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. 2022 Apr 12;13:1968. doi: 10.1038/s41467-022-29591-z

Fig. 6. SWI/SNF colocalises with Rtt106 and regulates TSS-associated nucleosome position at PDR network gene promoters.

Fig. 6

a Nucleosome positioning at the PDR5 promoter in the presence and absence of Snf2. Binding of the Swi3 SWI/SNF subunit (ChEC-seq) and nucleosome occupancy (MNase-seq) at the PDR5 promoter were extracted from published datasets20. TSS TSS-seq extracted from Malabat et al. 201549. Snf2 depletion resulted in shift of the +1 nucleosome at the PDR5 promoter (red rectangle). b Percentages of gene promoters strongly bound by SWI/SNF and those by Rtt106. The list of gene promoters strongly bound with SWI/SNF was obtained from Kubik et al. 201920. Promoters bound by Rtt106 were defined as in Fig. 2. c Changes in mRNA levels of genes with promoters bound by both SWI/SNF and Rtt106 (as in b), and correlation of snf2Δ and rtt106Δ effects in YPD. Magenta dashed line shows trend for Type A. Data represents means of three biological replicates. d GST pull-down analysis showing GST-Rtt106 interacts with SWI/SNF purified from yeast cells. e Nucleosome occupancies at Type A promoters bound by SWI/SNF (magenta lines) and promoters not bound by SWI/SNF (grey lines), and those in the absence of Snf2 (dashed lines). Datasets in Kubik et al. 201920 were utilised. Asterisk, region analysed in f and g. f, g Nucleosome occupancy change (f) and TBP binding change (g) caused by loss of Snf2 at Type A promoters bound by SWI/SNF. Normalised reads in regions spanning −100 to 0 bp from the dyad of the +1 nucleosome (indicated by asterisk in e) were extracted from published datasets20. For analysis of TBP binding change, promoters with low TBP binding (<50 normalised reads) were eliminated. Boxplots indicate median (middle line), interquartile range (box), outliers denoted by points greater than ±1.5 × interquartile range (single points) and the rest of the data distribution (whiskers). Mann–Whitney tests (two-sided). h Proposed roles of Rtt106 and SWI/SNF in transcription of the PDR network genes in S. cerevisiae (S288C). Rtt106 and SWI/SNF are recruited to the PDR network gene promoters dependent on Pdr3, to mediate Pdr3-dependent transcription during logarithmic growth phase, while SWI/SNF upregulates their Pdr1-dependent expression in response to ketoconazole.