Figure 4.

DNMT1 Knockdown Prevents SAHF Formation

(A) Replication-timing (RT) profiles of WI38 RAF cells at early stages of OIS. The data are displayed as log2 ratios of signals from early and late S-phase fractions. The positive scale corresponds to an early replication, and the negative scale corresponds to late replication timing.

(B) Washington University Genome browser shot. Top: mC tracks from IMR90 cells. The blue color indicates methylation levels and the gray background indicates coverage. Data are from NCBI roadmap to epigenomics. Middle: replication timing track of uninduced WI38 RAF cells (G1 phase to G2 phase). The classification of G1 to G2 phase is mentioned in the STAR Methods. Bottom: SAHDs falling in the displayed region.

(C) Schematic overview of the knockdown experiment. OISi, oncogene induction; RNAi, administration of siRNA. Day 0 (D0) to day 5 (D5).

(D) Representative DAPI staining images (z-slice) from oncogene-induced (D5) and control (NT) and upon depletion of HMGA1 + HMGA2, DNMT1, DNMT3A, DNMT3B, SUV420H1, SUV420H2, LRWD1, RIF1, GAPDH. Scale bar, 10 μm.

(E) Quantification of the changes in the SAHF score (details in STAR Methods) of the cells displayed in (D). Statistical significance was calculated using the Mann-Whitney test.

See also Figure S4.