Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data

Nucleic Acids Research

Volumn 42, Issue 7, 2014, Pages

  Trieu, Tuan ^a   Cheng, Jianlin ^a,b  

^a University of Missouri   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACUTE LYMPHOBLASTIC LEUKEMIA; ARTICLE; B LYMPHOCYTE; CHROMATIN STRUCTURE; CHROMOSOME ANALYSIS; CHROMOSOME STRUCTURE; COMPARTMENT MODEL; EUCHROMATIN; FLUORESCENCE IN SITU HYBRIDIZATION; GENETIC MODEL; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; MOLECULAR DOCKING; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; SCORING SYSTEM; VALIDATION PROCESS;

B-LYMPHOCYTES; CHROMOSOMES, HUMAN; HUMANS; LEUKEMIA, B-CELL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION;

EID: 84899014890     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1411     Document Type: Article

References (19)

1. Misteli, T. (2007) Beyond the sequence: cellular organization of genome function. Cell, 128, 787-800. (Pubitemid 46273571)
2. Miele, A. and Dekker, J. (2008) Long-range chromosomal interactions and gene regulation. Mol. Biosyst., 4, 1046-1057.
3. Fraser, P. and Bickmore, W. (2007) Nuclear organization of the genome and the potential for gene regulation. Nature, 447, 413-417. (Pubitemid 46816747)
4. Dekker, J. (2008) Gene regulation in the third dimension. Science, 319, 1793-1794. (Pubitemid 351451557)
5. West, A.G. and Fraser, P. (2005) Remote control of gene transcription. Hum. Mol. Genet., 14, R101-R111. (Pubitemid 40542626)
6. Dekker, J., Rippe, K., Dekker, M. and Kleckner, N. (2002) Capturing chromosome conformation. Science, 295, 1306-1311. (Pubitemid 34157624)
7. 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 longrange interactions reveals folding principles of the human genome. Science, 326, 289-293.
8. 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.
9. Rousseau, M., Fraser, J., Ferraiuolo, M.A., Dostie, J. and Blanchette, M. (2011) Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. BMC Bioinformatics, 12, 414.
10. Wang, Z., Cao, R., Taylor, K., Briley, A., Caldwell, C. and Cheng, J. (2013) The properties of genome conformation and spatial gene interaction and regulation networks of normal and malignant human cell types. PLoS One, 8, e58793.
11. 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.
12. 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.
13. Wolfe, P. (1969) Convergence conditions for ascent methods. SIAM Rev., 11, 226-235.
14. Mateos-Langerak, J., Bohn, M., De Leeuw, W., Giromus, O., Manders, E.M.M., Verschure, P.J., Indemans, M.H.G., Gierman, H.J., Heermann, D.W. and Van Driel, R. (2009) Spatially confined folding of chromatin in the interphase nucleus. Proc. Natl Acad. Sci. USA, 106, 3812-3817.
15. Wang, Z., Eickholt, J. and Cheng, J. (2011) APOLLO: a quality assessment service for single and multiple protein models. Bioinformatics, 27, 1715-1716.
16. Zhang, Y. and Skolnick, J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins., 57, 702-710. (Pubitemid 39626992)
17. 1-Norm and Related Methods. North Holland/Elsevier, Amsterdam, pp. 405-416.
18. Hoffman, R.M. (1984) Altered methionine metabolism, DNA methylation et oncogene expression in carcinogenesis: A review and synthesis. Biochim. Biophys. Acta, 738, 49-87. (Pubitemid 14067989)
19. Ehrlich, M. (2009) DNA hypomethylation in cancer cells. Epigenomics, 1, 239-259.