Mapping Cis- and Trans- chromatin interaction networks using chromosome conformation capture (3C)

Methods in Molecular Biology

Volumn 464, Issue , 2008, Pages 105-121

  Miele, Adriana ^a   Dekker, Job ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

Chromatin looping; DNA; Formaldehyde crosslinking; Long range gene regulation; Spatial organization; Trans regulation

Indexed keywords

MAMMALIA; SACCHAROMYCES CEREVISIAE;

EID: 60349092237     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-461-6_7     Document Type: Article

References (12)

1. Drissen, R., Palstra, R., Gillemano, N., Splinter, E., Grosveld, F., Philipsen, S., and de Laat, W. (2004) The active spatial organization of the β-globin locus requires the transcription factor EKLF. Genes Dev. 18, 2485-2490.
2. Vakoc, C., Letting, D.L., Gheldof, N., Sawado, T., Bender, M.A., Groudine, M., Weiss, M.J., Dekker, J., and Blobel, G.A. (2005) Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol. Cell 17, 453-462.
3. Dekker, J. (2002) Capturing chromosome conformation. Science 295,1306-1311.
4. Gheldof, N., Tabuchi, T.M., and Dekker, J. (2006) The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications. Proc. Natl. Acad. Sci. USA 103, 12463-12468.
5. Tolhuis, B., Palstra, R.J., Splinter, E., Grosveld, F., and de Laat, W. (2002) Looping interaction between hypersensitive sites in the active beta-globin locus. Mol. Cell 10, 1435-1465.
6. Palstra, R.J., Tolhuis, B., Splinter, E., Nijmeijer, R., Grosveld, F., and de Laat, W. (2003) The β-globin nuclear compartment in development and erythroid differentiation. Nat. Genet. 25, 190-194.
7. Dostie, J., Richmond, R.A., Arnaout, R.A., Selzer, R.R., Lee, W.L., Honan,. A., Rubio, E.D., Krumm, A., Lamb, J., Nusbaum, C., Green, R.D., and Dekker, J. (2006) Chromosome conformation capture carbon copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Res. 16, 1299-1309.
8. Liu, Z. and Garrard, W.T. (2005) Long-range interactions between three transcriptional enhancers, active Vkappa gene promoters, and a 3? boundary sequence spanning 46 kilobases. Mol. Cell. Biol. 25, 3220-3231.
9. Murrell, A., Heeson, S., and Reik, W. (2004) Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat. Genet. 36, 889-893.
10. Spilianakis, C.G., Lalioti, M.D., Town, T., Lee, G.R., and Flavell, R.A. (2005) Interchromosomal associations between alternatively expressed loci. Nature 435, 637-645.
11. Lomvardas, S., Barnea, G., Pisapia, D.J., Mendelsohn, M., Kirkland, J., and Axel, R. (2006) Interchromosomal interactions and olfactory receptor choice. Cell 126, 403-413.
12. Dekker, J. (2006) The three C's of chromosome conformation capture: controls, controls, controls. Nat. Methods 3, 17-21.