Analysis of interactions between genomic loci through chromosome conformation capture (3C)

Current Protocols in Cell Biology

Volumn 1, Issue SUPPL.56, 2012, Pages

  Kaderi, Belal El ^a   Medler, Scott ^a   Ansari, Athar ^a  

^a WAYNE STATE UNIVERSITY   (United States)

Author keywords

Chromosome conformation; DNA element interaction; Yeast

Indexed keywords

RIBONUCLEASE A; CROSS LINKING REAGENT;

ARTICLE; CELL DIFFERENTIATION; CELL PROLIFERATION; CHROMATIN; CHROMOSOME; CHROMOSOME CONFORMATION CAPTURE ASSAY; CONFORMATION; CONTROLLED STUDY; CROSS LINKING; DENSITOMETRY; DNA PURIFICATION; DNA REPLICATION; DNA TEMPLATE; ELECTROPHORESIS; FUNGAL GENE; GENE EXPRESSION; GENE LOCUS; NONHUMAN; PRIORITY JOURNAL; RESTRICTION SITE; CHEMISTRY; GENETIC PROCEDURES; GENETICS; METABOLISM; METHODOLOGY; POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE;

CHROMATIN; CHROMOSOMES, FUNGAL; CROSS-LINKING REAGENTS; DENSITOMETRY; GENETIC TECHNIQUES; NUCLEIC ACID CONFORMATION; POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE;

EID: 84872676459     PISSN: 19342500     EISSN: 19342616     Source Type: Journal    
DOI: 10.1002/0471143030.cb2215s56     Document Type: Article

References (25)

1. Ansari, A. and Hampsey, M. 2005. A role for the CPF 3-end processing machinery in RNAP IIdependent gene looping. Genes Dev. 19:2969-2978.
2. Bastia, D. and Singh, S.K. 2011. "Chromosome kissing" and modulation of replication termination. Bioarchitecture 1:24-28.
3. Berger, A.B., Cabal, G.G., Fabre, E., Duong, T., Buc, H., Nehrbass, U.,Olivo-Marin, J.C., Gadal, O., and Zimmer, C. 2008. High-resolution statistical mapping reveals gene territories in live yeast. Nat. Methods 5:1031-1037.
4. Cavalli, G. 2007. Chromosome kissing. Curr. Opin. Genet. Dev. 17:443-450.
5. Dekker, J., Rippe, K., Dekker, M., and Kleckner, N. 2002. Capturing chromosome conformation. Science 295:1306-1311.
6. Dostie, J., Richmond, T.A., Arnaout, R.A., Selzer, R.R., Lee, W.L., Honan, T.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.
7. El Kaderi, B., Medler, S., Raghunayakula, S., and Ansari, A. 2009. Gene looping is conferred by activator-dependent interaction of transcription initiation and termination machineries. J. Biol. Chem. 284:25015-25025.
8. Laine, J.P., Singh, B.N., Krishnamurthy, S., and Hampsey, M. 2009. A physiological role for gene loops in yeast. Genes Dev. 23:2604-2609.
9. 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., Sandstrom, R., Bernstein, B., Bender, M.A., Groudine, M., Gnirke, A., Stamatoyannopoulos, J., Mirny, L.A., Lander, E.S., and Dekker, J. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289-293.
10. Medler, S., Al Husini, N., Raghunayakula, S., Mukundan, B., Aldea, A., and Ansari, A. 2011. Evidence for a complex of transcription factor IIB with poly(A) polymerase and cleavage factor 1 subunits required for gene looping. J. Biol. Chem. 286:33709-33718.
11. Miele, A. and Dekker, J. 2008. Long-range chromosomal interactions and gene regulation. Mol. Biosyst. 4:1046-1057.
12. O'Sullivan, J.M., Tan-Wong, S.M., Morillon, A., Lee, B., Coles, J., Mellor, J., and Proudfoot, N.J. 2004. Gene loops juxtapose promoters and terminators in yeast. Nat. Genet. 36:1014-1018.
13. Papantonis, A. and Cook, P.R. 2010. Genome architecture and the role of transcription. Curr. Opin. Cell Biol. 22:271-276.
14. Parada, L. and Misteli, T. 2002. Chromosome positioning in the interphase nucleus. Trends Cell Biol. 12:425-432.
15. Perkins, K.J., Lusic, M., Mitar, I., Giacca, M., and Proudfoot, N.J. 2008. Transcription-dependent gene looping of the HIV-1 provirus is dictated by recognition of pre-mRNAprocessing signals. Mol. Cell 29:56-68.
16. Sanyal, A., Bau, D., Marti-Renom, M.A., and Dekker, J. 2011. Chromatin globules: A common motif of higher order chromosome structure? Curr. Opin. Cell Biol. 23:325-331.
17. Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B., and de Laat, W. 2006. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38:1348-1354.
18. Singh, B.N. and Hampsey, M. 2007. A transcription-independent role for TFIIB in gene looping. Mol. Cell 27:806-816.
19. Singh, B.N., Ansari, A., and Hampsey, M. 2009. Detection of gene loops by 3C in yeast. Methods 48:361-367.
20. Spector, D.L. 2003. The dynamics of chromosome organization and gene regulation. Annu. Rev. Biochem. 72:573-608.
21. 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.
22. Tan-Wong, S.M., French, J.D., Proudfoot, N.J., and Brown, M.A. 2008. Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene. Proc. Natl. Acad. Sci. U.S.A. 105:5160-5165.
23. Voytas, D. 2001. Agarose gel electrophoresis. Curr. Protoc. Mol. Biol. 51:2.5A.1-2.5A.9.
24. Zhou, G.L., Xin, L., Song, W., Di, L.J., Liu, G., Wu, X.S., Liu, D.P., and Liang, C.C. 2006. Active chromatin hub of the mouse alpha-globin locus forms in a transcription factory of clustered housekeeping genes. Mol. Cell Biol. 26:5096-5105.
25. Zimmer, C. and Fabre, E. 2011. Principles of chromosomal organization: Lessons from yeast. J. Cell Biol. 192:723-733.