PLAMseq enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a...

Chromatin immunoprecipitation and coimmunoprecipitation assays are common approaches to characterize the genomic localization and protein interactors, respectively, for a protein of interest. However, these approaches require the use of specific antibodies, which often face sensitivity and specificity issues. On the basis of TurboID, we developed proximity-labeled affinity-purified mass spectrometry and sequencing (PLAMseq), which enables, in the same workflow, identification of the genomic loci and the interacting proteome of a protein of interest. Moreover, PLAMseq can also be applied to specifically map protein interactions and ubiquitin(-like)-modified proteins. We validated PLAMseq with two well-characterized proteins, RNA polymerase II, and CTCF, with excellent robustness and reproducibility. Next, we applied PLAMseq to characterize histone H1 SUMOylation, in which study has remained elusive due to the lack of specific reagents, and found that SETDB1 binds to SUMOylated histones H1.2 and H1.4 that also colocalize with H3K9me3 at repetitive regions of the genome.