Open AccessMARCC (Matrix‐Assisted Reader Chromatin Capture): An Antibody‐Free Method to Enrich and Analyze Combinatorial Nucleosome Modifications
Author(s) -
Su Zhangli,
Denu John M.
Publication year - 2015
Publication title -
current protocols in molecular biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.533
H-Index - 42
eISSN - 1934-3647
pISSN - 1934-3639
DOI - 10.1002/0471142727.mb2132s111
Subject(s) - nucleosome , chromatin , computational biology , matrix (chemical analysis) , computer science , chemistry , biology , genetics , dna , chromatography
Combinatorial patterns of histone modifications are key indicators of different chromatin states. Most of the current approaches rely on the usage of antibodies to analyze combinatorial histone modifications. Here we detail an antibody‐free method named MARCC ( M atrix‐ A ssisted R eader C hromatin C apture) to enrich combinatorial histone modifications. The combinatorial patterns are enriched on native nucleosomes extracted from cultured mammalian cells and prepared by micrococcal nuclease digestion. Such enrichment is achieved by recombinant chromatin‐interacting protein modules, or so‐called reader domains, which can bind in a combinatorial modification‐dependent manner. The enriched chromatin can be quantified by immunoblotting or mass spectrometry for the co‐existence of histone modifications, while the associated DNA content can be analyzed by qPCR or next‐generation sequencing. Altogether, MARCC provides a reproducible, efficient and customizable solution to enrich and analyze combinatorial histone modifications. © 2015 by John Wiley & Sons, Inc.