Decoding the chromatin proteome of a single genomic locus by DNA sequencing
Fig 4
Chromatin rewiring upon HU treatment.
(A) DNA regions replicated in the HU arrest were determined by DNA copy number assessment. The DNA coverage in bins of 200 bp is plotted across the genome for untreated and HU-treated samples. The lower panel shows a zoom-in of chromosome IV, which contains the barcoded locus on the left arm (indicated by the arrow). Replication timing in the absence of HU was obtained from Alvino and colleagues [36]. The percentage of replicated DNA is plotted for each bin at 10, 12.5, 15, 17.5, 25, and 40 minutes after release from a G1 arrest, as indicated by the shades of grey. (B) RT-qPCR shows relative mRNA expression of KanMX/HphMX in untreated and HU-treated samples. The untreated samples were set to 1. The average of 3 biological replicates is shown; error bars indicate SD. (C) Volcano plots showing the ratio of binding in HU-treated/untreated for factors that were significantly enriched in either one or both of the conditions. The coloured dots are factors with significantly different binding scores (FDR < 0.05). BC_DN, downstream barcode; BC_UP, upstream barcode; FDR, false discovery rate; HU, hydroxyurea; ORC, origin recognition complex; RT-qPCR, quantitative reverse transcription PCR.