DNA methylation status of interspersed repetitive sequences in patients with migraine.

OBJECTIVE: To analyse the methylation status of the Long Interspersed Nuclear Element-1 (LINE-1) and Short Interspersed Nuclear Element Alu (Alu) of peripheral blood mononuclear cells (PBMCs) from patients with migraine compared with healthy control subjects. METHODS: This case-control study recruited patients with migraine without aura and age-matched healthy control subjects. PBMCs were purified from peripheral blood samples. Methylation levels and patterns of LINE-1 and Alu sequences were evaluated using combined bisulfite restriction analysis-interspersed repetitive sequences polymerase chain reaction. RESULTS: A total of 84 patients with migraine and 82 age-matched healthy controls were enrolled in the study. High levels of unmethylated cytosines in both the LINE-1 and Alu repetitive elements were observed in the migraine group compared with the control subjects. In addition, a significant difference was detected in the methylation level of LINE-1 between TT and CC genotype groups of the methylenetetrahydrofolate reductase gene. CONCLUSIONS: These results suggest that analysis of epigenetic biomarkers in PBMCs may help to identify patients at a higher risk of migraine development.

Molecular Mechanisms of Alu and LINE-1 Interspersed Repetitive Sequences Reveal Diseases of Visual System Dysfunction.

BACKGROUND: Short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINE-1s) are the abundant and well-characterized repetitive elements in the human genome. METHODS: For this review, all relevant original research studies were assessed by searching electronic databases, including PubMed, Google Scholar, and Web of Science, by using relevant keywords. Accumulating evidence indicates that the disorder of gene expression regulated by these repetitive sequences is one of the causes of the diseases of visual system dysfunction, including retinal degenerations, glaucoma, retinitis punctata albescens, retinitis pigmentosa, geographic atrophy, and age-related macular degeneration, suggesting that SINEs and LINE-1s may have great potential implications in ophthalmology. RESULTS: Alu elements belonging to the SINEs are present in more than one million copies, comprising 10% of the human genome. CONCLUSION: This study offers recent advances in Alu and LINE-1 mechanisms in the development of eye diseases. The current study could advance our knowledge of the roles of SINEs and LINE-1s in the developing process of eye diseases, suggesting new diagnostic biomarkers, therapeutic strategies, and significant points for future studies.

This study reveals the Alu and LINE-1 interspersed repetitive sequences involved in the diseases of visual system dysfunction.This study shows the disorder of gene expression regulated by SINEs and LINE-1s sequences is one of the causes of the diseases of visual system dysfunction.This study suggests recent advances in Alu and LINE-1 mechanisms are involved in eye diseases.

Genome-Wide Identification and Classification of MicroRNAs Derived from Repetitive Elements.

MicroRNAs (miRNAs) are known for their role in mRNA silencing via interference pathways. Repetitive elements (REs) share several characteristics with endogenous precursor miRNAs. In this study, 406 previously identified and 1,494 novel RE-derived miRNAs were sorted from the GENCODE v.19 database using the RepeatMasker program. They were divided into six major types, based on their genomic structure. More novel RE-derived miRNAs were confirmed than identified as RE-derived miRNAs. In conclusion, many miRNAs have not yet been identified, most of which are derived from REs.

Genome-Wide Identification and Classification of MicroRNAs Derived from Repetitive Elements

MicroRNAs (miRNAs) are known for their role in mRNA silencing via interference pathways. Repetitive elements (REs) share several characteristics with endogenous precursor miRNAs. In this study, 406 previously identified and 1,494 novel RE-derived miRNAs were sorted from the GENCODE v.19 database using the RepeatMasker program. They were divided into six major types, based on their genomic structure. More novel RE-derived miRNAs were confirmed than identified as RE-derived miRNAs. In conclusion, many miRNAs have not yet been identified, most of which are derived from REs.

A molecular and spatial clustering analysis of active pulmonary tuberculosis patients in Funing county of Jiangsu Province, China / 中华传染病杂志

Objective To describe the distribution and spatial clustering of active pulmonary tuberculosis patients in Funing county of Jiangsu Province,China,and to determine the rules of recent transmission in TB patients and help establish the strategy of TB control with the results of genetic typing of Mycobacterium tuberculosis (M.TB).Methods Newly reported and retreated tuberculosis patients registered in Funing county,Jiangsu Province between Jun 1,2009 and Nov 30,2010 were recruited as research subjects.Geographic information system was applied to analysis the spatial clustering of tuberculosis patients.The M.TB isolates were genotyped by mycobacterial interspersed repetitive units (MIRU).Cluster was defined as two or more patients' M.TB isolates harboring identical MIRU genotype.Results During the study period,there were a total of 681 active pulmonary tuberculosis patients reported.Global Moran's I value and local Moran's I value indicated a random and sporadical manner instead of global spatial clustering of tuberculosis patients in Funing county.Spatial scan statistics (SaTScan) showed that the patients in Guoshu town was statistically significant in spatial clustering (RR=1.85,P=0.036).Among 169 strains of M.TB,27 strains distributed in 12 clusters,which indicated recent transmission among patients within the cluster.Conclusions In rural areas with high tuberculosis incidence,it is less likely to have massive tuberculosis outbreak.Sporadic transmission of tuberculosis may have played an important role in the transmission of tuberculosis in high prevalence area.

Effects of particulate matter on genomic DNA methylation content and iNOS promoter methylation.

BACKGROUND: Altered patterns of gene expression mediate the effects of particulate matter (PM) on human health, but mechanisms through which PM modifies gene expression are largely undetermined. OBJECTIVES: We aimed at identifying short- and long-term effects of PM exposure on DNA methylation, a major genomic mechanism of gene expression control, in workers in an electric furnace steel plant with well-characterized exposure to PM with aerodynamic diameters < 10 microm (PM(10)). METHODS: We measured global genomic DNA methylation content estimated in Alu and long interspersed nuclear element-1 (LINE-1) repeated elements, and promoter DNA methylation of iNOS (inducible nitric oxide synthase), a gene suppressed by DNA methylation and induced by PM exposure in blood leukocytes. Quantitative DNA methylation analysis was performed through bisulfite PCR pyrosequencing on blood DNA obtained from 63 workers on the first day of a work week (baseline, after 2 days off work) and after 3 days of work (postexposure). Individual PM(10) exposure was between 73.4 and 1,220 microg/m(3). RESULTS: Global methylation content estimated in Alu and LINE-1 repeated elements did not show changes in postexposure measures compared with baseline. PM(10) exposure levels were negatively associated with methylation in both Alu [beta = -0.19 %5-methylcytosine (%5mC); p = 0.04] and LINE-1 [beta = -0.34 %5mC; p = 0.04], likely reflecting long-term PM(10) effects. iNOS promoter DNA methylation was significantly lower in postexposure blood samples compared with baseline (difference = -0.61 %5mC; p = 0.02). CONCLUSIONS: We observed changes in global and gene specific methylation that should be further characterized in future investigations on the effects of PM.

Evaluation of the Selected 12-locus MIRU for Genotyping Beijing Family Mycobacterium tuberculosis in Korea / 결핵및호흡기질환

BACKGROUND: Mycobacterial Interspersed Repetitive Units (MIRUs) that are located mainly in intergenic regions dispersed throughout the Mycobacterium tuberculosis genome. The selected MIRU loci, which were composed of a 12-locus set, demonstrated a high power for discrimination of Mycobacterium tuberculosis isolates collected from Kangwon province of Korea. To evaluate its ability to discriminate the M. tuberculosis strains, 45 clinical isolates were genotyped using the methods IS6110 RFLP and MIRU. METHODS: All the samples were collected during the period from January 2007 to December 2007 from TB patients, who were residents and registered to a public health center of Kangwon Province in Korea. A total of 45 DNAs were extracted from clinical isolated mycobacterial strains and genotyped using IS6110 RFLP, the MIRU method. RESULTS: We compared the 12-MIRU with IS6110 RFLP in the 45 samples, the 12-locus version offered less discriminatory power (Hunter-Gaston discriminatory index [HGDI]: 0.959 vs 0.998; 57.78% of clustered cases vs 8.89%). CONCLUSION: This 12-locus MIRU can be useful when additional combinations of other loci for genotyping M. tuberculosis in Korea where the Beijing family strains are dominant.