501
|
Guy CP, Atkinson J, Gupta MK, Mahdi AA, Gwynn EJ, Rudolph CJ, Moon PB, van Knippenberg IC, Cadman CJ, Dillingham MS, Lloyd RG, McGlynn P. Rep provides a second motor at the replisome to promote duplication of protein-bound DNA. Mol Cell 2009; 36:654-66. [PMID: 19941825 PMCID: PMC2807033 DOI: 10.1016/j.molcel.2009.11.009] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 10/20/2009] [Accepted: 11/09/2009] [Indexed: 10/28/2022]
Abstract
Nucleoprotein complexes present challenges to genome stability by acting as potent blocks to replication. One attractive model of how such conflicts are resolved is direct targeting of blocked forks by helicases with the ability to displace the blocking protein-DNA complex. We show that Rep and UvrD each promote movement of E. coli replisomes blocked by nucleoprotein complexes in vitro, that such an activity is required to clear protein blocks (primarily transcription complexes) in vivo, and that a polarity of translocation opposite that of the replicative helicase is critical for this activity. However, these two helicases are not equivalent. Rep but not UvrD interacts physically and functionally with the replicative helicase. In contrast, UvrD likely provides a general means of protein-DNA complex turnover during replication, repair, and recombination. Rep and UvrD therefore provide two contrasting solutions as to how organisms may promote replication of protein-bound DNA.
Collapse
Affiliation(s)
- Colin P Guy
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, UK
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
502
|
Shah SN, Opresko PL, Meng X, Lee MYWT, Eckert KA. DNA structure and the Werner protein modulate human DNA polymerase delta-dependent replication dynamics within the common fragile site FRA16D. Nucleic Acids Res 2009; 38:1149-62. [PMID: 19969545 PMCID: PMC2831333 DOI: 10.1093/nar/gkp1131] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Common fragile sites (CFS) are chromosomal regions that exhibit instability during DNA replication stress. Although the mechanism of CFS expression has not been fully elucidated, one known feature is a severely delayed S-phase. We used an in vitro primer extension assay to examine the progression of DNA synthesis through various sequences within FRA16D by the replicative human DNA polymerases δ and α, and with human cell-free extracts. We found that specific cis-acting sequence elements perturb DNA elongation, causing inconsistent DNA synthesis rates between regions on the same strand and complementary strands. Pol δ was significantly inhibited in regions containing hairpins and microsatellites, [AT/TA]24 and [A/T]19–28, compared with a control region with minimal secondary structure. Pol δ processivity was enhanced by full length Werner Syndrome protein (WRN) and by WRN fragments containing either the helicase domain or DNA-binding C-terminal domain. In cell-free extracts, stalling was eliminated at smaller hairpins, but persisted in larger hairpins and microsatellites. Our data support a model whereby CFS expression during cellular stress is due to a combination of factors—density of specific DNA secondary-structures within a genomic region and asymmetric rates of strand synthesis.
Collapse
Affiliation(s)
- Sandeep N Shah
- Department of Pathology, Gittlen Cancer Research Foundation and the Intercollege Graduate Degree Program in Genetics, College of Medicine, The Pennsylvania State University, Hershey, PA 17033, USA
| | | | | | | | | |
Collapse
|
503
|
Abstract
Yeasts used in the production of lagers belong to the genus Saccharomyces pastorianus. Species within this genus arose from a natural hybridization event between two yeast species that appear to be closely related to Saccharomyces cerevisiae and Saccharomyces bayanus. The resultant hybrids contain complex allopolyploid genomes and retain genetic characteristics of both parental species. Recent genome analysis using both whole genome sequencing and competitive genomic hybridization techniques has revealed the underlying composition of lager yeasts genomes. There appear to be at least 36 unique chromosomes, many of which are lager specific, resulting from recombination events between the homeologous parental chromosomes. The recombination events are limited to a defined set of genetic loci, which are highly conserved within strains of lager yeasts. In addition to the hybrid chromosomes, several non-reciprocal chromosomal translocations and inversions are also observed. Remarkably, in response to exposure to environmental stresses such as high temperatures and high osmotic pressure, the genomes appear to be highly dynamic and undergo recombination events at defined loci and alterations in the telomeric regions. The ability of environmental stress to alter the structure and composition of the genomes of lager yeasts may point to mechanisms of adaptive evolution in these species.
Collapse
Affiliation(s)
- Ursula Bond
- School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| |
Collapse
|
504
|
Chad Brenner J, Chinnaiyan AM. Translocations in epithelial cancers. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1796:201-15. [PMID: 19406209 PMCID: PMC2752494 DOI: 10.1016/j.bbcan.2009.04.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 04/21/2009] [Indexed: 01/09/2023]
Abstract
Genomic translocations leading to the expression of chimeric transcripts characterize several hematologic, mesenchymal and epithelial malignancies. While several gene fusions have been linked to essential molecular events in hematologic malignancies, the identification and characterization of recurrent chimeric transcripts in epithelial cancers has been limited. However, the recent discovery of the recurrent gene fusions in prostate cancer has sparked a revitalization of the quest to identify novel rearrangements in epithelial malignancies. Here, the molecular mechanisms of gene fusions that drive several epithelial cancers and the recent technological advances that increase the speed and reliability of recurrent gene fusion discovery are explored.
Collapse
Affiliation(s)
- J. Chad Brenner
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Howard Hughes Medical Institute, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Urology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| |
Collapse
|
505
|
Yurov YB, Vorsanova SG, Iourov IY. GIN'n'CIN hypothesis of brain aging: deciphering the role of somatic genetic instabilities and neural aneuploidy during ontogeny. Mol Cytogenet 2009; 2:23. [PMID: 19939257 PMCID: PMC2787505 DOI: 10.1186/1755-8166-2-23] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 11/25/2009] [Indexed: 08/30/2023] Open
Abstract
Genomic instability (GIN) and chromosome instability (CIN) are two closely related ways to produce a variety of pathogenic conditions, i.e. cancer, neurodegeneration, chromosomal and genomic diseases. The GIN and CIN manifestation that possesses the most appreciable impact on cell physiology and viability is aneuploidy. The latter has been consistently shown to be associated with aging. Classically, it has been considered that a failure of mitotic machinery leads to aneuploidy acquiring throughout aging in dividing cells. Paradoxically, this model is inapplicable for the human brain, which is composed of post-mitotic cells persisting throughout the lifetime. To solve this paradox, we have focused on mosaic neural aneuploidy, a remarkable biomarker of GIN and CIN in the normal and diseased brain (i.e. Alzheimer's disease and ataxia-telangiectasia). Looking through the available data on genomic variations in the developing and adult human central nervous system, we were able to propose a hypothesis suggesting that neural aneuploidy produced during early brain development plays a crucial role of genetic determinant of aging in the healthy and diseased brain.
Collapse
Affiliation(s)
- Yuri B Yurov
- National Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow 119152, Russia.
| | | | | |
Collapse
|
506
|
Stewart JA, Campbell JL, Bambara RA. Dna2 is a structure-specific nuclease, with affinity for 5'-flap intermediates. Nucleic Acids Res 2009; 38:920-30. [PMID: 19934252 PMCID: PMC2817469 DOI: 10.1093/nar/gkp1055] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Dna2 is a nuclease/helicase with proposed roles in DNA replication, double-strand break repair and telomere maintenance. For each role Dna2 is proposed to process DNA substrates with a 5′-flap. To date, however, Dna2 has not revealed a preference for binding or cleavage of flaps over single-stranded DNA. Using DNA binding competition assays we found that Dna2 has substrate structure specificity. The nuclease displayed a strong preference for binding substrates with a 5′-flap or some variations of flap structure. Further analysis revealed that Dna2 recognized and bound both the single-stranded flap and portions of the duplex region immediately downstream of the flap. A model is proposed in which Dna2 first binds to a flap base, and then the flap threads through the protein with periodic cleavage, to a terminal flap length of ∼5 nt. This resembles the mechanism of flap endonuclease 1, consistent with cooperation of these two proteins in flap processing.
Collapse
Affiliation(s)
- Jason A Stewart
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | | | | |
Collapse
|
507
|
Weinert T, Kaochar S, Jones H, Paek A, Clark AJ. The replication fork's five degrees of freedom, their failure and genome rearrangements. Curr Opin Cell Biol 2009; 21:778-84. [PMID: 19913398 DOI: 10.1016/j.ceb.2009.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 10/09/2009] [Accepted: 10/10/2009] [Indexed: 12/20/2022]
Abstract
Genome rearrangements are important in pathology and evolution. The thesis of this review is that the genome is in peril when replication forks stall, and stalled forks are normally rescued by error-free mechanisms. Failure of error-free mechanisms results in large-scale chromosome changes called gross chromosomal rearrangements, GCRs, by the aficionados. In this review we discuss five error-free mechanisms a replication fork may use to overcome blockage, mechanisms that are still poorly understood. We then speculate on how genome rearrangements may occur when such mechanisms fail. Replication fork recovery failure may be an important feature of the oncogenic process. (Feedback to the authors on topics discussed herein is welcome.).
Collapse
Affiliation(s)
- T Weinert
- Department of Molecular & Cell Biology, University of Arizona, Tucson, AZ 85721, USA.
| | | | | | | | | |
Collapse
|
508
|
Double-strand break repair pathways protect against CAG/CTG repeat expansions, contractions and repeat-mediated chromosomal fragility in Saccharomyces cerevisiae. Genetics 2009; 184:65-77. [PMID: 19901069 DOI: 10.1534/genetics.109.111039] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trinucleotide repeats can form secondary structures, whose inappropriate repair or replication can lead to repeat expansions. There are multiple loci within the human genome where expansion of trinucleotide repeats leads to disease. Although it is known that expanded repeats accumulate double-strand breaks (DSBs), it is not known which DSB repair pathways act on such lesions and whether inaccurate DSB repair pathways contribute to repeat expansions. Using Saccharomyces cerevisiae, we found that CAG/CTG tracts of 70 or 155 repeats exhibited significantly elevated levels of breakage and expansions in strains lacking MRE11, implicating the Mre11/Rad50/Xrs2 complex in repairing lesions at structure-forming repeats. About two-thirds of the expansions that occurred in the absence of MRE11 were dependent on RAD52, implicating aberrant homologous recombination as a mechanism for generating expansions. Expansions were also elevated in a sae2 deletion background and these were not dependent on RAD52, supporting an additional role for Mre11 in facilitating Sae2-dependent hairpin processing at the repeat. Mre11 nuclease activity and Tel1-dependent checkpoint functions were largely dispensable for repeat maintenance. In addition, we found that intact homologous recombination and nonhomologous end-joining pathways of DSB repair are needed to prevent repeat fragility and that both pathways also protect against repeat instability. We conclude that failure of principal DSB repair pathways to repair breaks that occur within the repeats can result in the accumulation of atypical intermediates, whose aberrant resolution will then lead to CAG expansions, contractions, and repeat-mediated chromosomal fragility.
Collapse
|
509
|
Negishi M, Chiba T, Saraya A, Miyagi S, Iwama A. Dmap1 plays an essential role in the maintenance of genome integrity through the DNA repair process. Genes Cells 2009; 14:1347-57. [DOI: 10.1111/j.1365-2443.2009.01352.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
510
|
Tuduri S, Crabbé L, Conti C, Tourrière H, Holtgreve-Grez H, Jauch A, Pantesco V, De Vos J, Thomas A, Theillet C, Pommier Y, Tazi J, Coquelle A, Pasero P. Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription. Nat Cell Biol 2009; 11:1315-24. [PMID: 19838172 DOI: 10.1038/ncb1984] [Citation(s) in RCA: 377] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 08/24/2009] [Indexed: 12/16/2022]
Abstract
Topoisomerase I (Top1) is a key enzyme in functioning at the interface between DNA replication, transcription and mRNA maturation. Here, we show that Top1 suppresses genomic instability in mammalian cells by preventing a conflict between transcription and DNA replication. Using DNA combing and ChIP (chromatin immunoprecipitation)-on-chip, we found that Top1-deficient cells accumulate stalled replication forks and chromosome breaks in S phase, and that breaks occur preferentially at gene-rich regions of the genome. Notably, these phenotypes were suppressed by preventing the formation of RNA-DNA hybrids (R-loops) during transcription. Moreover, these defects could be mimicked by depletion of the splicing factor ASF/SF2 (alternative splicing factor/splicing factor 2), which interacts functionally with Top1. Taken together, these data indicate that Top1 prevents replication fork collapse by suppressing the formation of R-loops in an ASF/SF2-dependent manner. We propose that interference between replication and transcription represents a major source of spontaneous replication stress, which could drive genomic instability during the early stages of tumorigenesis.
Collapse
Affiliation(s)
- Sandie Tuduri
- Institute of Human Genetics CNRS UPR1142, F-34396 Montpellier, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
511
|
Lotti M. Science and surmise. Arch Toxicol 2009; 83:885-6. [PMID: 19730821 DOI: 10.1007/s00204-009-0462-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
512
|
Bermejo R, Capra T, Gonzalez-Huici V, Fachinetti D, Cocito A, Natoli G, Katou Y, Mori H, Kurokawa K, Shirahige K, Foiani M. Genome-Organizing Factors Top2 and Hmo1 Prevent Chromosome Fragility at Sites of S phase Transcription. Cell 2009; 138:870-84. [DOI: 10.1016/j.cell.2009.06.022] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 04/10/2009] [Accepted: 06/10/2009] [Indexed: 12/18/2022]
|
513
|
Paulsen RD, Soni DV, Wollman R, Hahn AT, Yee MC, Guan A, Hesley JA, Miller SC, Cromwell EF, Solow-Cordero DE, Meyer T, Cimprich KA. A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability. Mol Cell 2009; 35:228-39. [PMID: 19647519 DOI: 10.1016/j.molcel.2009.06.021] [Citation(s) in RCA: 421] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 05/21/2009] [Accepted: 06/26/2009] [Indexed: 12/26/2022]
Abstract
Signaling pathways that respond to DNA damage are essential for the maintenance of genome stability and are linked to many diseases, including cancer. Here, a genome-wide siRNA screen was employed to identify additional genes involved in genome stabilization by monitoring phosphorylation of the histone variant H2AX, an early mark of DNA damage. We identified hundreds of genes whose downregulation led to elevated levels of H2AX phosphorylation (gammaH2AX) and revealed links to cellular complexes and to genes with unclassified functions. We demonstrate a widespread role for mRNA-processing factors in preventing DNA damage, which in some cases is caused by aberrant RNA-DNA structures. Furthermore, we connect increased gammaH2AX levels to the neurological disorder Charcot-Marie-Tooth (CMT) syndrome, and we find a role for several CMT proteins in the DNA-damage response. These data indicate that preservation of genome stability is mediated by a larger network of biological processes than previously appreciated.
Collapse
Affiliation(s)
- Renee D Paulsen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
514
|
McCord AM, Jamal M, Williams ES, Camphausen K, Tofilon PJ. CD133+ glioblastoma stem-like cells are radiosensitive with a defective DNA damage response compared with established cell lines. Clin Cancer Res 2009; 15:5145-53. [PMID: 19671863 PMCID: PMC6290462 DOI: 10.1158/1078-0432.ccr-09-0263] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE CD133+ glioblastoma tumor stem-like cells (TSC) have been defined as radioresistant. However, although previously classified relative to CD133- cells, the radiosensitivity of CD133+ TSCs with respect to the standard glioblastoma model, established glioma cell lines, has not been determined. Therefore, to better understand the radioresponse of this cancer stem cell, we have used established cell lines as a framework for defining their in vitro radioresponse. EXPERIMENTAL DESIGN The intrinsic radiosensitivity of CD133+ TSC cultures and established glioma cell lines was determined by clonogenic assay. The TSCs and established cell lines were also compared in terms of DNA double-strand break (DSB) repair capacity and cell cycle checkpoint activation. RESULTS Based on clonogenic analysis, each of the six TSC cultures evaluated was more sensitive to radiation than the established glioma cell lines. Consistent with increased radiosensitivity, the DSB repair capacity as defined by neutral comet assay and gammaH2AX and Rad51 foci was significantly reduced in TSCs compared with the cell lines. Although G2 checkpoint activation was intact, in contrast to the cell lines, DNA synthesis was not inhibited in TSCs after irradiation, indicating the absence of the intra-S-phase checkpoint. CONCLUSIONS These data indicate that the mechanisms through which CD133+ TSCs respond to radiation are significantly different from those of the traditional glioblastoma in vitro model, established glioma cell lines. If TSCs play a critical role in glioblastoma treatment response, then such differences are likely to be of consequence in the development and testing of radiosensitizing agents.
Collapse
Affiliation(s)
- Amy M McCord
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, USA
| | | | | | | | | |
Collapse
|
515
|
Abstract
Gastric cancer is the second most frequent cause of cancer death worldwide, although much geographical variation in incidence exists. Prevention and personalised treatment are regarded as the best options to reduce gastric cancer mortality rates. Prevention strategies should be based on specific risk profiles, including Helicobacter pylori genotype, host gene polymorphisms, presence of precursor lesions, and environmental factors. Although adequate surgery remains the cornerstone of gastric cancer treatment, this single modality treatment seems to have reached its maximum achievable effect for local control and survival. Minimally invasive techniques can be used for treatment of early gastric cancers. Achievement of locoregional control for advanced disease remains very difficult. Extended resections that are standard practice in some Asian countries have not been shown to be as effective in other developed countries. We present an update of the incidence, causes, pathology, and treatment of gastric cancer, consisting of surgery, new strategies with neoadjuvant and adjuvant chemotherapy or radiotherapy, or both, novel treatment strategies using gene signatures, and the effect of caseload on patient outcomes.
Collapse
Affiliation(s)
- Henk H Hartgrink
- Department of Surgery, Leiden University Medical Centre, Leiden, the Netherlands
| | | | | | | |
Collapse
|
516
|
Gambus A, van Deursen F, Polychronopoulos D, Foltman M, Jones RC, Edmondson RD, Calzada A, Labib K. A key role for Ctf4 in coupling the MCM2-7 helicase to DNA polymerase alpha within the eukaryotic replisome. EMBO J 2009; 28:2992-3004. [PMID: 19661920 DOI: 10.1038/emboj.2009.226] [Citation(s) in RCA: 203] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Accepted: 07/15/2009] [Indexed: 01/14/2023] Open
Abstract
The eukaryotic replisome is a crucial determinant of genome stability, but its structure is still poorly understood. We found previously that many regulatory proteins assemble around the MCM2-7 helicase at yeast replication forks to form the replisome progression complex (RPC), which might link MCM2-7 to other replisome components. Here, we show that the RPC associates with DNA polymerase alpha that primes each Okazaki fragment during lagging strand synthesis. Our data indicate that a complex of the GINS and Ctf4 components of the RPC is crucial to couple MCM2-7 to DNA polymerase alpha. Others have found recently that the Mrc1 subunit of RPCs binds DNA polymerase epsilon, which synthesises the leading strand at DNA replication forks. We show that cells lacking both Ctf4 and Mrc1 experience chronic activation of the DNA damage checkpoint during chromosome replication and do not complete the cell cycle. These findings indicate that coupling MCM2-7 to replicative polymerases is an important feature of the regulation of chromosome replication in eukaryotes, and highlight a key role for Ctf4 in this process.
Collapse
Affiliation(s)
- Agnieszka Gambus
- Cancer Research UK, Paterson Institute for Cancer Research, University of Manchester, Manchester, UK
| | | | | | | | | | | | | | | |
Collapse
|
517
|
Chromosomal translocations caused by either pol32-dependent or pol32-independent triparental break-induced replication. Mol Cell Biol 2009; 29:5441-54. [PMID: 19651902 DOI: 10.1128/mcb.00256-09] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Double-strand breaks (DSBs) are harmful DNA lesions that can generate chromosomal rearrangements or chromosome losses if not properly repaired. Despite their association with a number of genetic diseases and cancer, the mechanisms by which DSBs cause rearrangements remain unknown. Using a newly developed experimental assay for the analysis of translocations occurring between two chromosomes in Saccharomyces cerevisiae, we found that a single DSB located on one chromosome uses a short homologous sequence found in a third chromosome as a bridge to complete DSB repair, leading to chromosomal translocations. Such translocations are dramatically reduced when the short homologous sequence on the third chromosome is deleted. Translocations rely on homologous recombination (HR) proteins, such as Rad51, Rad52, and Rad59, as well as on the break-induced replication-specific protein Pol32 and on Srs2, but not on Ku70. Our results indicate that a single chromosomal DSB efficiently searches for short homologous sequences throughout the genome for its repair, leading to triparental translocations between heterologous chromosomes. Given the abundance of repetitive DNA in eukaryotic genomes, the results of this study open the possibility that HR rather than nonhomologous end joining may be a major source of chromosomal translocations.
Collapse
|
518
|
Hartgrink HH, Jansen EPM, van Grieken NCT, van de Velde CJH. Gastric cancer. LANCET (LONDON, ENGLAND) 2009. [PMID: 19625077 DOI: 10.1016/s0140-6736(09)] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Gastric cancer is the second most frequent cause of cancer death worldwide, although much geographical variation in incidence exists. Prevention and personalised treatment are regarded as the best options to reduce gastric cancer mortality rates. Prevention strategies should be based on specific risk profiles, including Helicobacter pylori genotype, host gene polymorphisms, presence of precursor lesions, and environmental factors. Although adequate surgery remains the cornerstone of gastric cancer treatment, this single modality treatment seems to have reached its maximum achievable effect for local control and survival. Minimally invasive techniques can be used for treatment of early gastric cancers. Achievement of locoregional control for advanced disease remains very difficult. Extended resections that are standard practice in some Asian countries have not been shown to be as effective in other developed countries. We present an update of the incidence, causes, pathology, and treatment of gastric cancer, consisting of surgery, new strategies with neoadjuvant and adjuvant chemotherapy or radiotherapy, or both, novel treatment strategies using gene signatures, and the effect of caseload on patient outcomes.
Collapse
Affiliation(s)
- Henk H Hartgrink
- Department of Surgery, Leiden University Medical Centre, Leiden, the Netherlands
| | | | | | | |
Collapse
|
519
|
Zhong XY, Wang P, Han J, Rosenfeld MG, Fu XD. SR proteins in vertical integration of gene expression from transcription to RNA processing to translation. Mol Cell 2009; 35:1-10. [PMID: 19595711 PMCID: PMC2744344 DOI: 10.1016/j.molcel.2009.06.016] [Citation(s) in RCA: 239] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Indexed: 12/25/2022]
Abstract
SR proteins have been studied extensively as a family of RNA-binding proteins that participate in both constitutive and regulated pre-mRNA splicing in mammalian cells. However, SR proteins were first discovered as factors that interact with transcriptionally active chromatin. Recent studies have now uncovered properties that connect these once apparently disparate functions, showing that a subset of SR proteins seem to bind directly to the histone 3 tail, play an active role in transcriptional elongation, and colocalize with genes that are engaged in specific intra- and interchromosome interactions for coordinated regulation of gene expression in the nucleus. These transcription-related activities are also coupled with a further expansion of putative functions of specific SR protein family members in RNA metabolism downstream of mRNA splicing, from RNA export to stability control to translation. These findings, therefore, highlight the broader roles of SR proteins in vertical integration of gene expression and provide mechanistic insights into their contributions to genome stability and proper cell-cycle progression in higher eukaryotic cells.
Collapse
Affiliation(s)
- Xiang-Yang Zhong
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651
| | - Pingping Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651
| | - Joonhee Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651
| | - Michael G. Rosenfeld
- Howard Hughes Medicine Institute, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651
| |
Collapse
|
520
|
Tjeertes JV, Miller KM, Jackson SP. Screen for DNA-damage-responsive histone modifications identifies H3K9Ac and H3K56Ac in human cells. EMBO J 2009; 28:1878-89. [PMID: 19407812 PMCID: PMC2684025 DOI: 10.1038/emboj.2009.119] [Citation(s) in RCA: 254] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 03/26/2009] [Indexed: 01/05/2023] Open
Abstract
Recognition and repair of damaged DNA occurs within the context of chromatin. The key protein components of chromatin are histones, whose post-translational modifications control diverse chromatin functions. Here, we report our findings from a large-scale screen for DNA-damage-responsive histone modifications in human cells. We have identified specific phosphorylations and acetylations on histone H3 that decrease in response to DNA damage. Significantly, we find that DNA-damage-induced changes in H3S10p, H3S28p and H3.3S31p are a consequence of cell-cycle re-positioning rather than DNA damage per se. In contrast, H3K9Ac and H3K56Ac, a mark previously uncharacterized in human cells, are rapidly and reversibly reduced in response to DNA damage. Finally, we show that the histone acetyl-transferase GCN5/KAT2A acetylates H3K56 in vitro and in vivo. Collectively, our data indicate that though most histone modifications do not change appreciably after genotoxic stress, H3K9Ac and H3K56Ac are reduced in response to DNA damage in human cells.
Collapse
Affiliation(s)
- Jorrit V Tjeertes
- The Gurdon Institute, University of Cambridge, Cambridge, UK
- These authors contributed equally to this work
| | - Kyle M Miller
- The Gurdon Institute, University of Cambridge, Cambridge, UK
- These authors contributed equally to this work
| | | |
Collapse
|
521
|
Ruan K, Bao S, Ouyang G. The multifaceted role of periostin in tumorigenesis. Cell Mol Life Sci 2009; 66:2219-30. [PMID: 19308325 PMCID: PMC11115806 DOI: 10.1007/s00018-009-0013-7] [Citation(s) in RCA: 257] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 02/24/2009] [Accepted: 02/27/2009] [Indexed: 12/18/2022]
Abstract
Periostin, also called osteoblast-specific factor 2 (OSF-2), is a member of the fasciclin family and a disulfide-linked cell adhesion protein that has been shown to be expressed preferentially in the periosteum and periodontal ligaments, where it acts as a critical regulator of bone and tooth formation and maintenance. Furthermore, periostin plays an important role in cardiac development. Recent clinical evidence has also revealed that periostin is involved in the development of various tumors, such as breast, lung, colon, pancreatic, and ovarian cancers. Periostin interacts with multiple cell-surface receptors, most notably integrins, and signals mainly via the PI3-K/Akt and other pathways to promote cancer cell survival, epithelial-mesenchymal transition (EMT), invasion, and metastasis. In this review, aspects related to the function of periostin in tumorigenesis are summarized.
Collapse
Affiliation(s)
- Kai Ruan
- Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, 361005 Xiamen, China
| | - Shideng Bao
- Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, 361005 Xiamen, China
- Present Address: Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 USA
| | - Gaoliang Ouyang
- Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, 361005 Xiamen, China
| |
Collapse
|
522
|
Goettel W, Messing J. Change of gene structure and function by non-homologous end-joining, homologous recombination, and transposition of DNA. PLoS Genet 2009; 5:e1000516. [PMID: 19521498 PMCID: PMC2686159 DOI: 10.1371/journal.pgen.1000516] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Accepted: 05/13/2009] [Indexed: 11/18/2022] Open
Abstract
An important objective in genome research is to relate genome structure to gene function. Sequence comparisons among orthologous and paralogous genes and their allelic variants can reveal sequences of functional significance. Here, we describe a 379-kb region on chromosome 1 of maize that enables us to reconstruct chromosome breakage, transposition, non-homologous end-joining, and homologous recombination events. Such a high-density composition of various mechanisms in a small chromosomal interval exemplifies the evolution of gene regulation and allelic diversity in general. It also illustrates the evolutionary pace of changes in plants, where many of the above mechanisms are of somatic origin. In contrast to animals, somatic alterations can easily be transmitted through meiosis because the germline in plants is contiguous to somatic tissue, permitting the recovery of such chromosomal rearrangements. The analyzed region contains the P1-wr allele, a variant of the genetically well-defined p1 gene, which encodes a Myb-like transcriptional activator in maize. The P1-wr allele consists of eleven nearly perfect P1-wr 12-kb repeats that are arranged in a tandem head-to-tail array. Although a technical challenge to sequence such a structure by shotgun sequencing, we overcame this problem by subcloning each repeat and ordering them based on nucleotide variations. These polymorphisms were also critical for recombination and expression analysis in presence and absence of the trans-acting epigenetic factor Ufo1. Interestingly, chimeras of the p1 and p2 genes, p2/p1 and p1/p2, are framing the P1-wr cluster. Reconstruction of sequence amplification steps at the p locus showed the evolution from a single Myb-homolog to the multi-gene P1-wr cluster. It also demonstrates how non-homologous end-joining can create novel gene fusions. Comparisons to orthologous regions in sorghum and rice also indicate a greater instability of the maize genome, probably due to diploidization following allotetraploidization.
Collapse
Affiliation(s)
- Wolfgang Goettel
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA
| | | |
Collapse
|
523
|
Meiosis drives extraordinary genome plasticity in the haploid fungal plant pathogen Mycosphaerella graminicola. PLoS One 2009; 4:e5863. [PMID: 19516898 PMCID: PMC2689623 DOI: 10.1371/journal.pone.0005863] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 03/27/2009] [Indexed: 11/24/2022] Open
Abstract
Meiosis in the haploid plant-pathogenic fungus Mycosphaerella graminicola results in eight ascospores due to a mitotic division following the two meiotic divisions. The transient diploid phase allows for recombination among homologous chromosomes. However, some chromosomes of M. graminicola lack homologs and do not pair during meiosis. Because these chromosomes are not present universally in the genome of the organism they can be considered to be dispensable. To analyze the meiotic transmission of unequal chromosome numbers, two segregating populations were generated by crossing genetically unrelated parent isolates originating from Algeria and The Netherlands that had pathogenicity towards durum or bread wheat, respectively. Detailed genetic analyses of these progenies using high-density mapping (1793 DArT, 258 AFLP and 25 SSR markers) and graphical genotyping revealed that M. graminicola has up to eight dispensable chromosomes, the highest number reported in filamentous fungi. These chromosomes vary from 0.39 to 0.77 Mb in size, and represent up to 38% of the chromosomal complement. Chromosome numbers among progeny isolates varied widely, with some progeny missing up to three chromosomes, while other strains were disomic for one or more chromosomes. Between 15–20% of the progeny isolates lacked one or more chromosomes that were present in both parents. The two high-density maps showed no recombination of dispensable chromosomes and hence, their meiotic processing may require distributive disjunction, a phenomenon that is rarely observed in fungi. The maps also enabled the identification of individual twin isolates from a single ascus that shared the same missing or doubled chromosomes indicating that the chromosomal polymorphisms were mitotically stable and originated from nondisjunction during the second division and, less frequently, during the first division of fungal meiosis. High genome plasticity could be among the strategies enabling this versatile pathogen to quickly overcome adverse biotic and abiotic conditions in wheat fields.
Collapse
|
524
|
Yaakov G, Duch A, García-Rubio M, Clotet J, Jimenez J, Aguilera A, Posas F. The stress-activated protein kinase Hog1 mediates S phase delay in response to osmostress. Mol Biol Cell 2009; 20:3572-82. [PMID: 19477922 DOI: 10.1091/mbc.e09-02-0129] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Control of cell cycle progression by stress-activated protein kinases (SAPKs) is essential for cell adaptation to extracellular stimuli. Exposure of yeast to osmostress activates the Hog1 SAPK, which modulates cell cycle progression at G1 and G2 by the phosphorylation of elements of the cell cycle machinery, such as Sic1 and Hsl1, and by down-regulation of G1 and G2 cyclins. Here, we show that upon stress, Hog1 also modulates S phase progression. The control of S phase is independent of the S phase DNA damage checkpoint and of the previously characterized Hog1 cell cycle targets Sic1 and Hsl1. Hog1 uses at least two distinct mechanisms in its control over S phase progression. At early S phase, the SAPK prevents firing of replication origins by delaying the accumulation of the S phase cyclins Clb5 and Clb6. In addition, Hog1 prevents S phase progression when activated later in S phase or cells containing a genetic bypass for cyclin-dependent kinase activity. Hog1 interacts with components of the replication complex and delays phosphorylation of the Dpb2 subunit of the DNA polymerase. The two mechanisms of Hog1 action lead to delayed firing of origins and prolonged replication, respectively. The Hog1-dependent delay of replication could be important to allow Hog1 to induce gene expression before replication.
Collapse
Affiliation(s)
- Gilad Yaakov
- Cell Signaling Unit, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | | | | | | | | | | | | |
Collapse
|
525
|
Chromatin remodelling beyond transcription: the INO80 and SWR1 complexes. Nat Rev Mol Cell Biol 2009; 10:373-84. [PMID: 19424290 DOI: 10.1038/nrm2693] [Citation(s) in RCA: 222] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chromatin-modifying factors have essential roles in DNA processing pathways that dictate cellular functions. The ability of chromatin modifiers, including the INO80 and SWR1 chromatin-remodelling complexes, to regulate transcriptional processes is well established. However, recent studies reveal that the INO80 and SWR1 complexes have crucial functions in many other essential processes, including DNA repair, checkpoint regulation, DNA replication, telomere maintenance and chromosome segregation. During these diverse nuclear processes, the INO80 and SWR1 complexes function cooperatively with their histone substrates, gamma-H2AX and H2AZ. This research reveals that INO80 and SWR1 ATP-dependent chromatin remodelling is an integral component of pathways that maintain genomic integrity.
Collapse
|
526
|
Atkinson J, McGlynn P. Replication fork reversal and the maintenance of genome stability. Nucleic Acids Res 2009; 37:3475-92. [PMID: 19406929 PMCID: PMC2699526 DOI: 10.1093/nar/gkp244] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The progress of replication forks is often threatened in vivo, both by DNA damage and by proteins bound to the template. Blocked forks must somehow be restarted, and the original blockage cleared, in order to complete genome duplication, implying that blocked fork processing may be critical for genome stability. One possible pathway that might allow processing and restart of blocked forks, replication fork reversal, involves the unwinding of blocked forks to form four-stranded structures resembling Holliday junctions. This concept has gained increasing popularity recently based on the ability of such processing to explain many genetic observations, the detection of unwound fork structures in vivo and the identification of enzymes that have the capacity to catalyse fork regression in vitro. Here, we discuss the contexts in which fork regression might occur, the factors that may promote such a reaction and the possible roles of replication fork unwinding in normal DNA metabolism.
Collapse
Affiliation(s)
- John Atkinson
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | | |
Collapse
|
527
|
Giardino D, Corti C, Ballarati L, Colombo D, Sala E, Villa N, Piombo G, Pierluigi M, Faravelli F, Guerneri S, Coviello D, Lalatta F, Cavallari U, Bellotti D, Barlati S, Croci G, Franchi F, Savin E, Nocera G, Amico FP, Granata P, Casalone R, Nutini L, Lisi E, Torricelli F, Giussani U, Facchinetti B, Guanti G, Di Giacomo M, Susca FP, Pecile V, Romitti L, Cardarelli L, Racalbuto E, Police MA, Chiodo F, Rodeschini O, Falcone P, Donti E, Grimoldi MG, Martinoli E, Stioui S, Caufin D, Lauricella SA, Tanzariello SA, Voglino G, Lenzini E, Besozzi M, Larizza L, Dalprà L. De novo balanced chromosome rearrangements in prenatal diagnosis. Prenat Diagn 2009; 29:257-65. [PMID: 19248039 DOI: 10.1002/pd.2215] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVE We surveyed the datasheets of 29 laboratories concerning prenatal diagnosis of de novo apparently balanced chromosome rearrangements to assess the involvement of specific chromosomes, the breakpoints distribution and the impact on the pregnancy outcome. METHOD By means of a questionnaire, data on 269.371 analyses performed from 1983 to 2006 on amniotic fluid, chorionic villus and fetal blood samples were collected. RESULTS A total of 246 balanced anomalies were detected at frequencies of 72% for reciprocal translocations, 18% for Robertsonian translocations, 7% for inversions and 3% for complex chromosome rearrangements. The total frequencies of balanced rearrangements were 0.09%, 0.08% and 0.05% on amniotic fluid, chorionic villus and fetal blood samples. CONCLUSION A preferential involvement of chromosomes 22, 7, 21, 3, 9 and 11 and a less involvement of chromosomes X, 19, 12, 6 and 1 was observed. A nonrandom distribution of the breakpoints across chromosomes was noticed. Association in the location of recurrent breakpoints and fragile sites was observed for chromosomes 11, 7, 10 and 22, while it was not recorded for chromosome 3. The rate of pregnancy termination was about 20%, with frequencies decreasing from complex chromosomal rearrangements (33%), reciprocal translocations (24%) to inversions (11%) and Robertsonian translocations (3%).
Collapse
Affiliation(s)
- Daniela Giardino
- Lab Citogenetica Medica e Genetica Molecolare, IRCCS Ist. Auxologico Italiano, Milano, Italy.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
528
|
Meyer R, Fofanov V, Panigrahi AK, Merchant F, Zhang N, Pati D. Overexpression and mislocalization of the chromosomal segregation protein separase in multiple human cancers. Clin Cancer Res 2009; 15:2703-10. [PMID: 19351757 PMCID: PMC2718850 DOI: 10.1158/1078-0432.ccr-08-2454] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Separase, an endopeptidase, plays a pivotal role in chromosomal segregation by separating sister chromatids during the metaphase to anaphase transition. Using a mouse mammary tumor model we have recently shown that overexpression of Separase induces aneuploidy and tumorigenesis (Zhang et al., Proc Natl Acad Sci 2008;105:13033). In the present study, we have investigated the expression level of Separase across a wide range of human tumors. EXPERIMENTAL DESIGN To examine the expression levels and localization of Separase in human tumors, we have performed immunofluorescence microscopy using human Separase antibody and tumor tissue arrays from osteosarcoma, colorectal, breast, and prostate cancers with appropriate normal controls. RESULTS We show that Separase is significantly overexpressed in osteosarcoma, breast, and prostate tumor specimens. There is a strong correlation of tumor status with the localization of Separase into the nucleus throughout all stages of the cell cycle. Unlike the normal control tissues, where Separase localization is exclusively cytoplasmic in nondividing cells, human tumor samples show significantly higher number of resting cells with a strong nuclear Separase staining. Additionally, overexpression of Separase transcript strongly correlates with high incidence of relapse, metastasis, and lower 5-year overall survival rate in breast and prostate cancer patients. CONCLUSION These results further strengthen our hypothesis that Separase might be an oncogene, whose overexpression induces tumorigenesis, and indicates that Separase overexpression and aberrant nuclear localization are common in many tumor types and may predict outcome in some human cancers.
Collapse
Affiliation(s)
- Rene Meyer
- Department of Pediatric Hematology/Oncology, Texas Children’s Cancer Center, Baylor College of Medicine, 6621 Fannin St., MC3-3320, Houston, TX, 77030
| | - Viacheslav Fofanov
- Department of Statistics, Rice University, 6100 Main St., Houston, Texas 77005
| | - Anil K. Panigrahi
- Department of Pediatric Hematology/Oncology, Texas Children’s Cancer Center, Baylor College of Medicine, 6621 Fannin St., MC3-3320, Houston, TX, 77030
| | - Fatima Merchant
- Department of Engineering Technology, University of Houston, 4800 Calhoun Rd., Houston, TX, 77204
| | - Nenggang Zhang
- Department of Pediatric Hematology/Oncology, Texas Children’s Cancer Center, Baylor College of Medicine, 6621 Fannin St., MC3-3320, Houston, TX, 77030
| | - Debananda Pati
- Department of Pediatric Hematology/Oncology, Texas Children’s Cancer Center, Baylor College of Medicine, 6621 Fannin St., MC3-3320, Houston, TX, 77030
| |
Collapse
|
529
|
|
530
|
G clustering is important for the initiation of transcription-induced R-loops in vitro, whereas high G density without clustering is sufficient thereafter. Mol Cell Biol 2009; 29:3124-33. [PMID: 19307304 DOI: 10.1128/mcb.00139-09] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
R-loops form cotranscriptionally in vitro and in vivo at transcribed duplex DNA regions when the nascent RNA is G-rich, particularly with G clusters. This is the case for phage polymerases, as used here (T7 RNA polymerase), as well as RNA polymerases in bacteria, Saccharomyces cerevisiae, avians, mice, and humans. The nontemplate strand is left in a single-stranded configuration within the R-loop region. These structures are known to form at mammalian immunoglobulin class switch regions, thus exposing regions of single-stranded DNA for the action of AID, a single-strand-specific cytidine deaminase. R-loops form by thread-back of the RNA onto the template DNA strand, and here we report that G clusters are extremely important for the initiation phase of R-loop formation. Even very short regions with one GGGG sequence can initiate R-loops much more efficiently than random sequences. The high efficiencies observed with G clusters cannot be achieved by having a very high G density alone. Annealing of the transcript, which is otherwise disadvantaged relative to the nontemplate DNA strand because of unfavorable proximity while exiting the RNA polymerase, can offer greater stability if it occurs at the G clusters, thereby initiating an R-loop. R-loop elongation beyond the initiation zone occurs in a manner that is not as reliant on G clusters as it is on a high G density. These results lead to a model in which G clusters are important to nucleate the thread-back of RNA for R-loop initiation and, once initiated, the elongation of R-loops is primarily determined by the density of G on the nontemplate DNA strand. Without both a favorable R-loop initiation zone and elongation zone, R-loop formation is inefficient.
Collapse
|
531
|
Thymidylate synthetase allelic imbalance in clear cell renal carcinoma. Cancer Chemother Pharmacol 2009; 64:1195-200. [PMID: 19306093 DOI: 10.1007/s00280-009-0986-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 03/06/2009] [Indexed: 10/21/2022]
Abstract
PURPOSE To investigate the allelic status of the thymidylate synthetase (TYMS) gene, located at chromosome band 18p11.32, in renal cell carcinoma (RCC). TYMS is a key target of the 5-fluorouracil (5-FU)-based class of drugs, frequently considered in combination therapies in advanced RCC. TYMS variants, such as the TYMS polymorphic 5'-untranslated region variable number tandem repeat sequence (VNTR), are under investigation to guide 5-FU treatment. Yet, no information is available with regard to changes in TYMS allele frequencies in RCC malignances. METHODS Blood and matched tumor samples were collected from 41 histological proven clear cell RCC affected patients (30 males, 11 females.). TYMS VNTR genotype was first determined in blood to identify heterozygotes employing PCR techniques. To evaluate for allelic imbalance, fragment analysis was performed both in blood and matched tumor DNA of the heterozygote patients. Microsatellite analysis, employing the markers D18S59 and D18S476 mapping, respectively, at the TYMS locus (18p11.32) and 1.5 Mb downstream of the TYMS gene sequence (18p11.31), was performed to confirm TYMS allelic imbalance in tumors. RESULTS Germ-line TYMS VNTR distribution was: 2R/2R (19.5%), TYMS 2R/3R (36.6%) and TYMS 3R/3R (43.9%). Allelic imbalance for the TYMS tandem repeat region was detected in 26.6% of the heterozygote patients. Microsatellite analysis confirmed the allelic imbalance detected by TYMS VNTR analysis and revealed that the overall frequence of allelic imbalance of chromosome band 18p11.32 was 35%, while the overall allelic imbalance of chromosome band 18p11.31 was 28%. CONCLUSIONS By focusing on the TYMS polymorphic variants in renal cancer, we here provide evidence, to our knowledge, for the first time showing loss of 18p11.32 and 18p11.31 in renal cell carcinomas. As allelic imbalances involving TYMS locus may be an important variable affecting 5-FU responsiveness, this study may contribute to explain different responses of advanced RCC in combined chemotherapeutic regimens incorporating fluoropyridines.
Collapse
|
532
|
Faza MB, Kemmler S, Jimeno S, González-Aguilera C, Aguilera A, Hurt E, Panse VG. Sem1 is a functional component of the nuclear pore complex-associated messenger RNA export machinery. ACTA ACUST UNITED AC 2009; 184:833-46. [PMID: 19289793 PMCID: PMC2699155 DOI: 10.1083/jcb.200810059] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The evolutionarily conserved protein Sem1/Dss1 is a subunit of the regulatory particle (RP) of the proteasome, and, in mammalian cells, binds the tumor suppressor protein BRCA2. Here, we describe a new function for yeast Sem1. We show that sem1 mutants are impaired in messenger RNA (mRNA) export and transcription elongation, and induce strong transcription-associated hyper-recombination phenotypes. Importantly, Sem1, independent of the RP, is functionally linked to the mRNA export pathway. Biochemical analyses revealed that, in addition to the RP, Sem1 coenriches with components of two other multisubunit complexes: the nuclear pore complex (NPC)-associated TREX-2 complex that is required for transcription-coupled mRNA export, and the COP9 signalosome, which is involved in deneddylation. Notably, targeting of Thp1, a TREX-2 component, to the NPC is perturbed in a sem1 mutant. These findings reveal an unexpected nonproteasomal function of Sem1 in mRNA export and in prevention of transcription-associated genome instability. Thus, Sem1 is a versatile protein that might stabilize multiple protein complexes involved in diverse pathways.
Collapse
|
533
|
Lee PS, Greenwell PW, Dominska M, Gawel M, Hamilton M, Petes TD. A fine-structure map of spontaneous mitotic crossovers in the yeast Saccharomyces cerevisiae. PLoS Genet 2009; 5:e1000410. [PMID: 19282969 PMCID: PMC2646836 DOI: 10.1371/journal.pgen.1000410] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Accepted: 02/06/2009] [Indexed: 12/04/2022] Open
Abstract
Homologous recombination is an important mechanism for the repair of DNA damage in mitotically dividing cells. Mitotic crossovers between homologues with heterozygous alleles can produce two homozygous daughter cells (loss of heterozygosity), whereas crossovers between repeated genes on non-homologous chromosomes can result in translocations. Using a genetic system that allows selection of daughter cells that contain the reciprocal products of mitotic crossing over, we mapped crossovers and gene conversion events at a resolution of about 4 kb in a 120-kb region of chromosome V of Saccharomyces cerevisiae. The gene conversion tracts associated with mitotic crossovers are much longer (averaging about 12 kb) than the conversion tracts associated with meiotic recombination and are non-randomly distributed along the chromosome. In addition, about 40% of the conversion events have patterns of marker segregation that are most simply explained as reflecting the repair of a chromosome that was broken in G1 of the cell cycle. Most higher organisms have two copies of several different types of chromosomes. For example, the human female has 23 pairs of chromosomes. Although the chromosome pairs have very similar sequences, they are not identical. Members of a chromosome pair can swap segments from one chromosome to the other; these exchanges are called “recombination.” Most previous studies of recombination have been done in cells undergoing meiosis, the process that leads to the formation of eggs and sperm (gametes). Recombination, however, can also occur in cells that are dividing mitotically. In our study, we examine the properties of mitotic recombination in yeast. We show that mitotic recombination differs from meiotic recombination in two important ways. First, the sizes of the chromosome segments that are non-reciprocally transferred during mitotic recombination are much larger than those transferred during meiotic exchange. Second, in meiosis, most recombination events involve the repair of a single chromosome break, whereas in mitosis, about half of the recombination events appear to involve the repair of two chromosome breaks.
Collapse
Affiliation(s)
- Phoebe S Lee
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | | | | | | | | | | |
Collapse
|
534
|
Recombination at DNA replication fork barriers is not universal and is differentially regulated by Swi1. Proc Natl Acad Sci U S A 2009; 106:4770-5. [PMID: 19273851 DOI: 10.1073/pnas.0807739106] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
DNA replication stress has been implicated in the etiology of genetic diseases, including cancers. It has been proposed that genomic sites that inhibit or slow DNA replication fork progression possess recombination hotspot activity and can form potential fragile sites. Here we used the fission yeast, Schizosaccharomyces pombe, to demonstrate that hotspot activity is not a universal feature of replication fork barriers (RFBs), and we propose that most sites within the genome that form RFBs do not have recombination hotspot activity under nonstressed conditions. We further demonstrate that Swi1, the TIMELESS homologue, differentially controls the recombination potential of RFBs, switching between being a suppressor and an activator of recombination in a site-specific fashion.
Collapse
|
535
|
Abstract
Tumour-associated cell cycle defects are often mediated by alterations in cyclin-dependent kinase (CDK) activity. Misregulated CDKs induce unscheduled proliferation as well as genomic and chromosomal instability. According to current models, mammalian CDKs are essential for driving each cell cycle phase, so therapeutic strategies that block CDK activity are unlikely to selectively target tumour cells. However, recent genetic evidence has revealed that, whereas CDK1 is required for the cell cycle, interphase CDKs are only essential for proliferation of specialized cells. Emerging evidence suggests that tumour cells may also require specific interphase CDKs for proliferation. Thus, selective CDK inhibition may provide therapeutic benefit against certain human neoplasias.
Collapse
Affiliation(s)
- Marcos Malumbres
- Cell Division and Cancer Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
| | | |
Collapse
|
536
|
de la Loza MCD, Wellinger RE, Aguilera A. Stimulation of direct-repeat recombination by RNA polymerase III transcription. DNA Repair (Amst) 2009; 8:620-6. [PMID: 19168400 DOI: 10.1016/j.dnarep.2008.12.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Revised: 12/13/2008] [Accepted: 12/15/2008] [Indexed: 11/18/2022]
Abstract
Eukaryotic cells have to regulate the progression and integrity of DNA replication forks through concomitantly transcribed genes. A transcription-dependent increase of recombination within protein-coding and ribosomal genes of eukaryotic cells is well documented. Here we addressed whether tRNA transcription and tRNA-dependent transcription-associated replication pausing leads to genetic instability. Thus, we designed a plasmid based, LEU2 direct-repeat containing system for the analysis of factors that contribute to tRNA(SUP53)-dependent genetic instability. We show that tRNA(SUP53) transcription is recombinogenic and that recombination can be further stimulated by deletion of the 5' to 3' helicase Rrm3. Furthermore, tRNA(SUP53)-dependent recombination was markedly increased in the presence of 4-NQO in rrm3Delta cells only. The frequency of recombination events mediated by tRNA(SUP53) transcription does not correlate with the appearance and intensity of replication fork pausing sites. Our results provide evidence that the convergent encounter of replication and RNA polymerase III transcription machineries stimulates recombination, although to a lesser extent than RNA polymerase I or II transcription. However, there is no correlation between recombination and the specific replication fork pausing sites found at the tRNA (SUP53) gene. Our results indicate that tRNA-specific replication fork pausing sites are poorly recombinogenic.
Collapse
Affiliation(s)
- M C Díaz de la Loza
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla - CSIC, Avda. Américo Vespucio s/n, 41092 Sevilla, Spain
| | | | | |
Collapse
|
537
|
Panigrahi AK, Pati D. Road to the crossroads of life and death: linking sister chromatid cohesion and separation to aneuploidy, apoptosis and cancer. Crit Rev Oncol Hematol 2009; 72:181-93. [PMID: 19162508 DOI: 10.1016/j.critrevonc.2008.12.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Revised: 12/02/2008] [Accepted: 12/11/2008] [Indexed: 01/22/2023] Open
Abstract
Genomic instability, aberrant cell proliferation and defects in apoptotic cell death are critical issues in cancer. The two most prominent hallmarks of cancer cells are multiple mutations in key genes encoding proteins that regulate important cell-survival pathways, and marked restructuring or redistribution of the chromosomes (aneuploidy) indicative of genomic instability. Both these aspects have been suggested to cause cancer, though a causal role for chromosomal restructuring in tumorigenesis has not been experimentally fully substantiated. This review is aimed at understanding the mechanisms of cell cycle (proliferation) and programmed cell death (apoptosis) and chromosomal instability governed by cohesin and other aneuploidy promoters, which will provide new insights into the process of carcinogenesis and new avenues for targeted treatment.
Collapse
Affiliation(s)
- Anil K Panigrahi
- Department of Pediatric Hematology/Oncology, Texas Children's Cancer Center, Baylor College of Medicine, 6621 Fannin St., MC3-3320, Houston, TX 77030, USA
| | | |
Collapse
|
538
|
Urtishak KA, Smith KD, Chanoux RA, Greenberg RA, Johnson FB, Brown EJ. Timeless Maintains Genomic Stability and Suppresses Sister Chromatid Exchange during Unperturbed DNA Replication. J Biol Chem 2008; 284:8777-85. [PMID: 19112184 DOI: 10.1074/jbc.m806103200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Genome integrity is maintained during DNA replication by coordination of various replisome-regulated processes. Although it is known that Timeless (Tim) is a replisome component that participates in replication checkpoint responses to genotoxic stress, its importance for genome maintenance during normal DNA synthesis has not been reported. Here we demonstrate that Tim reduction leads to genomic instability during unperturbed DNA replication, culminating in increased chromatid breaks and translocations (triradials, quadriradials, and fusions). Tim deficiency led to increased H2AX phosphorylation and Rad51 and Rad52 foci formation selectively during DNA synthesis and caused a 3-4-fold increase in sister chromatid exchange. The sister chromatid exchange events stimulated by Tim reduction were largely mediated via a Brca2/Rad51-dependent mechanism and were additively increased by deletion of the Blm helicase. Therefore, Tim deficiency leads to an increased reliance on homologous recombination for proper continuation of DNA synthesis. Together, these results indicate a pivotal role for Tim in maintaining genome stability throughout normal DNA replication.
Collapse
Affiliation(s)
- Karen A Urtishak
- Abramson Family Cancer Research Institute, Department of Cancer Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA."
| | | | | | | | | | | |
Collapse
|
539
|
Shen C, Zhou Y, Zhan J, Reske SN, Buck AK. Chromosome instability and tumor lethality suppression in carcinogenesis. J Cell Biochem 2008; 105:1327-41. [DOI: 10.1002/jcb.21937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
540
|
Conaway RC, Conaway JW. The INO80 chromatin remodeling complex in transcription, replication and repair. Trends Biochem Sci 2008; 34:71-7. [PMID: 19062292 DOI: 10.1016/j.tibs.2008.10.010] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 10/28/2008] [Accepted: 10/29/2008] [Indexed: 01/05/2023]
Abstract
The Ino80 ATPase is a member of the SNF2 family of ATPases and functions as an integral component of a multisubunit ATP-dependent chromatin remodeling complex. Although INO80 complexes from yeast and higher eukaryotes share a common core of conserved subunits, the complexes have diverged substantially during evolution and have acquired new subunits with apparently species-specific functions. Recent studies have shown that the INO80 complex contributes to a wide variety of chromatin-dependent nuclear transactions, including transcription, DNA repair and DNA replication.
Collapse
Affiliation(s)
- Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
| | | |
Collapse
|
541
|
Sikdar N, Banerjee S, Zhang H, Smith S, Myung K. Spt2p defines a new transcription-dependent gross chromosomal rearrangement pathway. PLoS Genet 2008; 4:e1000290. [PMID: 19057669 PMCID: PMC2585797 DOI: 10.1371/journal.pgen.1000290] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 11/03/2008] [Indexed: 01/18/2023] Open
Abstract
Large numbers of gross chromosomal rearrangements (GCRs) are frequently observed in many cancers. High mobility group 1 (HMG1) protein is a non-histone DNA-binding protein and is highly expressed in different types of tumors. The high expression of HMG1 could alter DNA structure resulting in GCRs. Spt2p is a non-histone DNA binding protein in Saccharomyces cerevisiae and shares homology with mammalian HMG1 protein. We found that Spt2p overexpression enhances GCRs dependent on proteins for transcription elongation and polyadenylation. Excess Spt2p increases the number of cells in S phase and the amount of single-stranded DNA (ssDNA) that might be susceptible to cause DNA damage and GCR. Consistently, RNase H expression, which reduces levels of ssDNA, decreased GCRs in cells expressing high level of Spt2p. Lastly, high transcription in the chromosome V, the location at which GCR is monitored, also enhanced GCR formation. We propose a new pathway for GCR where DNA intermediates formed during transcription can lead to genomic instability. Transmitting genetic information without creating deleterious genetic alternations is one of the cell's most important tasks. When cells cannot repair DNA damage properly, it leads to genomic instability and results in genetic disorders, including cancer. Many studies, including ours, have started to uncover pathways suppressing one type of genomic instability, gross chromosomal rearrangement (GCR). However, the pathogenic mechanism to promote GCR that could mimic the hyper-activation of oncogenes during tumorigenesis is not clearly understood. The high expression of HMG1 has been documented many times as a putative oncogene. Therefore, we tested whether high expression of its yeast homologue, Spt2p, could induce pathogenic effect including GCR formation. Excess Spt2p expression indeed induced GCR formation dependent on its role in transcription elongation and polyadenylation. Further studies to find mechanisms resided in GCR formation by Spt2p revealed that excess Spt2p increased single-stranded DNA to produce GCR. Our studies provide a mechanistic bridge between transcription and genomic instability.
Collapse
Affiliation(s)
- Nilabja Sikdar
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Soma Banerjee
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Han Zhang
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stephanie Smith
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kyungjae Myung
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| |
Collapse
|
542
|
Structure-function analysis of the barley genome: the gene-rich region of chromosome 2HL. Funct Integr Genomics 2008; 9:67-79. [PMID: 18958509 DOI: 10.1007/s10142-008-0099-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 09/03/2008] [Accepted: 10/13/2008] [Indexed: 10/21/2022]
Abstract
A major gene-rich region on the end of the long arm of Triticeae group 2 chromosomes exhibits high recombination frequencies, making it an attractive region for positional cloning. Traits known to be controlled by this region include chasmogamy/cleistogamy, frost tolerance at flowering, grain yield, head architecture, and resistance to Fusarium head blight and rusts. To assist these cloning efforts, we constructed detailed genetic maps of barley chromosome 2H, including 61 polymerase chain reaction markers. Colinearity with rice occurred in eight distinct blocks, including five blocks in the terminal gene-rich region. Alignment of rice sequences from the junctions of colinear chromosome segments provided no evidence for the involvement of long (>2.5 kb) inverted repeats in generating inversions. However, reuse of some junction sequences in two or three separate evolutionary breakage/fusion events was implicated, suggesting the presence of fragile sites. Sequencing across 91 gene fragments totaling 107 kb from four barley genotypes revealed the highest single nucleotide substitution and insertion-deletion polymorphism levels in the terminal regions of the chromosome arms. The maps will assist in the isolation of genes from the chromosome 2L gene-rich region in barley and wheat by providing markers and accelerating the identification of the corresponding points in the rice genome sequence.
Collapse
|
543
|
Genomic and epigenetic instability in colorectal cancer pathogenesis. Gastroenterology 2008; 135:1079-99. [PMID: 18773902 PMCID: PMC2866182 DOI: 10.1053/j.gastro.2008.07.076] [Citation(s) in RCA: 680] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 07/07/2008] [Accepted: 07/28/2008] [Indexed: 12/11/2022]
Abstract
Colorectal cancer arises as a consequence of the accumulation of genetic alterations (gene mutations, gene amplification, and so on) and epigenetic alterations (aberrant DNA methylation, chromatin modifications, and so on) that transform colonic epithelial cells into colon adenocarcinoma cells. The loss of genomic stability and resulting gene alterations are key molecular pathogenic steps that occur early in tumorigenesis; they permit the acquisition of a sufficient number of alterations in tumor suppressor genes and oncogenes that transform cells and promote tumor progression. Two predominant forms of genomic instability that have been identified in colon cancer are microsatellite instability and chromosome instability. Substantial progress has been made to identify causes of chromosomal instability in colorectal cells and to determine the effects of the different forms of genomic instability on the biological and clinical behavior of colon tumors. In addition to genomic instability, epigenetic instability results in the aberrant methylation of tumor suppressor genes. Determining the causes and roles of genomic and epigenomic instability in colon tumor formation has the potential to yield more effective prevention strategies and therapeutics for patients with colorectal cancer.
Collapse
|
544
|
Su X, Bernal JA, Venkitaraman AR. Cell-cycle coordination between DNA replication and recombination revealed by a vertebrate N-end rule degron-Rad51. Nat Struct Mol Biol 2008; 15:1049-58. [DOI: 10.1038/nsmb.1490] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Accepted: 08/12/2008] [Indexed: 11/09/2022]
|
545
|
Sadikovic B, Al-Romaih K, Squire J, Zielenska M. Cause and consequences of genetic and epigenetic alterations in human cancer. Curr Genomics 2008; 9:394-408. [PMID: 19506729 PMCID: PMC2691666 DOI: 10.2174/138920208785699580] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 05/06/2008] [Accepted: 05/08/2008] [Indexed: 12/16/2022] Open
Abstract
Both genetic and epigenetic changes contribute to development of human cancer. Oncogenomics has primarily focused on understanding the genetic basis of neoplasia, with less emphasis being placed on the role of epigenetics in tumourigenesis. Genomic alterations in cancer vary between the different types and stages, tissues and individuals. Moreover, genomic change ranges from single nucleotide mutations to gross chromosomal aneuploidy; which may or may not be associated with underlying genomic instability. Collectively, genomic alterations result in widespread deregulation of gene expression profiles and the disruption of signalling networks that control proliferation and cellular functions. In addition to changes in DNA and chromosomes, it has become evident that oncogenomic processes can be profoundly influenced by epigenetic mechanisms. DNA methylation is one of the key epigenetic factors involved in regulation of gene expression and genomic stability, and is biologically necessary for the maintenance of many cellular functions. While there has been considerable progress in understanding the impact of genetic and epigenetic mechanisms in tumourigenesis, there has been little consideration of the importance of the interplay between these two processes. In this review we summarize current understanding of the role of genetic and epigenetic alterations in human cancer. In addition we consider the associated interactions of genetic and epigenetic processes in tumour onset and progression. Furthermore, we provide a model of tumourigenesis that addresses the combined impact of both epigenetic and genetic alterations in cancer cells.
Collapse
Affiliation(s)
- B Sadikovic
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Canada
- The Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Canada
| | - K Al-Romaih
- The Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Canada
| | - J.A Squire
- The Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Canada
| | - M Zielenska
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Canada
| |
Collapse
|
546
|
Chen CC, Carson JJ, Feser J, Tamburini B, Zabaronick S, Linger J, Tyler JK. Acetylated lysine 56 on histone H3 drives chromatin assembly after repair and signals for the completion of repair. Cell 2008; 134:231-43. [PMID: 18662539 DOI: 10.1016/j.cell.2008.06.035] [Citation(s) in RCA: 316] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 05/02/2008] [Accepted: 06/16/2008] [Indexed: 11/28/2022]
Abstract
DNA damage causes checkpoint activation leading to cell cycle arrest and repair, during which the chromatin structure is disrupted. The mechanisms whereby chromatin structure and cell cycle progression are restored after DNA repair are largely unknown. We show that chromatin reassembly following double-strand break (DSB) repair requires the histone chaperone Asf1 and that absence of Asf1 causes cell death, as cells are unable to recover from the DNA damage checkpoint. We find that Asf1 contributes toward chromatin assembly after DSB repair by promoting acetylation of free histone H3 on lysine 56 (K56) via the histone acetyl transferase Rtt109. Mimicking acetylation of K56 bypasses the requirement for Asf1 for chromatin reassembly and checkpoint recovery, whereas mutations that prevent K56 acetylation block chromatin reassembly after repair. These results indicate that restoration of the chromatin following DSB repair is driven by acetylated H3 K56 and that this is a signal for the completion of repair.
Collapse
Affiliation(s)
- Chin-Chuan Chen
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | | | | | | | | | | |
Collapse
|
547
|
Vázquez MV, Rojas V, Tercero JA. Multiple pathways cooperate to facilitate DNA replication fork progression through alkylated DNA. DNA Repair (Amst) 2008; 7:1693-704. [PMID: 18640290 DOI: 10.1016/j.dnarep.2008.06.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 06/23/2008] [Accepted: 06/24/2008] [Indexed: 10/21/2022]
Abstract
Eukaryotic genomes are especially vulnerable to DNA damage during the S phase of the cell cycle, when chromosomes must be duplicated. The stability of DNA replication forks is critical to achieve faithful chromosome replication and is severely compromised when forks encounter DNA lesions. To maintain genome integrity, replication forks need to be protected by the S-phase checkpoint and DNA insults must be repaired. Different pathways help to repair or tolerate the lesions in the DNA, but their contribution to the progression of replication forks through damaged DNA is not well known. Here we show in budding yeast that, when the DNA template is damaged with the alkylating agent methyl methanesulfonate (MMS), base excision repair, homologous recombination and DNA damage tolerance pathways, together with a functional S-phase checkpoint, are essential for the efficient progression of DNA replication forks and the maintenance of cell survival. In the absence of base excision repair, replication forks stall reversibly in cells exposed to MMS. This repair reaction is necessary to eliminate the lesions that impede fork progression and has to be coordinated with recombination and damage tolerance activities to avoid fork collapse and allow forks to resume and complete chromosome replication.
Collapse
|
548
|
González-Aguilera C, Tous C, Gómez-González B, Huertas P, Luna R, Aguilera A. The THP1-SAC3-SUS1-CDC31 complex works in transcription elongation-mRNA export preventing RNA-mediated genome instability. Mol Biol Cell 2008; 19:4310-8. [PMID: 18667528 DOI: 10.1091/mbc.e08-04-0355] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The eukaryotic THO/TREX complex, involved in mRNP biogenesis, plays a key role in the maintenance of genome integrity in yeast. mRNA export factors such as Thp1-Sac3 also affect genome integrity, but their mutations have other phenotypes different from those of THO/TREX. Sus1 is a novel component of SAGA transcription factor that also associates with Thp1-Sac3, but little is known about its effect on genome instability and transcription. Here we show that Thp1, Sac3, and Sus1 form a functional unit with a role in mRNP biogenesis and maintenance of genome integrity that is independent of SAGA. Importantly, the effects of ribozyme-containing transcription units, RNase H, and the action of human activation-induced cytidine deaminase on transcription and genome instability are consistent with the possibility that R-loops are formed in Thp1-Sac3-Sus1-Cdc31 as in THO mutants. Our data reveal that Thp1-Sac3-Sus1-Cdc31, together with THO/TREX, define a specific pathway connecting transcription elongation with export via an RNA-dependent dynamic process that provides a feedback mechanism for the control of transcription and the preservation of genetic integrity of transcribed DNA regions.
Collapse
Affiliation(s)
- Cristina González-Aguilera
- Centro Andaluz de Biologia Molecular y Medicina Regenerativa, Universidad de Sevilla-CSIC, 41092 Sevilla, Spain
| | | | | | | | | | | |
Collapse
|
549
|
Abstract
Cellular senescence is associated with ageing and cancer in vivo and has a proven tumour-suppressive function. Common to both ageing and cancer is the generation of DNA damage and the engagement of the DNA-damage response pathways. In this Review, the diverse mechanisms that lead to DNA-damage generation and the activation of DNA-damage-response signalling pathways are discussed, together with the evidence for their contribution to the establishment and maintenance of cellular senescence in the context of organismal ageing and cancer development.
Collapse
|
550
|
Abstract
A regional analysis of nucleotide substitution rates along human genes and their flanking regions allows us to quantify the effect of mutational mechanisms associated with transcription in germ line cells. Our analysis reveals three distinct patterns of substitution rates. First, a sharp decline in the deamination rate of methylated CpG dinucleotides, which is observed in the vicinity of the 5' end of genes. Second, a strand asymmetry in complementary substitution rates, which extends from the 5' end to 1 kbp downstream from the 3' end, associated with transcription-coupled repair. Finally, a localized strand asymmetry, an excess of C-->T over G-->A substitution in the nontemplate strand confined to the first 1-2 kbp downstream of the 5' end of genes. We hypothesize that higher exposure of the nontemplate strand near the 5' end of genes leads to a higher cytosine deamination rate. Up to now, only the somatic hypermutation (SHM) pathway has been known to mediate localized and strand-specific mutagenic processes associated with transcription in mammalia. The mutational patterns in SHM are induced by cytosine deaminase, which just targets single-stranded DNA. This DNA conformation is induced by R-loops, which preferentially occur at the 5' ends of genes. We predict that R-loops are extensively formed in the beginning of transcribed regions in germ line cells.
Collapse
|