Migrations, admixture and genetic diversity in Central Argentinian Patagonia: analysis of autosomal Alu polymorphisms / Migraciones, mestizaje y diversidad genética en la Patagonia Central Argentina: análisis de polimorfismos autosómicos Alu

This study aimed to analyze autosomal Alu insertions in three localities from Patagonia Argentina belonging to the Andes region and the coast of the Chubut province. Knowledge of the genetic diversity of these populations, along with the genealogical data, will contribute to better understand historical information, differential migration process and bio-demographic composition of the Central Patagonia region. In order to achieve this objective, 16 autosomal Alu insertion polymorphisms were genotyped: ACE, APO-A1, TPA25, FXIIIB, A25, HS4.32, D1, HS4.69, HS2.43, Sb19.12, Yb8NBC120, Sb19.3, Yb8NBC125, Ya5NBC221, DM, and CD4. Our results showed that the Central Patagonia region presents a complex continental genetic admixture with marked Native American roots (39% ± 1.2), Eurasian (56% ± 1.73) and, to a lesser extent, African (5% ± 1.7). The genetic proximity of the Patagonian samples in relation to groups from Europe and Northern Africa, but with a displacement towards the native communities, constitutes a clear indicator of the differential admixture process that took place in different regions of Argentina. Moreover, genetic differences were observed between Patagonian localities and Bahía Blanca (Central region of Argentina). These observations warned us that population genetic constitution analysis cannot be approached without bearing in mind the regional particularities, which are the result of the different historical, migratory, social-economic and demographic processes that occurs in the country.

Este estudio tiene como objetivo el análisis de las inserciones autosómicas Alu en tres localidades de la Patagonia argentina localizadas en la región andina y costera de la provincia de Chubut. El conocimiento de la diversidad genética de estas poblaciones, junto con los datos genealógicos, contribuirán a una mejor comprensión de la información histórica, los procesos migratorios diferenciales y la composición bio-demográfica de la región central Patagónica. Para alcanzar este objetivo se analizaron 16 polimorfismos autosómicos de inserción Alu: ACE, APO-A1, TPA25, FXIIIB, A25, HS4.32, D1, HS4.69, HS2.43, Sb19.12, Yb8NBC120, Sb19.3, Yb8NBC125, Ya5NBC221, DM y CD4. Nuestros resultados mostraron que la región central Patagónica presenta una mezcla genética continental compleja de marcadas raíces nativo americanas 39% (± 1.2), eurasiáticas 56% (± 1.73) y, en menor medida, africanas 5% (± 1.7). La proximidad genética de las muestras patagónicas a los grupos de Europa y del Norte de África, pero con un mayor desplazamiento hacia las comunidades nativas, constituye un claro indicador del proceso de mezcla diferencial que tuvo lugar en las distintas regiones de la Argentina. Por otra parte, las diferencias genéticas observadas entre las localidades de Patagonia y Bahía Blanca (región central de la Argentina), nos advierten que no puede analizarse la constitución genética de las poblaciones sin tener en cuenta las particularidades regionales, que son el resultado de los diferentes procesos históricos, migratorios, socio-económicos y demográficos que ocurrieron en el interior del país.

Relationship between the overexpression of DNA methyltransferase 3B4 and clear cell renal cell carcinoma / 中国肿瘤临床

Objective:To determine the molecular role of DNA methyltransferase (DNMT) in kidney tumorigenesis. Methods:Tissue samples consisted of 15 cancer tissues and 15 matched adjacent tissues from clear cell renal cell carcinoma (ccRCC) patients who had undergone nephrectomy in 2012 at the First Affiliated Hospital of Baotou Medical College, Science and Technology University of Inner Mongolia were collected. Real-time PCR, Western blot, combined bisulfite restriction analysis (COBRA) and methylation specific PCR were used in this study. Real-time PCR was used to examine the mRNA expression levels of DNMT. The global methylation level, DNA methylation level, and the expression of the antioncogene RASSF1A in ccRCC tissues were concurrently detected. Results:Both mRNA and protein levels of DNMT3B4, a splice variant of DNMT3B, were elevated in renal cell carcinoma tissue compared with those in con-troll tissue. Additionally, Alu was hypomethylated in ccRCC tissue (0.106±0.04) compared with control tissue (0.115±0.03) (P<0.05). Fur-thermore, the methylation of the promoter for RASSF1A, a tumor-suppressor gene, moderately increased in renal cell carcinoma tis-sue. By contrast, RASF1A expression decreased. Conclusion:DNMT3B4 overexpression may play an important role in human kidney tu-morigenesis via chromosomal instability and the decreased expression of RASSF1A.

Association between the Alu Insertion/Deletion Polymorphism in the Tissue-Type Plasminogen Activator Gene and Mirtazapine Response in Koreans with Major Depression

OBJECTIVES: To determine the relationship between the Alu insertion/deletion (I/D) polymorphism in the tissue-type plasminogen activator (tPA) gene and the clinical outcome of mirtazapine treatment in Korean major depressive disorder (MDD) patients. METHODS: We enrolled 422 patients in this study. Symptoms were evaluated using the 21-item Hamilton Depression Rating (HAMD-21) Scale. After 1, 2, 4, and 8 weeks of mirtazapine treatment, the association between the Alu I/D polymorphism in the tPA gene and remission/response outcomes were evaluated. RESULTS: The proportion of I/I homozygotes in responders was higher than that in non-responders, whereas the proportion of D/D homozygotes in responders was lower than that in non-responders at 8 weeks of treatment (p = 0.032, OR = 1.57). The percentage decline of HAMD-21 scores in I allele carriers was larger than that of D/D homozygotes at 2 and 8 weeks of treatment (p = 0.035 and 0.007, respectively). I allele carriers were associated with remission at 8 weeks of treatment (p = 0.047, OR = 2.2). CONCLUSIONS: These results show that treatment response and remission to mirtazapine were associated with the Alu I/D polymorphism of the tPA gene. This suggests the Alu I/D polymorphism may be a potential genetic marker for the prediction of therapeutic response to mirtazapine treatment in patients with MDD.

Structural Variation of Alu Element and Human Disease

Transposable elements are one of major sources to cause genomic instability through various mechanisms including de novo insertion, insertion-mediated genomic deletion, and recombination-associated genomic deletion. Among them is Alu element which is the most abundant element, composing ~10% of the human genome. The element emerged in the primate genome 65 million years ago and has since propagated successfully in the human and non-human primate genomes. Alu element is a non-autonomous retrotransposon and therefore retrotransposed using L1-enzyme machinery. The 'master gene' model has been generally accepted to explain Alu element amplification in primate genomes. According to the model, different subfamilies of Alu elements are created by mutations on the master gene and most Alu elements are amplified from the hyperactive master genes. Alu element is frequently involved in genomic rearrangements in the human genome due to its abundance and sequence identity between them. The genomic rearrangements caused by Alu elements could lead to genetic disorders such as hereditary disease, blood disorder, and neurological disorder. In fact, Alu elements are associated with approximately 0.1% of human genetic disorders. The first part of this review discusses mechanisms of Alu amplification and diversity among different Alu subfamilies. The second part discusses the particular role of Alu elements in generating genomic rearrangements as well as human genetic disorders.

Detection of Human Hepatocarcinoma Cell Line PLC/PRF/5 Genome Hepatitis b Virus DNA Integration with Alu-PCR / 医学研究杂志

Objective In this research with the method of Alu -PCR we investigate the integration of hepatitis B virus ( HBV) DNA in human hepatocarcinoma cell line (PLC/PRF/5) genome DNA.Methods We at first extracted the genome DNA from PLC/PRF/5 cells, and then the potential integration fragments of HBV DNA and human genome DNA were amplified with according to the Alu -PCR after three rounds PCR .The Alu-PCR amplification products were observated with agarose gel electrophoresis , then integration positive electrophoresis bandings were chipped and purified for nucleic acid sequencing .At last he bioinformatics information was acquired by blast online.Results Through agarose gel electrophoresis after Alu -PCR amplification, we got four potential integration bindings , among which we got three integration sequences of HBV DNA in human genome DNA .These integration sequences could be individually located in the human chromosome of 03p21.31, 05p15.33, 12q13 and 12-q14.1.Conclusion With Alu-PCR we can accurately measure the integration of HBV DNA in human genome DNA , and Alu-PCR can be a a convenience and economic method in the study of HBV DNA ′s integration in human genome DNA .

Mechanism of the mitochondria damage of the nerve cells in mouse after chronic exposure to nano-alumina / 中国药理学与毒理学杂志

OBJECTIVE To explore the potential neurotoxicity of nano-alu mina (<50 n m)in vivo, we treated the ICR mouse with the nano-alu mina to investigate the mitochondrial da mage of nerve cells on morphology and function.METHODS Adult male mice were exposed to nano-alu mina (<50 n m)of 0,25,50 and 75 mg·kg -1 by nasal instillation for 1 month.Then we observed the mitochondrial ultra-structure of the nerve cells in CA3 region of hippoca mpus,and measured the mean dia meter in every group.The activities of Na +-K +-ATPase and Ca2 +-Mg2 +-ATPase were tested by the determination of the inorganic phosphorus,which was the deco mposition product of ATPase.Western blot analysis was used to detect the expression of COX-Ⅳ,Beclin1 ,LC3Ιand LC3Ⅱ.RESULTS Co mpared with 0 and 25 mg·kg -1 groups exposed to Al2 O3 nanopartilces (Al2 O3 NPs),the mitochondria of CA3 region in hip-poca mpus in 50 mg·kg -1 group beca me ede matous and swollen with sparse and broken cristae sur-rounding the nuclear,and the mean dia meter was higher(0.49 ±0.02 μm,P <0.05).But co mpared with 50 mg·kg -1 group,the mitochondria in 75 mg·kg -1 group beca me s maller with inner cristae of high density,and the mean dia meter was lower(0.36 ±0.02 μm,P<0.05).The enzy me activity of the mito-chondria in cerebral cortex decreased dose-dependently with exposure,the activities of Na +-K +-ATPase in 50 and 75 mg·kg -1 groups(6.37 ±0.22 kU·g -1 protein,5.48 ±1 .53 kU·g -1 protein)and Ca2 +-Mg2 +-ATPase in 50 and 75 mg·kg -1 groups (3.21 ±0.99 kU·g -1 protein,3.28 ±0.15 kU·g -1 protein)were lower than the 0 mg·kg -1 group(P<0.05).Meanwhile,the Ca2 +-Mg2 +-ATPase in 50 and 75 mg·kg -1 groups showed lower activities in co mparison with the 25 mg·kg -1 group.The 75 mg·kg -1 group expressed higher level of the COX-Ⅳ protein 1 .35 ±0.66(P<0.05)than other groups.Both expression of Beclin1 protein and rate of LC3Ⅱ/LC3Ⅰin 75 mg·kg -1 group were more than the 0 mg·kg -1 group. CONCLUSION The mitochondrial dysfunction may be the potential neurotoxicity of nano-alu mina,and the da maged mitochondria were cleared by autophagy.

Utilidad del bandeo cromosómico con la enzima ALU I para la identificación de zonas metiladas en cáncer de mama / Utility of chromosome banding with ALU I enzyme for identifying methylated areas in breast cancer

El cáncer es un conjunto de trastornos que comparten la característica común de un crecimiento celular descontrolado, teniendo la facultad de comenzar en las células, generando dos procesos sucesivos: el aumento de la proliferación celular (tumor o neoplasia) y la capacidad invasiva de estas células, proliferando y colonizando otros tejidos (metástasis). La metilación del DNA es un proceso epigenético que recurrentemente ha sido involucrado como un factor importante en la patogenia de esta enfermedad el cual participa en la regulación de la expresión génica directamente al impedir la unión de factores de trascripción, e indirectamente propiciando la estructura “cerrada” de la cromatina. El objetivo de este trabajo fue determinar regiones hipermetiladas en muestras de extendidos cromosómicos mediante la utilización de la endonucleasa de restricción Alu I y relacionar estas regiones con sitios de localización de genes supresores de tumores relacionados con el cáncer de mama. Se analizaron 60 muestras de sangre periférica de mujeres con diagnóstico de cáncer de mama a las cuales se les realizó cultivo celular; los extendidos cromosómicos fueron teñidos con Giemsa previamente digeridos con la enzima Alu I. Se observaron cromosomas con regiones centroméricas y no centroméricas teñidas en el 37% de los casos, comprobándose que en el 95,46% de los casos existen genes asociados descritos, como metilados en cáncer de mama. Ejemplo de ellos son los localizados en los cromosomas 1q, 2q, 6q, y regiones centroméricas no teñidas usualmente como en los cromosomas 3, 4, 8, 13, 14, 15, y 17. Se sugiere la importancia de esta técnica ya que permite la visualización total del genoma, pudiendo localizar genes metilados relacionados con cáncer de mama y, de esta manera dirigir la terapia de forma específica, logrando una mejor respuesta terapéutica.

Cancer is a group of disorders characterized by uncontrolled cell growth which is produced by two successive events: increased cell proliferation (tumor or neoplasia) and the invasive capacity of these cells (metastasis). DNA methylation is an epigenetic process which has been involved as an important pathogenic factor of cancer. DNA methylation participates in the regulation of gene expression, directly, by preventing the union of transcription factors, and indirectly, by promoting the “closed” structure of the chromatine. The objectives of this study were to identify hypermethyled chromosomal regions through the use of restriction Alu I endonuclease, and to relate cytogenetically these regions with tumor suppressive gene loci. Sixty peripheral blood samples of females with breast cancer were analyzed. Cell cultures were performed and cytogenetic spreads, previously digested with Alu I enzyme, were stained with Giemsa. Chromosomal centromeric and not centromeric regions were stained in 37% of cases. About 96% of stained hypermethyled chromosomal regions (1q, 2q, 6q) were linked with methylated genes associated with breast cancer. In addition, centromeric regions in chromosomes 3, 4, 8, 13, 14, 15 and 17, usually unstained, were found positive to digestion with Alu I enzime and Giemsa staining. We suggest the importance of this technique for the global visualization of the genome which can find methylated genes related to breast cancer, and thus lead to a specific therapy, and therefore a better therapeutic response.

Comparative study between the free DNA in peripheral blood and TNM staging in patients with colorectal cancer for prognostic evaluation in the university hospital of the State of Alagoas

Colorectal neoplasm is one of the most common cancers in developed countries and its incidence has grown progressively. The currently used attempts to prognostic assessment are limited, since they are restricted to the observation of tumor morphology, such as the TNM staging. The quantification of free DNA in peripheral blood aims to find a way to relate it to the clinical status of patients with cancer. OBJECTIVE: To evaluate the prognosis of patients with colorectal cancer with the quantification of ALU247 fragments in peripheral blood and TNM staging. METHODS: We evaluated 79 patients in the following groups: Operated, and Non-Operated and Control as to the ALU247 fragment dosage and its correlation with tumor staging. RESULTS: The amount of ALU247 fragments revealed very different results when comparing the different groups. The mean quantity in the Non-Operated group was 14.62 pg, while the mean was 0.48 pg for the Control Group and 0.93 pg for the Operated Group. Serum levels of ALU247 were higher in more advanced morphofunctional classes of the TNM staging. CONCLUSIONS: We suggest there is a relation between the advanced TNM stage and high doses of free DNA in peripheral blood with worse prognosis. (AU)

A neoplasia colorretal é uma das formas mais comuns de câncer nos países desenvolvidos e sua incidência tem crescido de maneira contínua. As tentativas de avaliação prognóstica usadas atualmente apresentam a grave limitação de se restringirem à observação da morfologia tumoral, como o estadiamento TNM. A quantificação do DNA livre no sangue periférico busca encontrar uma forma de relacioná-lo com o estado clínico dos portadores de câncer. OBJETIVO: Avaliar o prognóstico dos pacientes portadores do câncer colorretal por meio da quantificação de fragmentos de ALU247 no sangue periférico e do estadiamento TNM. MÉTODOS: Foram avaliados 79 pacientes nos Grupos Operados, Não Operados e Controle quanto à dosagem de fragmento de ALU247 e sua correlação com os estádios dos tumores. RESULTADOS: A quantidade de fragmentos ALU247 revelou resultados bastante distintos quando os diferentes grupos foram comparados. A média da quantificação nos Não Operados foi de 14,62 pg, de 0,48 pg no Grupo Controle e 0,93 pg no Grupo Operados. Os valores séricos do ALU247 encontraram-se mais elevados nas classes morfofuncionais mais avançadas do estadiamento TNM. CONCLUSÕES: Sugere-se uma relação entre o avanço do estádio TNM e a dosagem elevada do DNA livre no sangue periférico com pior prognóstico. (AU)

Transposable Elements: No More 'Junk DNA'

Since the advent of whole-genome sequencing, transposable elements (TEs), just thought to be 'junk' DNA, have been noticed because of their numerous copies in various eukaryotic genomes. Many studies about TEs have been conducted to discover their functions in their host genomes. Based on the results of those studies, it has been generally accepted that they have a function to cause genomic and genetic variations. However, their infinite functions are not fully elucidated. Through various mechanisms, including de novo TE insertions, TE insertion-mediated deletions, and recombination events, they manipulate their host genomes. In this review, we focus on Alu, L1, human endogenous retrovirus, and short interspersed element/variable number of tandem repeats/Alu (SVA) elements and discuss how they have affected primate genomes, especially the human and chimpanzee genomes, since their divergence.

Value of detection of fecal Alu repetitive sequences in the diagnosis of pancreatic cancer / 中华胰腺病杂志

ObjectiveTo detect the Alu expression in the stool of patients with pancreatic cancer and investigate its value in the diagnosis of pancreatic cancer.MethodsStool samples were obtained from patients with pancreatic cancer (PC) ( n =41 ),chronic pancreatitis (CP) ( n =27 ) and healthy subjects ( n =23 ),the DNA was extracted from the stool and the expression of Alu repetitive sequences was subjected to quantitative analysis by the real-time PCR.ResultsThe expressions of Alu repetitive sequences in PC,CP,and healthy subjects were (5.17 ± 0.99 ),( 3.79 ± 0.94),(0.28 ± 0.35 ) rig/g,and the difference among the three groups was statistically significant (P ＜0.05).The AUC of PC was 74.8％ with the 95％ CI 0.661 ～0.835,and the sensitivity,specificity was 75.6％ and 67.1％,respectively.ConclusionsAlu repetitive sequences are highly expressed in the stool of patients with pancreatic cancer,and it is of value in the diagnosis of pancreatic cancer.

Research of the origin of a particular Tunisian group using a physical marker and Alu insertion polymorphisms

The aim of this study was to show how, in some particular circumstances, a physical marker can be used along with molecular markers in the research of an ancient people movement. A set of five Alu insertions was analysed in 42 subjects from a particular Tunisian group (El Hamma) that has, unlike most of the Tunisian population, a very dark skin, similar to that of sub-Saharans, and in 114 Tunisian subjects (Gabes sample) from the same governorate, but outside the group. Our results showed that the El Hamma group is genetically midway between sub-Saharan populations and North Africans, whereas the Gabes sample is clustered among North Africans. In addition, The A25 Alu insertion, considered characteristic to sub-Saharan Africans, was present in the El Hamma group at a relatively high frequency. This frequency was similar to that found in sub-Saharans from Nigeria, but significantly different from those found in the Gabes sample and in other North African populations. Our molecular results, consistent with the skin color status, suggest a sub-Saharan origin of this particular Tunisian group.

Identification and characterization of two critical sequences in SV40PolyA that activate the green fluorescent protein reporter gene

Alu repeats or Line-1-ORF2 (ORF2) inhibit expression of the green fluorescent protein (GFP) gene when inserted downstream of this gene in the vector pEGFP-C1. In this work, we studied cis-acting elements that eliminated the repression of GFP gene expression induced by Alu and ORF2 and sequence characteristics of these elements. We found that sense and antisense PolyA of simian virus 40 (SV40PolyA, 240 bp) eliminated the repression of GFP gene expression when inserted between the GFP gene and the Alu (283 bp) repeats or ORF2 (3825 bp) in pAlu14 (14 tandem Alu repeats were inserted downstream of the GFP gene in the vector pEGFP-C1) or pORF2. Antisense SV40PolyA (PolyAas) induced stronger gene expression than its sense orientation (PolyA). Of four 60-bp segments of PolyAas (1F1R, 2F2R, 3F3R and 4F4R) inserted independently into pAlu14, only two (2F2R and 3F3R) eliminated the inhibition of GFP gene expression induced by Alu repeats. Deletion analysis revealed that a 17 nucleotide AT repeat (17ntAT; 5'-AAAAAAATGCTTTATTT-3') in 2F2R and the fragment 3F38d9 (5'-ATAAACAAGTTAACAACA ACAATTGCATT-3') in 3F3R were critical sequences for activating the GFP gene. Sequence and structural analyses showed that 17ntAT and 3F38d9 included imperfect palindromes and may form a variety of unstable stem-loops. We suggest that the presence of imperfect palindromes and unstable stem-loops in DNA enhancer elements plays an important role in GFP gene activation.

MCM3AP, a Novel HBV Integration Site in Hepatocellular Carcinoma and Its Implication in Hepatocarcinogenesis / 华中科技大学学报（医学）（英德文版）

A novel HBV integration site involved in hepatocarcinogenesis was investigated. The HBV DNA integration sites were detected by Alu-PCR in hepatocellular carcinoma tissues, matched surrounding liver tissues in 30 patients with hepatitis B-related hepatocellular carcinoma (HCC) and 3 cases of normal liver tissues. The integration sites and flanking sequences in human genome were sequenced and blasted, and the expression of integrated HBV genes was determined by reverse tran-scriptase-polymerase chain reaction (RT-PCR). The influence of the up-regulated expression of inte-grated genes on hepatocarcinogenesis was analyzed. Nineteen integration sites of HBV DNA into HCC tissues were obtained by RT-PCR and sequencing. These genes encoding proteins were: LOC51030, LOC 157777, minichromosome maintenance complex component 3 associated protein (MCM3AP), MCTP1, SH3 and multiple ankyrin repeat domains 2 isoform 2, CCDC40, similar to HCG2033532, mitochondrial ribosomal S5 pseudogene 4. One of them was integrated into the intron of MCM3AP. RT-PCR demonstrated that the expression levels of MCM3AP mRNA in HCC tissues, matched surrounding liver tissues and normal liver tissues were in a descendent order. The ratio of MCM3AP mRNA to the GAPDH mRNA in these three tissues was 1.07375, 0.21573, 0.06747 re-spectively, with the difference being statistically significant among them (P<0.05). Meanwhile, the expression levels of MCM3AP mRNA from HCC tissues in which HBV DNA integrated into MCM3AP were still significantly higher than those without HBV DNA integrated into MCM3AP. It was concluded that the HBV DNA integration sites into human genome were random, and MCM3AP was a new site. The up-regulated MCM3AP mRNA may affect flanking sequences which promote the hepatocarcinogenesis.

Estimating genomic instability mediated by Alu retroelements in breast cancer

Alu-PCR is a relatively simple technique that can be used to investigate genomic instability in cancer. This technique allows identification of the loss, gain or amplification of gene sequences based on the analysis of segments between two Alu elements coupled with quantitative and qualitative analyses of the profiles obtained from tumor samples, surgical margins and blood. In this work, we used Alu-PCR to identify gene alterations in ten patients with invasive ductal breast cancer. Several deletions and insertions were identified, indicating genomic instability in the tumor and adjacent normal tissue. Although not associated with specific genes, the alterations, which involved chromosomal bands 1p36.23, 1q41, 11q14.3, 13q14.2, occurred in areas of well-known genomic instability in breast and other types of cancer. These results indicate the potential usefulness of Alu-PCR in identifying altered gene sequences in breast cancer. However, caution is required in its application since the Alu primer can produce non-specific amplification.

Detection of hepatitis B virus DNA integration in hepatocellular carcinoma using hepatitis B virus-Alu-polymerase chain reaction / 中华传染病杂志

Objective To detect the integration of hepatitis B virus (HBV) DNA in HBVrelated human hepatocellular carcinomas (HCC). Methods Extracted DNA from the liver tissue samples and amplified by nested polymerase chain reaction (PCR) with specially designed U-base primers. According to the known genes and human Alu repeat sequences (Alu repeat) , primers were designed respectively. Integrated clones combined target HBV DNA and the adjacent cell gene sequences were established by PCR and products were sequenced by biotechnology companies.Accurate locations of HBV genes integrated in the human genomes were analyzed by national center for biotechnology information (NCBI) basic local alignment search tool (BLAST) and Map Viewer search. Results In 24 HBsAg positive HCC samples, 15 cases showed the integrations of HBV fragment. And the other 8 samples didn't show any evidence of integration. Among 14 samples with integration, forward insertions of HBV DNA into the host chromosomal DNA were found in 10 samples and reverse insertions were found in 8 samples while both forward and reverse insertions were found in 5 samples. Analysis from viral-cellular junctions suggested that the integrations were all happened with truncated viral DNA and could be in any locus of X gene. Conclusion HBV DNA integration is not distributed evenly throughout the host genome.

Identification of hRad21-Binding Sites in Human Chromosome

The aim of this study is to identify hRad21-binding sites in human chromosome, the core component of cohesin complex that held sister chromatids together. After chromatin immunoprecipitation with an hRad21 antibody, it was cloned the recovered DNA and sequenced 30 independent clones. Among them, 20 clones (67%) contained repetitive elements including short interspersed transposable elements (SINE or Alu elements), long terminal repeat (LTR) and long interspersed transposable elements (LINE), fourteen of these twenty (70%) repeats clones had Alu elements, which could be categorized as the old and the young Alu Subfamily, eleven of the fourteen (73%) Alu elements belonged to the old Alu Subfamily, and only three Alu elements were categorized as young Alu subfamily. There is no CpG island within these selected clones. Association of hRad21 with Alu was confirmed by chromatin immunoprecipitation-PCR using conserved Alu primers. The primers were designed in the flanking region of Alu, and the specific Alu element was shown in the selected clone. From these experiments, it was demonstrated that hRad21 could bind to SINE, LTRs, and LINE as well as Alu.

DETECTION OF STRAND BREAKS OF DNA IN HUMAN EARLY CHORIONIC VILLUS CELLS INDUCED BY DIAGNOSTIC ULTRASOUND USING 32p-LABELED ALU HYBRIDIZATION / 药物分析学报

Objective To explore if strand breaks of DNA in human early chorionic villus cells in uterus were induced by diagnostic ultrasound and to evaluate the method used for detection of single-stranded breaks and doublestranded breaks in human DNA. Methods 60 normal pregnant women aged 20-30, who underwent artificial abortion during 6-8 weeks of gestation, were randomly divided into 2 experimental groups: All 30 cases were exposed to diagnostic ultrasound in uterus for 10 minutes, and 24 hours later chorionic villi were extracted; the other 30 cases were taken as the control group. Single-stranded DNA and double-stranded DNA in villus cells in all cases were isolated by the alkaline unwinding combined with hydroxylapatite chromatography, and were quantitatively detected using32 P-labeled Alu probe for dot-blotting hybridization. Results There was no significant difference in quantity and percentage in single-stranded DNA and double-stranded DNA between 2 groups (P＞0.05). 32 P-Alu probe could only hybridize with human DNA, and could detect DNA isolated from as few as 2.5 × 103 chorionic villus cells and 0.45 ng DNA in human leukocytes. Conclusion The results suggested that there were no DNA strand damages in human chorionic villus cells when the uterus was exposed to diagnostic ultrasound for 10 minutes. The method, 32P-Alu probe for dot-blotting hybridization, was even more specific, sensitive and accurate than conventional approaches.

High Correlation between Alu Elements and the Conversion of 3' UTR of mRNAs Processed Pseudogenes

Even though it represents 6 13% of human genomic DNA, Alu sequences are rarely found in coding regions. When in exon region, over 80 % of them are found in 3' untranslated region (UTR). Pseudogenes are an important component of human genome. Their functions are not clearly known and the mechanism of how they are generated is still debatable. Both the Alu and Pseudogenes are important research problems in molecular biology. mRNA is thought to be a prime source of pseudogene and active research is going on its molecular mechanism. We report, for the first time, that mRNAs containing Alu repeats at 3' UTR has a significantly high correlation with processed pseudogenes, suggesting a possibility that Alu containing mRNAs have a high tendency to become processed pseudogenes. It is known that about 10% of all human genes have been transposed. Transposed genes at 3' UTR without Alu repeat have about two processed pseudogenes per gene on average while we found with statistical significance that a transposed gene with Alu had over three processed Pseudogenes on average. Therefore, we propose Alu repeats as a new and important factor in the generation of pseudogenes.

Alu and L1 Retroelements Are Correlated with the Tissue Extent and Peak Rate of Gene Expression, Respectively

We exploited the serial analysis of gene expression (SAGE) libraries and human genome database in silico to correlate the breadth of expression (BOE; housekeep-ing versus tissue-specific genes) and peak rate of expression (PRE; high versus low expressed genes) with the density distribution of the retroelements. The BOE status is linearly associated with the density of the sense Alus along the 100 kb nucleotides region upstream of a gene, whereas the PRE status is inversely correlated with the density of antisense L1s within a gene and in the up- and downstream regions of the 0-10 kb nucleotides. The radial distance of intranuclear position, which is known to serve as the global domain for transcription regulation, is reciprocally correlated with the fractions of Alu (toward the nuclear center) and L1 (toward the nuclear edge) elements in each chromosome. We propose that the BOE and PRE statuses are related to the reciprocal distribution of Alu and L1 elements that formulate local and global expression domains.

A case of X-linked agammaglobulinemia with deletion of introns 15-18 of Btk gene mediated by Alu-Alu recombination / 대한내과학회지

X-linked agammaglobulinemia (XLA) is characterized by early onset of recurrent bacterial infection, markedly reduced levels of all major classes of immunoglobulins in the serum and few mature B cells in the blood. XLA is known to be associated with mutations in Bruton's tyrosin kinase (Btk). The Btk protein consists of 5 functional domains; the pleckstrin homology (PH) domain, the Tec homology (TH) domain, the Src homology 3 (SH3) domain, the SH2 domain, and the kinase (SH1) domain. Mutations in all domains of the Btk gene have been shown to cause XLA. The large number of Alu elements within the human genome provides abundant opportunities for unequal homologous recombination events between Alu repeats, resulting in human disease. We present a case of XLA with deletion of introns 15-18 of Btk gene which were mediated by an Alu-Alu recombination event.