http://www.genomeintegrity.com The most accessed research articles published by Genome Integrity 2012-04-11T00:00:00Z Background: Cancers often arise within an area of cells (e.g. an epithelial patch) that is predisposed to the development of cancer, i.e. a "field of cancerization" or "field defect." Sporadic colon cancer is characterized by an elevated mutation rate and genomic instability. If a field defect were deficient in DNA repair, DNA damages would tend to escape repair and give rise to carcinogenic mutations.PurposeTo determine whether reduced expression of DNA repair proteins Pms2, Ercc1 and Xpf (pairing partner of Ercc1) are early steps in progression to colon cancer. Results: Tissue biopsies were taken during colonoscopies of 77 patients at 4 different risk levels for colon cancer, including 19 patients who had never had colonic neoplasia (who served as controls). In addition, 158 tissue samples were taken from tissues near or within colon cancers removed by resection and 16 tissue samples were taken near tubulovillous adenomas (TVAs) removed by resection. 568 triplicate tissue sections (a total of 1,704 tissue sections) from these tissue samples were evaluated by immunohistochemistry for 4 DNA repair proteins. Substantially reduced protein expression of Pms2, Ercc1 and Xpf occurred in field defects of up to 10 cm longitudinally distant from colon cancers or TVAs and within colon cancers. Expression of another DNA repair protein, Ku86, was infrequently reduced in these areas. When Pms2, Ercc1 or Xpf were reduced in protein expression, then either one or both of the other two proteins most often had reduced protein expression as well. The mean inner colon circumferences, from 32 resections, of the ascending, transverse and descending/sigmoid areas were measured as 6.6 cm, 5.8 cm and 6.3 cm, respectively. When combined with other measurements in the literature, this indicates the approximate mean number of colonic crypts in humans is 10 million. Conclusions: The substantial deficiencies in protein expression of DNA repair proteins Pms2, Ercc1 and Xpf in about 1 million crypts near cancers and TVAs suggests that the tumors arose in field defects that were deficient in DNA repair and that deficiencies in Pms2, Ercc1 and Xpf are early steps, often occurring together, in progression to colon cancer. http://www.genomeintegrity.com/content/3/1/3 Alexander Facista Huy Nguyen Cristy Lewis Anil Prasad Lois Ramsey Beryl Zaitlin Valentine Nfonsam Robert Krouse Harris Bernstein Claire Payne Stephen Stern Nicole Oatman Bhaskar Banerjee Carol Bernstein Genome Integrity 2012, null:3 2012-04-11T00:00:00Z doi:10.1186/2041-9414-3-3 /content/figures/2041-9414-3-3-toc.gif Genome Integrity 2041-9414 ${item.volume} 3 2012-04-11T00:00:00Z XML Products of various forms of DNA damage have been implicated in a variety of important biological processes, such as aging, neurodegenerative diseases, and cancer. Therefore, there exists great interest to develop methods for interrogating damaged DNA in the context of sequencing. Here, we demonstrate that single-molecule, real-time (SMRT®) DNA sequencing can directly detect damaged DNA bases in the DNA template - as a by-product of the sequencing method - through an analysis of the DNA polymerase kinetics that are altered by the presence of a modified base. We demonstrate the sequencing of several DNA templates containing products of DNA damage, including 8-oxoguanine, 8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine, 5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thymine dimers, and show that these base modifications can be readily detected with single-modification resolution and DNA strand specificity. We characterize the distinct kinetic signatures generated by these DNA base modifications. http://www.genomeintegrity.com/content/2/1/10 Tyson Clark Kristi Spittle Stephen Turner Jonas Korlach Genome Integrity 2011, null:10 2011-12-20T00:00:00Z doi:10.1186/2041-9414-2-10 /content/figures/2041-9414-2-10-toc.gif Genome Integrity 2041-9414 ${item.volume} 10 2011-12-20T00:00:00Z XML Background: Investigating the cellular and molecular signatures in eukaryotic cells following exposure to nanoparticles will further our understanding on the mechanisms mediating nanoparticle induced effects. This study illustrates the molecular effects of silver nanoparticles (Ag-np) in normal human lung cells, IMR-90 and human brain cancer cells, U251 with emphasis on gene expression, induction of inflammatory mediators and the interaction of Ag-np with cytosolic proteins. Results: We report that silver nanoparticles are capable of adsorbing cytosolic proteins on their surface that may influence the function of intracellular factors. Gene and protein expression profiles of Ag-np exposed cells revealed up regulation of many DNA damage response genes such as Gadd 45 in both the cell types and ATR in cancer cells. Moreover, down regulation of genes necessary for cell cycle progression (cyclin B and cyclin E) and DNA damage response/repair (XRCC1 and 3, FEN1, RAD51C, RPA1) was observed in both the cell lines. Double strand DNA damage was observed in a dose dependant manner as evidenced in γH2AX foci assay. There was a down regulation of p53 and PCNA in treated cells. Cancer cells in particular showed a concentration dependant increase in phosphorylated p53 accompanied by the cleavage of caspase 3 and PARP. Our results demonstrate the involvement of NFκB and MAP kinase pathway in response to Ag-np exposure. Up regulation of pro-inflammatory cytokines such as interleukins (IL-8, IL-6), macrophage colony stimulating factor, macrophage inflammatory protein in fibroblasts following Ag-np exposure were also observed. Conclusion: In summary, Ag-np can modulate gene expression and protein functions in IMR-90 cells and U251 cells, leading to defective DNA repair, proliferation arrest and inflammatory response. The observed changes could also be due to its capability to adsorb cytosolic proteins on its surface. http://www.genomeintegrity.com/content/3/1/2 P AshaRani Swaminathan Sethu Hui Kheng Lim Ganapathy Balaji Suresh Valiyaveettil M Prakash Hande Genome Integrity 2012, null:2 2012-02-10T00:00:00Z doi:10.1186/2041-9414-3-2 /content/figures/2041-9414-3-2-toc.gif Genome Integrity 2041-9414 ${item.volume} 2 2012-02-10T00:00:00Z XML Cellular senescence is a normal biological process that is initiated in response to a range of intrinsic and extrinsic factors that functions to remove irreparable damage and therefore potentially harmful cells, from the proliferative pool. Senescence can therefore be thought of in beneficial terms as a tumour suppressor. In contrast to this, there is a growing body of evidence suggesting that senescence is also associated with the disruption of the tissue microenvironment and development of a pro-oncogenic environment, principally via the secretion of senescence-associated pro-inflammatory factors. The fraction of cells in a senescent state is known to increase with cellular age and from exposure to various stressors including ionising radiation therefore, the implications of the detrimental effects of the senescent phenotype are important to understand within the context of the increasing human exposure to ionising radiation. This review will discuss what is currently understood about senescence, highlighting possible associations between senescence and cancer and, how exposure to ionising radiation may modify this. http://www.genomeintegrity.com/content/2/1/7 Rebecca Sabin Rhona Anderson Genome Integrity 2011, null:7 2011-08-11T00:00:00Z doi:10.1186/2041-9414-2-7 /content/figures/2041-9414-2-7-toc.gif Genome Integrity 2041-9414 ${item.volume} 7 2011-08-11T00:00:00Z XML DNA double-strand breaks are among the most serious types of DNA damage and their signaling and repair is critical for all cells and organisms. The repair of both induced and programmed DNA breaks is fundamental as demonstrated by the many human syndromes, neurodegenerative diseases, immunodeficiency and cancer associated with defective repair of these DNA lesions. Homologous recombination and non-homologous end-joining pathways are the two major DNA repair pathways responsible for mediating the repair of DNA double-strand breaks. The signaling of DNA double-strand breaks is critical for cells to orchestrate the repair pathways and maintain genomic integrity. This signaling network is highly regulated and involves a growing number of proteins and elaborated posttranslational modifications including phosphorylation and ubiquitylation. Here, we highlight the recent progress in the signaling of DNA double-strand breaks, the major proteins and posttranslational modifications involved and the diseases and syndromes associated with impaired signaling of these breaks. http://www.genomeintegrity.com/content/1/1/15 Toshiyuki Bohgaki Miyuki Bohgaki Razqallah Hakem Genome Integrity 2010, null:15 2010-11-05T00:00:00Z doi:10.1186/2041-9414-1-15 /content/figures/2041-9414-1-15-toc.gif Genome Integrity 2041-9414 ${item.volume} 15 2010-11-05T00:00:00Z XML Radiation therapy is a widely used therapeutic approach for cancer. To improve the efficacy of radiotherapy there is an intense interest in combining this modality with two broad classes of compounds, radiosensitizers and radioprotectors. These either enhance tumour-killing efficacy or mitigate damage to surrounding non-malignant tissue, respectively. Radiation exposure often results in the formation of DNA double-strand breaks, which are marked by the induction of H2AX phosphorylation to generate γH2AX. In addition to its essential role in DDR signalling and coordination of double-strand break repair, the ability to visualize and quantitate γH2AX foci using immunofluorescence microscopy techniques enables it to be exploited as an indicator of therapeutic efficacy in a range of cell types and tissues. This review will explore the emerging applicability of γH2AX as a marker for monitoring the effectiveness of radiation-modifying compounds. http://www.genomeintegrity.com/content/2/1/3 Li-Jeen Mah Christian Orlowski Katherine Ververis Raja Vasireddy Assam El-Osta Tom Karagiannis Genome Integrity 2011, null:3 2011-01-25T00:00:00Z doi:10.1186/2041-9414-2-3 /content/figures/2041-9414-2-3-toc.gif Genome Integrity 2041-9414 ${item.volume} 3 2011-01-25T00:00:00Z XML Background: Genome instability is associated with human cancers and chromosome breakage syndromes, including Bloom's syndrome, caused by inactivation of BLM helicase. Numerous mutations that lead to genome instability are known, yet how they interact genetically is poorly understood. Results: We show that spontaneous translocations that arise by nonallelic homologous recombination in DNA-damage-checkpoint-defective yeast lacking the BLM-related Sgs1 helicase (sgs1Δ mec3Δ) are inhibited if cells lack Mec1/ATR kinase. Tel1/ATM, in contrast, acts as a suppressor independently of Mec3 and Sgs1. Translocations are also inhibited in cells lacking Dun1 kinase, but not in cells defective in a parallel checkpoint branch defined by Chk1 kinase. While we had previously shown that RAD51 deletion did not inhibit translocation formation, RAD59 deletion led to inhibition comparable to the rad52Δ mutation. A candidate screen of other DNA metabolic factors identified Exo1 as a strong suppressor of chromosomal rearrangements in the sgs1Δ mutant, becoming even more important for chromosomal stability upon MEC3 deletion. We determined that the C-terminal third of Exo1, harboring mismatch repair protein binding sites and phosphorylation sites, is dispensable for Exo1's roles in chromosomal rearrangement suppression, mutation avoidance and resistance to DNA-damaging agents. Conclusions: Our findings suggest that translocations between related genes can form by Rad59-dependent, Rad51-independent homologous recombination, which is independently suppressed by Sgs1, Tel1, Mec3 and Exo1 but promoted by Dun1 and the telomerase-inhibitor Mec1. We propose a model for the functional interaction between mitotic recombination and the DNA-damage checkpoint in the suppression of chromosomal rearrangements in sgs1Δ cells. http://www.genomeintegrity.com/content/2/1/8 Lillian Doerfler Lorena Harris Emilie Viebranz Kristina Schmidt Genome Integrity 2011, null:8 2011-10-31T00:00:00Z doi:10.1186/2041-9414-2-8 /content/figures/2041-9414-2-8-toc.gif Genome Integrity 2041-9414 ${item.volume} 8 2011-10-31T00:00:00Z XML Ionizing radiation is an invaluable diagnostic and treatment tool used in various clinical applications. On the other hand, radiation is a known cytotoxic with a potential DNA damaging and carcinogenic effects. However, the biological effects of low and high linear energy transfer (LET) radiations are considerably more complex than previously thought. In the past decade, evidence has mounted for a novel biological phenomenon termed as "bystander effect" (BE), wherein directly irradiated cells transmit damaging signals to non-irradiated cells thereby inducing a response similar to that of irradiated cells. BE can also be induced in various cells irrespective of the type of radiation, and the BE may be more damaging in the longer term than direct radiation exposure. BE is mediated either through gap-junctions or via soluble factors released by irradiated cells. DNA damage response mechanisms represent a vital line of defense against exogenous and endogenous damage caused by radiation and promote two distinct outcomes: survival and the maintenance of genomic stability. The latter is critical for cancer avoidance. Therefore, efforts to understand and modulate the bystander responses will provide new approaches to cancer therapy and prevention. This review overviews the emerging role of BE of low and high LET radiations on the genomic instability of bystander cells and its possible implications for carcinogenesis. http://www.genomeintegrity.com/content/1/1/13 Rajamanickam Baskar Genome Integrity 2010, null:13 2010-09-12T00:00:00Z doi:10.1186/2041-9414-1-13 /content/figures/2041-9414-1-13-toc.gif Genome Integrity 2041-9414 ${item.volume} 13 2010-09-12T00:00:00Z XML Background: In order to maintain cellular viability and genetic integrity cells must respond quickly following the induction of cytotoxic double strand DNA breaks (DSB). This response requires a number of processes including stabilisation of the DSB, signalling of the break and repair. It is becoming increasingly apparent that one key step in this process is chromatin remodelling. Results: Here we describe the chromodomain helicase DNA-binding protein (CHD4) as a target of ATM kinase. We show that ionising radiation (IR)-induced phosphorylation of CHD4 affects its intranuclear organization resulting in increased chromatin binding/retention. We also show assembly of phosphorylated CHD4 foci at sites of DNA damage, which might be required to fulfil its function in the regulation of DNA repair. Consistent with this, cells overexpressing a phospho-mutant version of CHD4 that cannot be phosphorylated by ATM fail to show enhanced chromatin retention after DSBs and display high rates of spontaneous damage. Conclusion: These results provide insight into how CHD4 phosphorylation might be required to remodel chromatin around DNA breaks allowing efficient DNA repair to occur. http://www.genomeintegrity.com/content/2/1/1 Aaron Urquhart Magtouf Gatei Derek Richard Kum Kum Khanna Genome Integrity 2011, null:1 2011-01-10T00:00:00Z doi:10.1186/2041-9414-2-1 /content/figures/2041-9414-2-1-toc.gif Genome Integrity 2041-9414 ${item.volume} 1 2011-01-10T00:00:00Z XML Background: Telomeres are protective cap structures at the ends of the linear eukaryotic chromosomes, which provide stability to the genome by shielding from degradation and chromosome fusions. The cap consists of telomere-specific proteins binding to the respective single- and double-stranded parts of the telomeric sequence. In addition to the nucleation of the chromatin structure the telomere-binding proteins are involved in the regulation of the telomere length. However, the telomeric sequences are highly diverged among yeast species. During the evolution this high rate of divergency presents a challenge for the sequence recognition of the telomere-binding proteins. Results: We found that the Saccharomyces castellii protein Rap1, a negative regulator of telomere length, binds a 12-mer minimal binding site (MBS) within the double-stranded telomeric DNA. The sequence specificity is dependent on the interaction with two 5 nucleotide motifs, having a 6 nucleotide centre-to-centre spacing. The isolated DNA-binding domain binds the same MBS and retains the same motif binding characteristics as the full-length Rap1 protein. However, it shows some deviations in the degree of sequence-specific dependence in some nucleotide positions. Intriguingly, the positions of most importance for the sequence-specific binding of the full-length Rap1 protein coincide with 3 of the 4 nucleotides utilized by the 3' overhang binding protein Cdc13. These nucleotides are very well conserved within the otherwise highly divergent telomeric sequences of yeasts. Conclusions: Rap1 and Cdc13 are two very distinct types of DNA-binding proteins with highly separate functions. They interact with the double-stranded vs. the single-stranded telomeric DNA via significantly different types of DNA-binding domain structures. However, we show that they are dependent on coinciding nucleotide positions for their sequence-specific binding to telomeric sequences. Thus, we conclude that during the molecular evolution they act together to preserve a core sequence of the telomeric DNA. http://www.genomeintegrity.com/content/2/1/2 Jenny Rhodin Edso Cecilia Gustafsson Marita Cohn Genome Integrity 2011, null:2 2011-01-14T00:00:00Z doi:10.1186/2041-9414-2-2 /content/figures/2041-9414-2-2-toc.gif Genome Integrity 2041-9414 ${item.volume} 2 2011-01-14T00:00:00Z XML