Identification of alternative topological domains in chromatin

Algorithms for Molecular Biology

Volumn 9, Issue 1, 2014, Pages

  Filippova, Darya ^a,b   Patro, Rob ^a   Duggal, Geet ^a,b   Kingsford, Carl ^a  

^a Carnegie Mellon University   (United States)

^b CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

Alternative topological domains; Chromatin conformation capture; Dynamic programming

Indexed keywords

EID: 84900425608     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-9-14     Document Type: Article

References (25)

1. de Wit E, de Laat W. A decade of 3C technologies: insights into nuclear organization. Genes Dev 2012, 26:11-24. 10.1101/gad.179804.111, 3258961, 22215806.
2. Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell 2013, 49(5):773-782. 10.1016/j.molcel.2013.02.011, 3741673, 23473598.
3. Cavalli G, Misteli T. Functional implications of genome topology. Nat Struct Mol Biol 2013, 20(3):290-299. 10.1038/nsmb.2474, 23463314.
4. Fudenberg G, Getz G, Meyerson M, Mirny LA. High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nat Biotechnol 2011, 29(12):1109-13. 10.1038/nbt.2049, 3268007, 22101486.
5. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012, 485(7398):376-80. 10.1038/nature11082, 3356448, 22495300.
6. Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G. Three-dimensional folding and functional organization principles of the drosophila genome. Cell 2012, 148(3):458-472. 10.1016/j.cell.2012.01.010, 22265598.
7. Hou C, Li L, Qin ZS, Corces VG. Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains. Mol Cell 2012, 48(3):471-84. 10.1016/j.molcel.2012.08.031, 3496039, 23041285.
8. Kölbl AC, Weigl D, Mulaw M, Thormeyer T, Bohlander SK, Cremer T, Dietzel S. The radial nuclear positioning of genes correlates with features of megabase-sized chromatin domains. Chromosome Res 2012, 20(6):735-52. 10.1007/s10577-012-9309-9, 23053570.
9. Lin YC, Benner C, Mansson R, Heinz S, Miyazaki K, Miyazaki M, Chandra V, Bossen C, Glass CK, Murre C. Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. Nat Immunol 2012, 13(12):1196-204. 10.1038/ni.2432, 3501570, 23064439.
10. Bickmore WA, van Steensel B. Genome Architecture: domain organization of interphase chromosomes. Cell 2013, 152(6):1270-1284. 10.1016/j.cell.2013.02.001, 23498936.
11. Tanay A, Cavalli G. Chromosomal domains: epigenetic contexts and functional implications of genomic compartmentalization. Curr Opin Genet Dev 2013, 23(2):197-203. 10.1016/j.gde.2012.12.009, 23414654.
12. Goldberg AV. Finding a maximum density subgraph Tech. Rep. 171, University of California, Berkeley, CA 1984.
13. Schaeffer SE. Graph clustering. Comput Sci Rev 2007, 1:27-64.
14. Filippova D, Gadani A, Kingsford C. Coral: an integrated suite of visualizations for comparing clusterings. BMC Bioinformatics 2012, 13:276. 10.1186/1471-2105-13-276, 3576325, 23102108.
15. Huang L, Chiang D. Better k-best parsing. Proceedings of the Ninth International Workshop on Parsing Technology 2005, 53-64. Stroudsburg, PA, USA: Association for Computational Linguistics.
16. Kleinberg J, Tardos E. Algorithm Design. Boston 2005, MA: Addison-Wesley.
17. Yaffe E, Tanay A. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet 2011, 43(11):1059-1065. 10.1038/ng.947, 22001755.
18. Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007, 128(6):1231-1245. 10.1016/j.cell.2006.12.048, 2572726, 17382889.
19. Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. A map of the cis-regulatory sequences in the mouse genome. Nature 2012, 488:116-120. 10.1038/nature11243, 22763441.
20. Meilǎ M. Comparing clusterings by the variation of information. Learn Theory Kernel Mach 2777, 2003:173-187.
21. Duggal G, Wang H, Kingsford C. Higher-order chromatin domains link eQTLs with the expression of far-away genes. Nucleic Acids Res Adv Access 2013, 42(1):87-96.
22. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326(5950):289-293. 10.1126/science.1181369, 2858594, 19815776.
23. Zhou X, Lowdon RF, Li D, Lawson HA, Madden PA, Costello JF, Wang T. Exploring long-range genome interactions using the WashU Epigenome Browser. Nat Methods 2013, 10(5):375-376. 10.1038/nmeth.2440, 3820286, 23629413.
24. Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 2013, 502(7469):59-64. 10.1038/nature12593, 3869051, 24067610.
25. Filippova D, Patro R, Duggal G, Kingsford C. Multiscale Identification of Topological Domains in Chromatin. Proceedings of 13th Workshop on Algorithms in Bioinformatics (WABI), Volume 8126 2013, 300-3012. Heidelberg, Germany.