Genome-wide MNase-ChIP profile of transfected Strep-LIN9 in WT and LIN37-/- HCT116 cells

We performed MNase-ChIP seq with deep digestion to identify the MuvB associated nucleosomes in WT and LIN37 -/- HCT116 cells in G1 arrested and cycling cells. Strep-LIN9 as well as a mutant of the protein (Strep-4xLIN9: R174A/R175A/F180A/F181A) which is unable to associate with LIN37 or RbAP48 were transiently transfected in WT and LIN37 -/- HCT116 cells. At 24 hours after transfection, cells were treated with Nutlin-3a to induce G1 arrest; cells were harvested 48 hours following treatment. For several samples, Nutlin-3a treatment was omitted to maintain cycling conditions. Cells were then cross-linked with formaldehyde, lysed and treated with micrococcal nuclease. Chromatin fragments were precipitated with Streptactin-XT magnetic beads after which DNA was purified and libraries were prepared and sequenced using NovaSeq 6000 platform in 150bp paired-end mode. We find that LIN9 precipitates to +1 nucleosomes of target genes in arrested HCT116 and LIN37 -/- cells. The precipitation of this nucleosome is diminished in cycling cells as well as in arrested cells transfected with the Strep-4xLIN9 mutant. Overall design: MNase-ChIP seq profiles of transiently transfected Strep-LIN9 proteins and a LIN9 mutant in HCT116 WT and HCT116 LIN37 -/- in cycling and arrested conditions