Fig. 4
From: Multiple epigenetic factors co-localize with HMGN proteins in A-compartment chromatin
Chromatin profiling by ChIP–MS identifies proteins that reside nucleosome-long proximity to HMGN-occupied regions of chromatin. A Schematic overview of ChIP–MS assay. Mouse embryonic stem cells and MEF cells were cross-linked, and the chromatin was isolated, sonicated, and immunoprecipitated. DKO cells served as a negative control. Overall, there were 16 samples: two immunoprecipitations (HMGN1 and HMGN2), two cell types (ES and MEF), two genotypes (WT and DKO), and two biological replicates. Proteins, co-purified with HMGN and identified by UHPLC/MS/MS, represent HMGN binding partners. B ChIP DNA visualized by the Agilent TapeStation System after the optimized sonication step. More than 70% of total DNA fragments ranged from shorter than 505 bp to longer than 58 bp. C The table with the total number of identified proteins in individual samples. The number of proteins selected as HMGN binding partners with various (WT/DKO) cutoff limits in various cells