A novel variable number of tandem repeats (VNTR) polymorphism containing Sp1 binding elements in the promoter of XRCC5 is a risk factor for human bladder cancer

Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences

Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ≥7 bp. We detected 35 638 VNTR loci and classified 5676 as commonly polymorphic (i.e. with non-reference alleles occurring in >5% of the population). Commonly polymorphic VNTR loci were found to be enriched in genomic regions with regulatory function, i.e. transcription start sites and enhancers. Investigation of the commonly polymorphic VNTRs in the context of population ancestry revealed that 1096 loci contained population-specific alleles and that those could be used to classify individuals into super-populations with near-perfect accuracy. Search for quantitative trait loci (eQTLs), among the VNTRs proximal to genes, indicated that in 187 genes expression differences correlated with VNTR genotype. We validated our predictions in several ways, including experimentally, through the identification of predicted alleles in long reads, and by comparisons showing consistency between sequencing platforms. This study is the most comprehensive analysis of minisatellite VNTRs in the human population to date.

Radio-adaptive response and correlation of non-homologous end joining repair gene polymorphisms [XRRC5 (3R/2R/1R/0R), XRCC6(C/G) and XRCC7 (G/T)] in human peripheral blood mononuclear cells exposed to gamma radiation

BACKGROUND

Radio-adaptive response (RAR) is transient phenomena, where cells conditioned with a small dose (priming) of ionizing radiation shows significantly reduced DNA damage with a subsequent high challenging dose. The role of DNA double strand break repair gene polymorphism in RAR is not known. In the present study attempt was made to find out the influence of NHEJ repair gene polymorphisms [a VNTR; XRCC5 (3R/2R/1R/0R); two single nucleotide polymorphisms (SNPs); XRCC6 (C/G) and XRCC7 (G/T)] with DNA damage, repair and mRNA expression in human PBMCs in dose and adaptive response studies. Genomic DNA extracted from venous blood samples of 20 random healthy donors (16 adaptive and 4 non-adaptive) and genotyping of NHEJ repair genes was carried out using PCR amplified length polymorphism.

RESULTS

The dose response study revealed significant positive correlation of genotypes at XRRC5 (3R/2R/1R/0R), XRCC6(C/G) and XRCC7 (G/T) with DNA damage. Donors having genotypes with 2R allele at XRCC5 showed significant positive correlation with mRNA expression level (0R/2R: r = 0.846, P = 0.034; 1R/2R: r = 0.698, P = 0.0001 and 2R/2R: r = 0.831, P = 0.0001) for dose response. Genotypes C/C and C/G of XRCC6 showed a significant positive correlation (P = 0.0001), whereas, genotype T/T of XRCC7 showed significant negative correlation (r = - 0.376, P = 0.041) with mRNA expression.

CONCLUSION

Interestingly, adaptive donors having C/G genotype of XRCC6 showed significantly higher (P < 0.05) mRNA expression level in primed cells suggesting their role in RAR. In addition, NHEJ repair gene polymorphisms play crucial role with radio-sensitivity and RAR in human PBMCs.

The role of double-strand break repair, translesion synthesis, and interstrand crosslinks in colorectal cancer progression-clinicopathological data and survival

BACKGROUND AND OBJECTIVES

DNA repair is a new and important pathway that explains colorectal carcinogenesis. This study will evaluate the prognostic value of molecular modulation of double-strand break repair (XRCC2 and XRCC5); DNA damage tolerance/translesion synthesis (POLH, POLK, and POLQ), and interstrand crosslink repair (DCLRE1A) in sporadic colorectal cancer (CRC).

METHODS

Tumor specimens and matched healthy mucosal tissues from 47 patients with CRC who underwent surgery were assessed for gene expression of XRCC2, XRCC5, POLH, POLK, POLQ, and DCLRE1A; protein expression of Polk, Ku80, p53, Ki67, and mismatch repair MLH1 and MSH2 components; CpG island promoter methylation of XRCC5, POLH, POLK, POLQ, and DCLRE1A was performed.

RESULTS

Neoplastic tissues exhibited induction of POLK (P < .001) and DCLRE1A (P < .001) expression and low expression of POLH (P < .001) and POLQ (P < .001) in comparison to healthy paired mucosa. Low expression of POLH was associated with mucinous histology and T1-T2 tumors (P = .038); low tumor expression of POLK was associated with distant metastases (P = .042). CRC harboring POLK promoter methylation exhibited better disease-free survival (DFS) (P = .005).

CONCLUSIONS

This study demonstrated that low expression or unmethylated POLH and POLK were related to worse biological behavior tumors. However, POLK methylation was associated with better DFS. POLK and POLH are potential prognostic biomarkers in CRC.

Genetic association of XRCC5 gene polymorphisms with breast cancer among Jordanian women

Purpose

Breast cancer (BC) is a complex disease that is governed by several different environmental and inherited factors. There are many genes have been linked with BC development by screening specific genetic variants within these genes. In this study, we aim to investigate the correlation between Variable Number Tandem Repeat (VNTR) in XRCC5 gene and BC.

Materials and methods

Polymerase Chain Reaction (PCR) and Gel electrophoresis were used to genotype the XRCC5 gene polymorphism in 200 cases with breast cancer and 200 healthy individuals. All participants were Jordanian women from Arab descents. Clinical and pathological characteristics for BC patients were summarized and categorized according to their medical records.

Results

In this study, we found a strong correlation between the VNTR polymorphism in the XRCC5 gene and BC risk (P-value<0.0001). Remarkably, three different genotypes (2R\2R, 3R\2R and 3R\3R) showed significant association with BC (P-value<0.0001). This study also reported a significant difference in the distribution of allele frequencies between BC patients and healthy individuals (3R; P-value<0.0001 and 2R; P-value<0.001). However, we propose that VNTR of XRCC5 gene did not interfere with BC prognosis.

Conclusion

We speculate that the VNTR of XRCC5 gene may influence BC development. More investigations are needed in this regard to clarify the underlying role of the XRCC5 genetic variant in tumorgenesis including BC development.

Association between selenium, cadmium, and arsenic levels and genetic polymorphisms in DNA repair genes (XRCC5, XRCC6) in gastric cancerous and non-cancerous tissue

Gastric cancer is one of the most prevalent cancers in northern Iran. The DNA repair genes X-ray repair cross-complementing (XRCC) group 5, XRCC6, which are important members of non-homologous end-joining repair system, play an important role in repairing the DNA double-strand breaks. Chronic exposure to heavy metals has long been recognized as being capable of augmenting gastric cancer incidence among exposed human populations. Since trace elements could directly or indirectly damage DNA, and polymorphism in DNA DSBs-repair genes can alter the capacity of system repair, we assumed that XRCC5 VNTR and XRCC6-61C >G polymorphism also impress the DSBs-repair system ability and contribute to gastric cancer. Therefore, the objective of this research was to evaluate the tissue accumulation of Selenium (Se), Cadmium (Cd) and Arsenic (As), and XRCC5 VNTR, XRCC6-61C >G polymorphisms in cancerous and non-cancerous tissues in Golestan province. The study population included 46 gastric cancer patients and 43 cancer-free controls. Two polymorphisms of XRCC5, XRCC6 were genotyped using polymerase chain reaction (PCR) or polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Further employed was atomic absorption spectroscopy so as to determine the levels of Se, Cd and As. Finally, the data were analyzed by SPSS (version 16) statistical software. The Se level was significantly higher in tumors as compared to non-tumor tissues, but there was no significant correlation between As and Cd in cancerous and noncancerous tissues. Allele frequencies of the selected genes were not statistically different between groups regarding XRCC6 (-61C>G). XRCC5 0R/0R, 0R/1R, 1R/1R, and 0R/2R genotypes were more common in cancerous group. High levels of Se in cancerous tissues vs. non-cancerous tissues may be one of the carcinogenic factors; in Golestan province, unlike other regions of Iran and the world, the level of Se is high, hence the higher risks of gastric cancer.

The single nucleotide polymorphism g.133A>C in the stearoyl CoA desaturase gene (SCD) promoter affects gene expression and quali-quantitative properties of river buffalo milk

The stearoyl-CoA desaturase (SCD) gene has been investigated in depth in ruminants because of its effect on milk fat composition. In river buffalo, the single nucleotide polymorphism (SNP) g.133A>C in the gene promoter has been associated with milk quality and yield. However, the biological reason for such effects remains unexplored. In this study, we combined mRNA profile analysis, an electromobility shift assay, and quantitative PCR to elucidate the role of this SNP on gene transcription and its effects on milk fat traits. A preliminary genotyping of g.133A>C was carried out on a group of 303 river buffaloes to choose individuals for the downstream applications. Analysis of allele frequencies showed an increase in the minor allele C (0.25) compared with previous findings (0.16). Six animals (2 for each genotype) were chosen for cloning and 216 positive cDNA recombinant clones for SCD (72 per genotype) were analyzed by PCR. All clones showed the same length on agarose gel; therefore, random clones were chosen for sequencing. No qualitative differences were found and all gene transcripts assembled correctly. An electrophoretic mobility shift assay was performed to evaluate the binding of the transcription factor Sp1 to DNA sequences including g.133A>C. Genotype CC showed a higher binding (mean ± standard error of the mean) than genotype AA in 2 different conditions [Enzo buffer (EB), Enzo Life Science Inc., Farmingdale, NY: 201.77 ± 4.06 vs. 141.65 ± 3.77 band intensity values and Poletto buffer (PB): 95.90 ± 1.15 vs. 67.30 ± 2.14 band intensity values]. The subsequent quantitative PCR confirmed the upregulation of the CC genotype compared with the AA and AC genotypes. The association study with milk fat traits revealed a favorable effect of allele C. The heterozygous genotype had the highest values for monounsaturated fatty acids, oleic acid (C18:1 cis-9), polyunsaturated fatty acids, and odd- and branched-chain fatty acids, and the lowest values for saturated fatty acids and atherogenic and thrombogenic indices; the heterozygous genotype differed significantly from the AA genotype. The AC genotype has previously been associated with higher milk yield. Therefore, the g.133A>C SNP is a marker with dual effects and is an interesting candidate for assisted selection programs in river buffalo. These data clarified the biological role of the SNP g.133A>C in the SCD promoter and how it affects gene function, providing important knowledge on the genetic background of lipid metabolism, including the future possibility of selecting alleles with quantitatively or qualitatively favorable effects.

Overexpression of CLC-3 is regulated by XRCC5 and is a poor prognostic biomarker for gastric cancer

Background

Recently, many potential prognostic biomarkers for gastric cancer (GC) have been identified, but the prognosis of advanced GC patients remains poor. Chloride channels are promising cancer biomarkers, and their family member chloride channel-3 (CLC-3) is involved in multiple biological behaviors. However, whether CLC-3 is a prognostic biomarker for GC patients is rarely reported. The molecular mechanisms by which CLC-3 is regulated in GC are unclear.

Methods

The expression of CLC-3 and XRCC5 in human specimens was analyzed using immunohistochemistry. The primary biological functions and pathways related to CLC-3 were enriched by RNA sequencing. A 5′-biotin-labeled DNA probe with a promoter region between − 248 and + 226 was synthesized to pull down CLC-3 promoter-binding proteins. Functional studies were detected by MTS, clone formation, wound scratch, transwell, and xenograft mice model. Mechanistic studies were investigated by streptavidin-agarose-mediated DNA pull-down, mass spectrometry, ChIP, dual-luciferase reporter assay system, Co-IP, and immunofluorescence.

Results

The results showed that CLC-3 was overexpressed in human GC tissues and that overexpression of CLC-3 was a poor prognostic biomarker for GC patients (P = 0.012). Furthermore, higher expression of CLC-3 was correlated with deeper tumor invasion (P = 0.006) and increased lymph node metastasis (P = 0.016), and knockdown of CLC-3 inhibited cell proliferation and migration in vitro. In addition, X-ray repair cross-complementing 5 (XRCC5) was identified as a CLC-3 promoter-binding protein, and both CLC-3 (HR 1.671; 95% CI 1.012–2.758; P = 0.045) and XRCC5 (HR 1.795; 95% CI 1.076–2.994; P = 0.025) were prognostic factors of overall survival in GC patients. The in vitro and in vivo results showed that the expression and function of CLC-3 were inhibited after XRCC5 knockdown, and the inhibition effects were rescued by CLC-3 overexpression. Meanwhile, the expression and function of CLC-3 were promoted after XRCC5 overexpression, and the promotion effects were reversed by the CLC-3 knockdown. The mechanistic study revealed that knockdown of XRCC5 suppressed the binding of XRCC5 to the CLC-3 promoter and subsequent promoter activity, thus regulating CLC-3 expression at the transcriptional level by interacting with PARP1.

Conclusions

Our findings indicate that overexpression of CLC-3 is regulated by XRCC5 and is a poor prognostic biomarker for gastric cancer. Double targeting CLC-3 and XRCC5 may provide the promising therapeutic potential for GC treatment.

Electronic supplementary material

The online version of this article (10.1186/s13045-018-0660-y) contains supplementary material, which is available to authorized users.

XRCC5 VNTR, XRCC6 -61C>G, and XRCC7 6721G>T Gene Polymorphisms Associated with Male Infertility Risk: Evidences from Case-Control and In Silico Studies

We evaluate the association between genetic polymorphisms of XRCC5 VNTR, XRCC6 -61C>G, and XRCC7 6721G>T with male infertility susceptibility. A total of 392 men including 178 infertile males (102 idiopathic azoospermia and 76 severe oligozoospermia) and 214 healthy controls were recruited. XRCC6 -61C>G and XRCC7 6721G>T genotyping was performed by PCR-RFLP whereas XRCC5 VNTR was performed by PCR. The 2R allele and 2R allele carriers of XRCC5 VNTR polymorphism significantly decreased risk of male infertility. The mutant GG genotypes and carriers of the CG and GG genotypes of XRCC6 -61C>G showed increased risk for the male infertility. Furthermore, the G allele of the XRCC6 -61C>G was correlated with increased susceptibility to male infertility. Likewise, the T allele of the XRCC7 6721G>T polymorphism was associated with increased susceptibility to male infertility in azoospermia. In silico analysis predicted that the presence of tandem repeats in XRCC5 gene prompter can be sequence to bind to more nuclear factors. Also, rs2267437 (C>G) variant was located in a well-conserved region in XRCC6 promoter and this variation might lead to differential allelic expression. The XRCC7 6721G>T gene polymorphism occurred in an acceptor-splicing site, but this polymorphism has no severe modification on XRCC7 mRNA splicing. Our results indicate the association of XRCC5 VNTR, XRCC6 -61C>G, and XRCC7 6721G>T gene polymorphisms with male infertility in Iranian men.

Differences of Variable Number Tandem Repeats in XRCC5 Promoter Are Associated with Increased or Decreased Risk of Breast Cancer in BRCA Gene Mutation Carriers

Ku80 is a subunit of the Ku heterodimer that binds to DNA double-strand break ends as part of the non-homologous end joining (NHEJ) pathway. Ku80 is also involved in homologous recombination (HR) via its interaction with BRCA1. Ku80 is encoded by the XRCC5 gene that contains a variable number tandem repeat (VNTR) insertion in its promoter region. Different VNTR genotypes can alter XRCC5 expression and affect Ku80 production, thereby affecting NHEJ and HR pathways. VNTR polymorphism is associated with multiple types of sporadic cancer. In this study, we investigated its potential association with familial breast cancer at the germline level. Using PCR, PAGE, Sanger sequencing, and statistical analyses, we compared VNTR genotypes in the XRCC5 promoter between healthy individuals and three types of familial breast cancer cases: mutated BRCA1 (BRCA1⁺), mutated BRCA2 (BRCA2⁺), and wild-type BRCA1/BRCA2 (BRCAx). We observed significant differences of VNTR genotypes between control and BRCA1⁺ group (P < 0.0001) and BRCA2⁺ group (P = 0.0042) but not BRCAx group (P = 0.2185), and the differences were significant between control and cancer-affected BRCA1⁺ cases (P < 0.0001) and BRCA2⁺ cases (P = 0.0092) but not cancer-affected BRCAx cases (P = 0.4251). Further analysis indicated that 2R/2R (OR = 1.94, 95%CI = 1.26–2.95, P = 0.0096) and 2R/1R (OR = 1.58, 95%CI = 1.11–2.26, P = 0.0388) were associated with increased risk but 1R/1R (OR = 0.55, 95%CI = 0.35–0.84, P = 0.0196) and 1R/0R (OR = 0, 95%CI = 0–0.29, P = 0.0012) were associated with decreased risk in cancer-affected BRCA1⁺ group; 2R/1R (OR = 1.94, 95%CI = 1.14–3.32, P = 0.0242) was associated with increased risk in cancer-affected BRCA2⁺ group. No correlation was observed for the altered risk between cancer-affected or -unaffected carriers and between different age of cancer diagnosis in cancer-affected carriers. The frequently observed VNTR association with in BRCA1⁺ and BRCA2⁺ breast cancer group indicates that VNTR polymorphism in the XRCC5 promoter is associated with altered risk of breast cancer in BRCA1⁺ and BRCA2⁺ carriers.

Sp1 and the 'hallmarks of cancer'

For many years, transcription factor Sp1 was viewed as a basal transcription factor and relegated to a role in the regulation of so-called housekeeping genes. Identification of Sp1's role in recruiting the general transcription machinery in the absence of a TATA box increased its importance in gene regulation, particularly in light of recent estimates that the majority of mammalian genes lack a TATA box. In this review, we briefly consider the history of Sp1, the founding member of the Sp family of transcription factors. We review the evidence suggesting that Sp1 is highly regulated by post-translational modifications that positively and negatively affect the activity of Sp1 on a wide array of genes. Sp1 is over-expressed in many cancers and is associated with poor prognosis. Targeting Sp1 in cancer treatment has been suggested; however, our review of the literature on the role of Sp1 in the regulation of genes that contribute to the 'hallmarks of cancer' illustrates the extreme complexity of Sp1 functions. Sp1 both activates and suppresses the expression of a number of essential oncogenes and tumor suppressors, as well as genes involved in essential cellular functions, including proliferation, differentiation, the DNA damage response, apoptosis, senescence and angiogenesis. Sp1 is also implicated in inflammation and genomic instability, as well as epigenetic silencing. Given the apparently opposing effects of Sp1, a more complete understanding of the function of Sp1 in cancer is required to validate its potential as a therapeutic target.

Susceptibility to gastric cancer and polymorphisms of insertion/deletion at the intron 3 of the XRCC4 and VNTR at the promoter region of the XRCC5

The genes encoding X-ray repair cross-complementing group 4 (XRCC4; OMIM: 194363) and 5 (XRCC5; OMIM: 194364) are involved in repair of DNA double-strand breaks. To investigating the associations between polymorphisms of Insertion/Deletion (I/D, rs28360071) in the intron 3 of the XRCC4 and VNTR in the promoter region of the XRCC5 and risk of gastric cancer, the present study was carried out. We included 159 (56 females, 103 males) with gastric cancer and 242 (75 females, 167 males) healthy blood donors frequency matched for age and gender. Using PCR-based methods, the genotypes of the study polymorphisms were determined. The alleles of VNTR XRCC5 polymorphism divided into two groups: L (0 and 1 repeats) and H (2 and 3 repeats) alleles. For the I/D XRCC4 polymorphism, after stratification of the subjects according to their family history (FH) of cancer, either the ID (OR = 3.19, 95%CI: 1.35-7.50, P = 0.008) or the DD genotypes (OR = 4.62, 95%CI: 1.63-13.0, P = 0.004) among positive FH persons, increased the risk of gastric cancer compared with the reference group (persons who have negative FH and II genotype). For the VNTR XRCC5 polymorphism, the LH + HH genotypes among positive FH persons, increased the risk of gastric cancer compared with the reference group (persons who have negative FH and LL genotype) (OR = 2.88, 95%CI: 1.34-6.18, P = 0.006). Sensitivity analysis showed that the above mentioned associations were not occurred due to the maldistribution of the genotypes among missing data. The present study suggests that both polymorphisms of the XRCC4 and XRCC5 might be risk factors for gastric cancer development especially among persons with positive FH.

Association of XRCC5 VNTR polymorphism with the development of chronic myeloid leukemia

Double-strand breaks (DSBs) inducing agents influence the fidelity of DNA repair in both normal cells and leukemic cells, causing major genomic instability. In eukaryotic cells, non-homologous end joining pathway (NHEJ) is the major mechanism for DSB repair. Human X-ray repair cross-complementing 5 (XRCC5) gene encodes for the protein KU86, an important component of NHEJ pathway. Variable number of tandem repeats (VNTR) polymorphism (rs 6147172) in the promoter region of XRCC5 gene was shown to have effect on gene expression and was found to be associated with the development of several cancers. We analyzed VNTR polymorphism of XRCC5 gene in 461 chronic myeloid leukemia (CML) cases and 408 controls by polymerase chain reaction. Our results showed that frequency of 0R/0R genotype was significantly elevated in CML cases compared to that of controls (p = 0.05). Significant difference in the genotype distribution was observed between cases and controls (p = 0.02). The risk of CML development was found to be elevated for individuals carrying lower repeats (1R p = 0.03; 0R p = 0.007). Elevated 0R/0R genotype frequency was found to be significantly associated with early age at onset (≤ 30 years) and slightly elevated in chronic phase and poor hematologic response to imatinib mesylate. The influence of zero repeat on enhanced expression of XRCC5 might confer risk to error-prone repair leading to genomic instability and CML. Hence, the VNTR polymorphism in the promoter region of XRCC5 gene could serve as an important prognostic marker in CML development.

A combination of two electrophoretical approaches for detailed proteome-based characterization of SCLC subtypes

CONTEXT

Small cell lung cancers (SCLC) are heterogeneous and tumours differ in growth characteristics and treatment resistance.

OBJECTIVE

To get insight into the underlying protein profiles responsible for this heterogeneity, two subtypes of SCLC cells mutually differing in chemo resistance properties and growth characteristics are analysed.

MATERIALS AND METHODS

Two different electrophoresis approaches in combination with mass spectrometry were used to detect differences between the SCLC cell lines GLC1 and GLC1M13: IEF/SDS-PAGE as well as cetyltrimethylammonium bromide (CTAB)-SDS-PAGE.

RESULTS

Altogether 60 non redundant differentially expressed proteins were found of which 5 were verified by Western Blot analysis.

DISCUSSION

Most of these proteins identified are involved in processes of tumour progression. Therefore, these proteins are interesting candidates for further functional analysis.

CONCLUSION

Additional CTAB-SDS page is a complementary method to IEF-SDS page revealing a complete new subset of proteins differentially expressed between GLC1 and GLC1 M13 cells SCLC subtypes.

Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements

Tandem repeats are genomic elements that are prone to changes in repeat number and are thus often polymorphic. These sequences are found at a high density at the start of human genes, in the gene’s promoter. Increasing empirical evidence suggests that length variation in these tandem repeats can affect gene regulation. One class of tandem repeats, known as microsatellites, rapidly alter in repeat number. Some of the genetic variation induced by microsatellites is known to result in phenotypic variation. Recently, our group developed a novel method for measuring the evolutionary conservation of microsatellites, and with it we discovered that human microsatellites near transcription start sites are often highly conserved. In this study, we examined the properties of microsatellites found in promoters. We found a high density of microsatellites at the start of genes. We showed that microsatellites are statistically associated with promoters using a wavelet analysis, which allowed us to test for associations on multiple scales and to control for other promoter related elements. Because promoter microsatellites tend to be G/C rich, we hypothesized that G/C rich regulatory elements may drive the association between microsatellites and promoters. Our results indicate that CpG islands, G-quadruplexes (G4) and untranslated regulatory regions have highly significant associations with microsatellites, but controlling for these elements in the analysis does not remove the association between microsatellites and promoters. Due to their intrinsic lability and their overlap with predicted functional elements, these results suggest that many promoter microsatellites have the potential to affect human phenotypes by generating mutations in regulatory elements, which may ultimately result in disease. We discuss the potential functions of human promoter microsatellites in this context.

The novel allele (3R) of the VNTR polymorphism in the XRCC5 promoter region dramatically decreases the gene expression

Polymorphism of variable number of tandem repeats (VNTR) in the promoter region of X-ray repair cross-complementing 5 (MIM: 194364, XRCC5; rs6147172) was reported. The aim of the present study is to evaluate the influence of this polymorphism on XRCC5 mRNA levels. Genotypes of XRCC5 VNTR were determined by high resolution of melting analysis (HRMA). The quantitative XRCC5 mRNA expression (compared to ß-actin expression) among 0R/1R, 1R/2R, and 1R/3R genotypes was investigated. There was a negative correlation between the overall number of tandem repeats and XRCC5 expression (r=-0.965, df=7, P<0.001). The mRNA level of XRCC5 decreased as function of number of tandem repeats. The 3R allele of the VNTR polymorphism in the XRCC5 promoter region dramatically decreases the gene expression.

Detection of dispersed short tandem repeats using reversible jump Markov chain Monte Carlo

Tandem repeats occur frequently in biological sequences. They are important for studying genome evolution and human disease. A number of methods have been designed to detect a single tandem repeat in a sliding window. In this article, we focus on the case that an unknown number of tandem repeat segments of the same pattern are dispersively distributed in a sequence. We construct a probabilistic generative model for the tandem repeats, where the sequence pattern is represented by a motif matrix. A Bayesian approach is adopted to compute this model. Markov chain Monte Carlo (MCMC) algorithms are used to explore the posterior distribution as an effort to infer both the motif matrix of tandem repeats and the location of repeat segments. Reversible jump Markov chain Monte Carlo (RJMCMC) algorithms are used to address the transdimensional model selection problem raised by the variable number of repeat segments. Experiments on both synthetic data and real data show that this new approach is powerful in detecting dispersed short tandem repeats. As far as we know, it is the first work to adopt RJMCMC algorithms in the detection of tandem repeats.

Role of the XRCC5/XRCC6 dimer in carcinogenesis and pharmacogenomics

Over the past few decades, the incidence of cancer has rapidly increased all over the world and cancer remains a major threat to public health. It is believed that cancer results from a series of genetic alterations that lead to the progressive disorder of the normal mechanisms controlling cell proliferation, differentiation, death and/or genomic stability. The response of the cell to genetic injury and its ability to maintain genomic stability by means of a variety of DNA repair mechanisms are therefore essential in preventing tumor initiation and progression. From the same viewpoint, the relative role of DNA repair as a biomarker for prognosis, predictor of drug and therapy responses or indeed as a target for novel gene therapy, is very promising. In this article, we have summarized the studies investigating the association between the XRCC5/XRCC6 dimer and the susceptibility to multiple cancers and discuss its role in carcinogenesis and its potential application to anticancer drug discovery.

Novel allelic variants in the canine cyclooxgenase-2 (Cox-2) promoter are associated with renal dysplasia in dogs

Renal dysplasia (RD) in dogs is a complex disease with a highly variable phenotype and mode of inheritance that does not follow a simple Mendelian pattern. Cox-2 (Cyclooxgenase-2) deficient mice have renal abnormalities and a pathology that has striking similarities to RD in dogs suggesting to us that mutations in the Cox-2 gene could be the cause of RD in dogs. Our data supports this hypothesis. Sequencing of the canine Cox-2 gene was done from clinically affected and normal dogs. Although no changes were detected in the Cox-2 coding region, small insertions and deletions of GC boxes just upstream of the ATG translation start site were found. These sequences are putative SP1 transcription factor binding sites that may represent important cis-acting DNA regulatory elements that govern the expression of Cox-2. A pedigree study of a family of Lhasa apsos revealed an important statistical correlation of these mutant alleles with the disease. We examined an additional 22 clinical cases from various breeds. Regardless of the breed or severity of disease, all of these had one or two copies of the Cox-2 allelic variants. We suggest that the unusual inheritance pattern of RD is due to these alleles, either by changing the pattern of expression of Cox-2 or making Cox-2 levels susceptible to influences of other genes or environmental factors that play an unknown but important role in the development of RD in dogs.