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. 2009 Jun 26;34(6):722-34.
doi: 10.1016/j.molcel.2009.05.022.

Highly Transcribed RNA Polymerase II Genes Are Impediments to Replication Fork Progression in Saccharomyces Cerevisiae

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Free PMC article

Highly Transcribed RNA Polymerase II Genes Are Impediments to Replication Fork Progression in Saccharomyces Cerevisiae

Anna Azvolinsky et al. Mol Cell. .
Free PMC article

Abstract

Replication forks face multiple obstacles that slow their progression. By two-dimensional gel analysis, yeast forks pause at stable DNA protein complexes, and this pausing is greatly increased in the absence of the Rrm3 helicase. We used a genome-wide approach to identify 96 sites of very high DNA polymerase binding in wild-type cells. Most of these binding sites were not previously identified pause sites. Rather, the most highly represented genomic category among high DNA polymerase binding sites was the open reading frames (ORFs) of highly transcribed RNA polymerase II genes. Twice as many pause sites were identified in rrm3 compared with wild-type cells, as pausing in this strain occurred at both highly transcribed RNA polymerase II genes and the previously identified protein DNA complexes. ORFs of highly transcribed RNA polymerase II genes are a class of natural pause sites that are not exacerbated in rrm3 cells.

Figures

Figure 1
Figure 1. High occupancy DNA Pol2-MYC and Rrm3-MYC sites by genomic class in WT and rrm3 cells
A. The proportion of the 96 DNA Pol2-MYC WT, 192 DNA Pol2-MYC rrm3, 115 Rrm3-MYC, and 99 untagged high occupancy sites that overlap with listed genomic features (white bars) and expected proportions (black bars) are plotted. Because high occupancy sites may overlap with more than one genomic feature, numbers do not add up to the total number of high occupancy sites. Numbers in parentheses are the actual number of high occupancy sites that overlap with the indicated feature. Asterisks denote class enrichments that were significantly different from both the expected proportion and the number of sites that overlapped with the particular genomic class in the untagged control. See supplemental methods for p values. B. Rrm3-MYC and DNA Pol2-MYC both WT and rrm3 cells are highly associated with highly transcribed genes while Rrm3-sensitive sites are enriched only in DNA Pol2-MYC rrm3 cells. The plots are DNA Pol2-MYC normalized log(2) values with 250 bp sliding window averages of arrayed elements using ChIPOTle from untagged (black broken line), DNA Pol2-MYC WT (black), DNA Pol2-MYC rrm3 (gray), and Rrm3-MYC (dashed black). Enrichment values are plotted along 12 kb of chromosome VII (Fig 1B, top; includes highly transcribed TDH3) and 17 kb of chromosome XVI (Fig. 1B, bottom; includes highly transcribed TEF1). Annotations corresponding to the coordinates are shown below the plot (dark gray, characterized ORF; light gray, uncharacterized ORF, tRNA, or origin of replication). tW(CCA)G2 adjacent to TDH3 and inactive ARS1625 adjacent to TEF1 were significant DNA Pol2-MYC binding sites in rrm3 cells only.
Figure 2
Figure 2. DNA Pol2-MYC in rrm3 cells is associated with inactive and late/rarely active origins of replication
A. Distribution of classes of origins of replication (see supplemental methods for description of origin classes). B. Distribution of origin classes among the 57 origins in the 192 high occupancy DNA Pol2-MYC binding sites in rrm3 cells. C. Pattern of binding within the ARS313/ARS314 region in Rrm3-MYC and DNA Pol2-MYC in WT and rrm3 cells. This region is a high occupancy DNA Pol2-MYC site in rrm3 but not WT cells. See Fig. 1B for details. D. ARS313 and 314 are Rrm3-sensitive replication sites. DNA from WT and rrm3 cells was EcoRV digested, separated on 2D gels, and analyzed by Southern blotting. Schematic indicates the locations of the inactive ARS313 and rarely active ARS314. Gray circles indicate inactive origins; open circle indicates the nearest efficient replication origin (ARS315) whose activation is usually responsible for replicating this region (Poloumienko et al., 2001). Arrows denote pauses. E. DNA Pol2-MYC is associated with late/inactive and inactive origins in rrm3 (left panel) but not WT cells (right panel). Sliding window average of enrichment values versus distance from replication origins within an origin class. The positions of all probes on the arrays were mapped relative to the positions of early, inactive/late, and inactive origins (Fig. 2A). A sliding window (30 bp, 1 bp step size) was used to calculate the average DNA Pol2-MYC enrichment from the origins (0 bp to 4.5 kb away) in both WT and rrm3 cells. Moving averages of DNA Pol2-MYC ChIP enrichments are plotted for inactive (black solid line), inactive/late (solid gray), and early origins (black broken line) in rrm3 (left) and WT (right) cells. Rrm3-MYC and untagged plots are similar to Pol2-MYC WT for all origins (data not shown).
Figure 3
Figure 3. Rrm3-sensitive replication sites are often high occupancy DNA Pol2-MYC binding sites in rrm3 but not WT cells
A. Venn diagram of overlapping high occupancy DNA Pol2-MYC WT and DNA Pol2-MYC rrm3 sites. B. The number of sites in common between DNA Pol2-MYC WT and rrm3 cells (overlap, black bars), DNA Pol2-MYC WT only (white bars), and DNA Pol2-MYC rrm3 only (gray bars) are plotted by genomic classes (Fig 1A). As more than 1 site within a single telomere may be associated with DNA Pol2, the number of telomeric loci and number of telomeres associated with DNA Pol2 are not equal.
Figure 4
Figure 4. Highly transcribed genes are high occupancy DNA Pol2-MYC sites in WT and rrm3 cells as well as high occupancy Rrm3-MYC sites
A. Association of DNA Pol2-MYC in WT and rrm3 cells and Rrm3-MYC with 12 kb regions on chromosomes XII, II and III, as in Fig. 1B. These regions contain the highly transcribed PDC1, TEF2, and PGK1 genes. Each gene was significantly associated with DNA Pol2-MYC in WT and rrm3 cells and with Rrm3-MYC. B. Schematics of restriction enzyme digested DNA with replication intermediates as visualized by 2D gels: 1N, non-replicating fragment; 2N, almost fully replicated fragment; P, replication pause; dotted line, arc of linear DNA molecules. C. DNA from WT and rrm3 cells was restriction enzyme digested, separated on 2D gels, and analyzed by Southern blotting at the indicated gene (restriction enzymes: EcoRV, TEF1 and PGK1; PstI, TEF2 and PDC1; BglII, RPS3; NdeI, TEF2). Brackets mark ORFs; arrows mark pauses. Pausing within TEF2 was also detectable in NdeI digested DNA when the pause was ~80% through the arc of replication intermediates.
Figure 5
Figure 5. DNA Pol2-MYC binding at highly transcribed genes is within ORFs, not promoters
A. Diagrams (left) of the PGK1 region on chromosome III, TEF1 region on chromosome XVI, and TEF2 region on chromosome II including positions of nearest early firing replication origin. Forks moving from these origins are responsible for replication of the nearby genes in most cells. Gray arrows indicate ORFs and direction of transcription. Horizontal bars indicate positions of amplified segments (RT probe). Cells expressing DNA Pol2-MYC or Rrm3-MYC were processed for ChIP and qPCR. Results are plotted as % of input DNA in the immunoprecipitate (% IP’ed). Error bars are standard deviations from 3 to 8 biological replicates with two real-time PCR replicates per biological replicate. The sequence being amplified is indicated on the x-axis (ORFs, gray bars; promoters, white bars). The difference in DNA Pol2-MYC binding within the ORF versus its promoter was significant for PGK1, TEF1, and TEF2 (p=0.005, 0.03, and 0.01, respectively) and for Rrm3-MYC binding for PGK1, TEF1, and TEF2 (p= 0.007, 0.03, and 0.0006 respectively). B. DNA Pol2-MYC is highly associated with ORFs, not promoters, of highly transcribed RNA Pol II genes. Enrichment values of ORFs (red) and promoters (blue) are plotted as a function of transcription rate (TR, mRNAs/hour) (Holstege et al., 1998) for untagged, Pol2-MYC WT, DNA Pol2-MYC rrm3, and Rrm3-MYC cells. Arrows indicate 25 mRNAs/hr. C. DNA Pol2-MYC and Rrm3-MYC are more likely to be highly associated with ORFs whose TRs require more than one simultaneous transcription event. The enrichments arrayed ORFs are plotted as a function of the difference between the actual and theoretical number of mRNAs produced for the corresponding ORF in one hour for untagged, Pol2-MYC WT, DNA Pol2-MYC rrm3, and Rrm3-MYC cells. Actual number of mRNAs produced is based on measured transcription rates (Holstege et al., 1998).
Figure 6
Figure 6. High association of DNA Pol2-MYC with highly transcribed genes is not Rap1 dependent
A. Diagram of GAL7 and GAL10 region on chromosome II (see Fig 5A for symbols). B. High DNA Pol2-MYC binding in WT and rrm3 cells is enriched within the GAL7 and GAL10 ORFs only in galactose grown cells (galactose, black bars; raffinose, white bars) (p=0.01 and 0.0006 for GAL7 in WT and rrm3, respectively. p=0.02 and 0.0073 for GAL10 in WT and rrm3, respectively). C. DNA Pol2-MYC enrichment at highly transcribed TEF2 and PGK1, whose transcription is carbon source independent, is not affected by carbon source (galactose, black bars; raffinose, white bars; p=0.73 and 0.07 for TEF2 and PGK1 in WT cells, and 0.27 and 0.85 for TEF2 and PGK1 in rrm3 cells, respectively). D. Diagram of modified RPL24A-RPL30 region integrated at URA3 and endogenous RPL24A-RPL30 genes on chromosome VII (see Fig 5A for symbols). RR, two Rap1 binding sites. E. mRNA abundance and transcription rate (Holstege et al., 1998) of the endogenous RPL30 and RPL24A genes and the predicted abundance and transcription rate of the mutated (rr) construct. F. Cultures expressing DNA Pol2-MYC with the integrated reporter construct (panel D) with either WT Rap1 binding sites (RR) or mutated Rap1 binding sites (rr) were processed for ChIP and qPCR. Amplifed sequences are indicated on x-axis. G. Association of DNA Pol2-MYC with GFP ORF was indistinguishable in RR and rr strains (p=0.12).
Figure 7
Figure 7. DNA polymerase and Rrm3 are associated with highly transcribed RNA Pol II genes only during replication
WT cells expressing both DNA Pol2-HA and Rrm3-MYC were arrested in G1 phase with alpha factor. After removal from alpha factor, cells were grown at 17° C and allowed to proceed synchronously through the cell cycle as monitored by FACS (panel B). At 12 minute intervals, samples were taken for FACS and cultures were split, processed for ChIP using either HA or MYC antibodies and then analyzed by qPCR. ChIP of Rrm3-MYC (black squares) and Pol2-HA (gray squares) from the same culture. See Fig. 5A for structures of the PGK1, TEF1, and TEF2 regions and positions of PCR primers. Real-time primers are indicated in top left corner.

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