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Zech J, Godfrey EL, Masai H, Hartsuiker E, Dalgaard JZ. The DNA-Binding Domain of S. pombe Mrc1 (Claspin) Acts to Enhance Stalling at Replication Barriers. PLoS One 2015. [PMID: 26201080 PMCID: PMC4511789 DOI: 10.1371/journal.pone.0132595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During S-phase replication forks can stall at specific genetic loci. At some loci, the stalling events depend on the replisome components Schizosaccharomyces pombe Swi1 (Saccharomyces cerevisiae Tof1) and Swi3 (S. cerevisiae Csm3) as well as factors that bind DNA in a site-specific manner. Using a new genetic screen we identified Mrc1 (S. cerevisiae Mrc1/metazoan Claspin) as a replisome component involved in replication stalling. Mrc1 is known to form a sub-complex with Swi1 and Swi3 within the replisome and is required for the intra-S phase checkpoint activation. This discovery is surprising as several studies show that S. cerevisiae Mrc1 is not required for replication barrier activity. In contrast, we show that deletion of S. pombe mrc1 leads to an approximately three-fold reduction in barrier activity at several barriers and that Mrc1’s role in replication fork stalling is independent of its role in checkpoint activation. Instead, S. pombe Mrc1 mediated fork stalling requires the presence of a functional copy of its phylogenetically conserved DNA binding domain. Interestingly, this domain is on the sequence level absent from S. cerevisiae Mrc1. Our study indicates that direct interactions between the eukaryotic replisome and the DNA are important for site-specific replication stalling.
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Affiliation(s)
- Juergen Zech
- Warwick Medical School, University of Warwick, Gibbet Hill Campus, CV47AL Coventry, United Kingdom
- * E-mail: (JZ); (JZD)
| | - Emma Louise Godfrey
- Warwick Medical School, University of Warwick, Gibbet Hill Campus, CV47AL Coventry, United Kingdom
| | - Hisao Masai
- Genome Dynamics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156–8613, Japan
| | - Edgar Hartsuiker
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Wales, LI57 2UW, United Kingdom
| | - Jacob Zeuthen Dalgaard
- Warwick Medical School, University of Warwick, Gibbet Hill Campus, CV47AL Coventry, United Kingdom
- * E-mail: (JZ); (JZD)
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Rattan R, Bielinska AU, Banaszak Holl MM. Quantification of cytosolic plasmid DNA degradation using high-throughput sequencing: implications for gene delivery. J Gene Med 2015; 16:75-83. [PMID: 24700644 DOI: 10.1002/jgm.2761] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 03/06/2014] [Accepted: 03/31/2014] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Although cytosolic DNA degradation plays an important role in decreasing transgene expression, the plasmid degradation pattern remains largely unexplored. METHODS Illumina dye sequencing was employed to provide degradation site information for S1 and cytosolic nucleases. S1 nuclease provided a positive control for a comparison between the agarose gel method and sequencing approaches. RESULTS The poly(A) region between the β-lactamase gene and the cytomegalovirus (CMV) promoter was identified as the most likely cut site for polyplex-treated cytosol. The second most likely site, at the 5' end of the β-lactamase gene, was identified by gel electrophoresis and sequencing. Additional sites were detected in the OriC region, the SV40/poly(A) region, the luciferase gene and the CMV promoter. Sequence analysis of plasmid treated with cytosol from control cells showed the greatest cut activity in the OriC region, the β-lactamase gene and the poly(A) region following the luciferase gene. Additional regions of cut activity include the SV40 promoter and the β-lactamase poly(A) termination sequence. Both cytosolic nucleases and the S1 nuclease showed substantial activity at the bacterial origin of replication (OriC). CONCLUSIONS High-throughput plasmid sequencing revealed regions of the luciferase plasmid DNA sequence that are sensitive to cytosolic nuclease degradation. This provides new targets for improving plasmid and/or polymer design to optimize the likelihood of protein expression.
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Affiliation(s)
- Rahul Rattan
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI, USA
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Liu G, Myers S, Chen X, Bissler JJ, Sinden RR, Leffak M. Replication fork stalling and checkpoint activation by a PKD1 locus mirror repeat polypurine-polypyrimidine (Pu-Py) tract. J Biol Chem 2012; 287:33412-23. [PMID: 22872635 DOI: 10.1074/jbc.m112.402503] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA sequences prone to forming noncanonical structures (hairpins, triplexes, G-quadruplexes) cause DNA replication fork stalling, activate DNA damage responses, and represent hotspots of genomic instability associated with human disease. The 88-bp asymmetric polypurine-polypyrimidine (Pu-Py) mirror repeat tract from the human polycystic kidney disease (PKD1) intron 21 forms non-B DNA secondary structures in vitro. We show that the PKD1 mirror repeat also causes orientation-dependent fork stalling during replication in vitro and in vivo. When integrated alongside the c-myc replicator at an ectopic chromosomal site in the HeLa genome, the Pu-Py mirror repeat tract elicits a polar replication fork barrier. Increased replication protein A (RPA), Rad9, and ataxia telangiectasia- and Rad3-related (ATR) checkpoint protein binding near the mirror repeat sequence suggests that the DNA damage response is activated upon replication fork stalling. Moreover, the proximal c-myc origin of replication was not required to cause orientation-dependent checkpoint activation. Cells expressing the replication fork barrier display constitutive Chk1 phosphorylation and continued growth, i.e. checkpoint adaptation. Excision of the Pu-Py mirror repeat tract abrogates the DNA damage response. Adaptation to Chk1 phosphorylation in cells expressing the replication fork barrier may allow the accumulation of mutations that would otherwise be remediated by the DNA damage response.
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Affiliation(s)
- Guoqi Liu
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435, USA.
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Bagshaw ATM, Pitt JPW, Gemmell NJ. Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots. BMC Genomics 2006; 7:179. [PMID: 16846522 PMCID: PMC1543642 DOI: 10.1186/1471-2164-7-179] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Accepted: 07/18/2006] [Indexed: 11/17/2022] Open
Abstract
Background Meiotic recombination events have been found to concentrate in 1–2.5 kilo base regions, but these recombination hot spots do not share a consensus sequence and why they occur at specific sites is not fully understood. Some previous evidence suggests that poly-purine/poly-pyrimidine (poly-pu/py) tracts (PPTs), a class of sequence with distinctive biochemical properties, could be involved in recombination, but no general association of PPTs with meiotic recombination hot spots has previously been reported. Results We used computational methods to investigate in detail the relationship between PPTs and hot spots. We show statistical associations of PPT frequency with hot spots of meiotic recombination initiating lesions, double-strand breaks, in the genome of the yeast S. cerevisiae and with experimentally well characterized human meiotic recombination hot spots. Supporting a possible role of poly-pu/py-rich sequences in hot spot recombination, we also found that all three single nucleotide polymorphisms previously shown to be associated with human hot spot activity changes occur within sequence contexts of 14 bp or longer that are 85% or more poly-pu/py and at least 70% G/C. These polymorphisms are all close to the hot spot mid points. Comparing the sequences of experimentally characterized human hot spots with the orthologous regions of the chimpanzee genome previously shown not to contain hot spots, we found that in all five cases in which comparisons for the hot spot central regions are possible with publicly available sequence data, there are differences near the human hot spot mid points within sequences 14 bp or longer consisting of more than 80% poly-pu/py and at least 50% G/C. Conclusion Our results, along with previous evidence for the unique biochemical properties and recombination-stimulating potential of poly-pu/py-rich sequences, suggest that the possible functional involvement of this type of sequence in meiotic recombination hot spots deserves further experimental exploration.
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Affiliation(s)
- Andrew TM Bagshaw
- School of Biological Sciences, University of Canterbury, New Zealand
| | - Joel PW Pitt
- Bioprotection and Ecology Division, Lincoln University, New Zealand
| | - Neil J Gemmell
- School of Biological Sciences, University of Canterbury, New Zealand
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Shimotai Y, Minami H, Saitoh Y, Onodera Y, Mishima Y, Kelm RJ, Tsutsumi KI. A binding site for Pur alpha and Pur beta is structurally unstable and is required for replication in vivo from the rat aldolase B origin. Biochem Biophys Res Commun 2005; 340:517-25. [PMID: 16376299 DOI: 10.1016/j.bbrc.2005.12.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Accepted: 12/06/2005] [Indexed: 11/27/2022]
Abstract
The rat aldolase B promoter acts as a replication origin in vivo, as well as an autonomously replicating sequence (ARS). Here, we examined roles of a polypurine stretch (site PPu) in this origin, which is indispensable to the ARS activity. Purification of site PPu-binding protein revealed that site PPu binds Puralpha and Purbeta, i.e., single-stranded DNA-binding proteins whose roles in replication have been implicated, but less clear. Biochemical analyses showed that site PPu even in a longer DNA fragment is unstable in terms of double-helix, implying that Puralpha/beta may stabilize single-stranded state. Deletion of site PPu from the origin DNA, which was ectopically positioned in the mouse chromosome, significantly reduced replicator activity. Chromatin immunoprecipitation experiments showed that deletion of site PPu abolishes binding of the Puralpha/beta proteins to the origin. These observations suggest functional roles of site PPu and Puralpha/beta proteins in replication initiation.
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Affiliation(s)
- Yoshitaka Shimotai
- Laboratory of Functional Genomics, United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
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Amiri H, Nekhotiaeva N, Sun JS, Nguyen CH, Grierson DS, Good L, Zain R. Benzoquinoquinoxaline derivatives stabilize and cleave H-DNA and repress transcription downstream of a triplex-forming sequence. J Mol Biol 2005; 351:776-83. [PMID: 16045927 DOI: 10.1016/j.jmb.2005.03.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Revised: 03/15/2005] [Accepted: 03/16/2005] [Indexed: 11/29/2022]
Abstract
Oligopyrimidine*oligopurine sequences with potential to form intramolecular triple helix structures (H-DNA) have been found mainly in high eukaryote genomes. However, the natural occurrence and function of H-DNA remains elusive largely because we lack appropriate reagents to demonstrate the formation of these structures in cells. We examined whether a triple-helix specific stabilizing compound, benzoquinoquinoxaline (BQQ), and its 1,10-phenanthroline derivative can be efficiently utilized to study the formation and stabilization of an intramolecular triple-helical DNA structure in growing Escherichia coli cells and in vitro. Cell uptake of BQQ was confirmed by fluorescence microscopy. A plasmid carrying an H-DNA forming sequence upstream of a reporter gene was used to assess the effects of H-DNA formation and stabilization in growing cells. The presence of the H-DNA forming sequence dramatically repressed beta-lactamase expression, and sub-growth-inhibitory doses of BQQ caused a further 40% reduction. Most importantly, repression was dependent on the triple-helix forming sequence and correlated with the addition of BQQ. As the abundance of the H-DNA forming plasmid was not affected by the addition of BQQ, the dose-dependent reduction at the protein level observed here is likely caused by repression of transcription. Finally, the triple-helix specific interaction of BQQ with the target DNA sequence was demonstrated using a triple-helix directed cleavage assay by BQQ-1,10-phenanthroline conjugate in vitro.
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Affiliation(s)
- Haleh Amiri
- Department of Molecular Biology and Functional Genomics, Stockholm University, S-10691 Stockholm, Sweden
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Wang G, Vasquez KM. Naturally occurring H-DNA-forming sequences are mutagenic in mammalian cells. Proc Natl Acad Sci U S A 2004; 101:13448-53. [PMID: 15342911 PMCID: PMC518777 DOI: 10.1073/pnas.0405116101] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Naturally occurring DNA sequences can form noncanonical structures such as H-DNA, which are abundant and regulate the expression of several disease-linked genes. Here, we show that H-DNA-forming sequences are intrinsically mutagenic in mammalian cells. This finding suggests that DNA is a causative factor in mutagenesis and not just the end product. By using the endogenous H-DNA-forming sequence found in the human c-myc promoter, mutation frequencies in a reporter gene were increased approximately 20-fold over background in COS-7 cells. H-DNA-induced double-strand breaks (DSBs) were detected near the H-DNA locus. The structures of the mutants revealed microhomologies at the breakpoints, consistent with a nonhomologous end-joining repair of the DSBs. These results implicate H-DNA-induced DSBs in c-myc gene translocations in diseases such as Burkitt's lymphoma and t(12;15) BALB/c plasmacytomas, where most breakpoints are found near the H-DNA-forming site. Thus, our findings suggest that H-DNA is a source of genetic instability resulting from DSBs and demonstrate that naturally occurring DNA sequences are mutagenic in mammals, perhaps contributing to genetic evolution and disease.
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Affiliation(s)
- Guliang Wang
- Department of Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Science Park-Research Division, 1808 Park Road 1-C, Smithville, TX 78957, USA
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Maiti AK, Brahmachari SK. Poly purine.pyrimidine sequences upstream of the beta-galactosidase gene affect gene expression in Saccharomyces cerevisiae. BMC Mol Biol 2001; 2:11. [PMID: 11696239 PMCID: PMC59624 DOI: 10.1186/1471-2199-2-11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2001] [Accepted: 10/08/2001] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Poly purine.pyrimidine sequences have the potential to adopt intramolecular triplex structures and are overrepresented upstream of genes in eukaryotes. These sequences may regulate gene expression by modulating the interaction of transcription factors with DNA sequences upstream of genes. RESULTS A poly purine.pyrimidine sequence with the potential to adopt an intramolecular triplex DNA structure was designed. The sequence was inserted within a nucleosome positioned upstream of the beta-galactosidase gene in yeast, Saccharomyces cerevisiae, between the cycl promoter and gal 10 Upstream Activating Sequences (UASg). Upon derepression with galactose, beta-galactosidase gene expression is reduced 12-fold in cells carrying single copy poly purine.pyrimidine sequences. This reduction in expression is correlated with reduced transcription. Furthermore, we show that plasmids carrying a poly purine.pyrimidine sequence are not specifically lost from yeast cells. CONCLUSION We propose that a poly purine.pyrimidine sequence upstream of a gene affects transcription. Plasmids carrying this sequence are not specifically lost from cells and thus no additional effort is needed for the replication of these sequences in eukaryotic cells.
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Affiliation(s)
- Amit K Maiti
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - Samir K Brahmachari
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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Giovannangeli C, Hélène C. Progress in developments of triplex-based strategies. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1997; 7:413-21. [PMID: 9303193 DOI: 10.1089/oli.1.1997.7.413] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recognition of B-DNA by oligonucleotides that form triple helices is a unique method to specifically recognize sequences of double-stranded DNA. Recently, some significant limitations of the triple-based applications have been overcome. Stable intermolecular triplexes can be formed under physiologic conditions. Binding affinities of modified oligonucleotides to their target sequence due to Hoogsteen or reverse Hoogsteen hydrogen bonding interactions are now in the range of those obtained for duplex formation via Watson-Crick hydrogen bonding interactions even if the kinetics may be quite different. Progress has been made toward developing general procedures to determine the molecular mechanisms of action of triplex-forming oligonucleotides (TFO) administered to cultured cells to provide a rational proof-of-concept for antigene strategies. The antigene strategy has reached a point where TFOs can be used to interfere with several biologic progresses (replication, transcription, recombination, repair) in relevant systems both in vitro and ex vivo.
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Affiliation(s)
- C Giovannangeli
- Laboratoire de Biophysique, INSERM U.201, CNRS URA 481, Paris, France
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