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Biology

يرتبط فخ كروموسوم لتحديد الحمض النووي تفاعلات طويلة المدى

doi: 10.3791/2621 Published: April 23, 2011

Materials

Name Company Catalog Number Comments
RPMI1640 medium Invitrogen 22400-105
acrylamide Invitrogen 15512-023
ATP solution, 10mM Invitrogen AM8110G
fetal bovine serum Invitrogen 16000-044
penicillin-streptomycin Invitrogen 15140-122
1M Tris pH8.0 Invitrogen AM9856
RNase A Invitrogen 12091-039
SDS Invitrogen 15525-017
urea Invitrogen 15505-035
BamH I New England Biolabs R0136T
Bgl II New England Biolabs R0144M
Dpn II New England Biolabs R0543T
Msp I New England Biolabs R0106S
dNTPs New England Biolabs N0447L
proteinase K New England Biolabs P8102S
T4 DNA ligase New England Biolabs M0202T
37% formaldehyde Sigma-Aldrich F8775
Bis-acrylamide Sigma-Aldrich 146072
dithiothreitol Sigma-Aldrich 43815
glycine Sigma-Aldrich 50046
PMSF Sigma-Aldrich 93482
proteinase inhibitor Sigma-Aldrich S8830
Nonidet P-40 Roche Group 11754599001
KlenTaq1 Ab peptides 1001
dCTP alpha P32 PerkinElmer, Inc. BLU513H250UC
PTC-100 Thermal Cycler MJ Research mjptc100
Power Supply Bio-Rad 164-5056
OmniPAGE Maxi Aurogene Life Science VS20D
Typhoon 9400 GE Healthcare 63-0055-78

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References

  1. Dekker, J., Rippe, K., Dekker, M., Kleckner, N. Capturing chromosome conformation. Science. 295, 1306-1311 (2002).
  2. Apostolou, E., Thanos, D. Virus Infection Induces NF-kappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression. Cell. 134, 85-96 (2008).
  3. Duan, Z. A three-dimensional model of the yeast genome. Nature. 465, 363-367 (2010).
  4. Lomvardas, S. Interchromosomal interactions and olfactory receptor choice. Cell. 126, 403-413 (2006).
  5. Murrell, A., Heeson, S., Reik, W. Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat Genet. 36, 889-893 (2004).
  6. Schoenfelder, S. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet. 42, 53-61 (2010).
  7. Spilianakis, C. G., Lalioti, M. D., Town, T., Lee, G. R., Flavell, R. A. Interchromosomal associations between alternatively expressed loci. Nature. 435, 637-645 (2005).
  8. Vakoc, C. R. Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol Cell. 17, 453-462 (2005).
  9. Xu, N., Tsai, C. L., Lee, J. T. Transient homologous chromosome pairing marks the onset of X inactivation. Science. 311, 1149-1152 (2006).
  10. Lieberman-Aiden, E. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 326, 289-293 (2009).
  11. Berkum, N. L. van Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp. (2010).
  12. Ling, J. Q. CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science. 312, 269-272 (2006).
  13. Dekker, J. The three 'C's of chromosome conformation capture: controls, controls, controls. Nat Methods. 3, 17-21 (2006).
يرتبط فخ كروموسوم لتحديد الحمض النووي تفاعلات طويلة المدى
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Cite this Article

Ling, J., Hoffman, A. R. Associated Chromosome Trap for Identifying Long-range DNA Interactions. J. Vis. Exp. (50), e2621, doi:10.3791/2621 (2011).More

Ling, J., Hoffman, A. R. Associated Chromosome Trap for Identifying Long-range DNA Interactions. J. Vis. Exp. (50), e2621, doi:10.3791/2621 (2011).

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