Fig. 4

ChIP-seq and transcriptome analysis reveal the genes directly regulated by SIN3 220. a Western blot for SIN3 of whole cell extracts prepared from GFP RNAi or Sin3A knockdown (KD) cells. β-Actin was used as a loading control. b Scatter plot showing the correlation between genes bound by SIN3 220HA and those that change in expression following Sin3A knockdown. Green dots denote genes regulated by SIN3 220 but not bound. Red dots indicate genes that are regulated by SIN3 220 and bound by both SIN3 isoforms. Black dots refer to genes uniquely bound and regulated by the SIN3 220 isoform. c Average ChIP signal of SIN3 220HA over the genes as identified in (b). d qRT-PCR verification of genes identified by RNA-seq to change in expression upon Sin3A knockdown versus GFP RNAi. P-value ** <0.01, *** <0.0001. e Gene-ontology analysis of the genes identified in (b) are represented as bar plots. The Y-axis lists the broad GO categories. Red: categories of genes that are directly repressed. Blue: categories of genes directly activated. P-value (gene ontology categories) <0.05