Replication timing of many genes is unchanged in ES mutants. (a) Replication timing analysis of Oct4, Esg1, Nkx2.9 and Mash1 in wild-type (white bars; OS25, G9a WT, Suv39 h1/h2 WT, Dicer WT) and mutant (gray bars; Mll KO, Eed KO, Dnmt 1 KO, Dnmt3a/3b DKO, Mbd3 KO, G9a KO, Suv39 h1/h2 DKO and Dicer KO) ES cells. The histograms show the relative locus replication within each cell cycle fraction as measured by qPCR for all the wild-type and mutant ES cells analyzed. The mean values and standard error of at least two independent experiments are shown. (b,c) Summary of replication timing of candidate genes (b) and loci surrounding the Rex1 gene (c). In (c), positions of genes are indicated by black boxes and the two regions changing replication timing upon ES cell differentiation are indicated by red bars. (d) Replication timing categories and color code. Early replication (E) is defined by peak abundance in the G1-S and/or S1 fractions, mid-early (ME) by peak replication in S2, middle (M) in S2 and S3, mid-late (ML) in S3 and late (L) replicating loci have peak abundance in S4 and/or G2.