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Utilization of ribonucleotides and RNA primers by Tetrahymena telomerase.

Telomerase is a ribonucleoprotein (RNP) DNA polymerase involved in telomere synthesis. A short sequence within the telomerase RNA component provides a template for de novo addition of the G-rich strand of a telomeric simple sequence repeat onto chromosome termini. In vitro, telomerase can elongate single-stranded DNA primers processively: one primer can be extended by multiple rounds of template copying before product dissociation. Telomerase will incorporate dNTPs or ddNTPs and will elongate any G-rich, single-stranded primer DNA. In this report, we show that Tetrahymena telomerase was able to incorporate a ribonucleotide, rGTP, into product polynucleotide. Synthesis of the product [d(TT)r(GGGG)]n was processive, suggesting that the chimeric product remained associated with the enzyme both at the active site and at a second, previously characterized, template-independent product binding site. As predicted by this finding, RNA-containing oligonucleotides served as primers for elongation. More than 3 nt of RNA at a primer 3' end decreased the quantity of product synthesis but increased the affinity of the primer for telomerase. Thus, RNA-containing primers were effective as competitive inhibitors of DNA primer elongation by telomerase. These results support the possible evolutionary origin of telomerase as an RNA-dependent RNA polymerase.

Animals↗

Linkage studies in alcohol-responsive myoclonic dystonia.

A large German family with "myoclonic dystonia with lightning jerks responsive to alcohol" was identified. Eleven affected pedigree members and six obligate gene carriers from five generations were identified. A description of one branch of this pedigree was published in 1964. Our examination 30 years after the initial report confirms the clinical syndrome of a nonprogressive movement disorder characterized by myoclonic jerks affecting the proximal muscles and the muscles of the trunk, accompanied by mild dystonic features in some affected family members. Segregation analysis favors autosomal dominant inheritance with high, but incomplete, penetrance in males and much lower penetrance in females. Linkage analysis was performed using simple sequence repeat polymorphisms (CA repeats) closely associated with or spanning the chromosomal regions containing 15 candidate genes: the gene for early-onset generalized torsion dystonia, DYT1 (chromosome 9q34); the genes for subunits alpha 2, beta 1, and gamma 1 (chromosome 4p12-4q13); for alpha 1, alpha 6, beta 2, and gamma 2 (chromosome 5q31.1-5q31.3); for alpha 4, alpha 5, beta 3, and gamma 3 (chromosome 15q11-15q13); for rho 1 and rho 2 (chromosome 6q14-6q21) of the gamma-aminobutyric acid A receptor; and for the alpha subunit of the glycine receptor (chromosome 5q31). By a combination of pairwise and multipoint linkage analysis, it could be excluded that any of these candidate gene-bearing chromosomal regions contain the disease gene in this family. We also excluded major portions of three chromosomal regions syntenic with mouse chromosome 3, which carries the murine beta subunit of the glycine receptor.

Adolescent↗

The region responsible for stroke on chromosome 4 in the stroke-prone spontaneously hypertensive rat.

To detect genetic loci responsible for stroke susceptibility, we produced 107 male F2 progenies crossed between stroke-prone spontaneously hypertensive rats (SHRSP/Izm) and normotensive Wistar Kyoto rats (WKY/Izm) and followed them up until they developed cerebral stroke. One hundred and twenty-five simple sequence repeat (SSR) markers were analyzed in these F2 rats. Nine of 107 F2 rats suffered from macroscopically overt stroke. In these 9 rats, the segregation ratio of 3 genotypes at 6 SSR marker loci on chromosomes 2, 4, 9, and 10 was highly distorted from the expected value (the observed sp/sp:sp/wky:wky/ wky ratio was either 6:3:0 or 6:2:1, while the expected was 1:2:1, p < 0.01 by chi 2 test). Further, the brain weight was significantly heavier (p < 0.001) in the F2 rats suffering from stroke, suggesting that the brain weight was a parameter for stroke. The brain weight of F2 rats cosegregated with D4Mit19, D4Mgh7, and D4Mgh8 (p = 0.0015, 0.0014, and 0.0040 by ANOVA, respectively) on chromosome 4 supporting genetic effects of this genetic loci on the pathogenesis of cerebral stroke. Blood pressure did not cosegregate with these markers on chromosome 4. These results suggest that a region on chromosome 4, independently of hypertension, determines genetic susceptibility to cerebral stroke.

Animals↗

Isolation of full-length cDNA of mouse PAX4 gene and identification of its human homologue.

Recent genetic studies have suggested that PAX4, a member of the paired box (PAX) gene family, is involved in the mechanism regulating the fate of pancreatic islet endocrine progenitor cells. Murine PAX4 was originally identified by genomic screening and, to date, only a partial sequence of PAX4 has been reported. In this study, we cloned the full-length cDNA of mouse PAX4 by RACE (rapid amplification of cDNA ends) using RNA from MIN6 cells, a mouse insulinoma cell line. The full length of cDNA was 1.38 kb, consistent with the estimated size of the transcript by Northern blot. The deduced mouse PAX4 protein was 349 amino acids and had the predicted molecular weight of 38 kDa. Two DNA binding motifs, a 128-amino acid paired domain and a 61-amino acid paired-type homeodomain exhibit the highest amino acid homology with PAX6 (71.2%, 65.0%, respectively), another member of the PAX gene family. However, the sequence of the C-terminal segment of PAX4 diverged and showed no significant homology with any other known PAX genes. As to the genomic DNA, the coding region of the mouse PAX4 gene spanned approximately 5.5 kb and was composed of 10 exons. In the public DNA database, a human cosmid (g1572c264), which was localized on human chromosome 7q31.3, was found to contain a gene homologous to PAX4. The nucleotide and protein sequence homologies between mouse PAX4 and its human homologue were 83.1% and 80.0%, respectively. Interestingly, the ARP5 (ADP-ribosylation factor 5) gene was also found in the same cosmid g1572c264, suggesting the ARP5 gene to be adjacent to the human PAX4 homologue. The human cosmid g1572c264 contains at least four SSRPs (simple sequence repeat polymorphism), which could be used for genetic linkage studies of the locus. The results of this study, i.e. isolation of the full-length cDNA sequence of PAX4 and identification of the homologous human gene, will facilitate further functional and genetic studies of the PAX4 gene.

Alternative Splicing↗

A PCR-based linkage map of human chromosome 1.

A genetic linkage map of human chromosome 1 based entirely on PCR-typable markers has been developed using 38 simple sequence repeat (SSR) polymorphisms. These SSRs include 36 dinucleotide repeats and 2 tetranucleotide repeats. The average heterozygosity at these markers was 0.73 and ranged from 0.52 to 0.95. Multipoint linkage analysis was used to develop a map of these 38 markers in which the relative placement of each locus is supported by likelihood odds > 1000:1. This PCR-based map was anchored at the centromere by the D1Z5 alpha-satellite polymorphism, and the ends of the map were defined by D1Z2 and D1S68, which are the most distal loci in the CEPH consortium map of chromosome 1. The sex-averaged, male, and female maps extend for 328, 273, and 409 cM, respectively. The average distance between markers on the sex-averaged map is 8 cM, and the largest interval is 32 cM. This map of highly informative PCR-based markers will provide a rapid means of screening human chromosome 1 for the presence of disease genes.

Base Sequence↗

High-resolution linkage map in the vicinity of the host resistance locus Bcg.

The mouse chromosome 1 locus Bcg determines natural resistance/susceptibility of inbred mouse strains to infection with antigenically unrelated intracellular parasites, including several Mycobacterium species, Salmonella typhimurium, and Leishmania donovani. In our effort to clone Bcg, we have constructed a high-resolution genetic linkage map in the vicinity of the gene. We have developed eight new highly polymorphic markers (simple sequence repeats) corresponding to cloned genes (Vil, Inha, Des), microdissected chromosome 1 anonymous probes (lambda Mm1C136, lambda Mm1C163, lambda Mm1C165), or novel DNA markers from the region obtained by chromosome walking (D1Mcg101 and D1Mcg105). We have followed the cosegregation of these markers with respect to Bcg in a novel panel of 1000 (C57L/J x C57BL/6J) x C57BL/6J segregating backcross mice. Additional segregation analyses were carried out in preexisting panels of intra- and interspecific backcross mice and recombinant inbred strains. Three of these markers were found to be very tightly linked to Bcg: lambda Mm1C165 did not show recombination with Bcg in 1424 meioses analyzed, while D1Mcg105 and lambda Mm1C136 were located 0.1 cM proximal and 0.2 cM distal to Bcg, respectively. This analysis enabled us to define further the proximal and distal boundaries of the Bcg interval: the proximal limit was defined by a single crossover occurring between D1Mcg105 and Bcg/lambda Mm1C165/Vil, and the distal limit by 1 cross-over between Bcg/lambda Mm1C165/Vil and lambda Mm1C136 in 1683 and 575 informative meioses, respectively, for a maximal interval of 0.3 cM.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Genetic map of 12 polymorphic loci on rat chromosome 1.

Twelve polymorphic markers identified by restriction fragment length polymorphism (RFLP) analysis or simple sequence repeat (SSR) polymorphism analysis were assigned to rat chromosome 1 by linkage analysis of F2 intercross progeny of F344/N and LEW/N inbred rat strains. One linkage group, covering 46.3 cM, consisted of eight markers including five genes, TNT (fast skeletal troponin T), IGF2 (insulin-like growth factor 2), MYL2 (MLC2 gene for muscle myosin light chain 2), ALDOA (aldolase A), and HBB (hemoglobin beta-chain); one anonymous locus, D1N64; one marker related to the carboxypeptidase B gene, CARB07-related sequence; and one marker related to the parathyroid hormone gene, PTH-related sequence. A second linkage group, covering 45.0 cM, consisted of three markers including two anonymous loci, 2B1 and D1N40, and one gene, TCP1 (T-complex 1). INS1 (insulin 1), which has been previously assigned to rat chromosome 1, was not linked to these markers. The SSR markers were highly polymorphic in 13 inbred rat strains (SHR/N, WKY/N, MNR/N, MR/N, LOU/MN, BN/SsN, BUF/N, WBB1/N, WBB2/N, ACl/N, LER/N, F344/N, and LEW/N). These markers, located on chromosome 1, will be useful in genetic studies in rats.

Alleles↗

High-resolution comparative mapping of mouse chromosome 17.

We have constructed a high-resolution genetic linkage map spanning the proximal 32 cM of mouse chromosome 17 including the t complex. Simple sequence repeats at D17Tu1 and D17Mit6 were employed to identify 121 recombinants among 374 offspring of a (C57BL/6 x CAST/Ei) x C57BL/6 backcross. In contrast to previously reported interspecific Mus domesticus x Mus spretus backcrosses, we did not observe inversion polymorphisms with our cross. This and the relatively high frequency of DNA polymorphisms between C57BL/6 and CAST/Ei allowed us to put 32 RFLV markers and 32 PCR markers on a single map. We present the localization of four new DNA markers and determined map positions for 10 other loci, which previously had been assigned to intervals of the t complex only through the study of partial t haplotype chromosomes.

Animals↗

Linkage map of nine loci defined by polymorphic DNA markers assigned to rat chromosome 13.

A genetic map of nine loci defined by polymorphic DNA markers was created using a single cross of F344/N and LEW/N rats. The markers contained polymorphic simple sequence repeats identified in five genes, renin (Ren), cardiac troponin T (Tnnt3), synaptotagmin (Syt2), Na+,K(+)-ATPase catalytic subunit (Atp1a2), and the Asp-, Gly-, Glu-, and Leu-tRNA gene cluster (Trnegl), as well as four anonymous DNA segments. Analysis of the segregation of the alleles of these markers in F2 intercross progeny of F344/N and LEW/N rats indicated the following locus order and distances between pairs of loci: D13N1-5 cM-Ren-1 cM-Tntt3-0 cM-Syt2-12 cM-D13N2-25 cM-Atp1a2-0 cM-Trnegl-7 cM-D13N3-4 cM-D13N4. Three of the loci, Ren, Trnegl, and Atp1a2, have previously been assigned to rat chromosome 13. Except for Ren, none of the loci have previously been mapped by linkage analysis. The markers for these loci were characterized in a total of 13 inbred rat strains (F344/N, LEW/N, LOU/MN, WBB1/N, WBB2/N, MR/N, MNR/N, ACI/N, SHR/N, WKY/N, BN/SsN, BUF/N, and LER/N) and were found to be highly polymorphic, with two to eight alleles detected for each marker. These markers expand the genetic map of the rat and should be valuable tools for future genetic studies. An examination of human and mouse comparative map information for all loci assigned to rat chromosome 13 shows significant synteny conservation with the q arm of human chromosome 1 and the distal portion of mouse chromosome 1.

Animals↗

Linkage mapping of 40 randomly isolated liver cDNA clones in the mouse.

We report the chromosomal mapping of 43 loci for 40 randomly isolated mouse liver cDNA clones by linkage analysis in an interspecific backcross of ((C57BL/6J x Mus spretus) x C57BL/6J). The clones were sequenced from both sides and a subset was examined for expression in various mouse tissues. Fifteen of the 40 mapped cDNA clones are either identical or strongly related to known sequences in GenBank, while 25 represent new genes. Additional loci mapped in this cross include 53 simple sequence repeat polymorphisms and 40 restriction fragment length variants from previously characterized cDNA markers. Nine homologous human genes were identified for 7 mouse liver cDNA clones. One clone that maps to mouse chromosome 3 (D3Ucla1) identified a novel homologous segment (synteny) on human chromosome 18q23 (D18S372E). These studies provide linkage mapping and initial characterization of random cDNA clones that may provide a resource for the positional candidate cloning of disease genes.

Animals↗

Large linkage analysis in 100 families with autosomal recessive spinal muscular atrophy (SMA) and 11 CEPH families using 15 polymorphic loci in the region 5q11.2-q13.3.

The autosomal recessive proximal spinal muscular atrophy (SMA) gene was mapped to the region 5q11.2-q13.3 in 1990. Here, we present a large genetic linkage study of 100 SMA families and 11 CEPH families using 14 polymorphic simple sequence repeats (SSRs) and one RFLP in the region 5q11.2-q13.3. The genetic interval between the closest SMA flanking loci D5S435 and D5S557 comprises 1 cM at zmax = 27.94. Two recombinants were identified between the SMA gene and the closest telomeric marker D5S557 (theta = 0.02 at zmax = 8.63). The first places the SMA gene centromeric to this marker; the second suggests a double recombinant at D5S557, which is very unlikely. More likely explanations are discussed in the paper. No recombinant was found between D5S435 and the SMA gene (theta = 0.00 at zmax = 25.36). We localized a recently described polymorphic marker, D5S351 (Hudson et al., 1992), close to the SMA (theta = 0.00 at zmax = 19.01) and the 3'MAP1B gene (theta = 0.01 at zmax = 38.76). Due to its high PIC value of 0.70, it represents a very useful marker for prenatal diagnosis. In addition, we developed a new reverse primer for the nearest centromeric locus D5S435 (Soares et al., 1993), a useful marker for prenatal diagnosis, which has been very difficult to amplify in the past. Three of the markers presented here are newly developed polymorphic SSRs (one tetranucleotide repeat, D5S507/W15CATT, and two dinucleotide repeats, D5S544/C88.2GT and D5S682/C88.3GT). These markers are too far from the SMA gene to be relevant for cloning; nevertheless, as part of the human genome project, they are contributing to the fine genetic mapping of the region 5q11.2-q13.3. The most likely order of the loci based on two-point and multipoint linkage analyses as well as on specific recombination events and physical mapping studies is D5S76-D5S507- D5S6-D5S125-D5S680-D5S435-SMA-D5S557- D5S351-5'MAP1B-3'MAP1B-JK53CA1/2-(D5S127- D5S39)-(D5S544-D5S682). In general, the genetic distances obtained from the SMA and CEPH families are comparable.

Base Sequence↗

Gene order is conserved within the human chromosome 21 linkage group on mouse chromosome 10.

One hundred progeny from each of two intersubspecific mouse backcrosses were used to construct a comparative genetic map of a region of mouse chromosome 10 (MMU10) that is homologous to the distal tip of the long arm of human chromosome 21 (HSA21). The analysis included five genes and three simple sequence repeat markers, two of which flanked the HSA21-homologous cluster on either side. Analysis of 200 backcross progeny detected at least one crossover between each pair of adjacent genes and demonstrated that the proximal to distal orientation of the cluster was reversed between human and mouse. The order was determined to be Fyn-1-D10Mit20-S100b-Col6a1-Itgb2-Pfkl+ ++/D10Mit7-D10Mit11. Comparative mapping supports the order of corresponding markers on HSA21 determined using pulsed-field gel electrophoresis and radiation hybrid line data. However, sequence tagged site content mapping of human yeast artificial chromosomes (YACs) yielded conflicting data on the relative positions of human COL6A1 and S100B on HSA21. This discrepancy was resolved here by demonstrating that several key YACs used in the human contig analysis were mistyped for S100B. The murine map reported here provides a scaffold for construction of physical maps and yeast artificial chromosome contigs that will be useful in the development of mouse models for the study of Down syndrome.

Animals↗

Deletion map of the coloboma (Cm) locus on mouse chromosome 2.

The extent of the semidominant coloboma (Cm) mutation on mouse Chromosome 2 was determined by deletion mapping using interspecific hybrid mice. The Cm deletion mutation results in ophthalmic dysmorphology and behavioral deficits, including profound hyperactivity, and has been shown to encompass the gene Snap. In addition to Snap, the gene encoding phospholipase C beta-1 (Plcb-1), which maps 0.60 +/- 0.60 cM proximal to Snap, and simple sequence repeat (SSR) loci D2Mit19, D2Mit46, D2Mit28, and D2Mit136 were shown to be deleted at the Cm locus. In contrast, analysis of other closely linked SSRs and genes either proximal (Bmp-2a) or distal (Nec-1) to Snap, as well as a complementation test with the closely linked mutation lethal milk (lm), indicates that these gene sequences are unaffected by the Cm mutation. These data demonstrate that the Cm deletion represents a contiguous gene defect encompassing 1.1 to 2.2 cM that may be probed for genes, both in the mouse and in the syntenic region of human Chr 20, that independently affect elements of neurological behavior and eye development.

Animals↗

The mouse neurofibromatosis type 2 gene maps to chromosome 11.

Neurofibromatosis type 2 (NF2) is a dominantly inherited disease characterized by the development of bilateral vestibular schwannomas and meningiomas, which together represent 30% of primary brain tumors. The NF2 gene, which has recently been isolated, maps to the long arm of human chromosome 22. Using recombinant inbred mice, we have determined the chromosomal position of the mouse homologue of the NF2 gene. Analysis of the allele distribution in AKXD recombinant inbred strains using a simple sequence repeat polymorphism (D11Mcg1) in the 3' untranslated region of the mouse cDNA maps the mouse NF2 gene to the proximal region of chromosome 11, closely linked to Pmv-2. This region also contains the genes for leukemia inhibitory factor and neurofilament heavy-chain polypeptide and thus represents a region of conserved synteny between human chromosome 22 and mouse chromosome 11. Using additional polymorphic markers, we established the following locus order from the centromere: D11Mit1/D11Mit72/D11Mcg1-D11Mit74-Pmv-2-D11Mi t2-D11Mit77/D11Mit78/D11Mit63.

Alleles↗

Similar origins of two mouse minisatellites within transposon-like LTRs.

Tandem arrays of simple sequence repeat units are among the most unstable regions of mammalian genomes. Mutational instability at such loci depends on both repeat unit sequence and DNA sequences external to the tandem array, which have been recently implicated in polarized variability at human minisatellites. The characteristics of DNA sequences flanking the mouse minisatellite Ms6-hm have been investigated. This locus has a high mutation rate both in the germline and during early somatic development and is composed of a hypervariable tandem array of 500-2000 pentanucleotide repeat units flanked by a transposon-like long terminal repeat sequence of the mouse transcript (MT) family. A subpopulation of MT elements in the mouse genome are shown to flank a 1.1-kb internal sequence, consistent with their classification within a newly defined mammalian retrotransposon-like superfamily (MaLR). A second mouse minisatellite, Hm-2, also originates from within a MaLR LTR. Hm-2 is related to Ms6-hm in repeat unit sequence and profiles of germline and somatic instability; at both loci the tandem array has amplified from precisely the same point within the LTR. The similar origins of Ms6-hm and Hm-2 suggest that flanking MaLR sequences may be involved in mutational processes at these loci.

Animals↗

A PCR-based genetic map for human chromosome 3.

Oligonucleotide primers for 125 simple sequence repeat microsatellite-based genetic markers have been assayed by polymerase chain reaction (PCR) in the CEPH reference family panel. These microsatellites include 101 dinucleotide repeats as well as 24 new tetranucleotide repeats. The average heterozygosity of this marker set was 72.4%. Genetic data were analyzed with the genetic mapping package LINKAGE. A subset of these microsatellite markers define a set of 56 uniquely ordered loci (> 1000:1 against local inversion) that span 271 cM. Sixty-seven additional loci were tightly linked to markers on the uniquely ordered map, but could not be ordered with such high precision. These markers were positioned by CMAP into confidence intervals. One hundred thirteen of the microsatellite markers were also tested on a chromosome 3 framework somatic cell hybrid panel that divides this chromosome into 23 cytogenetically defined regions, integrating the genetic and physical maps of this chromosome. The high density, high heterozygosity, and PCR format of this genetically and physically mapped set of markers will accelerate the mapping and positional cloning of new chromosome 3 genes.

Animals↗

Molecular mapping of SSRs for Pgm1 and C8b in the vicinity of the rat fatty locus.

Recessive mutations at the rat fatty locus (fa, facp), which produce obesity, insulin resistance, and diabetes, provide useful experimental models for similar phenotypes in humans. The molecular pathogenesis of the metabolic phenotype in animals segregating for fa is unknown and difficult to study once the confounding metabolic effects of obesity are present. Although various experimental methods distinguish preobese from lean rats (phenotypic markers and molecular markers genetically linked to fatty), technical difficulties limit their utility. We report the identification of two (GT)n simple sequence repeats (SSRs) near the rat phosphoglucomutase gene (Pgm1) gene and two SSRs, (GA)n and (GT)n, near the rat complement component 8 beta gene (C8b). These SSRs map to an approximately 4-cM interval flanking the fatty locus on rat chromosome 5. Use of these molecular markers in combination offers an improved method for early assessment of gene dosage for fa and hence for studying the fundamental molecular physiology underlying the derangements of metabolism and behavior resulting from mutations in this gene.

Alleles↗

Microsatellite-centromere mapping in the zebrafish (Danio rerio).

Ten (CA)n microsatellite simple sequence repeat (SSR) markers, 1, 2, 12, 14, 16, 18, 20, 22, 26, and 29, were used to show high chiasma interference and to determine centromere-marker map distances in the zebrafish (Danio rerio). Of these, SSR 12 exhibited no recombinant tetratypes among 175 half-tetrad embryos, placing this marker within 1 cM of the centromere of Linkage Group XVII. Fractions of heterozygous half-tetrads for the remaining nine markers ranged from 0.64 to 0.89. Of these, six recombinant fractions were more than 0.67 (P < 0.05), indicating strong chiasma interference during female meiosis in the zebrafish. Consistent with previous mapping data, SSRs 2 and 20 of Linkage Group VI were tightly linked. Half-tetrad analysis will allow the mapping of the remaining centromeres and may be useful in the mapping of new genes and mutations in the zebrafish.

Animals↗