Chromatin-bound protein colocalization analysis using bedGraph2Cluster and PanChIP

Hanjun Lee; Ioannis Sanidas; Nicholas J Dyson; Michael S Lawrence

doi:10.1016/j.xpro.2022.101991

Chromatin-bound protein colocalization analysis using bedGraph2Cluster and PanChIP

STAR Protoc. 2023 Mar 17;4(1):101991. doi: 10.1016/j.xpro.2022.101991. Epub 2023 Jan 5.

Authors

Hanjun Lee¹, Ioannis Sanidas², Nicholas J Dyson³, Michael S Lawrence⁴

Affiliations

¹ Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. Electronic address: hanjun@mit.edu.
² Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA; Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY 14203, USA.
³ Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.
⁴ Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Electronic address: mslawrence@mgh.harvard.edu.

Abstract

Computational pipelines for chromatin immunoprecipitation sequencing analysis can neglect colocalization events that occur in a mere subset of the genome. Here, we detail a streamlined approach for assessing colocalization of chromatin-bound proteins using the bedGraph2Cluster and PanChIP algorithms. Using histone modifications as an example, bedGraph2Cluster performs clustering analysis on chromatin binding patterns of target proteins. PanChIP then compares these clusters with a reference library of chromatin binding patterns and measures the overlap in peaks, capturing the heterogeneity in chromatin binding and colocalization patterns. For complete details on the use and execution of this protocol, please refer to Sanidas et al. (2022).¹.

Keywords: Bioinformatics; ChIPseq; Sequence analysis.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Chromatin Immunoprecipitation / methods
Chromatin Immunoprecipitation Sequencing / methods
Chromatin* / genetics
Genome
High-Throughput Nucleotide Sequencing* / methods

Substances

Chromatin

Grants and funding

R01 CA236538/CA/NCI NIH HHS/United States