C3D: a tool to predict 3D genomic interactions between cis-regulatory elements

Tahmid Mehdi; Swneke D Bailey; Paul Guilhamon; Mathieu Lupien

doi:10.1093/bioinformatics/bty717

C3D: a tool to predict 3D genomic interactions between cis-regulatory elements

Bioinformatics. 2019 Mar 1;35(5):877-879. doi: 10.1093/bioinformatics/bty717.

Authors

Tahmid Mehdi^{1

2}, Swneke D Bailey¹, Paul Guilhamon¹, Mathieu Lupien^{1

3

4}

Affiliations

¹ Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
² Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada.
³ Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
⁴ Ontario Institute for Cancer Research, Toronto, ON, Canada.

PMID: 30816925
DOI: 10.1093/bioinformatics/bty717

Abstract

Motivation: The 3D genome architecture influences the regulation of genes by facilitating chromatin interactions between distal cis-regulatory elements and gene promoters. We implement Cross Cell-type Correlation based on DNA accessibility (C3D), a customizable computational tool that predicts chromatin interactions using an unsupervised algorithm that utilizes correlations in chromatin measurements, such as DNaseI hypersensitivity signals.

Results: C3D accurately predicts 32.7%, 18.3% and 24.1% of interactions, validated by ChIA-PET assays, between promoters and distal regions that overlie DNaseI hypersensitive sites in K562, MCF-7 and GM12878 cells, respectively.

Availability and implementation: Source code is open-source and freely available on GitHub (https://github.com/LupienLabOrganization/C3D) under the GNU GPLv3 license. C3D is implemented in Bash and R; it runs on any platform with Bash (≥4.0), R (≥3.1.1) and BEDTools (≥2.19.0). It requires the following R packages: GenomicRanges, Sushi, data.table, preprocessCore and dynamicTreeCut.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromatin Immunoprecipitation
Genome*
Genomics*
Regulatory Sequences, Nucleic Acid
Software

Grants and funding

CIHR/Canada