Fig. 4

Transcription-tied-up SUMOylation in HS. a GRO-seq (plus-strand) and SUMO2/3 ChIP-seq signals at HS-inducible HSPA1A and UBB loci in K562 cells in control (blue) and in HS conditions (red). Numbers depict the maximum signal. b Heat map showing SUMO2/3 ChIP-seq (in ±2 kb window using false-color scale) and GRO-seq signal densities (minus-strand, cyan; plus-strand, magenta) at TSSs arranged according to control GRO-seq signal. c Whisker-plot of SUMO2/3 control (blue boxes) and HS (red boxes) ChIP-seq signals at the promoters of transcribed and non-transcribed genes, and at promoters of genes divided into four groups of 2,417 genes according to increasing transcription in control or in HS. Gray line indicates background signal intensity. d GRO-seq plus- and minus-strand signals and SUMO2/3 signals in control (blue) and HS (red) at HS-inducible intergenic SUMO2/3 peak. e Heat map showing the same as in (b) but (instead for TSSs) for intergenic SUMO2/3-binding sites. Heat map is divided into three parts according to control (C; blue bar) and HS (red bar) SUMO2/3-binding sites. f Whisker-plot of SUMO2/3 control (blue boxes) and HS (red boxes) ChIP-seq signals at four groups of 135 eRNA enhancers with increasing transcription in control or HS. Gray line indicates background signal intensity. g Correlation between gene transcription and SUMO2/3 binding. Whisker-plot showing gene body GRO-seq signal (in RPKM (reads per kilobase per million mapped reads)) of transcribed genes in C and HS conditions. In each comparison, transcribed genes were divided into two groups based on their promoter or intergenic SUMO2/3 association (+, association; -, no association) in control (blue) or HS conditions (red). Gray depicts transcribed genes not associated with particular SUMO2/3 category. h Correlation between promoter pausing and SUMO2/3 binding. Promoter pausing index (PPI) was calculated by dividing promoter GRO-seq RPKM value with gene body RPKM value. SUMO2/3 peak associations are the same as in (g). i Correlation between SUMO2/3 binding and HS-induced changes in transcription. SUMO2/3 peak associations are the same as in (g). HS-induced change in gene transcription was measured from gene-body GRO-seq signal (gene body RPKM in HS divided by gene body RPKM in control) and shown as log₂(HS/C). In all whisker-blots, stars depict P values (***P <0.001, **P <0.01, ns = not significant) of Student’s t-test (g, h, i) or Kruskall-Wallis/Dunn’s multiple comparison tests (c, f). Line represents median, box edges are 25 % and 75 % boundaries, and whiskers 10 % and 90 % of the data