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1.
RNA Biol ; 12(4): 457-77, 2015.
Article in English | MEDLINE | ID: mdl-25757558

ABSTRACT

MicroRNA (miRNA) genes generally share many features common to those of protein coding genes. Various transcription factors (TFs) and co-regulators are also known to regulate miRNA genes. Here we identify novel p53 and NFκB p65/RelA responsive miRNAs and demonstrate that these 2 TFs bind to the regulatory sequences of miR-100, -146a and -150 in both mouse striatal and human cervical carcinoma cells and regulate their expression. p53 represses the miRNAs while NFκB p65/RelA induces them. Further, we provide evidence that exogenous p53 inhibits NFκB p65/RelA activity by reducing its nuclear content and competing with it for CBP binding. This suggests for the existence of a functional cross-talk between the 2 TFs in regulating miRNA expression. Moreover, promoter occupancy assay reveals that exogenous p53 excludes NFκB p65/RelA from its binding site in the upstream sequence of miR-100 gene thereby causing its repression. Thus, our work identifies novel p53 and NFκB p65/RelA responsive miRNAs in human and mouse and uncovers possible mechanisms of co-regulation of miR-100. It is to be mentioned here that cross-talks between p53 and NFκB p65/RelA have been observed to define the outcome of several biological processes and that the pro-apoptotic effect of p53 and the pro-survival functions of NFκB can be largely mediated via the biological roles of the miRNAs these TFs regulate. Our observation with cell lines thus provides an important platform upon which further work is to be done to establish the biological significance of such co-regulation of miRNAs by p53 and NFκB p65/RelA.


Subject(s)
Gene Expression Regulation , MicroRNAs/genetics , Transcription Factor RelA/metabolism , Tumor Suppressor Protein p53/metabolism , Animals , Cell Line, Tumor , HeLa Cells , Humans , Mice , MicroRNAs/metabolism , Promoter Regions, Genetic
2.
Cell Death Differ ; 20(3): 430-42, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23099851

ABSTRACT

The spindle assembly checkpoint (SAC) is a 'wait-anaphase' mechanism that has evolved in eukaryotic cells in response to the stochastic nature of chromosome-spindle attachments. In the recent past, different aspects of the SAC regulation have been described. However, the role of microRNAs in the SAC is vaguely understood. We report here that Mad1, a core SAC protein, is repressed by human miR-125b. Mad1 serves as an adaptor protein for Mad2 - which functions to inhibit anaphase entry till the chromosomal defects in metaphase are corrected. We show that exogenous expression of miR-125b, through downregulation of Mad1, delays cells at metaphase. As a result of this delay, cells proceed towards apoptotic death, which follows from elevated chromosomal abnormalities upon ectopic expression of miR-125b. Moreover, expressions of Mad1 and miR-125b are inversely correlated in a variety of cancer cell lines, as well as in primary head and neck tumour tissues. We conclude that increased expression of miR-125b inhibits cell proliferation by suppressing Mad1 and activating the SAC transiently. We hypothesize an optimum Mad1 level and thus, a properly scheduled SAC is maintained partly by miR-125b.


Subject(s)
Apoptosis , Cell Cycle Proteins/metabolism , MicroRNAs/metabolism , Mitosis , Nuclear Proteins/metabolism , 3' Untranslated Regions , Anaphase , Base Sequence , Calcium-Binding Proteins/metabolism , Cell Cycle Proteins/antagonists & inhibitors , Cell Cycle Proteins/genetics , Cell Line, Tumor , Cell Proliferation , Chromosome Aberrations , Down-Regulation , HCT116 Cells , Hep G2 Cells , Humans , M Phase Cell Cycle Checkpoints , Mad2 Proteins , MicroRNAs/genetics , Nuclear Proteins/antagonists & inhibitors , Nuclear Proteins/genetics , Repressor Proteins/metabolism
3.
Nucleic Acids Res ; 38(3): 878-92, 2010 Jan.
Article in English | MEDLINE | ID: mdl-19934260

ABSTRACT

Earlier we have shown that exogenous expression of HIPPI, a molecular partner of Huntingtin interacting protein HIP-1, induces apoptosis and increases expression of caspases-1, -8 and -10 in HeLa and Neuro2A cells. The C-terminal pseudo death effector domain of HIPPI (pDED-HIPPI) specifically interacts with the putative promoter sequences of these genes. In the present manuscript, we predict from structural modeling of pDED-HIPPI that R393 of HIPPI is important for such interaction. R393E mutation in pDED-HIPPI decreases the interaction with the putative promoter of caspase-1 in cells. Expression of caspase-1 is decreased in cells expressing mutant pDED-HIPPI in comparison to that observed in cells expressing wild type pDED-HIPPI. Using HIP-1 knocked down cells as well as over expressing HIP-1 with mutation at its nuclear localization signal and other deletion mutations, we demonstrate that translocation of HIPPI to the nucleus is mediated by HIP-1 for the increased expression of caspase-1. HIPPI-HIP-1 heterodimer is detected in cytoplasm as well as in the nucleus and is associated with transcription complex in cells. Taking together, we are able to show the importance of R393 of HIPPI and the role of HIPPI-HIP-1 heterodimer in the transcription regulation of caspase-1.


Subject(s)
Adaptor Proteins, Signal Transducing/chemistry , Caspase 1/genetics , DNA-Binding Proteins/metabolism , Gene Expression Regulation , Transcription, Genetic , Active Transport, Cell Nucleus , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/metabolism , Amino Acid Sequence , Amino Acid Substitution , Apoptosis , Caspase 1/metabolism , Cell Line , Cell Nucleus/metabolism , DNA/chemistry , DNA-Binding Proteins/chemistry , Dimerization , HeLa Cells , Humans , Models, Molecular , Molecular Sequence Data , Promoter Regions, Genetic
4.
FEBS J ; 274(15): 3886-99, 2007 Aug.
Article in English | MEDLINE | ID: mdl-17623017

ABSTRACT

To investigate the mechanism of increased expression of caspase-1 caused by exogenous Hippi, observed earlier in HeLa and Neuro2A cells, in this work we identified a specific motif AAAGACATG (- 101 to - 93) at the caspase-1 gene upstream sequence where HIPPI could bind. Various mutations in this specific sequence compromised the interaction, showing the specificity of the interactions. In the luciferase reporter assay, when the reporter gene was driven by caspase-1 gene upstream sequences (- 151 to - 92) with the mutation G to T at position - 98, luciferase activity was decreased significantly in green fluorescent protein-Hippi-expressing HeLa cells in comparison to that obtained with the wild-type caspase-1 gene 60 bp upstream sequence, indicating the biological significance of such binding. It was observed that the C-terminal 'pseudo' death effector domain of HIPPI interacted with the 60 bp (- 151 to - 92) upstream sequence of the caspase-1 gene containing the motif. We further observed that expression of caspase-8 and caspase-10 was increased in green fluorescent protein-Hippi-expressing HeLa cells. In addition, HIPPI interacted in vitro with putative promoter sequences of these genes, containing a similar motif. In summary, we identified a novel function of HIPPI; it binds to specific upstream sequences of the caspase-1, caspase-8 and caspase-10 genes and alters the expression of the genes. This result showed the motif-specific interaction of HIPPI with DNA, and indicates that it could act as transcription regulator.


Subject(s)
Adaptor Proteins, Signal Transducing/metabolism , Caspase 10/genetics , Caspase 1/genetics , Caspase 8/genetics , Promoter Regions, Genetic/genetics , Adaptor Proteins, Signal Transducing/genetics , Amino Acid Motifs , Animals , Caspase 1/metabolism , Caspase 10/metabolism , Caspase 8/metabolism , Death Domain Receptor Signaling Adaptor Proteins/genetics , Death Domain Receptor Signaling Adaptor Proteins/metabolism , Gene Expression Regulation , Genes, Reporter/genetics , HeLa Cells , Humans , Mutation/genetics , Protein Binding
5.
Mol Cell Biochem ; 297(1-2): 31-9, 2007 Mar.
Article in English | MEDLINE | ID: mdl-17096185

ABSTRACT

Curcumin (diferuloylmethane), a natural cancer chemopreventive compound, has been tested for its action in acute myeloblastic leukemia cell line HL-60. The results clearly show that curcumin induces apoptosis in these cells as evidenced by the release of cytochrome c from mitochondria to the cytosol and increase in the DNA content in sub G1 region as observed in FACS analysis. Apoptosis is apparently mediated by up-regulation of apoptotic gene bax and simultaneous down-regulation of anti-apoptotic gene bcl-2 followed by activation of caspases 3 and 8 and degradation of PARP. Telomerase, a reverse transcriptase, has been found to be activated in more than 80% of human cancers and, therefore, can be considered as a potential marker for tumorigenesis. Certain natural compounds have the potential of inhibiting telomerase activity leading to suppression of cell viability and induction of apoptosis. The present study shows that curcumin-induced apoptosis coincides with the inhibition of telomerase activity in a dose dependent manner.


Subject(s)
Antineoplastic Agents/pharmacology , Apoptosis/drug effects , Curcumin/pharmacology , Leukemia/enzymology , Leukemia/pathology , Telomerase/antagonists & inhibitors , Apoptosis Regulatory Proteins/metabolism , Caspase 3/metabolism , Caspase 8/metabolism , Cytochromes c/metabolism , DNA, Neoplasm/analysis , Dose-Response Relationship, Drug , Flow Cytometry , HL-60 Cells , Humans , Poly(ADP-ribose) Polymerases/metabolism , Protein Processing, Post-Translational/drug effects , Proto-Oncogene Proteins c-bcl-2/metabolism , bcl-2-Associated X Protein/metabolism
6.
Biochem Biophys Res Commun ; 353(1): 80-5, 2007 Feb 02.
Article in English | MEDLINE | ID: mdl-17173859

ABSTRACT

To investigate the mechanism of increased expression of caspase-1 in Hippi expressing HeLa and Neuro 2A cells, reported earlier, we report here that HIPPI directly interacted with upstream sequence of caspase-1 gene (-700 to +17, 717 bp). Deletion of this 717 bp sequence and further analysis by electrophoretic mobility shift assay and fluorescence quenching revealed that HIPPI interacted with 60 bp (-151 to -92) upstream sequence of caspase-1. We also observed by chromatin immunoprecipitation assay that HIPPI interacted with the 717 bp sequence in vivo. In luciferase assay, when expression of the reporter gene was driven by either 717 bp or 60 bp caspase-1 upstream sequences, luciferase activity was increased in GFP-Hippi expressing HeLa cells in comparison to that obtained with parental HeLa cells with the same constructs. Similar result was obtained in Neuro2A cells with 717 bp caspase-1 upstream sequence. In summary, we showed that HIPPI could interact with the putative promoter sequence of caspase-1 and increased the expression of the downstream gene suggesting that HIPPI could act as transcription regulator.


Subject(s)
Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/metabolism , Caspase 1/genetics , Caspase 1/metabolism , Neurons/metabolism , Promoter Regions, Genetic/genetics , Transcriptional Activation/physiology , Binding Sites , Cell Line , HeLa Cells , Humans , Protein Binding
7.
Mutat Res ; 596(1-2): 81-90, 2006 Apr 11.
Article in English | MEDLINE | ID: mdl-16445949

ABSTRACT

Telomerase, a reverse transcriptase that maintains telomere length, is highly activated in tumor cells and practically absent in somatic cells and hence considered a potential marker for tumorigenesis. A connection between telomerase activity and resistance to apoptosis has been established. Telomerase, therefore, has been proposed to represent a novel and potentially selective target for cancer therapy. Several synthetic compounds have been developed in recent years with a view to inhibit telomerase activity with telomere shortening below a critical length resulting in apoptosis. Such compounds are always highly toxic. Many plant-derived products act through the induction of apoptosis as a mechanism to suppress carcinogenesis. Curcumin, a phenolic compound isolated from the rhizome of the plant Curcuma longa Linn., has been reported to possess anti-tumor, apoptotic and anti-angiogenic properties. Apoptosis has emerged as the major mechanism by which anti-tumor agents eliminate pre-neoplastic cells or cells progressed to malignancy. The present study was undertaken to examine the mechanism of curcumin-induced apoptosis in human leukemia cell line K-562 with particular emphasis on the role of curcumin on telomerase activity. Induction of apoptosis by curcumin is initiated by the release of cytochrome c from mitochondria into the cytosol, and evidenced by the increase in DNA content in the sub-G1 region as obtained from FACS analysis. Apoptosis is mediated by the activation of caspases 3 and 8, up-regulation of the apoptotic gene bax with concomitant down-regulation of the anti-apoptotic gene bcl-2. Using TRAP assay it has been observed that curcumin inhibits telomerase activity in a dose and time-dependent manner, the inhibition being due to suppression of translocation of telomerase reverse transcriptase (TERT), a catalytic subunit, from cytosol to nucleus. Most significantly, the inhibition of telomerase activity by curcumin correlates with several parameters of apoptosis. The results suggest that telomerase status plays an important role in the induction of apoptosis in K-562 cells by curcumin.


Subject(s)
Apoptosis/drug effects , Curcumin/pharmacology , Telomerase/antagonists & inhibitors , Caspases/drug effects , Caspases/metabolism , Cytochromes c/analysis , DNA-Binding Proteins/drug effects , DNA-Binding Proteins/metabolism , Flow Cytometry , Humans , K562 Cells , Kinetics , Telomerase/drug effects , Telomerase/metabolism
8.
Ann Hum Genet ; 68(Pt 3): 189-95, 2004 May.
Article in English | MEDLINE | ID: mdl-15180699

ABSTRACT

Friedreich ataxia (FRDA), the most common type of ataxia worldwide, is an autosomal recessive disease. Homozygous expansion of GAA repeats in the first intron of the frataxin gene constitute the major type of mutation that causes the disease. The prevalence of FRDA in diverse ethnic populations of India has not been widely studied. We have studied the distribution of polymorphic GAA repeats in the frataxin gene among 6 clinically diagnosed patients and 160 ethnically matched normal individuals, to gather information on the prevalence of FRDA in the eastern part of India. Homozygous expansion in the range of 250-730 GAA repeats was detected among the patients. Among normal individuals, we observed a unimodal distribution of GAA repeats, consisting of 10 different alleles ranging from 7 to 16 GAA repeats, where the 9 repeat allele had maximal frequency. Only 5.9% of all chromosomes were found to harbour >12 GAA repeats. Haplotype analysis using closely linked four bi-allelic markers in and around the frataxin gene indicated that 66.7% of the expanded alleles harbour the ATCC haplotype that has been reported worldwide. This haplotype was present in 53.3% of the chromosomes with >12 GAA repeats, and accounted for only 3.8% of chromosomes with 7 to 12 GAA repeats. We found one novel haplotype, ACCT, among the expanded alleles as well as among normal individuals, though at low frequency; this haplotype may be characteristic of Indian populations.


Subject(s)
Friedreich Ataxia/genetics , Haplotypes/genetics , Iron-Binding Proteins/genetics , Polymorphism, Genetic/genetics , Trinucleotide Repeat Expansion/genetics , Adolescent , Case-Control Studies , Child , Female , Friedreich Ataxia/epidemiology , Gene Frequency , Genetic Markers , Homozygote , Humans , India/epidemiology , Male , Frataxin
9.
Acta Neurol Scand ; 108(6): 407-14, 2003 Dec.
Article in English | MEDLINE | ID: mdl-14616293

ABSTRACT

OBJECTIVES: MJD1/SCA3 is the most common type of spinocerebellar ataxia (SCA) worldwide. To explain the low prevalence of the disease among SCA patients from eastern India, we analysed CAG repeats and two bi-allelic intragenic markers at SCA3 locus among 412 normal individuals and 10 patients. MATERIALS AND METHODS: For CAG repeat analysis, PCR amplified fragments were run on polyacrylamide gel, transferred to a membrane, probed with (CAG)10 and detected on an autoradiograph. Bi-allelic markers were analysed using allele specific PCR amplification. RESULTS: Large normal alleles (>33 CAG repeats) were 0.015 in pooled populations. All the patients had the common haplotype C-A as observed worldwide. Frequency of C-A haplotype among large normal alleles was 0.75. CONCLUSIONS: Observed low prevalence of SCA3 could be because of the low prevalence of large normal alleles that might act as the reservoir for the expanded alleles. SCA3 mutation in Indian populations had the same origin as found worldwide.


Subject(s)
Genetic Variation , Machado-Joseph Disease/genetics , Nerve Tissue Proteins/genetics , Trinucleotide Repeats , Ataxin-3 , Humans , India , Nuclear Proteins , Polymerase Chain Reaction , Polymorphism, Genetic , Repressor Proteins , Sampling Studies
10.
Ann Hum Genet ; 67(Pt 1): 26-34, 2003 Jan.
Article in English | MEDLINE | ID: mdl-12556232

ABSTRACT

It has been proposed that a constellation of three TP53 polymorphisms (intron 3 16 bp duplication, codon 72 BstUI, and intron 6 Nci I RFLP at nt 13494) constitute a haplotype predictive of increased cancer risk. We have estimated the allele frequency of these polymorphisms in three endogamous Indian ethnic populations from three different geographic locations (viz. Iyer from south India, Brahmin from central India and Mahishya from eastern India), as well as in head and neck squamous cell carcinoma (HNSCC) patients, and in ethnically matched normal individuals from the eastern region of India. The genotype distributions and allele frequencies of the three polymorphisms in all but one population, as well as in patients, showed a good fit to Hardy-Weinberg equilibrium. Strong linkage disequilibria were observed between all loci in every population examined, except for the 16bp-Nci I haplotype in the Mahishya population. The Mahishya population differed significantly from the other two populations with respect to differences in allele frequency and haplotype frequency. Although there were no significant differences in genotypic frequency at any of the loci between HNSCC patients and the matched control population, the minor allele frequency of codon 72 and intron 3 16 bp polymorphisms showed significant variation. Variation in overall haplotype frequency between patients and normal individuals was significant (p = 0.036) when two rare haplotypes 2-1-2 and 1-2-1 were combined. The rare haplotype 2-1-2 was found to be modestly over represented in HNSCC patients as compared to normal individuals.


Subject(s)
Gene Frequency , Genes, p53/genetics , Genetics, Population , Haplotypes , Head and Neck Neoplasms/genetics , Linkage Disequilibrium , DNA/blood , DNA/genetics , Genetic Predisposition to Disease , Head and Neck Neoplasms/epidemiology , Humans , India
11.
Cancer Chemother Pharmacol ; 48(4): 312-8, 2001 Oct.
Article in English | MEDLINE | ID: mdl-11710632

ABSTRACT

PURPOSE: To characterize a methotrexate-resistant Chinese hamster cell line, designated as M5, which had previously been shown to be resistant to gamma radiation, at the cellular and molecular levels. METHODS: Sensitivity towards a number of chemotherapeutic drugs was determined by colony-forming ability and compared with that of parental V79 cells. Expression of the hamster homologue of the human mismatch repair gene hmsh3 was also determined by RT-PCR. RESULTS: Induced killing by chemotherapeutic agents cis-diamminedichloroplatinum II (cisplatin). the antimetabolite 6-thioguanine (6-TG), camptothecin, a topoisomerase I inhibitor, and 4-(9-acridinyl-amino)-methanesulfon-m-anisidide (mAMSA), an inhibitor of topoisomerase II, was less in M5 cells than in the parental V79 cells. The IC50 values, defined as the concentration of the drug that reduced the survival to 50% that of the untreated control, in V79 cells for mAMSA and camptothecin treatment were 0.35 +/- 0.02 microg/ml and 84.3 +/- 16.0 ng/ml, respectively. For M5 cells, equivalent values were 0.52 +/- 0.10 microg/ml and 186 +/- 40.8 ng/ml. Treatment with 30 microM cisplatin reduced the survival of V79 cells to 0.09 +/- 0.07, whereas the same treatment reduced the survival of M5 cells to 0.67 +/- 0.16. Treatment of M5 cells with 6-TG did not induce appreciable killing up to the concentrations studied. However, for V79 cells, 6-TG was very toxic. We further observed that the dihydrofolate reductase (dhfr) gene as well as the hamster homologue of the human mismatch repair gene hmsh3 was amplified in the methotrexate-resistant M5 cells. CONCLUSION: Resistance to this group of chemotherapeutic drugs observed in M5 cells could be due to the amplification of the hamster homologue of hMSH3, which in turn possibly sequesters all the hMSH2 making M5 cells functionally deficient in the mismatch repair system.


Subject(s)
Antimetabolites, Antineoplastic/pharmacology , Antineoplastic Agents/pharmacology , DNA-Binding Proteins/biosynthesis , Drug Resistance, Neoplasm/genetics , Gene Amplification , Methotrexate/pharmacology , Multidrug Resistance-Associated Proteins , Tetrahydrofolate Dehydrogenase/genetics , Animals , Base Pair Mismatch , Cell Survival , Cricetinae , Cricetulus , DNA Repair , Drug Screening Assays, Antitumor , Humans , MutS Homolog 3 Protein , Reverse Transcriptase Polymerase Chain Reaction , Tumor Cells, Cultured
12.
Indian J Biochem Biophys ; 38(1-2): 42-7, 2001.
Article in English | MEDLINE | ID: mdl-11563329

ABSTRACT

While studying the inhibition of telomerase activity in Chinese hamster V79 cells using polymerase chain reaction (PCR) based telomeric repeat amplification protocol (TRAP) assay, we had earlier observed that 7-deaza deoxy guanosine triphosphate (7-deaza dGTP) and oligonucleotide (TTAGGG)4 inhibited telomerase activity in vitro. In the present study, we report inhibition of telomerase activity by modified base 7-deaza deoxy adenosine triphosphate (7-deaza dATP) and phosphorothioate TTAGGG (PS-TTAGGG). Both the compounds inhibited telomerase activity in a concentration dependent manner; 8.5 microM of 7-deaza dATP and 0.1 microM of PS-TTAGGG being the concentration for 50% of the maximum inhibition. This observation supports our earlier hypothesis that incorporation of a modified nucleotide into telomere possibly interferes with the recognition of the telomerase and TTAGGG interferes with the RNA component of telomerase. We have further shown that treatment of cells with nicotinamide (NA) and benzamide (BA), well known inhibitors of poly (ADP-ribose) polymerase, reduced telomerase activity. We speculate that modification of the telomeric binding proteins or other components by poly (ADP-ribosyl)ation may be involved in such inhibition.


Subject(s)
Telomerase/antagonists & inhibitors , Telomerase/metabolism , Animals , Benzamides/pharmacology , Cell Line , Cricetinae , Cricetulus , Densitometry , Deoxyguanine Nucleotides/pharmacology , Dose-Response Relationship, Drug , Niacinamide/pharmacology , Polymerase Chain Reaction , Protein Binding , Telomere/metabolism
13.
Hum Genet ; 108(4): 310-7, 2001 Apr.
Article in English | MEDLINE | ID: mdl-11379877

ABSTRACT

The frequencies of haplotypes based upon the (CTG)n repeat and three other biallelic markers in and around the myotonic dystrophy (DM) locus were estimated in 13 ethnically, linguistically and geographically diverse sub-populations of India. The range of CTG repeats in caste populations was 5-31, while in tribal populations the range was shorter (5-23). Extensive variation in frequencies of large (CTG)n alleles (> or =18 repeats) was found in Indian populations. The implications of this finding on DM epidemiology are discussed. Haplotype diversity was found to be very high in most populations. The majority of the Indian DM patients carried a haplotype that is commonly found among DM patients globally; this is the most common haplotype in the class of large (> or =18 repeats) CTG alleles. However, one haplotype was found to be present in particularly high frequency in Indian populations; this haplotype was also found among Indian DM patients. This haplotype may be a characteristic of Indian and possibly of other East Asian populations.


Subject(s)
Myotonic Dystrophy/genetics , Polymorphism, Genetic , Trinucleotide Repeats , Alleles , Alu Elements , Deoxyribonucleases, Type II Site-Specific , Gene Frequency , Genetic Variation , Haplotypes , Humans , India
14.
Int J Cancer ; 92(4): 555-61, 2001 May 15.
Article in English | MEDLINE | ID: mdl-11304691

ABSTRACT

Genomic instability in simple repeated sequences has been observed in several human cancers. We have analyzed 50 squamous cell carcinomas of the head and neck (SCCHN) and 5 pre-malignant severe dysplastic tissues from Indian patient populations for microsatellite instability in 18 different loci spread over eight different chromosomes. Among the tumors analyzed, 45% exhibited instability at two or more loci, and 15% exhibited instability at 40% of the markers tested. Similar analysis of SCCHN tumors from other populations (British, American and French) showed much less frequency of instability. SCCHN tumors in the present study did not show any instability in the mononucleotide repeat sequences. There is also a clear distinction in the nature of the instability in these tumors in comparison with colorectal tumors. These results suggest that the underlying mechanism generating this type of instability is different from those reported for colorectal tumors.


Subject(s)
Carcinoma, Squamous Cell/genetics , Head and Neck Neoplasms/genetics , Microsatellite Repeats , Trinucleotide Repeat Expansion , Adult , Age Factors , Aged , Alleles , Chromosome Mapping , Colorectal Neoplasms/genetics , Female , Humans , India , Loss of Heterozygosity , Male , Middle Aged , Polymerase Chain Reaction
15.
Hum Mutat ; 16(4): 372, 2000 Oct.
Article in English | MEDLINE | ID: mdl-11013451

ABSTRACT

We have studied the CTG repeat sizes in the DMPK gene and six biallelic markers which are in complete linkage disequlibrium with Caucasian DM patients, to identify any common founder haplotype in 30 clinically diagnosed unrelated DM patients from eastern India. Our results revealed that in 27 patients (90%), CTG expansion took place on a DraIII(-) - HhaI(-) - Alu(+) - HinfI(+) - Fnu4H I(-) - TaqI(+) haplotype (haplotype I), similar to what have been published for Caucasoid and other DM patients. However, in three patients (10%), the expansion of CTG repeat was on DraIII(+) - HhaI(+) - Alu(+) - HinfI(-) - Fnu4H I(+) - TaqI(-) background (haplotype II), indicating a new haplotype. The distribution of haplotypes in 52 normal individuals of eastern India revealed that percentage of haplotypes I and II were 23.1% and 7.7% respectively in normal chromosomes. Haplotype II is absent among Caucasian DM patients as well as normal individuals indicating that this particular haplotype may be characteristic of the Indian population. Hum Mutat 16:372, 2000.


Subject(s)
Myotonic Dystrophy/enzymology , Myotonic Dystrophy/genetics , Protein Kinases/genetics , Protein Serine-Threonine Kinases , Trinucleotide Repeat Expansion/genetics , Adolescent , Adult , Alleles , Female , Haplotypes/genetics , Humans , India/epidemiology , Male , Middle Aged , Myotonic Dystrophy/epidemiology , Myotonin-Protein Kinase
16.
Eur J Hum Genet ; 8(9): 678-82, 2000 Sep.
Article in English | MEDLINE | ID: mdl-10980573

ABSTRACT

We have analysed the distribution of CAG and adjacent polymorphic CCG repeats in the Huntingtin gene in 28 clinically diagnosed unrelated Huntington's disease (HD) patients and in normal individuals belonging to different ethnic groups of India. The range of expanded CAG repeats in HD patients varied from 41 to 56 repeats, whereas in normal individuals this number varied between 11 and 31 repeats. We identified six CCG alleles from a total of 380 normal chromosomes that were pooled across different ethnic populations of India. There were two predominant alleles: (CCG)7 (72.6%) and (CCG)10 (20%). We report here for the first time one four-repeat CCG allele which has not been found in any population so far. We found 30 haplotypes (two loci CAG-CCG) for 380 normal chromosomes. In the present study, no statistically significant preponderance of expanded HD alleles was found on either (CCG)7 or (CCG)10 backgrounds. Our studies suggest that the overall prevalence of HD in Indian populations may not be as high as in Western populations. Further studies are necessary to identify the origin of HD mutation in these populations.


Subject(s)
Huntington Disease/genetics , Nerve Tissue Proteins/genetics , Nuclear Proteins/genetics , Trinucleotide Repeat Expansion/genetics , Adolescent , Adult , Aged , Alleles , Ethnicity/genetics , Ethnicity/statistics & numerical data , Female , Haplotypes , Humans , Huntingtin Protein , Huntington Disease/blood , Huntington Disease/epidemiology , Huntington Disease/ethnology , India/epidemiology , India/ethnology , Male , Middle Aged , Nerve Tissue Proteins/blood , Nuclear Proteins/blood , Polymorphism, Genetic/genetics , Sequence Analysis, DNA
17.
Hum Genet ; 106(6): 597-604, 2000 Jun.
Article in English | MEDLINE | ID: mdl-10942107

ABSTRACT

To identify various subtypes of spinocerebellar ataxias (SCAs) among 57 unrelated individuals clinically diagnosed as ataxia patients we analysed the SCA1, SCA2, SCA3, SCA6, SCA7 and DRPLA loci for expansion of CAG repeats. We detected CAG repeat expansion in 6 patients (10.5%) at the SCA1 locus. Ten of the 57 patients (17.5%) had CAG repeat expansion at the SCA2 locus, while four had CAG expansion at the SCA3/MJD locus (7%). At the SCA6 locus there was a single patient (1.8%) with 21 CAG repeats. We have not detected any patient with expansion in the SCA7 and DRPLA loci. To test whether the frequencies of the large normal alleles in SCA1, SCA2 and SCA6 loci can reflect some light on prevalence of the subtypes of SCAs we studied the CAG repeat variation in these loci in nine ethnic sub-populations of eastern India from which the patients originated. We report here that the frequency of large normal alleles (>31 CAG repeats) in SCA1 locus to be 0.211 of 394 chromosomes studied. We also report that the frequency of large normal alleles (>22 CAG repeats) at the SCA2 locus is 0.038 while at the SCA6 locus frequency of large normal alleles (>13 repeats) is 0.032. We discussed our data in light of the distribution of normal alleles and prevalence of SCAs in the Japanese and white populations.


Subject(s)
Nerve Tissue Proteins/genetics , Spinocerebellar Ataxias/ethnology , Spinocerebellar Ataxias/genetics , Trinucleotide Repeats/genetics , White People/genetics , Adolescent , Adult , Alleles , Ataxin-1 , Ataxin-3 , Ataxin-7 , Ataxins , Calcium Channels/genetics , Child , Ethnicity/genetics , Female , Gene Frequency , Genetic Carrier Screening , Genetic Testing , Humans , India/ethnology , Male , Middle Aged , Nuclear Proteins/genetics , Proteins/genetics , Repressor Proteins , Spinocerebellar Ataxias/diagnosis , Trinucleotide Repeat Expansion/genetics
18.
Genome Res ; 9(8): 711-9, 1999 Aug.
Article in English | MEDLINE | ID: mdl-10447506

ABSTRACT

From the historically prevalent social structure of Indian populations it may be predicted that there has been very little male gene flow across ethnic boundaries. To test this finding, we have analyzed DNA samples of individuals belonging to 10 ethnic groups, speaking Indo-European or Austroasiatic languages and inhabiting the eastern and northern regions of India. Eight Y-chromosomal markers, two biallelic and six microsatellite, were studied. All populations were monomorphic for the deletion allele at the YAP (DYS287) locus and for the 119-bp allele at the DYS288 locus. Y-chromosomal haplotypes were constructed on the basis of one RFLP locus and five microsatellite loci. The haplotype distribution among the groups showed that different ethnic groups harbor nearly disjoint sets of haplotypes. This indicates that there has been virtually no male gene flow among ethnic groups. Analysis of molecular variance revealed that there was significant haplotypic variation between castes and tribes, but nonsignificant variation among ranked caste clusters. Haplotypic variation attributable to differences in geographical regions of habitat was also nonsignificant.


Subject(s)
DNA/analysis , Ethnicity/genetics , Gene Frequency/genetics , Polymorphism, Genetic/genetics , Y Chromosome/genetics , Genetic Markers/genetics , Genetics, Population , Haplotypes , Humans , India , Male
19.
Hum Mutat ; 13(1): 84, 1999.
Article in English | MEDLINE | ID: mdl-10189221

ABSTRACT

To determine the founder of Indian myotonic dystrophy mutation, we have studied the expansion of CTG repeats in myotonin protein kinase gene and two intragenic linked loci Alu(ins) / Alu(del) and G/T intron 9 HinfI polymorphism in ten unrelated DM patients from eastern India. Out of these ten patients, reconstruction of haplotype was possible for five patients unambiguously. In the other five cases, haplotype for the normal allele was assumed to be the most common haplotype found in normal individuals from Indian populations. Such analysis showed that in nine cases, the expansion of CTG repeats took place on Alu(ins)-HinfI-2 background indicating common founder with other DM mutation published. However, in one case we observed a different haplotype [Alu(ins)-HinfI-1] which could be a new mutation or due to admixture.


Subject(s)
Myotonic Dystrophy/genetics , Protein Serine-Threonine Kinases/genetics , Trinucleotide Repeats/genetics , Deoxyribonucleases, Type II Site-Specific/genetics , Humans , India , Introns/genetics , Trinucleotide Repeat Expansion/genetics
20.
Biochem Biophys Res Commun ; 251(2): 620-4, 1998 Oct 20.
Article in English | MEDLINE | ID: mdl-9792823

ABSTRACT

To investigate the nature of telomerase activity and its inhibition in Chinese hamster V79 cells, we have detected telomerase activity in Chinese hamster cells using Telomeric Repeat Amplification Protocol (TRAP) assay. We have further studied inhibition characteristics of this enzyme in vitro by nucleotide analogue 7-deaza-2'-deoxy guanosine triphosphate (7-deaza-dGTP) and oligonucleotide (TTAGGG)4. Both the inhibitors inhibited the telomerase activity in a dose dependent manner. To attain 50% inhibition of the telomerase activity, we needed about 4.5 microM of 7-deaza-dGTP. Similarly, preincubation at 37 degreesC of the cell extract with 1.25 x 10(-3) microgram oligonucleotide (TTAGGG)4 showed 50% inhibition of the control value. Inhibition of telomerase activity by 7-deaza-dGTP could be due to the incorporation of the modified nucleotide in the telomeric repeat and thus altering the further binding/extension by the enzyme. (TTAGGG)4 could have possibly interacted with RNA component of telomerase and inhibited its activity.


Subject(s)
Deoxyguanosine/analogs & derivatives , Oligodeoxyribonucleotides/pharmacology , Telomerase/metabolism , Animals , Base Sequence , Cell Line , Cricetinae , Cricetulus , Deoxyguanosine/pharmacology , Kinetics , Polymerase Chain Reaction , Telomerase/antagonists & inhibitors
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