Transcription shapes DNA replication initiation and termination in human cells

Chen, Yu-Hung; Keegan, Sarah; Kahli, Malik; Tonzi, Peter; Fenyö, David; Huang, Tony T.; Smith, Duncan J.

doi:10.1038/s41594-018-0171-0

Cited by 130 publications

(185 citation statements)

References 44 publications

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“…However, there are also substantial differences, as cyclin E overexpression has not been connected to Chk1 inhibitor sensitivity. Recent evidence suggests that transcription and DNA replication initiation sites are closely linked (Chen et al, 2019). We found that cyclin F regulates E2F1 only in the G2/M phase of the cell cycle.…”

Section: Discussionmentioning

confidence: 56%

“…It has been shown that cyclin E accumulation leads to reduced DNA replication origin assembly (Ekholm-Reed et al, 2004). Recent evidence suggests that transcription and DNA replication initiation sites are closely linked (Chen et al, 2019). This process predisposes cells to the deleterious consequences of transcription replication collisions and results in the formation of DSBs (Macheret & Halazonetis, 2018).…”

Section: Of 18mentioning

confidence: 99%

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E2F1 proteolysis via SCF ‐cyclin F underlies synthetic lethality between cyclin F loss and Chk1 inhibition

et al. 2019

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Cyclins are central engines of cell cycle progression in conjunction with cyclin‐dependent kinases (CDKs). Among the different cyclins controlling cell cycle progression, cyclin F does not partner with a CDK, but instead forms via its F‐box domain an SCF (Skp1‐Cul1‐F‐box)‐type E3 ubiquitin ligase module. Although various substrates of cyclin F have been identified, the vulnerabilities of cells lacking cyclin F are not known. Thus, we assessed viability of cells lacking cyclin F upon challenging them with more than 180 different kinase inhibitors. The screen revealed a striking synthetic lethality between Chk1 inhibition and cyclin F loss. Chk1 inhibition in cells lacking cyclin F leads to DNA replication catastrophe. Replication catastrophe depends on accumulation of the transcription factor E2F1 in cyclin F‐depleted cells. We find that SCF‐cyclin F controls E2F1 ubiquitylation and degradation during the G2/M phase of the cell cycle and upon challenging cells with Chk1 inhibitors. Thus, Cyclin F restricts E2F1 activity during the cell cycle and upon checkpoint inhibition to prevent DNA replication stress. Our findings pave the way for patient selection in the clinical use of checkpoint inhibitors.

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Section: Discussionmentioning

confidence: 56%

Section: Of 18mentioning

confidence: 99%

E2F1 proteolysis via SCF ‐cyclin F underlies synthetic lethality between cyclin F loss and Chk1 inhibition

et al. 2019

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“…an association also seen in other eukaryotes (8,10), although the mechanisms might differ. It is unclear how epigenetic dynamics dictate DNA replication activity in L. major.…”

Section: Discussionmentioning

confidence: 69%

“…In contrast, with the exception of Saccharomyces and closely related yeasts (3), replication origins in eukaryotes are not defined by conserved sequences. Instead, more elusive features, such as chromatin accessibility, transcription level and epigenetic elements (4)(5)(6)(7)(8)(9)(10), are determinants of replication initiation activity. What is common to all known eukaryotic origins is that they are licensed through binding by the origin recognition complex (ORC), which recruits the replicative helicase, MCM2-7, during G1 (11).…”

Section: Introductionmentioning

confidence: 99%

Genome duplication inLeishmania majorrelies on DNA replication outside S phase

Damasceno

Marques

Beraldi

et al. 2019

Preprint

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Once every cell cycle, DNA replication takes place to allow cells to duplicate their genome and segregate the two resulting copies into offspring cells. In eukaryotes, the number of DNA replication initiation loci, termed origins, is proportional to chromosome size. However, previous studies have suggested that in Leishmania, a group of single-celled eukaryotic parasites, DNA replication starts from just a single origin per chromosome, which is predicted to be insufficient to secure complete genome duplication within S phase.Here, we show that the paucity of origins activated in early S phase is balanced by DNA synthesis activity outside S phase. Simultaneous recruitment of acetylated histone H3 (AcH3), modified base J and the kinetochore factor KKT1 is exclusively found at the origins used in early S phase, while subtelomeric DNA replication can only be linked to AcH3 and displays persistent activity through the cell cycle, including in G2/M and G1 phases. We also show that subtelomeric DNA replication, unlike replication from the previously mapped origins, is sensitive to hydroxyurea and dependent on subunits of the 9-1-1 complex.Our work indicates that Leishmania genome transmission relies on an unconventional DNA replication programme, which may have implications for genome stability in this important parasite. sequence read depth in the former relative to the latter. As result, DNA synthesis very late in S-phase, or that occurs outside of S-phase, would escape detection. To test this, we modified the MFA-seq approach in order that DNA content enrichment could be calculated in replicating cells relative to naturally occurring non-replicative cells. Mapping origins of replication by calculating DNA enrichment in exponentially growing cells versus cells in a stationary state has been used successfully in bacteria (42) and yeast (43). Thus, we reasoned that L. major in stationary phase could also serve as a non-replicative control for normalization in MFA-seq analysis compared with cells that are growing exponentially. To test this, we used flow cytometry to compare DNA content of exponentially growing and stationary phase cells and, in addition, compared the capacity of the two cell populations to incorporate the thymidine analogue 5-ethynyl-2'deoxyuridine (EdU; Fig. 1A,B). Flow cytometry showed that the proportion of cells in S phase (with DNA content between 1C and 2C) was substantially lower in a population of stationary cells compared with exponentially growing cells (Fig. 1A). Concomitantly, stationary phase cells, unlike exponentially growing cells, failed to incorporate EdU, even upon relatively long periods of incubation ( Fig. 1B). Thus, L. major cells in stationary phase do not perform any detectable DNA synthesis and were therefore deemed suitable to be used as the non-replicative sample in MFA-seq analysis.Next, we compared MFA-seq profiles using read depth ratios from FACS-sorted early S (ES) and G2 cells, and from exponentially growing cells (EXP) and stationary (STA) cells (Fig. 1C). As reported ...

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“…Such a general mechanism may also be relevant to higher eukaryotes. Interestingly, in mammalian cells, replication mainly initiates within gene promoters (Miotto et al 2016;Chen et al 2019). Replication initiation efficiency nicely correlates with transcription initiation strength, which itself correlates with the accessibility of the NDR (Brown et al 2018;Chen et al 2019).…”

Section: A Common Model For All Eukaryotic Ndrs?mentioning

confidence: 99%

Fine chromatin-driven mechanism of transcription interference by antisense noncoding transcription

Gill

Maffioletti

García-Molinero

et al. 2019

Preprint

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AbstractEukaryotic genomes are almost entirely transcribed by RNA polymerase II (RNAPII). Consequently, the transcription of long noncoding RNAs (lncRNAs) often overlaps with coding gene promoters triggering potential gene repression through a poorly characterized mechanism of transcription interference. In this study, we propose a global model of chromatin-based transcription interference in Saccharomyces cerevisiae (S. cerevisiae). By using a noncoding transcription inducible strain, we analyzed the relationship between antisense elongation and coding sense repression, nucleosome occupancy and transcription-associated histone modifications using near-base pair resolution techniques. We show that antisense noncoding transcription leads to the deaceylation of a subpopulation of −1/+1 nucleosomes associated with increased H3K36 trimethylation (H3K36me3). Reduced acetylation results in decreased binding of the RSC chromatin remodeler at −1/+1 nucleosomes and subsequent sliding into the Nucleosome-Depleted Region (NDR) hindering Pre-Initiation Complex (PIC) association. Finally, we extend our model by showing that natural antisense noncoding transcription significantly represses around 20% of S. cerevisiae genes through this chromatin-based transcription interference mechanism.HighlightsInduction of antisense noncoding transcription leads to −1/+1 nucleosome sliding that competes with sense transcription PIC deposition.Antisense induction leads to a subpopulation of H3K36me3 nucleosomes differently positioned compared to H3K18ac nucleosomes.RSC chromatin remodeler recruitment to −1/+1 nucleosomes is modulated by histone acetylation levels.20% of S. cerevisiae genes are significantly repressed by this antisense-dependent chromatin-based transcription interference mechanism.

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Transcription shapes DNA replication initiation and termination in human cells

Cited by 130 publications

References 44 publications

E2F1 proteolysis via SCF ‐cyclin F underlies synthetic lethality between cyclin F loss and Chk1 inhibition

E2F1 proteolysis via SCF ‐cyclin F underlies synthetic lethality between cyclin F loss and Chk1 inhibition

Genome duplication inLeishmania majorrelies on DNA replication outside S phase

Fine chromatin-driven mechanism of transcription interference by antisense noncoding transcription

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