Abstract
SummaryAs transcription and replication use DNA as substrate, conflicts between transcription and replication can occur, leading to genome instability with direct consequences for human health. To determine how the two processes are coordinated throughout S phase, we characterize both processes together at high resolution. We find that transcription occurs during DNA replication, with transcription start sites (TSSs) not fully replicated along with surrounding regions and remaining under-replicated until late in the cell cycle. TSSs undergo completion of DNA replication specifically when cells enter mitosis, when RNA polymerase II is removed. Intriguingly, G2/M DNA synthesis occurs at high frequency in unperturbed cell culture, but it is not associated with increased DNA damage and is fundamentally separated from mitotic DNA synthesis. TSSs duplicated in G2/M are characterized by a series of specific features, including high levels of antisense transcription, making them difficult to duplicate during S phase.
Highlights
A large body of evidence has established that RNA transcription can impair DNA replication progression, inducing replication stress and DNA damage (Brewer and Fangman, 1988; Deshpande and Newlon, 1996; Huertas and Aguilera, 2003; Helmrich et al, 2011; Alzu et al, 2012; Akamatsu and Kobayashi, 2015)
Our findings provide an insight into how DNA replication and RNA polymerase II (RNAPII) transcription affect one another, with important consequences for completion of the DNA replication program and genome stability maintenance
As these assays were not able to assess whether transcription and replication could affect each other, we decided to investigate the coordination between transcription and replication using a combination of genome-wide approaches
Summary
A large body of evidence has established that RNA transcription can impair DNA replication progression, inducing replication stress and DNA damage (Brewer and Fangman, 1988; Deshpande and Newlon, 1996; Huertas and Aguilera, 2003; Helmrich et al, 2011; Alzu et al, 2012; Akamatsu and Kobayashi, 2015). To avoid head-to-head collisions between the transcription and replication machineries, bacterial genomes have transcription of major genes in a codirectional orientation with the replication fork emanating from the replication origin (Brewer, 1988) Such organization is not possible in higher eukaryotes because of the inherent variability of cell-type-specific transcription and replication programs (Hansen et al, 2010). Replication timing and distribution of replication origins are affected by RNAPII transcription, with early-replicated regions and replication origins enriched around transcribed genes (Cayrou et al, 2015; Petryk et al, 2016) It is unclear how this reciprocal relationship is arranged in mammalian cells, despite its importance for genome stability and direct links to several human diseases (Gaillard and Aguilera, 2016)
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