1. Schleif, R. DNA looping. Annu. Rev. Biochem. 61, 199-223 (1992
2. Cremer, T., & Cremer, C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2, 292-301 (2001
3. Fraser P., & Bickmore, W. Nuclear organization of the genome and the potential for gene regulation. Nature 447, 413-417 (2007
4. Dekker, J. Gene regulation in the third dimension. Science 319, 1793-1794 (2008
5. Fudenberg G., Getz, G., Meyerson, M., & Mirny, L. A. High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nat. Biotechnol. 29, 1109-1113 (2011
6. Zhang Y. et al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell 148, 908-921 (2012
7. Dekker J., Marti-Renom, M. A., & Mirny, L. A. Exploring the threedimensional organization of genomes: interpreting chromatin interaction data. Nat. Rev. Genet. 14, 390-403 (2013
8. Gorkin D. U., Leung, D., & Ren, B. The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell 14, 762-775 (2014
9. Mercer, T. R., & Mattick, J. S. Understanding the regulatory and transcriptional complexity of the genome through structure. Genome Res. 23, 1081-1088 (2013
10. Dixon J. R., et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376-380 (2012
11. Shen Y., et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116-120 (2012
12. Splinter E., et al. CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev. 20, 2349-2354 (2006
13. Phillips, J. E., & Corces, V. G. CTCF: master weaver of the genome. Cell 137, 1194-1211 (2009
14. Hou, C., Zhao, H., Tanimoto, K., & Dean, A. CTCF-dependent enhancerblocking by alternative chromatin loop formation. Proc. Natl Acad. Sci. USA 105, 20398-20403 (2008
15. Vakoc C. R., et al. Proximity among distant regulatory elements at the betaglobin locus requires GATA-1 and FOG-1. Mol. Cell 17, 453-462 (2005
16. Drissen R., et al. The active spatial organization of the b-globin locus requires the transcription factor EKLF. Genes Dev. 18, 2485-2490 (2004
17. Rao S. S. P., et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680 (2014
18. Zhou, Q., & Wong, W. H. CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proc. Natl Acad. Sci. USA 101, 12114-12119 (2004
19. Gerstein M. B., et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91-100 (2012
20. Das, D., Banerjee, N., & Zhang, M. Q. Interacting models of cooperative gene regulation. Proc. Natl Acad. Sci. USA 101, 16234-16239 (2004
21. Blanchette M., et al. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res. 16, 656-668 (2006
22. Gertz J., et al. Distinct properties of cell-Type-specific and shared transcription factor binding sites. Mol. Cell 52, 25-36 (2013
23. Boyle A. P., et al. Comparative analysis of regulatory information and circuits across distant species. Nature 512, 453-456 (2014
24. Dempster, A. P. Covariance Selection. Biometrics 28, 157-175 (1972
25. Friedman, J., Hastie, T., & Tibshirani, R. Sparse inverse covariance estimation with the graphical lasso. Biostatistics 9, 432-441 (2008
26. Liu, H., Han, F., Yuan, M., Lafferty, J., & Wasserman, L. High-dimensional semiparametric gaussian copula graphical models. Ann. Stat. 40, 2293-2326 (2012
27. Margolin A. A. et al. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7 (Suppl 1): S7 2006
28. Schaffter, T., Marbach, D., & Floreano, D. GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods. Bioinformatics 27, 2263-2270 (2011
29. Chan H. M., & La Thangue, N. B. p300/CBP proteins: HATs for transcriptional bridges and scaffolds. J. Cell Sci. 114, 2363-2373 2001
30. Kalkhoven, E. CBP and p300: HATs for different occasions. Biochem. Pharmacol. 68, 1145-1155 (2004
31. Mayr, B., & Montminy, M. Transcriptional regulation by the phosphorylationdependent factor CREB. Nat. Rev. Mol. Cell. Biol. 2, 599-609 (2001
32. Wen, A. Y., Sakamoto, K. M., & Miller, L. S. The role of the transcription factor CREB in immune function. J. Immunol. 185, 6413-6419 (2010
33. Nechanitzky R., et al. Transcription factor EBF1 is essential for the maintenance of B cell identity and prevention of alternative fates in committed cells. Nat. Immunol. 14, 867-875 (2013
34. Cobaleda, C., Schebesta, A., Delogu, A., & Busslinger, M. Pax5: the guardian of B cell identity and function. Nat. Immunol. 8, 463-470 (2007
35. Liu P., et al. Bcl11a is essential for normal lymphoid development. Nat. Immunol. 4, 525-532 (2003
36. Zhuang, Y., Cheng, P., & Weintraub, H. B-lymphocyte development is regulated by the combined dosage of three basic helix-loop-helix genes, E2A, E2-2, and HEB. Mol. Cell. Biol. 16, 2898-2905 (1996
37. Sun, H., Lu, B., Li, R. Q., Flavell, R. A., & Taneja, R. Defective T cell activation and autoimmune disorder in Stra13-deficient mice. Nat. Immunol. 2, 1040-1047 (2001
38. Sims, 3rd R. J., Belotserkovskaya, R., & Reinberg, D. Elongation by RNA polymerase II: the short and long of it. Genes Dev. 18, 2437-2468 (2004
39. Faiola F., et al. Dual regulation of c-Myc by p300 via acetylation-dependent control of Myc protein turnover and coactivation of Myc-induced transcription. Mol. Cell Biol. 25, 10220-10234 (2005
40. Zhang, K., Faiola, F., & Martinez, E. Six lysine residues on c-Myc are direct substrates for acetylation by p300. Biochem. Biophys. Res. Commun. 336, 274-280 (2005
41. Dinkel A., et al. The transcription factor early growth response 1 (Egr-1) advances differentiation of pre-B and immature B cells. J. Exp. Med. 188, 2215-2224 (1998
42. Welter, D., et al. The NHGRI GWAS Catalog, a curated resource of SNP-Trait associations. Nucleic Acids Res. 42, D1001-D1006 (2014
43. Newman, M. E. J. Finding community structure in networks using the eigenvectors of matrices. Phys. Rev. E 74, 036104-1-046104-19 (2006
44. Heidari N., et al. Genome-wide map of regulatory interactions in the human genome. Genome Res. 24, 1905-1917 (2014
45. Parelho V., et al. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132, 422-433 (2008
46. Lin J. X., et al. Critical role of STAT5 transcription factor tetramerization for cytokine responses and normal immune function. Immunity 36, 586-599 (2012
47. Betz B. C., et al. Batf coordinates multiple aspects of B and T cell function required for normal antibody responses. J. Exp. Med. 207, 933-942 (2010
48. Ge, B., Li, O., Wilder, P., Rizzino, A., & McKeithan, T. W. NF-kappa B regulates BCL3 transcription in T lymphocytes through an intronic enhancer. J. Immunol. 171, 4210-4218 (2003
49. Gerondakis, S., & Siebenlist, U. Roles of the NF-kappaB pathway in lymphocyte development and function. Cold Spring Harb. Perspect. Biol. 2, a000182 (2010
50. Michaelis, C., Ciosk, R., & Nasmyth, K. Cohesins: chromosomal proteins that prevent premature separation of sister chromatids. Cell 91, 35-45 (1997
51. Kagey M. H., et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430-435 (2010
52. Bailey S. D., et al. ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters. Nat. Commun. 2, 6186 (2015
53. Ogawa, S., Satake, M., & Ikuta, K. Physical and functional interactions between STAT5 and Runx transcription factors. J. Biochem. 143, 695-709 (2008
54. Hirata M., et al. C/EBPbeta and RUNX2 cooperate to degrade cartilage with MMP-13 as the target and HIF-2alpha as the inducer in chondrocytes. Hum. Mol. Genet. 21, 1111-1123 (2012
55. Hirata, M., et al C/EBPbeta promotes transition from proliferation to hypertrophic differentiation of chondrocytes through transactivation of p57. PLoS ONE 4 e4543 2009
56. Zervos, A. S., Gyuris, J., & Brent, R. Mxi1, a protein that specifically interacts with Max to bind Myc-Max recognition sites. Cell 72, 223-232 (1993
57. Luo, H., et al c-Myc rapidly induces acute myeloid leukemia in mice without evidence of lymphoma-Associated antiapoptotic mutations. Blood 106 2452-2461 (2005
58. Salvatori B., et al. Critical role of c-Myc in acute myeloid leukemia involving direct regulation of miR-26a and histone methyltransferase EZH2. Genes Cancer 2, 585-592 (2011
59. Wyszomierski, S. L., & Rosen, J. M. Cooperative effects of STAT5 (signal transducer and activator of transcription 5) and C/EBPb (CCAAT/enhancerbinding protein-beta) on b-casein gene transcription are mediated by the glucocorticoid receptor. Mol. Endocrinol. 15, 228-240 (2001
60. Xu, M., Nie, L., Kim, S. H., & Sun, X. H. STAT5-induced Id-1 transcription involves recruitment of HDAC1 and deacetylation of C/EBPbeta. EMBO J. 22, 893-904 (2003
61. Martens J. H., et al. PML-RARalpha/RXR alters the epigenetic landscape in acute promyelocytic leukemia. Cancer Cell 17, 173-185 (2010
62. Arvey, A., Agius, P., Noble, W. S., & Leslie, C. Sequence and chromatin determinants of cell-Type-specific transcription factor binding. Genome Res. 22, 1723-1734 (2012
63. Machanick, P., & Bailey, T. L. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27, 1696-1697 (2011
64. Whitington, T., Frith, M. C., Johnson, J., & Bailey, T. L. Inferring transcription factor complexes from ChIP-seq data. Nucleic Acids Res. 39, e98 (2011
65. Ferjoux, G., Auge, B., Boyer, K., & Haenlin, M. Waltzer L. A GATA/RUNX cis-regulatory module couples Drosophila blood cell commitment and differentiation into crystal cells. Dev. Biol. 305, 726-734 (2007
66. Waltzer, L., Ferjoux, G., Bataille, L., & Haenlin, M. Cooperation between the GATA and RUNX factors Serpent and Lozenge during Drosophila hematopoiesis. EMBO J. 22, 6516-6525 (2003
67. Consortium, E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012
68. Zhang Y., et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008
69. Eppstein, D., Loffler, M., & Strash, D. Listing all maximal cliques in sparse graphs in near-optimal time. Lect. Notes Comput. Sci. 6506, 403-414 (2010
70. Chatr-Aryamontri A., et al. The BioGRID interaction database: 2015 update. Nucleic Acids Res. 43, D470-D478 (2015