A torrent of data: Mapping chromatin organization using 5C and high-throughput sequencing

Methods in Enzymology

Volumn 513, Issue , 2012, Pages 113-141

  Fraser, James ^a   Ethier, Sylvain D ^a   Miura, Hisashi ^a   Dostie, Josée ^a  

^a MCGILL UNIVERSITY   (Canada)

Author keywords

3C carbon copy; Chromatin architecture; Chromosome conformation capture; Epigenetics; High throughput sequencing; Ion Torrent; Looping

Indexed keywords

HOX PROTEIN;

ARTICLE; CHROMATIN; DATA PROCESSING; GENE AMPLIFICATION; GENE CLUSTER; GENE EXPRESSION; GENE LIBRARY; GENE MAPPING; GENE SEQUENCE; HIGH THROUGHPUT SCREENING; HUMAN; PRIORITY JOURNAL; PURIFICATION; QUALITY CONTROL;

EID: 84865503094     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-391938-0.00005-7     Document Type: Chapter

References (46)

1. P.M. Ayton, and M.L. Cleary Transformation of myeloid progenitors by MLL oncoproteins is dependent on Hoxa7 and Hoxa9 Genes & Development 17 2003 2298 2307
2. D. Bau, A. Sanyal, B.R. Lajoie, E. Capriotti, M. Byron, and J.B. Lawrence The three-dimensional folding of the alpha-globin gene domain reveals formation of chromatin globules Nature Structural and Molecular Biology 18 2011 107 114
3. D. Blankenberg, G. Vonkuster, N. Coraor, G. Ananda, R. Lazarus, and M. Mangan Galaxy: A web-based genome analysis tool for experimentalists Current Protocols in Molecular Biology 2010 Chapter 19, Unit 19.10.11-21
4. T. Cremer, and M. Cremer Chromosome territories Cold Spring Harbor Perspectives in Biology 2 2010 a003889
5. J. Dekker, K. Rippe, M. Dekker, and N. Kleckner Capturing chromosome conformation Science 295 2002 1306 1311
6. J. Dostie, and J. Dekker Mapping networks of physical interactions between genomic elements using 5C technology Nature Protocols 2 2007 988 1002
7. J. Dostie, T.A. Richmond, R.A. Arnaout, R.R. Selzer, W.L. Lee, and T.A. Honan Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements Genome Research 16 2006 1299 1309
8. J. Dostie, Y. Zhan, and J. Dekker Chromosome conformation capture carbon copy technology Current Protocols in Molecular Biology 2007 Chapter 21, Unit 21.14
9. Z. Duan, M. Andronescu, K. Schutz, S. McIlwain, Y.J. Kim, and C. Lee A three-dimensional model of the yeast genome Nature 465 2010 363 367
10. S.D. Ethier, H. Miura, and J. Dostie Discovering genome regulation with 3C and 3C-related technologies Biochimica et Biophysica Acta 1819 5 2012 401 410
11. M.A. Ferraiuolo, M. Rousseau, C. Miyamoto, S. Shenker, X.Q. Wang, and M. Nadler The three-dimensional architecture of Hox cluster silencing Nucleic Acids Research 38 2010 7472 7484
12. J. Fraser, and J. Dostie 2009 http://Dostielab.biochem.mcgill.ca
13. J. Fraser, M. Rousseau, M. Blanchette, and J. Dostie Computing chromosome conformation Methods in Molecular Biology 674 2010 251 268
14. J. Fraser, M. Rousseau, S. Shenker, M.A. Ferraiuolo, Y. Hayashizaki, and M. Blanchette Chromatin conformation signatures of cellular differentiation Genome Biology 10 2009 R37
15. B. Giardine, C. Riemer, R.C. Hardison, R. Burhans, L. Elnitski, and P. Shah Galaxy: A platform for interactive large-scale genome analysis Genome Research 15 2005 1451 1455
16. J. Goecks, A. Nekrutenko, and J. Taylor Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biology 11 2010 R86
17. R. Kalhor, H. Tjong, N. Jayathilaka, F. Alber, and L. Chen Genome architectures revealed by tethered chromosome conformation capture and population-based modeling Nature Biotechnology 30 2011 90 98
18. E. Kroon, J. Krosl, U. Thorsteinsdottir, S. Baban, A.M. Buchberg, and G. Sauvageau Hoxa9 transforms primary bone marrow cells through specific collaboration with Meis1a but not Pbx1b The EMBO Journal 17 1998 3714 3725
19. B.R. Lajoie, and J. Dekker 2009 http://my5c.umassmed.edu/welcome/welcome. php
20. B.R. Lajoie, N.L. van Berkum, A. Sanyal, and J. Dekker My5C: Web tools for chromosome conformation capture studies Nature Methods 6 2009 690 691
21. B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biology 10 2009 R25
22. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
23. H. Li, and R. Durbin Fast and accurate long-read alignment with Burrows-Wheeler transform Bioinformatics 26 2010 589 595
24. H. Li, J. Ruan, and R. Durbin Mapping short DNA sequencing reads and calling variants using mapping quality scores Genome Research 18 2008 1851 1858
25. E. Lieberman-Aiden, N.L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, and A. Telling Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 2009 289 293
26. J.Q. Ling, T. Li, J.F. Hu, T.H. Vu, H.L. Chen, and X.W. Qiu CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1 Science 312 2006 269 272
27. A. Miele, N. Gheldof, T.M. Tabuchi, J. Dostie, and J. Dekker Mapping chromatin interactions by Chromosome Conformation Capture (3C) F.M. Ausubel, R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith, Current protocols in molecular biology 2006 John Wiley & Sons Hoboken, NJ 21.11.20 21.11.21
28. Z. Ning, A.J. Cox, and J.C. Mullikin SSAHA: A fast search method for large DNA databases Genome Research 11 2001 1725 1729
29. A. Pession, V. Martino, R. Tonelli, C. Beltramini, F. Locatelli, and G. Biserni MLL-AF9 oncogene expression affects cell growth but not terminal differentiation and is downregulated during monocyte-macrophage maturation in AML-M5 THP-1 cells Oncogene 22 2003 8671 8676
30. A. Pombo, and M.R. Branco Functional organisation of the genome during interphase Current Opinion in Genetics and Development 17 2007 451 455
31. M.M. Pomerantz, N. Ahmadiyeh, L. Jia, P. Herman, M.P. Verzi, and H. Doddapaneni The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer Nature Genetics 41 2009 882 884
32. J.M. Rothberg, W. Hinz, T.M. Rearick, J. Schultz, W. Mileski, and M. Davey An integrated semiconductor device enabling non-optical genome sequencing Nature 475 2011 348 352
33. D. Schmidt, P.C. Schwalie, C.S. Ross-Innes, A. Hurtado, G.D. Brown, and J.S. Carroll A CTCF-independent role for cohesin in tissue-specific transcription Genome Research 20 2010 578 588
34. M. Simonis, P. Klous, E. Splinter, Y. Moshkin, R. Willemsen, and E. de Wit Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C) Nature Genetics 38 2006 1348 1354
35. T.F. Smith, and M.S. Waterman Identification of common molecular subsequences Journal of Molecular Biology 147 1981 195 197
36. C.G. Spilianakis, and R.A. Flavell Long-range intrachromosomal interactions in the T helper type 2 cytokine locus Nature Immunology 5 2004 1017 1027
37. E. Splinter, H. Heath, J. Kooren, R.J. Palstra, P. Klous, and F. Grosveld CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus Genes & Development 20 2006 2349 2354
38. H. Suzuki, A.R. Forrest, E. van Nimwegen, C.O. Daub, P.J. Balwierz, and K.M. Irvine The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line Nature Genetics 41 2009 553 562
39. U. Thorsteinsdottir, G. Sauvageau, M.R. Hough, W. Dragowska, P.M. Lansdorp, and H.J. Lawrence Overexpression of HOXA10 in murine hematopoietic cells perturbs both myeloid and lymphoid differentiation and leads to acute myeloid leukemia Molecular and Cellular Biology 17 1997 495 505
40. B. Tolhuis, R.J. Palstra, E. Splinter, F. Grosveld, and W. de Laat Looping and Interaction between hypersensitive sites in the active beta-globin locus Molecular Cell 10 2002 1453 1465
41. I. Torrent/Applications 2011 http://www.iontorrent.com/applications/
42. I. Torrent/Applications 2012 http://www.invitrogen.com/site/us/en/home/ Products-and-Services/Applications/Sequencing/Semiconductor-Sequencing/ Publications.html
43. B.D. Towbin, P. Meister, and S.M. Gasser The nuclear envelope - A scaffold for silencing? Current Opinion in Genetics and Development 19 2009 180 186
44. M.A. Umbarger, E. Toro, M.A. Wright, G.J. Porreca, D. Bau, and S.H. Hong The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation Molecular Cell 44 2011 252 264
45. H. Würtele, and P. Chartrand Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology Chromosome Research 14 2006 477 495
46. Z. Zhao, G. Tavoosidana, M. Sjolinder, A. Gondor, P. Mariano, and S. Wang Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions Nature Genetics 38 2006 1341 1347