Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Ay, Ferhat ^a   Vu, Thanh H ^b   Zeitz, Michael J ^b   Varoquaux, Nelle ^c,d,e   Carette, Jan E ^f   Vert, Jean Philippe ^c,d,e   Hoffman, Andrew R ^b   Noble, William S ^a,g  

^a UNIVERSITY OF WASHINGTON   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c PSL RESEARCH UNIVERSITY   (France)

^d INSTITUT CURIE   (France)

^e INSERM U900   (France)

^f STANFORD UNIVERSITY   (United States)

^g University of Washington   (United States)

Author keywords

Chromatin conformation capture; Genome architecture; Leukemia; Multi locus chromatin contacts; Near haploid human cells; Three dimensional modeling

Indexed keywords

AGAROSE; CHROMATIN;

ARTICLE; BIOASSAY; CHROMOSOME STRUCTURE; CONFORMATION; CONTROLLED STUDY; GENE LOCUS; GENETIC DISTANCE; GENOME ANALYSIS; GENOME IMPRINTING; HAPLOIDY; HUMAN; HUMAN CELL; POLYMERASE CHAIN REACTION; RESTRICTION MAPPING; SEQUENCE ANALYSIS; TETHERED MULTIPLE CHROMATIN CONFORMATION CAPTURE ASSAY; CHROMATIN; GENETICS; HUMAN GENOME; LEUKEMIA; PATHOLOGY; TUMOR CELL LINE;

EUKARYOTA;

CELL LINE, TUMOR; CHROMATIN; GENOME, HUMAN; HUMANS; LEUKEMIA; RESTRICTION MAPPING;

EID: 84925254058     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1236-7     Document Type: Article

References (36)

1. Langer-Safer PR, Levine M, Ward DC. Immunological method for mapping genes on Drosophila polytene chromosomes. Proc Nat Acad Sci USA. 1982; 79(14):4381-5.
2. Manders EMM, Visser AE, Koppen A, de Leeuw WC, van Liere R, Brakenhof GJ, et al. Four-dimensional imaging of chromatin dynamics during the assembly of the interphase nucleus. Chromosome Res. 2003; 11:537-47.
3. Cremer M, Grasser F, Lanctot C, Muller S, Neusser M, Zinner R, Solovei I, et al. Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes. Methods Mol Biol. 2008; 463:205-39.
4. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009; 326(5950):289-93.
5. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012; 485(7398):376-80.
6. Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature. 2013; 503(7475):290-4.
7. Zhang Y, McCord RP, Ho Y, Lajoie BR, Hildebrand DG, Simon AC, et al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell. 2012; 148:1-14.
8. Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, et al. A three-dimensional model of the yeast genome. Nature. 2010; 465:363-7. [PMC2874121].
9. Umbarger MA, Toro E, Wright MA, Porreca GJ, Bau D, Hong S, et al. The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation. Molecular Cell. 2011; 44:252-64.
10. Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, et al. Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome. Cell. 2012; 148(3):458-72.
11. Ay F, Bunnik EM, Varoquaux N, Bol SM, Prudhomme J, Vert JP, et al. Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression. Genome Res. 2014; 24:974-88.
12. Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, et al. Organization of the mitotic chromosome. Science. 2013; 342(6161):948-53.
13. Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol. 2011; 30:90-8.
14. Cook PR. The organization of replication and transcription. Science. 1999; 284:1790-5.
15. Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, et al. Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation. Cell. 2012; 148:84-98.
16. Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature. 2004; 430:88-93.
17. Gavrilov AA, Chetverina HV, Chermnykh ES, Razin SV, Chetverin AB. Quantitative analysis of genomic element interactions by molecular colony technique. Nucleic Acids Res. 2014; 42(5):e36.
18. Bolzer A, Kreth G, Solovei I, Koehler D, Saracoglu K, Fauth C, et al. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol. 2005; 3(5):e157.
19. Kotecki M, Reddy PS, Cochran BH. Isolation and characterization of a near-haploid human cell line. Exp Cell Res. 1999; 252(2):273-80.
20. Bürckstümmer T, Banning C, Hainzl P, Schobesberger R, Kerzendorfer C, Pauler FM, et al. A reversible gene trap collection empowers haploid genetics in human cells. Nat Methods. 2013; 10(10):965-71.
21. Bartolomei M, Zemel S, Tilghman SM. Parental imprinting of the mouse H19 gene. Nature. 1991; 351(6322):153-5.
22. Ling JQ, Li T, Hu JF, Vu TH, Chen HL, Qiu XW, et al. CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science. 2006; 312(5771):269-72.
23. Vu T, Nguyen AH, Hoffman AR. Loss of IGF2 imprinting is associated with abrogation of long-range intrachromosomal interactions in human cancer cells. Hum Mol Genet. 2010; 19(5):901-19.
24. Murrell A, Heeson S, Reik W. Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat Genetics. 2004; 36(8):889-93.
25. ENCODE Project Consortium. An Integrated Encyclopedia of DNA Elements in the Human Genome. Nature. 2012; 489:57-74. [PMC3439153].
26. Qiu X, Vu TH, Lu Q, Ling JQ, Li T, Hou A, et al. A complex deoxyribonucleic acid looping configuration associated with the silencing of the maternal Igf2 allele. Mol Endocrinol. 2008; 22(6):1476-88.
27. Varoquaux N, Ay F, Noble WS, Vert JP. A statistical approach for inferring the 3D structure of the genome. Bioinformatics. 2014; 30(12):i26-i33.
28. Ferraiuolo MA, Rousseau M, Miyamoto C, Shenker S, Wang XQ, Nadler M, et al. The three-dimensional architecture of Hox cluster silencing. Nucleic Acids Res. 2010; 21:7472-84.
29. Carette JE, Guimaraes CP, Varadarajan M, Park A S, Wuethrich I, Godarova A, et al. Haploid genetic screens in human cells identify host factors used by pathogens. Science. 2009; 326(5957):1231-5.
30. Mahy NL, Perry PE, Bickmore WA. Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J Cell Biol. 2002; 159:753-63.
31. Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature. 2013; 502(7469):59-64.
32. Bau D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, et al. The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol. 2011; 18:107-14.
33. Zhang Z, Li G, Toh KC, Sung WK. Inference of spatial organizations of chromosomes using semi-definite embedding approach and Hi-C data In: Deng M, Jiang R, Sun F, Zhang X, editors. Proceedings of the 17th International Conference on Research in Computational Molecular, Biology, Volume 7821 of Lecture Notes in Computer Science. Berlin, Heidelberg: Springer-Verlag: 2013. p. 317-332.
34. Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods. 2012; 9:999-1003.
35. Ay F, Bailey TL, Noble WS. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res. 2014; 24:999-1011.
36. Fudenberg G, Mirny LA. Higher-order chromatin structure: bridging physics and biology. Curr Opin Genet Dev. 2012; 22(2):115-24.