Global Chromatin Profiling

Global chromatin profiling technology is a mass spectrometry-based assay to identify and quantify post-translational modifications on histone proteins from bulk chromatin. We use quantitative standards to enable consistent measurements across large sample sets. Around 60 different combinations of histone modifications can be quantified on H3, with even more possible combinations on H4, H2A (including isoforms), and H2B.

We like to think of chromatin profiling as orthogonal to ChIP-Seq. Instead of characterizing one histone mark at a time with locus resolution across the genome, we profile almost all combinations of histone marks together in bulk chromatin with no genomic resolution. The technique is particularly useful in assessing the functional consequences of genetic mutations to the epigenetic machinery, and has been used to discover novel cancer alleles. Ultiamtely, it is a signature generation technology that can be employed to make connections among biological conditions and perturbations An application of the technology can be found in our recent Nature Genetics paper.

GCP Signatures of knockdowns of epigenetic genes by shRNA

Each gene was knocked down with a single hairpin in triplicate in 293T cells. Cells are colored by z-score relative to the row. Clustering was performed using a Pearson correlation metric. Inset shows the signature of knocking down the EZH2 methyltransferase.