A complex network framework for unbiased statistical analyses of DNA-DNA contact maps

Nucleic Acids Research

Volumn 41, Issue 2, 2013, Pages 701-710

  Kruse, Kai ^a   Sewitz, Sven ^a,b   Madan Babu, M ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; COMPLEX NETWORK FRAMEWORK; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA BINDING; DNA REPLICATION; GENE LOCUS; GENE MAPPING; GENETIC RECOMBINATION; MEIOSIS; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN LOCALIZATION; SACCHAROMYCES CEREVISIAE; STATISTICAL ANALYSIS; STATISTICAL PARAMETERS; TRANSCRIPTION INITIATION SITE;

CELL CYCLE PROTEINS; CHROMOSOMAL PROTEINS, NON-HISTONE; CHROMOSOMES, FUNGAL; DATA INTERPRETATION, STATISTICAL; DNA; DNA, FUNGAL; GENES, FUNGAL; GENOME, FUNGAL; GENOMICS; MEIOSIS; NUCLEIC ACID CONFORMATION; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84875430845     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1096     Document Type: Article

References (50)

1. Dekker, J., Rippe, K., Dekker, M. and Kleckner, N. (2002) Capturing chromosome conformation. Science, 295, 1306-1311. (Pubitemid 34157624)
2. Osborne, C.S., Ewels, P.A. and Young, A.N.C. (2011) Meet the neighbours: tools to dissect nuclear structure and function. Brief. Funct. Genom., 10, 11-17.
3. Zhao, Z., Tavoosidana, G., Sjö linder, M., Gö ndö r, A., Mariano, P., Wang, S., Kanduri, C., Lezcano, M., Sandhu, K.S., Singh, U. et al. (2006) Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-and interchromosomal interactions. Nat. Genet., 38, 1341-1347. (Pubitemid 44646299)
4. Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B. and de Laat, W. (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet., 38, 1348-1354. (Pubitemid 44646300)
5. 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. (Pubitemid 44506963)
6. Rodley, C.D.M., Bertels, F., Jones, B. and O'Sullivan, J.M. (2009) Global identification of yeast chromosome interactions using Genome conformation capture. Fungal Genet. Biol. FG & B, 46, 879-886.
7. van Berkum, N.L., Lieberman-Aiden, E., Williams, L., Imakaev, M., Gnirke, A., Mirny, L.A., Dekker, J. and Lander, E.S. (2010) Hi-C: a method to study the three-dimensional architecture of genomes. J. Vis. Exp. JoVE, 39, 1-7.
8. 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.
9. Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F. and Chen, L. (2012) Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat. Biotechnol., 30, 90-98.
10. Splinter, E., de Wit, E., Nora, E.P., Klous, P., van de Werken, H.J.G., Zhu, Y., Kaaij, L.J.T., van Ijcken, W., Gribnau, J., Heard, E. et al. (2011) The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev., 25, 1371-1383.
11. Duan, Z., Andronescu, M., Schutz, K., McIlwain, S., Kim, Y.J., Lee, C., Shendure, J., Fields, S., Blau, C.A. and Noble, W.S. (2010) A three-dimensional model of the yeast genome. Nature, 465, 363-367.
12. Tanizawa, H., Iwasaki, O., Tanaka, A., Capizzi, J.R., Wickramasinghe, P., Lee, M., Fu, Z. and Noma, K.-I. (2010) Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. Nucleic Acids Res., 38, 8164-8177.
13. Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A. and Cavalli, G. (2012) Three-dimensional folding and functional organization principles of the Drosophila genome. Cell, 148, 458-472.
14. Moissiard, G., Cokus, S.J., Cary, J., Feng, S., Billi, A.C., Stroud, H., Husmann, D., Zhan, Y., Lajoie, B.R., McCord, R.P. et al. (2012) MORC family ATPases required for heterochromatin condensation and gene silencing. Science, 336, 1448-1451.
15. 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.
16. Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N. and Barabá si, A.L. (2000) The large-scale organization of metabolic networks. Nature, 407, 651-654.
17. Shen-Orr, S.S., Milo, R., Mangan, S. and Alon, U. (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet., 31, 64-68.
18. Maslov, S. and Sneppen, K. (2002) Specificity and stability in topology of protein networks. Science, 296, 910-913. (Pubitemid 34464896)
19. Jothi, R., Balaji, S., Wuster, A., Grochow, J.A., Gsponer, J., Przytycka, T.M., Aravind, L. and Babu, M.M. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol. Syst. Biol., 5, 294.
20. Strogatz, S.H. (2001) Exploring complex networks. Nature, 410, 268-276. (Pubitemid 32216604)
21. Janga, S.C., Collado-Vides, J. and Babu, M.M. (2008) Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes. Proc. Natl Acad. Sci. USA, 105, 15761-15766.
22. Barabá si, A.-L. and Oltvai, Z.N. (2004) Network biology: understanding the cell's functional organization. Nat. Rev. Genet., 5, 101-113. (Pubitemid 38160277)
23. Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D. and Alon, U. (2002) Network motifs: simple building blocks of complex networks. Science, 298, 824-827. (Pubitemid 35231534)
24. Itzkovitz, S., Milo, R., Kashtan, N., Ziv, G. and Alon, U. (2003) Subgraphs in random networks. Phys. Rev. E, 68, 1-8.
25. Itzkovitz, S. and Alon, U. (2005) Subgraphs and network motifs in geometric networks. Phys. Rev. E, 71, 1-9.
26. Mancera, E., Bourgon, R., Brozzi, A., Huber, W. and Steinmetz, L.M. (2008) High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature, 454, 479-485.
27. Venters, B.J., Wachi, S., Mavrich, T.N., Andersen, B.E., Jena, P., Sinnamon, A.J., Jain, P., Rolleri, N.S., Jiang, C., Hemeryck-Walsh, C. et al. (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol. Cell, 41, 480-492.
28. Cherry, J.M., Hong, E.L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E.T., Christie, K.R., Costanzo, M.C., Dwight, S.S., Engel, S.R. et al. (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res., 40, D700-D705.
29. Witten, D.M. and Noble, W.S. (2012) On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements. Nucleic Acids Res., 1-7.
30. Soffer, S. and Vá zquez, A. (2005) Network clustering coefficient without degree-correlation biases. Phys. Rev. E, 71, 2-5.
31. Bansal, S., Khandelwal, S. and Meyers, L.A. (2009) Exploring biological network structure with clustered random networks. BMC Bioinform., 10, 405.
32. Westfall, P.H. and Young, S.S. (1993) Resampling-Based Multiple Testing. John Wiley & Sons Hoboken, NJ 07030-5774, United States of America.
33. Kendziorski, C. and Wang, P. (2006) A review of statistical methods for expression quantitative trait loci mapping. Mamm. Genome: Off. J. Int. Mamm. Genome Soc., 17, 509-517.
34. Botta, M., Haider, S., Leung, I.X.Y., Lio, P. and Mozziconacci, J. (2010) Intra-and inter-chromosomal interactions correlate with CTCF binding genome wide. Mol. Syst. Biol., 6, 426.
35. Rajapakse, I., Scalzo, D., Tapscott, S.J., Kosak, S.T. and Groudine, M. (2010) Networking the nucleus. Mol. Syst. Biol., 6, 395.
36. Erdö s, P. and Renyi, A. (1959) On random graphs. 290-297.
37. Artzy-Randrup, Y. and Stone, L. (2005) Generating uniformly distributed random networks. Phys. Rev. E, 72, 1-7. (Pubitemid 41777857)
38. Basler, G., Ebenhö h, O., Selbig, J. and Nikoloski, Z. (2011) Mass-balanced randomization of metabolic networks. Bioinformatics (Oxford, England), 27, 1397-1403.
39. Dai, Z. and Dai, X. (2012) Nuclear colocalization of transcription factor target genes strengthens coregulation in yeast. Nucleic Acids Res., 40, 27-36.
40. Tanaka, T., Cosma, M.P., Wirth, K. and Nasmyth, K. (1999) Identification of cohesin association sites at centromeres and along chromosome arms. Cell, 98, 847-858. (Pubitemid 29446901)
41. Blat, Y. and Kleckner, N. (1999) Cohesins bind to preferential sites along yeast chromosome III, with differential regulation along arms versus the centric region. Cell, 98, 249-259. (Pubitemid 29344912)
42. De, S. and Michor F 2011 DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nat. Biotechnol 29 1103-1108.
43. Branco, M.R. and Pombo, A. (2006) Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol., 4, e138.
44. Fudenberg, G., Getz, G., Meyerson, M. and Mirny, L.A. (2011) High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nat. Biotechnol., 29, 1109-1113.
45. Tjong, H., Gong, K., Chen, L. and Alber, F. (2012) Physical tethering and volume exclusion determine higher-order genome organization in budding yeast. Genome Res., 22, 1295-1305.
46. Dorsett, D. and Strö m, L. (2012) The ancient and evolving roles of cohesin in gene expression and DNA repair. Curr. Biol., 22, R240-R250.
47. Ocampo-Hafalla, M.T. and Uhlmann, F. (2011) Cohesin loading and sliding. J. Cell Sci., 124, 685-691.
48. Merkenschlager, M. (2010) Cohesin: a global player in chromosome biology with local ties to gene regulation. Curr. Opin. Genet. Dev., 555-561.
49. Li, H., Ruan, J. and Durbin, R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-1858.
50. Yang, S.C.-H., Rhind, N. and Bechhoefer, J. (2010) Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing. Mol. Syst. Biol., 6, 404.