Locus-specific proteomics identifies new aspects of the chromatin context involved in V region somatic hypermutation

Abstract

AbstractActivation-induced cytidine deaminase (AID) somatically hypermutates the immunoglobulin heavy chain variable region (IGHV) gene to create the antibody diversity required to resist infections. This hypermutational process involves many pathways including transcription, DNA structural change and repair. While many of the proteins involved have been identified, their relative abundance, organization and regulation have not been resolved and additional factors and pathways need to be identified. To identify the proteome occupying IGHV, we have utilized dCas9-APEX targeted by guide RNAs to biotinylate and enrich the proteins associated with the mutating V region chromatin in the Ramos human B cell line and compared them to the non-mutating downstream constant region (C) chromatin. We identified hundreds of proteins specifically enriched on the V or C region. We confirmed the functionality of selected factors by examining the changes in the V region-specific proteome after inhibiting transcriptional elongation and somatic mutation with the Dot1L inhibitor EPZ004777.SummaryLocus-specific proteomics using dCas9-APEX identifies new aspects of the chromatin context involved in V region somatic hypermutation (SHM) in the human Ramos B cell line. An inhibitor of Dot1L which participates in SHM is used to identify functional SHM-related factors.