Capturing Chromosome Conformation

@article{Dekker2002CapturingCC,
  title={Capturing Chromosome Conformation},
  author={Job Dekker and Karsten Rippe and Martinus Bernardus Dekker and Nancy Kleckner},
  journal={Science},
  year={2002},
  volume={295},
  pages={1306 - 1311}
}
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… 

Topics from this paper

A Three-Dimensional Model of the Yeast Genome
TLDR
A method to globally capture intra- and inter-chromosomal interactions is developed and applied to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae, which recapitulates known features of genome organization, thereby validating the method, and identifies new features.
A Three-Dimensional Model of the Yeast Genome
TLDR
A method to globally capture intra- and inter-chromosomal interactions is developed and applied to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae, which recapitulates known features of genome organization, thereby validating the method, and identifies new features.
Mapping Chromatin Interactions by Chromosome Conformation Capture
TLDR
This unit describes detailed protocols for performing 3C with yeast Saccharomyces cerevisiae and mammalian cells.
Dynamic Trans Interactions in Yeast Chromosomes
TLDR
A case of inducible trans interaction in chromosomes of the budding yeast S. cerevisiae is described, where special DNA sequences, inserted in two ectopic chromosomal loci positioned in trans, pair with one another in an in Ducible manner.
Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions
TLDR
An integrated computational-molecular study that produces an ensemble of high-resolution 3-dimensional conformations of the budding yeast genome supports a link between structure and transcription that occurs within the context of a flexible genome organization.
Analysis of interactions between genomic loci through Chromosome Conformation Capture (3C).
TLDR
A modified 3C procedure is described that can detect transient, short-range interactions of DNA elements separated by a distance of less than 700 bp and can be used for detecting similar interactions of other genomic regions.
Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
TLDR
A computational method is developed to translate the TCC data into physical chromatin contacts in a population of three-dimensional genome structures, demonstrating that the indiscriminate properties of interchromosomal interactions are consistent with the well-known architectural features of the human genome.
Detecting Spatial Chromatin Organization by Chromosome Conformation Capture II: Genome-Wide Profiling by Hi-C.
TLDR
Two alternative methods for Hi-C are described, depending on the size of the genome, and the major computational approaches to convert the raw sequencing data into meaningful models of how genomes are organized are discussed.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 37 REFERENCES
Collisions between yeast chromosomal loci in vivo are governed by three layers of organization.
TLDR
It is suggested that pairing may exist to promote juxtaposition of homologous regions within irregular genome complements, which provides a framework for assessing the role of chromosome disposition in cellular processes such as DNA repair and gene expression.
Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure.
The recent determination of the complete sequence of chromosome III from the yeast Saccharomyces cerevisiae allows, for the first time, the investigation of the long range primary structure of a
Clustering of meiotic double-strand breaks on yeast chromosome III.
  • F. Baudat, A. Nicolas
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 1997
TLDR
The distribution of meiotic DSBs along the 340 kb of chromosome III indicates that they are likely to initiate most crossovers along chromosome III, but some discrepancies remain to be explained.
Meiotic chromosomes: integrating structure and function.
TLDR
The current article reviews recent information on diverse aspects of chromosome morphogenesis, notably relationships between sisters, development of axial structure, and variations in chromatin status in an historical context.
Chromosomal Addresses of the Cohesin Component Mcd1p
TLDR
The mapping of new Mcd1p-binding sites (cohesin-associated regions [CARs]) in single-copy sequences of several chromosomes establish their spacing, their sequestration to intergenic regions, and their association with AT-rich sequences as general genomic properties of CARs.
Polymer models for interphase chromosomes.
TLDR
The overall geometry of chromosomes in mammalian cells during interphase is analyzed and makes a testable prediction: that for two markers a given number of base pairs apart on a given chromosome, the average geometric separation is larger if the configuration is near one end of the chromosomes than if it is near the center of the chromosome.
Chromatin organization at meiosis
  • P. Moens, R. Pearlman
  • Biology, Medicine
    BioEssays : news and reviews in molecular, cellular and developmental biology
  • 1988
TLDR
The dissection of meiotic chromosome structures has become a realistic challenge through the arrival of isolated symptonemal complexes, monoclonal and polyclonal antibodies against SCs, the possibility for screening expression libraries for genes that encode SC proteins, the isolation of SC‐associated DNA, and the development of techniques for the in situ recognition of DNA sequences in the context of the meiotic chromosomes structure.
Chromosome bands, their chromatin flavors, and their functional features.
  • G. Holmquist
  • Biology, Medicine
    American journal of human genetics
  • 1992
To show that the input pattern of chromosomal mutations is highly organized relative to the band patterns along human chromosomes, a new term, "metaphase chromatin flavor," is introduced. Five
...
1
2
3
4
...