MARCC (Matrix‐Assisted Reader Chromatin Capture): ChIP‐less Analysis Of Chromatin States

Abstract

Histone post-translational modifications (PTMs) are key epigenetic regulators in chromatin-based processes. The combinations of histone PTMs rather than individual PTMs are thought to define functional chromatin states. Here we demonstrate MARCC, an antibody-free method for interrogating epigenetic states. At the heart of the workflow are recombinant chromatin reader domains, which target distinct chromatin states with combinatorial PTM patterns. Utilizing combinatorial histone peptide microarray, we showed three reader domains displayed greater specificity towards combinatorial PTM patterns than corresponding commercial antibodies. Such specific recognitions were employed to develop MARCC. We successfully applied MARCC to capture unique chromatin states and quantitatively profiled inter-connections between nucleosomal histone PTMs. A newly identified signature that harbored H3K4me0, H3K9me2/3, H3K79me0 and H4K20me2/3 within the same nucleosome was enriched in heterochromatin, as revealed by the associated DNA. Our results suggest the broad utility of recombinant reader domains as an enrichment tool specific to combinatorial PTM patterns. The reader affinity platform is compatible with downstream analyses to investigate the physical co-existence of nucleosomal PTM states associated with specific genomic loci. Collectively, the reader-based workflow will greatly facilitate our understanding of how distinct chromatin states and reader domains function in gene regulatory mechanisms. This work was supported by National Institutes of Health (Grant #GM059785-15/P250VA).