Unexpectedly high variability of the histone H4 gene in Leishmania

The sequence of the cDNA of the histone H4 gene of Leishmania tarentolae is reported herein. The predicted 100-amino-acid-long protein has the highest degree of identity with the histone H4 gene of L. infantum and shares with it a 5′ region that shows a very low degree of identity with the corresponding region of histone H4 genes from other organisms. However, between these two genes is a 7.7% nucleotide difference that results in seven different amino acids, located in the 5′, central, and 3′ regions of the coding sequence. Such a divergence in the H4 gene, which is considered to be one of the most highly conserved genes, between closely related members of the genus Leishmania is unexpected and may reflect some unusual features of these important proteins in kinetoplastid flagellates. Received: 16 August 1999 / Accepted: 10 September 1999     

Catalog of 668 SNPs detected among 31 genes encoding potential drug targets on the cell surface

 We have been publishing a series of detailed maps of single-nucleotide polymorphisms (SNPs) detected within the genomic loci of 145 genes encoding drug-metabolizing enzymes and transporters. As an addition to the maps reported earlier, we provide here high-density SNP maps of 31 genes encoding various receptors and adhesion molecules of medical importance. By examining a total of approximately 382 kb of genomic DNA encompassing these 31 genes, we identified 668 SNPs among 48 healthy Japanese individuals: 86 in 5′ flanking regions, 27 in 5′ untranslated regions, 45 in coding regions, 399 in introns, 47 in 3′ untranslated regions, and 64 in 3′ flanking regions. We also discovered 113 variations of other types. Of the 668 SNPs, 371 (55.5%) appeared to be novel, on the basis of comparisons with the dbSNP database of the National Center for Biotechnology Information (US) or with previous publications. The maps constructed in this study will serve as an additional resource for studies of complex genetic diseases and drug-response phenotypes to be mapped by linkage-disequilibrium analyses. Received: November 6, 2002 / Accepted: November 7, 2002 Correspondence to:Y. Nakamura     

Catalog of 605 single-nucleotide polymorphisms (SNPs) among 13 genes encoding human ATP-binding cassette transporters: ABCA4, ABCA7, ABCA8, ABCD1, ABCD3, ABCD4, ABCE1, ABCF1, ABCG1, ABCG2, ABCG4, ABCG5, and ABCG8

 Single-nucleotide polymorphisms (SNPs) at some gene loci are useful as markers of individual risk for adverse drug reactions or susceptibility to complex diseases. We have been focusing on identifying SNPs in and around genes encoding drug-metabolizing enzymes and transporters, and have constructed several high-density SNP maps of such regions. Here we report SNPs at additional loci, specifically 13 genes belonging to the superfamily of ATP-binding cassette transporters (ABCA4, ABCA7, ABCA8, ABCD1, ABCD3, ABCD4, ABCE1, ABCF1, ABCG1, ABCG2, ABCG4, ABCG5, and ABCG8). Sequencing a total of 416 kb of genomic DNA from 48 Japanese volunteers identified 605 SNPs among these 13 loci: 14 in 5′ flanking regions, 5 in 5′ untranslated regions, 37 within coding elements, 529 in introns, 8 in 3′ untranslated regions, and 12 in 3′ flanking regions. By comparing our data with SNPs deposited in the dbSNP database of the National Center for Biotechnology Information (US) and with published reports, we determined that 491 (81%) of the SNPs reported here were novel. We also detected 107 genetic variations of other types among the loci examined (insertion–deletions or mono- di-, or trinucleotide polymorphisms). The high-density SNP maps we constructed on the basis of these data should provide useful information for investigating associations between genetic variations and common diseases or responsiveness to drug therapy. Received: February 26, 2002 / Accepted: March 5, 2002     

Catalog of 46 single-nucleotide polymorphisms (SNPs) in the microsomal glutathione S-transferase 1 (MGST1) gene

A major goal in our laboratory is to understand the role of common genetic variations among individual patients as regards susceptibility to common diseases and differences in therapeutic efficacy and/or side effects of drugs. As an addition to the high-density SNP (single-nucleotide polymorphism) maps of 12 glutathione S-transferase and related genes reported earlier, we provide here an SNP map of the microsomal glutathione S-transferase 1 (MGST1) gene. Among 48 healthy Japanese volunteers examined, we identified a total of 46 SNPs at this locus, 36 of which had not been reported before: 4 in the promoter region, 34 in introns, 3 in the 3′ untranslated region, and 5 in the 3′ flanking region. No SNP was found in 5′ untranslated or coding regions. The ratio of transition to transversion was approximately 1.2 : 1. Among the 13 insertion–deletion polymorphisms was a 2-bp deletion in the coding region of MGST1 in DNA from one of the volunteers, which resulted in a frame-shift mutation. Since the gene product encoded by this mutant allele would lack the C-terminal half including the MAPEG (membrane-associated proteins in eicosanoid and glutathione metabolism) domain, MGST1 activity is likely to be reduced in the carrier's cells. The SNP map presented here adds to the archive of tools for studying complex genetic diseases, population migration patterns, and a variety of pharmacogenetic possibilities. Received: June 27, 2001 / Accepted: July 16, 2001     

Catalog of 86 single-nucleotide polymorphisms (SNPs) in three uridine diphosphate glycosyltransferase genes: <Emphasis Type="Italic">UGT2A1</Emphasis>, <Emphasis Type="Italic">UGT2B15</Emphasis>, and <Emphasis Type="Italic">UGT8</Emphasis>

We report here three high-density maps of variations found among 48 Japanese individuals in three uridine diphosphate glycosyltransferase (UGT) genes, UGT2A1, UGT2B15, and UGT8. A total of 86 single-nucleotide polymorphisms (SNPs) were identified through systematic screening of genomic regions containing these genes: 8 in 5′ flanking regions, 7 in coding regions, 67 in introns, 3 in 3′ untranslated regions, and 1 in a 3′ flanking region. We also discovered 14 variations of other types. Of the 86 SNPs, 63 (73%) were considered to be novel on the basis of comparison of our data with the Database of SNPs (dbSNP) of the National Center for Biotechnology Information. Among the seven SNPs identified in exonic sequences, five were non-synonymous changes that would result in amino-acid substitutions. The collection of SNPs derived from this study will serve as an additional resource for studies of complex genetic diseases and responsiveness to drug therapy. Received: June 12, 2002 / Accepted: June 13, 2002     

The organization of mitochondrial atp6 gene region in male fertile and CMS lines of pepper (Capsicum annuum L.)

The mitochondrial atp6 gene in male fertile (N) and CMS (S) pepper has previously been compared and was found to be present in two copies (Kim et al. in J Kor Soc Hort Sci 42:121–127 2001). In the current study, these atp6 copies were amplified by an inverse PCR technique, and the coding region as well as the 5′ and 3′ flanking regions were sequenced. The atp6 copies in CMS pepper were detected as one intact gene and one pseudogene, truncated at the 3′ coding region. When the atp6 genes in pepper were compared to other plant species, pepper, potato, and petunia all possessed a sequence of 12 identical amino acids at the 3′ extended region, which was considered a hallmark of the Solanaceae family. Northern blot analysis showed differences in mRNA band patterns between CMS and restorer lines, indicating that atp6 gene is one of the candidates for CMS in pepper. GenBank accession number: DQ126682 (atp6-1 genomic sequence common to fertile and CMS pepper), DQ126681 (Fertile atp6-2 genomic sequence), DQ126680 (CMS pseudo-atp6-2 genomic sequence)     

Catalog of 320 single nucleotide polymorphisms (SNPs) in 20 quinone oxidoreductase and sulfotransferase genes

Single nucleotide polymorphisms (SNPs) in genes encoding drug-metabolizing enzymes, transporters, receptors, and other drug targets have been widely implicated as contributors to differences among individuals as regards the efficacy and toxicity of many medications, as well as the susceptibility to complex diseases. By combining the polymerase chain reaction (PCR) technique with direct sequencing, we screened genomic DNAs from 48 Japa-nese volunteers for SNPs in genes encoding three quinone oxidoreductases (NQO1, NQO2, and PIG3) and 17 sulfotransferases (SULT1A1, SULT1A2, SULT1A3, SULT1C1, SULT1C2, SULT2A1, SULT2B1, ST1B2, TPST1, TPST2, SULTX3, STE, CST, HNK-1 ST, CHST2, CHST4, and CHST5). In all, we identified 320 SNPs from these 20 loci: 22 within coding elements, 21 in 5′ flanking regions, 10 in 5′ untranslated regions, 223 in introns, 19 in 3′ untranslated regions, and 25 in 3′ flanking regions. The ratio of transitions to transversions was approximately 2.3 to 1. Of the 22 coding SNPs, 6 were nonsynonymous substitutions that resulted in amino-acid substitutions. The high-density SNP maps we constructed from this data for each of the quinone oxidoreductases and sulfotransferases examined here should provide useful information for investigations designed to detect association(s) between genetic variations and common diseases or responsiveness to drug therapy. Received: January 12, 2001 / Accepted: January 19, 2001     

Catalog of 258 single-nucleotide polymorphisms (SNPs) in genes encoding three organic anion transporters, three organic anion-transporting polypeptides, and three NADH:ubiquinone oxidoreductase flavoproteins

We present here a series of high-density maps of single-nucleotide polymorphisms (SNPs) detected in genes encoding three organic-anion transporters, three organic anion-transporting polypeptides, and three nicotinamide adenine dinucleotide, reduced:ubiquinone oxidoreductase flavoproteins. A total of 258 SNPs were identified among these nine genes through systematic screening of DNA from 48 Japanese individuals: 17 in 5′ flanking regions, three in 5′ untranslated regions, 13 in coding regions, 211 in introns, six in 3′ untranslated regions, and 8 in 3′ flanking regions. By comparing our data with SNPs deposited in the dbSNP database in the National Center for Biotechnology Information, we determined that 236 (91.5%) were novel. In addition, 46 genetic variations of other types were discovered within these loci. These high-resolution maps will serve as a useful resource for analyzing potential associations between variations in these nine genes and differences in human susceptibilities to common diseases or response to drug therapies. Received: August 15, 2001 / Accepted: August 23, 2001     

Structural analysis of the chimeric <Emphasis Type="Italic">CYP21P/CYP21</Emphasis> gene in steroid 21-hydroxylase deficiency

Congenital adrenal hyperplasia (CAH) is a common autosomal recessive disorder mainly caused by defects in the steroid 21-hydroxylase (CYP21) gene. More than 90% of CAH cases are caused by mutations of the CYP21 gene. Approximately 75% of the defective CYP21 genes are generated through intergenic recombination, termed “apparent gene conversion,” from the neighboring CYP21P pseudogene. A chimeric CYP21P/CYP21 gene with its 5′ end corresponding to CYP21P and 3′ end corresponding to CYP21 has been identified. This type of gene is nonfunctional because it produces a truncated protein. We found two distinct chimeric genes in CAH patients. Both genes had a sequence with −300 nucleotides of the 5′ head as the CYP21P gene. The coding region consisted of a fusion molecule with the CYP21P gene in two different regions. One of the junctions was located in the chi-like sequence of GCTGGGC in the third intron and the other was in the minisatellite consensus TGGCAGGAGG of exon 5 of the CYP21P gene. In addition, analysis of restriction fragment length polymorphism for these two 3.3-kb chimeric molecules showed that these sequences arose as a consequence of unequal crossover between the CYP21P and CYP21 genes. It is plausible that both consensus sequences are responsible for the gene conversion of these two chimeric genes. Received: March 13, 2002 / Accepted: June 17, 2002     

High-resolution SNP map in the 55-kb region containing the selectin gene family on chromosome 1q24–q25

 Immunoglobulin A nephropathy (IgAN) is the most common form of glomerulonephritis characterized by predominant IgA deposits in glomerular mesangium. By means of a genome-wide case-control association study, we previously demonstrated that eight single-nucleotide polymorphisms (SNPs) within the selectin gene cluster are significantly associated with IgAN. Here we provide more detailed information of variations corresponding to selectin loci, consisting of 88 SNPs and two insertion–deletion polymorphisms in the Japanese population: 27 in 5′ flanking regions, 1 in 5′ untranslated regions, 6 within coding regions, 46 in introns, 4 within 3′ untranslated regions, and 4 in 3′ flanking regions. The SNP map presented here will be a useful resource not only for examining the relationships between selectin genotypes and susceptibility to the IgAN phenotype, but also for analyzing gene scans of complex diseases mapped to this local segment on chromosome 1. Received: November 18, 2002 / Accepted: November 22, 2002 Correspondence to:Y. Nakamura     

High-density single-nucleotide polymorphism (SNP) map of the 150-kb region corresponding to the human ATP-binding cassette transporter A1 (<Emphasis Type="Italic">ABCA1</Emphasis>) gene

Highly dense catalogs of human genetic variations, in combination with high-throughput genotyping technologies, are expected to clarify individual genetic differences in pharmacological responsiveness and predispositions to common diseases. Here we report single-nucleotide polymorphisms (SNPs) present among 48 Japanese individuals at the locus for the human ATP-binding cassette transporter A1 (ABCA1) gene. ABCA1 plays a key role in apolipoprotein-mediated cholesterol transport, and mutations in this gene are responsible for Tangier disease and familial high-density lipoprotein deficiency associated with reduced cholesterol efflux. We identified a total of 162 SNPs, 149 of which were novel, within the 150-kb region encompassing the entire ABCA1 gene. Eight of the SNPs lie within coding elements, two in 5′ flanking regions, 147 in introns, and five in 3′ untranslated regions, but none were found in 5′ untranslated or 3′ flanking regions. The ratio of transitions to transversions was approximately 2.37 to 1. Our dense SNP map of this region could serve as a powerful resource for studies of complex genetic diseases that may be associated with ABCA1 and of individual responses to drug therapy. Received: May 22, 2001 / Accepted: June 12, 2001     

Sulfate assimilation in Aspergillus terreus: analysis of genes encoding ATP-sulfurylase and PAPS-reductase

Two genes for the sulfate assimilation pathway in Aspergillus terreus were cloned. The genes sAT (coding for PAPS-reductase) and sCT (coding for ATP-sulfurylase) form a small gene cluster. Both genes are similar to their homologs in A. nidulans (sA and sC), Penicillium chrysogenum (aps) and Saccharomyces cerevisiae (MET3 and MET16). In the coding sequence of the sCT gene, a typical non-functional APS-kinase-like domain is present. The sCT gene is expressed in A. nidulans, but its expression there is less sensitive to methionine level than in the original species. Two regions 5′ upstream of sAT were found to be similar to those of sA. Received: 23 February 2000 / Accepted: 8 June 2000     

Human organic cation transporter (OCT1 and OCT2) gene polymorphisms and therapeutic effects of metformin

Organic cation transporters (OCTs) are responsible for the hepatic and renal transport of metformin. In this study we analyzed variants of OCT1 and OCT2 genes in 33 patients (24 responders and nine non-responders) based on the hypothesis that polymorphisms in both genes contribute to large inter-patient variability in the clinical efficacy of metformin. The sequences of the 5′-flanking and coding regions of the two genes of interest were screened by single-strand conformation polymorphism (SSCP) analysis. To compare the causative factors between responders and non-responders, we performed stepwise discriminant functional analysis. Age, body mass index (BMI) and treatment with lipid-lowering agents were demonstrated as positive predictors, and two mutations in the OCT1 gene, −43T > G in intron 1 and 408Met > Val (1222A > G) in exon 7, were negative and positive predictors, respectively, for the efficacy of metformin; the predictive accuracy was 55.5% (P < 0.05). Subsequent study indicated that OCT1 mRNA levels tended to be lower in human livers with the 408Met (1222A) variant, though the differences did not reach the level of significance. In this study it is suggested that OCT1 and OCT2 gene polymorphisms have little contribution to the clinical efficacy of metformin.     

Thirteen single-nucleotide polymorphisms (SNPs) in the alcohol dehydrogenase 4 (ADH4) gene locus

The human alcohol dehydrogenase 4 (ADH4) gene encodes the class II ADH4 pi subunit, which contributes to the metabolization of a wide variety of substrates, including ethanol, retinol, other aliphatic alcohols, hydroxysteroids, and lipid peroxidation products. Here we report the results of systematic screening for single-nucleotide polymorphisms (SNPs) in the ADH4 gene by means of direct sequencing combined with a polymerase chain reaction method. A total of 16 genetic variations including 13 SNPs were found; 4 in the 5′ flanking region, 4 in the 5′ untranslated region, and 8 within introns. No variation was found in coding, 3′ untranslated, or 3′ flanking regions. Eight of the 13 SNPs were not reported in the NCBI dbSNP database or any previous publications. Our SNP map presented here should provide tools to evaluate the role of ADH4 in complex genetic diseases and a variety of pharmacogenetic effects. Received: September 26, 2001 / Accepted: October 11, 2001     

Effect of +36T > C in intron 1 on the glutamine: fructose-6-phosphate amidotransferase 1 gene and its contribution to type 2 diabetes in different populations

Glutamine: fructose-6-phosphate amidotransferase 1 (GFPT1) acts as a rate-limiting enzyme in the hexosamine biosynthetic pathway, which is an alternative branch of glucose metabolism. To evaluate GFPT1 as a susceptibility gene to type 2 diabetes, we surveyed the polymorphisms related with the gene function of GFPT1 and assessed its contribution to type 2 diabetes with a case-control association study. Screening of the 5′-flanking and all coding regions of GFPT1 revealed eight polymorphisms, one in the 5′-flanking region, one synonymous polymorphism in exon 8, five in introns and one in 3′-UTR, but no mis-sense or non-sense polymorphism. With in silico simulation, a putative promoter region was apparently predicted between 1 kb upstream and 1 kb downstream of the start codon. In this region, +36T > C polymorphism was located on the GC box sequence in intron 1, and its functional effect on promoter activity was confirmed by luciferase reporter assay, introducing a new functional polymorphism of the GFPT1 gene. To examine its association with type 2 diabetes, we analyzed 2,763 Japanese (1,461 controls and 1,302 cases) and 330 Caucasians (190 controls and 140 cases). One possible association of +36T > C was observed in Caucasians, but no association of polymorphisms including +36T > C in intron 1 or haplotypes was observed in Japanese. Although we could not completely rule out a contribution to specific sub-groups or other populations, genetic variation of GFPT1 is unlikely to have a major role in the susceptibility to type 2 diabetes in Japanese.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.