Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation (original) (raw)
Figure 5
Replication Timing and Transcription Changes during Differentiation
(A and B) Average replication-timing ratios of replication domains were plotted against their “present” (i.e., transcriptionally active) gene density for ESCs (A) and NPCs (B). Pearson _R_2 values are shown.
(C and D) Correlation between early replication and the probability of expression. Genes were ranked by their replication-timing ratio and divided into bins of 100 genes, the height of which represents the percentage of active (i.e., ”present”) genes within each bin. The width and position of each bin represents its range of replication-timing ratios. Logistic regression (inner line) and 95% confidence intervals (outer lines) reveal a clear correlation in both ESCs (C) and NPCs (D). By the Likelihood Ratio test (a goodness-of-fit test), the fitted model is significantly different (p < 2 × 10−16 for both ESCs and NPCs) from that of a null hypothesis in which replication timing has no correlation to transcription.
(E) Box plots showing the fold changes in transcription [i.e., log2(NPC/ESC)] of LtoE, EtoL, LtoL, and EtoE genes. RefSeq genes with the 5% greatest replication timing changes were defined as EtoL and LtoE, whereas those with the least changes (lowest 20%) that maintained replication timing ratio of above 0.5 or below −0.5 were defined as EtoE and LtoL, respectively.
(F) Percentage of 2-fold up- or down-regulated genes within LtoE, EtoL, LtoL, and EtoE domains defined in Figure 4G.
(G) Summary of expression patterns of genes within LtoE, EtoL, LtoL, and EtoE domains. Definitions are as follows: “Up” and “Down,” above 2-fold up- and down-regulation, respectively; “Unchanged,” below 2-fold up-/down-regulation; “Unchanged Only,” domains with both active and silent genes that do not change by 2-fold; and “Silent Only,” domains with only silent genes in both states.
(H) LINE-1 transposable elements are actively transcribed in ESCs but become inactive in NPCs as assayed by RNA-FISH. Mean and standard error of mean (SEM) of the number of RNA-FISH signals per nucleus is shown (n = 30 from two biological replicates). The _p_-value was obtained from a two-tailed _t_-test for comparison of two unpaired groups.