A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions

Nucleic Acids Research

Volumn 42, Issue 18, 2014, Pages

  Paulsen, Jonas ^a   Rødland, Einar A ^b   Holden, Lars ^c   Holden, Marit ^c   Hovig, Eivind ^a,b  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b OSLO UNIVERSITY HOSPITAL   (Norway)

^c NORWEGIAN COMPUTING CENTER   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN; TRANSCRIPTION FACTOR RUNX1;

CHEMISTRY; CHROMATIN; DNA SEQUENCE; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; STATISTICAL MODEL;

CHROMATIN; CORE BINDING FACTOR ALPHA 2 SUBUNIT; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MODELS, STATISTICAL; SEQUENCE ANALYSIS, DNA;

EID: 84922391809     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku738     Document Type: Article

References (41)

1. Cavalli, G. And Misteli, T. (2013) Functional implications of genome topology. Nat. Struct. Mol. Biol., 20, 290-299.
2. Cullen, K. E., Kladde, M. P. And Seyfred, M. A. (1993) Interaction between transcription regulatory regions of prolactin chromatin. Science, 261, 203-206.
3. Tolhuis, B., Palstra, R. J., Splinter, E., Grosveld, F. And de Laat, W. (2002) Looping and interaction between hypersensitive sites in the active-globin locus. Mol. Cell, 10, 1453-1465.
4. Vernimmen, D., De Gobbi, M., Sloane-Stanley, J., Wood, W. G. And Higgs, D. R. (2007) Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J., 26, 2041-2051.
5. Fullwood, M. J., Liu, M. H., Pan, Y., Liu, J., Xu, H., Mohamed, Y. B., Orlov, Y. L., Velkov, S., Ho, A., Mei, P. H. et al. (2009) An oestrogen-receptor-bound human chromatin interactome. Nature, 462, 58-64.
6. Kagey, M. H., Newman, J. J., Bilodeau, S., Zhan, Y., Orlando, D. A., van Berkum, N. L., Ebmeier, C. C., Goossens, J., Rahl, P. B., Levine, S. S. et al. (2010) Mediator and cohesin connect gene expression and chromatin architecture. Nature, 467, 430-435.
7. Ren, X., Siegel, R., Kim, U. And Roeder, R. G. (2011) Direct interactions of OCA-B and TFII-I regulate immunoglobulin heavy-chain gene transcription by facilitating enhancer-promoter communication. Mol. Cell, 42, 342-355.
8. Dunham, I., Kundaje, A., Aldred, S. F., Collins, P. J., Davis, C. A., Doyle, F., Epstein, C. B., Frietze, S., Harrow, J., Kaul, R. et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
9. Bernstein, B. E., Stamatoyannopoulos, J. A., Costello, J. F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M., Beaudet, A. L., Ecker, J. R. et al. (2010) The NIH roadmap epigenomics mapping consortium. Nat. Biotechnol., 28, 1045-1048.
10. Dekker, J., Rippe, K., Dekker, M. And Kleckner, N. (2002) Capturing chromosome conformation. Science, 295, 1306-1311.
11. Handoko, L., Xu, H., Li, G., Ngan, C. Y., Chew, E., Schnapp, M., Lee, C. W. H., Ye, C., Ping, J. L. H., Mulawadi, F. et al. (2011) CTCF-mediated functional chromatin interactome in pluripotent cells. Nat. Genet., 43, 630-638.
12. Li, G., Ruan, X., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P., Poh, H. M., Goh, Y., Lim, J., Zhang, J. et al. (2012) Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell, 148, 84-98.
13. Li, G., Fullwood, M. J., Xu, H., Mulawadi, F. H., Velkov, S., Vega, V., Ariyaratne, P. N., Mohamed, Y. B., Ooi, H. S., Tennakoon, C. Et al. (2010) ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol., 11, R22.
14. Zhang, J., Poh, H. M., Peh, S. Q., Sia, Y. Y., Li, G., Mulawadi, F. H., Goh, Y., Fullwood, M. J., Sung, W. K., Ruan, X. et al. (2012) ChIA-PET analysis of transcriptional chromatin interactions. Methods, 58, 289-299.
15. Chepelev, I., Wei, G., Wangsa, D., Tang, Q. And 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, 490-503.
16. Sanyal, A., Lajoie, B. R., Jain, G. And Dekker, J. (2012) The long-range interaction landscape of gene promoters. Nature, 489, 109-113.
17. Paulsen, J., Lien, T. G., Sandve, G. K., Holden, L., Borgan, Ø., Glad, I. And Hovig, E. (2013) Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements. Nucleic Acids Res., 41, 5164-5174.
18. Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O. et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326, 289-293.
19. Duan, Z., Andronescu, M., Schutz, K., McIlwain, S., Kim, Y. J., Lee, C., Shendure, J., Fields, S., Blau, C. A. And Noble, W. S. (2009) A three-dimensional model of the yeast genome. Nature, 465, 363-367.
20. Yaffe, E. And Tanay, A. (2011) Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat. Genet., 43, 1059-1065.
21. Imakaev, M., Fudenberg, G., McCord, R. P., Naumova, N., Goloborodko, A., Lajoie, B. R., Dekker, J. And Mirny, L. A. (2012) Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods, 9, 999-1003.
22. Ay, F., Bailey, T. L. And Noble, W. S. (2014) Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res., doi:10. 1101/gr. 160374. 113.
23. Harkness, W. L. (1965) Properties of the extended hypergeometric distribution. Ann. Math. Stat., 36, 938-945.
24. Heyse, J. (2011) A false discovery rate procedure for categorical data. Recent Adv. Biostat. : False Discov. Rates Surviv. Anal. Relat. Top., 4, 43-58.
25. Cox, D. R. And Hinkley, D. V. (1979) Theoretical Statistics. Chapman and Hall, London.
26. Zhang, Y., Wong, C. H., Birnbaum, R. Y., Li, G., Favaro, R., Ngan, C. Y., Lim, J., Tai, E., Poh, H. M., Wong, E. et al. (2013) Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature, 504, 306-310.
27. Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
28. Dean, A. (2011) In the loop: long range chromatin interactions and gene regulation. Brief. Funct. Genomics, 10, 3-10.
29. Bàu, D., Sanyal, A., Lajoie, B. R., Capriotti, E., Byron, M., Lawrence, J. B., Dekker, J. And Marti-Renom, M. (2010) The three-dimensional folding of the-globin gene domain reveals formation of chromatin globules. Nat. Struct. Mol. Biol., 18, 107-114.
30. Jarman, A. P., Wood, W. G., Sharpe, J. A., Gourdon, G., Ayyub, H. And Higgs, D. R. (1991) Characterization of the major regulatory element upstream of the human alpha-globin gene cluster. Mol. Cell. Biol., 11, 4679-4689.
31. Mahajan, M. C., Karmakar, S., Newburger, P. E., Krause, D. S. And Weissman, S. M. (2009) Dynamics of-globin locus chromatin structure and gene expression during erythroid differentiation of human CD34+ cells in culture. Exp. Hematol., 37, 1143-1156.
32. Splinter, E., Heath, H., Kooren, J., Palstra, R. J., Klous, P., Grosveld, F., Galjart, N. And de Laat, W. (2006) CTCF mediates long-range chromatin looping and local histone modification in the-globin locus. Genes Dev., 20, 2349-2354.
33. Dostie, J., Richmond, T. A., Arnaout, R. A., Selzer, R. R., Lee, W. L., Honan, T. A., Rubio, E. D., Krumm, A., Lamb, J., Nusbaum, C. Et al. (2006) Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Res., 16, 1299-1309.
34. Fraser, P., Pruzina, S., Antoniou, M. And Grosveld, F. (1993) Each hypersensitive site of the human beta-globin locus control region confers a different developmental pattern of expression on the globin genes. Genes Dev., 7, 106-113.
35. Rae, J., Johnson, M. D., Scheys, J. O., Cordero, K. E., Larios, J. M. And Lippman, M. E. (2005) GREB1 is a critical regulator of hormone dependent breast cancer growth. Breast Cancer Res. Treat., 92, 141-149.
36. Deschênes, J., Bourdeau, V., White, J. H. And Mader, S. (2007) Regulation of GREB1 transcription by estrogen receptor -through a multipartite enhancer spread over 20 kb of upstream flanking sequences. J. Biol. Chem., 282, 17335-17339.
37. Otto, F., Lübbert, M. And Stock, M. (2003) Upstream and downstream targets of RUNX proteins. J. Cell. Biochem., 89, 9-18.
38. Ghozi, M. C., Bernstein, Y., Negreanu, V., Levanon, D. And Groner, Y. (1996) Expression of the human acute myeloid leukemia gene AML1 is regulated by two promoter regions. Proc. Natl. Acad. Sci. U. S. A., 93, 1935-1940.
39. Markova, E. N., Kantidze, O. L. And Razin, S. V. (2011) Transcriptional regulation and spatial organisation of the human AML1/RUNX1 gene. J. Cell. Biochem., 112, 1997-2005.
40. Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M. et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473, 43-49.
41. Ørom, U. A. And Shiekhattar, R. (2011) Long non-coding RNAs and enhancers. Curr. Opin. Genet. Dev., 21, 194-198.