Cut&RUN GCN5 Control Primary mouse hepatocytes

Pre-processed CUT&RUN files for ACLY and GCN5 were normalized to effective genome size.
For each file, background signal was calculated in heterochromatin regions using negative
ATAC-seq signal mask, and subsequently removed from the overall coverage. CUT&RUN
coverage heatmaps and profiles around the TSS of expressed genes were produced using
computeMatrix, plotHeatmap functions from deepTools v3.5.2 package51. The list of expressed
genes was inferred from the mouse primary hepatocyte RNA-seq data using variance
stabilizing transformation of the expression matrix and selecting genes with values > 0 for all
replicates. Peak calling on each replicate was performed using MACS252 v.2.2.7.1, and the
consensus overlapping peaks between all replicates were considered as reproducible for the
corresponding dataset. Number of overlapping peaks between conditions was calculated in R
with subsetByOverlaps (GenomicRanges v.1.54.1)57, and nearest genes were annotated to
peaks using biomaRt.
For the correlation of ChIP peaks with gene expression, all expressed genes derived from
RNA-seq data were divided into 4 equal groups based on their expression levels (quartiles (Q)
1 to 4). Promoter regions of those genes (± 1kb TSS) were extracted using the Rsubread
v.2.16.0)59 package, and the CUT&RUN signal was quantified with multiBigwigSummary from
deepTools package