Fig. 3

BAF60 binds nucleosome-free regions of transcribed genes. a Comparison between BAF60 and input of tag density in the region ±5 kb around the BAF60 peaks. ChIP-seq was performed on 14-day-old BAF60-CFP overexpressing plants (OE BAF60-CFP_1) grown under LD conditions. b Pie chart representation of the distribution of BAF60 peaks identified by ChIP-seq in four different genomic regions. The definition of each region is described above. TES transcription end site, TSS transcription start site. c Mean profile of BAF60 ChIP-seq and MNase-seq read density with respect to a gene model from TSS to TES. Normalization of coverage using spline algorithm was performed over the genes and flanking 2-kb region. d Merged profiles of BAF60 ChIP-seq and ATAC-seq read density over TSS and flanking 2-kb region. e Average enrichment profile of BAF60 is correlated with gene expression variation. Gene expression is categorized from low (first quantile) to high (fourth quantile) expression. Mean-normalized ChIP-seq densities of equal bins along the gene and 2-kb region flanking the TSS or the TES are plotted. Highly expressed genes show higher enrichment for binding of BAF60. f Co-ocurrence matrix representing the colocalization of H3K9ac marks and BAF60 binding along the BAF60 targets