Rxivist logo

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

By Jonas Ibn-Salem, Miguel A. Andrade-Navarro

Posted 01 Feb 2018
bioRxiv DOI: 10.1101/257584 (published DOI: 10.1186/s12864-019-6088-0)

We present a computational method to gain knowledge of the three-dimensional structure of the genome from ChIP-seq datasets. While not designed to detect contacts, the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, genomic regions that interact with the protein binding-site via chromatin looping are co-immunoprecipitated and sequenced. This produces minor ChIP-seq signals around CTCF motif pairs at loop anchor regions. Together with genomic sequence features, these signals predict whether loop anchors interact or not. Our method, Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs (7C), is available as an R/Bioconductor package: http://bioconductor.org/packages/sevenC .

Download data

  • Downloaded 1,408 times
  • Download rankings, all-time:
    • Site-wide: 6,093 out of 84,482
    • In genomics: 996 out of 5,454
  • Year to date:
    • Site-wide: 40,839 out of 84,482
  • Since beginning of last month:
    • Site-wide: 39,812 out of 84,482

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News