Publications from the Lab


Ferraiuolo MA, Rousseau M, Miyamoto C, Shenker S, Wang XQ, Nadler M, Blanchette M, and Dostie J., The three-dimensional architecture of Hox cluster silencing., Nucleic Acids Research, Nov 1 2010 Link

Crutchley JL, Wang XQ, Ferraiuolo MA, Dostie J., Chromatin conformation signatures: ideal human disease biomarkers? Biomarkers in Medecine, Aug 4 2010 Link

Fraser J, Rousseau M, Blanchette M, Dostie J., Computing chromosome conformation. Methods in Molecular Biology: Computation Biology of Transcription Factor Binding, 2010 Link

Fraser, J., Rousseau, M., Shenker, S., Ferraiuolo, M., Hayashizaki, Y., Blanchette, M., and Dostie, J., Chromatin conformation signatures of cellular differentiation., Genome Biology, Apr 19 2009, Link

- Raw data is available for download here.

Resources


Chromosome Conformation Capture (3C)

Dekker, J., Rippe, K., Dekker, M., and Kleckner, N. (2002) Capturing Chromosome Conformation, Science 295, 1306-1311.

Dekker, J. (2003) A closer look at long-range chromosomal interactions, Trends Biochem. Sci. 28, 277-280.

Gheldof, N., and Dekker, J. (2004) Spatial organization of genomes, Current Genomics 5, 157-168.

Splinter, E., Grosveld, F., and de Laat, W. (2004) 3C technology: analyzing the spatial organization of genomic loci in vivo., Methods Enzymol. 375, 493-507.

Dekker, J. (2006) The 3 C's of Chromosome Conformation Capture: Controls, Controls, Controls, Nat Methods 3, 17-21.

Miele, A., Gheldof, N., Tabuchi, T. M., Dostie, J., and Dekker, J. (2006) Mapping chromatin interactions by Chromosome Conformation Capture (3C), in Current Protocols in Molecular Biology (Ausubel, F. M., R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith, and K. Struhl, Ed.), pp 21.11.21-21.11-20, John Wiley & Sons, Hoboken, N.J.

Wurtele, H., and Chartrand, P. (2006) Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology, Chromosome Res 14, 477-495.

Lanzuolo, C., Roure, V., Dekker, J., Bantignies, F., and Orlando, V. (2007) Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex, Nat Cell Biol 9, 1167-1174.

Chromosome Conformation Capture Carbon Copy (5C)

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.

Dostie, J., and Dekker, J. (2007) Mapping networks of physical interactions between genomic elements using 5C technology, Nat Protoc 2, 988-1002.

Dostie, J., Zhan, Y., and Dekker, J. (2007) High-throughput mapping of chromatin interactions using 5C technology, in Current Protocols in Molecular Biology (Ausubel, F. M., R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith, and K. Struhl, Ed.), John Wiley & Sons, Hoboken, N.J.

Dostie, J., Zhan, Y., and Dekker, J. (2007) Chromosome conformation capture carbon copy technology, Curr Protoc Mol Biol Chapter 21, Unit 21 14.