UMass Chan Medical School Faculty Publications


Simultaneous profiling of multiple chromatin proteins in the same cells

UMMS Affiliation

Department of Molecular, Cell, and Cancer Biology; Program in Bioinformatics and Integrative Biology; Program in Systems Biology; Garber Lab; Graduate School of Biomedical Sciences

Publication Date


Document Type



Amino Acids, Peptides, and Proteins | Bioinformatics | Cell Biology | Genomics | Molecular Biology | Nucleic Acids, Nucleotides, and Nucleosides


Methods derived from CUTandRUN and CUTandTag enable genome-wide mapping of the localization of proteins on chromatin from as few as one cell. These and other mapping approaches focus on one protein at a time, preventing direct measurements of co-localization of different chromatin proteins in the same cells and requiring prioritization of targets where samples are limiting. Here, we describe multi-CUTandTag, an adaptation of CUTandTag that overcomes these hurdles by using antibody-specific barcodes to simultaneously map multiple proteins in the same cells. Highly specific multi-CUTandTag maps of histone marks and RNA Polymerase II uncovered sites of co-localization in the same cells, active and repressed genes, and candidate cis-regulatory elements. Single-cell multi-CUTandTag profiling facilitated identification of distinct cell types from a mixed population and characterization of cell-type-specific chromatin architecture. In sum, multi-CUTandTag increases the information content per cell of epigenomic maps, facilitating direct analysis of the interplay of different chromatin proteins.


H3K27ac, H3K27me3, RNA polymerase, chromatin, histones, profiling, single-cell, transcription

DOI of Published Version



Gopalan S, Wang Y, Harper NW, Garber M, Fazzio TG. Simultaneous profiling of multiple chromatin proteins in the same cells. Mol Cell. 2021 Nov 18;81(22):4736-4746.e5. doi: 10.1016/j.molcel.2021.09.019. Epub 2021 Oct 11. PMID: 34637755; PMCID: PMC8604773. Link to article on publisher's site


This article is based on a previously available preprint in bioRxiv.

Related Resources

Link to Article in PubMed

Journal/Book/Conference Title

Molecular cell

PubMed ID