BPS2026 – LEDGF and HDGF2 differentially remodel histone-DNA interactions in H3K36 methylation-mimetic nucleosomes

Lens epithelium-derived growth factor (LEDGF) and hepatoma-derived growth factor 2 (HDGF2) are nucleosome chaperones that facilitate transcription without ATP hydrolysis. LEDGF is known for its role as a primary host co-factor for HIV-1 chromatin integration, while HDGF2 is a secondary co-factor. LEDGF and HDGF2 contain HIV integrase binding domains (IBDs) that bind the HIV-1 intasome (INS). Both proteins also have methyl-lysine-binding PWWP domains that recognize epigenetic di- and trimethylation (H3K36me2/3) marks on histone H3 tails. LEDGF/HDGF2-mediated INS tethering to H3K36me3 nucleosomes has been suggested as a mechanism of HIV integration targeting. Studies on the abundance and genomic distribution of H3K36 methylation suggest that dimethylated (H3K36me2) are more abundantly found in the H3 histone. Furthermore, H3K36me3 is strongly correlated with actively transcribed genes, while H3K36me2 is found more in intergenic regions. To quantify the differences between the LEDGF/HDGF2-mediated nucleosome chaperone activity on these two H3K36 methylated nucleosome contexts, we applied optical tweezers and atomic force microscopy (AFM). We measured in vitro effects of the chaperones on the stability and unfolding/refolding kinetics of single nucleosome arrays reconstituted with unmodified or H3K36me2- or me3-mimetic histones. We conclude that LEDGF can destabilize the outer turn of DNA in H3K36me3-mimetic nucleosomes, multimerize on these nucleosomes, deform nucleosomal DNA, and tether INS, in a manner that enhances HIV-1 integration. In contrast, HDGF2 more weakly destabilizes H3K36me3-mimetic nucleosomes but more strongly promotes nucleosome re-assembly, emphasizing its role in facilitating transcription of H3K36me3-marked chromatin regions. We hypothesize that H3K36me2-mimetic nucleosomes will demonstrate less chaperone-mediated destabilization than nucleosomes with H3K36me3-mimetic marks.