Normalization of a chromosomal contact map

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Cournac, Axel ^a   Marie Nelly, Hervé ^b,c,d   Marbouty, Martial ^b,c   Koszul, Romain ^b,c   Mozziconacci, Julien ^a  

^a UNIVERSITÉ PIERRE ET MARIE CURIE   (France)

^b INSTITUT PASTEUR   (France)

^c CNRS   (France)

^d SORBONNE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTION FACTOR CTCF; TRANSFER RNA;

ARTICLE; CHROMOSOMAL CONTACT MAP; CHROMOSOME STRUCTURE; CONTROLLED STUDY; DATA ANALYSIS; DNA STRUCTURE; ERROR; GENE INTERACTION; GENE MAPPING; GENETIC DATABASE; HUMAN; NONHUMAN; QUANTITATIVE ANALYSIS; SACCHAROMYCES CEREVISIAE;

ANIMALS; BINDING SITES; CHROMOSOME MAPPING; CHROMOSOMES, FUNGAL; CHROMOSOMES, HUMAN; DNA POLYMERASE III; DNA, CIRCULAR; GENOME; HUMANS; REPRESSOR PROTEINS; RNA, TRANSFER; ROC CURVE; SACCHAROMYCES CEREVISIAE;

MAMMALIA; SACCHAROMYCETALES;

EID: 84865483795     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-436     Document Type: Article

References (30)

1. Misteli T. Beyond the sequence: cellular organization of genome function. Cell 2007, 128(4):787-800. 10.1016/j.cell.2007.01.028, 17320514.
2. Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 2012, 148(1-2):84-98. 10.1016/j.cell.2011.12.014, 22265404.
3. Knott SRV, Peace JM, Ostrow AZ, Gan Y, Rex AE, Viggiani CJ, Tavaré S, Aparicio OM. Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae. Cell 2012, 148(1-2):99-111. 10.1016/j.cell.2011.12.012, 22265405.
4. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science 2002, 295:1306-1311. 10.1126/science.1067799, 11847345.
5. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 2006, 38(11):1348-1354. 10.1038/ng1896, 17033623.
6. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, Green RD, Dekker J. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 2006, 16(10):1299-1309. 10.1101/gr.5571506, 1581439, 16954542.
7. Hakim O, Misteli T. SnapShot: Chromosome confirmation capture. Cell 2012, 148(5):1068.e1-1068.e2.
8. 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.
9. Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol 2012, 30:90-98.
10. Zhang Y, McCord RP, Ho YJ, Lajoie BR, Hildebrand DG, Simon AC, Becker MS, Alt FW, Dekker J. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell 2012, 148(5):908-921. 10.1016/j.cell.2012.02.002, 3320767, 22341456.
11. 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):376-380. 10.1038/nature11082, 3356448, 22495300.
12. Tanizawa H, Iwasaki O, Tanaka A, Capizzi JR, Wickramasinghe P, Lee M, Fu Z, ichi Noma K. Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. Nucleic Acids Res 2010, 38(22):8164-8177. 10.1093/nar/gkq955, 3001101, 21030438.
13. Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS. A three-dimensional model of the yeast genome. Nature 2010, 465(7296):363-367. 10.1038/nature08973, 2874121, 20436457.
14. Rodley CDM, Bertels F, Jones B, O'Sullivan JM. Global identification of yeast chromosome interactions using Genome conformation capture. Fungal Genet Biol 2009, 46(11):879-886. 10.1016/j.fgb.2009.07.006, 19628047.
15. 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.
16. Dekker J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat Methods 2006, 3:17-21. 10.1038/nmeth823, 16369547.
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. Gascoigne DK, Ryan MP, Taft J, Mattick JS. Reassessmentof the Hi-C analysis of human genome architecture. 2011,
19. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36(16):e105. 10.1093/nar/gkn425, 2532726, 18660515.
20. Shore D, Langowski J, Baldwin RL. DNA flexibility studied by covalent closure of short fragments into circles. Proc Natl Acad Sci U S A 1981, 78(8):4833-4837. 10.1073/pnas.78.8.4833, 320266, 6272277.
21. Du Q, Smith C, Shiffeldrim N, Vologodskaia M, Vologodskii A. Cyclization of short DNA fragments and bending fluctuations of the double helix. Proc Natl Acad Sci U S A 2005, 102(15):5397-5402. 10.1073/pnas.0500983102, 556251, 15809441.
22. Ruault M, Meyer AD, Loïodice I, Taddei A. Clustering heterochromatin: Sir3 promotes telomere clustering independently of silencing in yeast. J Cell Biol 2011, 192(3):417-431. 10.1083/jcb.201008007, 3101097, 21300849.
23. Therizols P, Duong T, Dujon B, Zimmer C, Fabre E. Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres. Proc Natl Acad Sci U S A 2010, 107(5):2025-2030. 10.1073/pnas.0914187107, 2836701, 20080699.
24. Tjong H, Gong K, Chen L, Alber F. Physical tethering and volume exclusion determine higher-order genome organization in budding yeast. Genome Res 2012, 22(7):1295-1305. 10.1101/gr.129437.111, 22619363.
25. Rienzi SCD, Collingwood D, Raghuraman MK, Brewer BJ. Fragile genomic sites are associated with origins of replication. Genome Biol Evol 2009, 1:350-363. 2817429, 20333204.
26. Haeusler RA, Pratt-Hyatt M, Good PD, Gipson TA, Engelke DR. Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes. Genes Dev 2008, 22(16):2204-2214. 10.1101/gad.1675908, 2518813, 18708579.
27. Thompson M, Haeusler RA, Good PD, Engelke DR. Nucleolar clustering of dispersed tRNA genes. Science 2003, 302(5649):1399-1401. 10.1126/science.1089814, 14631041.
28. Phillips JE, Corces VG. CTCF: master weaver of the genome. Cell 2009, 137(7):1194-1211. 10.1016/j.cell.2009.06.001, 3040116, 19563753.
29. Botta M, Haider S, Leung IXY, Lio P, Mozziconacci J. Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide. Mol Syst Biol 2010, 6:426. 3010120, 21045820.
30. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.