Supplementary Figure 5: Links between nucleosome occupancy and transcriptional regulation.
From: Opposing chromatin remodelers control transcription initiation frequency and start site selection
a, Scatterplot showing relationship between TBP binding change at gene promoters and RNAPII binding change in corresponding gene bodies following SWI-SNF depletion, for all genes with a well-defined TSS; Pearson R value shown. b, Scatterplot showing relationship between TBP binding and nucleosome occupancy changes following SWI-SNF depletion at down-regulated genes. c, Average plots displaying nucleosome occupancy, RNAPII and TBP ChIP signals, in the presence and absence of SWI-SNF, for those genes down-regulated upon SWI-SNF depletion. d-f, Average plots displaying nucleosome occupancy together with RNAPII and TBP ChIP-seq signals for genes up-regulated by INO80 depletion (d), down-regulated by INO80 depletion (e), or up-regulated by ISW2 depletion (f), in each case with or without (+/-) the indicated CR. g, Scatter plot displaying the relationship between TBP binding and nucleosome occupancy changes following double “puller” depletion at genes where transcription was affected (see Fig. 5b, c). h, Scatterplot displaying the TBP - RNAPII ChIP-seq signal relationship at all genes following double “puller” depletion. i-k, Average plots displaying nucleosome occupancy together with RNAPII and TBP ChIP-seq signals for genes down-regulated upon ISW1 depletion (i), up-regulated upon ISW1 depletion (j), or up-regulated upon CHD1 depletion (k), in each case with or without (+/-) the indicated CR.
