Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling.

ABSTRACT:

Background

Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mechanism of gene expression regulation. Chromosome Conformation Capture Carbon Copy (5C) and its variant Hi-C are techniques used to measure the interaction frequency (IF) between specific regions of the genome. Our goal is to use the IF data generated by these experiments to computationally model and analyze three-dimensional chromatin organization.

Results

We formulate a probabilistic model linking 5C/Hi-C data to physical distances and describe a Markov chain

SUBMITTER: Rousseau M 

PROVIDER: S-EPMC3245522 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature