Capturing Chromosome Conformation
10.1126/science.1067799
Crossref journal-article
American Association for the Advancement of Science (AAAS)
Science (221)
Abstract

We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in organisms from bacteria to human. Using the yeast Saccharomyces cerevisiae , we could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis. We also analyzed yeast chromosome III at the G 1 stage of the cell cycle. We found that chromatin is highly flexible throughout. Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring.

Bibliography

Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002). Capturing Chromosome Conformation. Science, 295(5558), 1306–1311.

Authors 4
  1. Job Dekker (first)
  2. Karsten Rippe (additional)
  3. Martijn Dekker (additional)
  4. Nancy Kleckner (additional)
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  44. In some cases a very small amount of ligation product was detected in the absence of cross-linking but this was always 5% or less than the amount detected after cross-linking with 1% formaldehyde.
  45. We thank Kleckner lab members for discussions. We are especially grateful to J. M. Perry and A. J. M. Walhout for valuable comments on the experiments and the manuscript. Part of the work by K.R. was done at the division “Biophysik der Makromoleküle” of the Deutsches Krebsforschungszentrum in Heidelberg. Supported by EMBO long-term fellowship ALTF-223-1998 and a fellowship from the Medical Foundation/Charles A. King Trust (J.D.) the Volkswagen Foundation program “Junior Research Groups at German Universities” (K.R.) and NIH grants GM44794 and GM25326 (N.K.).
Dates
Type When
Created 23 years ago (July 27, 2002, 5:35 a.m.)
Deposited 1 year, 7 months ago (Jan. 9, 2024, 5:25 p.m.)
Indexed 2 minutes ago (Aug. 25, 2025, 10 p.m.)
Issued 23 years, 6 months ago (Feb. 15, 2002)
Published 23 years, 6 months ago (Feb. 15, 2002)
Published Print 23 years, 6 months ago (Feb. 15, 2002)
Funders 0

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@article{Dekker_2002, title={Capturing Chromosome Conformation}, volume={295}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.1067799}, DOI={10.1126/science.1067799}, number={5558}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Dekker, Job and Rippe, Karsten and Dekker, Martijn and Kleckner, Nancy}, year={2002}, month=feb, pages={1306–1311} }