Figure 3.
Replication timing correlates with the transcription profile of the chromosome. (A) RNA Pol II density delineates early and late-replicating domains. Spatial plot of the moving average (n = 100) of RNA Pol II enrichment along the chromosome, represented as a heat map (red, most dense; white, least dense). The gray regions on either end of the chromosome represent regions with insufficient data for the moving average. The smoothed timing data was plotted as black curve. (B) Actively transcribed regions replicate early. The moving average (n = 100) of RNA Pol II enrichment using windows of 180 Kb plotted as a function of replication timing. An R2-value of 0.361 was calculated for the correlation (without using a moving average). (C) Transcription over large domains influences replication timing. An R2-value was calculated for the correlation between replication timing and the density of either RNA Pol II (red), gene expression (green), annotated genes (blue), or a mock immunoprecipitation (black) using windows of increasing sequence.