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E Zietkiewicz

Publications and source records attributed to E Zietkiewicz.

35 records · Page 2Linked to original sources
PubMed1994

Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification.

Simple sequence repeats (SSR), or microsatellites, are ubiquitous in eukaryotic genomes. Here we demonstrate the utility of microsatellite-directed DNA fingerprinting by polymerase chain reaction (PCR) amplification of the interrepeat region. No sequencing is required to design the oligonucleotide primers. We tested primers anchored at 3' or 5' termini of the (CA)n repeats, extended into the flanking sequence by 2 to 4 nucleotide residues [3'-anchored primers: (CA)8RG, (CA)8RY, and (CA)7RTCY; and 5'-anchored primers: BDB(CA)7C, DBDA(CA)7, VHVG(TG)7 and HVH(TG)7T]. Radioactively labeled amplification products were analyzed by electrophoresis, revealing information on multiple genomic loci in a single gel lane. Complex, species-specific patterns were obtained from a variety of eukaryotic taxa. Intraspecies polymorphisms were also observed and shown to segregate as Mendelian markers. Inter-SSR PCR provides a novel fingerprinting approach applicable for taxonomic and phylogenetic comparisons and as a mapping tool in a wide range of organisms. This application of (CA)n repeats may be extended to different microsatellites and other common dispersed elements.

Animals↗
PubMed1994

Evolution of secondary structure in the family of 7SL-like RNAs.

Primate and rodent genomes are populated with hundreds of thousands copies of Alu and B1 elements dispersed by retroposition, i.e., by genomic reintegration of their reverse transcribed RNAs. These, as well as primate BC200 and rodent 4.5S RNAs, are ancestrally related to the terminal portions of 7SL RNA sequence. The secondary structure of 7SL RNA (an integral component of the signal recognition particle) is conserved from prokaryotes to distant eukaryotic species. Yet only in primates and rodents did this molecule give rise to retroposing Alu and B1 RNAs and to apparently functional BC200 and 4.5S RNAs. To understand this transition and the underlying molecular events, we examined, by comparative analysis, the evolution of RNA structure in this family of molecules derived from 7SL RNA. RNA sequences of different simian (mostly human) and prosimian Alu subfamilies as well as rodent B1 repeats were derived from their genomic consensus sequences taken from the literature and our unpublished results (prosimian and New World Monkey). RNA secondary structures were determined by enzymatic studies (new data on 4.5S RNA are presented) and/or energy minimization analyses followed by phylogenetic comparison. Although, with the exception of 4.5S RNA, all 7SL-derived RNA species maintain the cruciform structure of their progenitor, the details of 7SL RNA folding domains are modified to a different extent in various RNA groups. Novel motifs found in retropositionally active RNAs are conserved among Alu and B1 subfamilies in different genomes. In RNAs that do not proliferate by retroposition these motifs are modified further. This indicates structural adaptation of 7SL-like RNA molecules to novel functions, presumably mediated by specific interactions with proteins; these functions were either useful for the host or served the selfish propagation of RNA templates within the host genome.

Animals↗
PubMed1993

3-Hydroxy-3-methylglutaryl coenzyme A lyase (HL): cloning and characterization of a mouse liver HL cDNA and subchromosomal mapping of the human and mouse HL genes.

3-Hydroxy-3-methylglutaryl coenzyme A lyase (HL) is a homodimeric mitochondrial matrix enzyme that catalyzes the last step of ketogenesis. Using a human HL cDNA as a probe, we isolated a 1.4-kb mouse HL cDNA (HLM) from a mouse liver library and extended the sequence in the 5' direction, using RACE PCR to include the complete coding sequence. The nucleotide sequence of the mouse HL coding region is 85.7% identical to human HL, and 52.6% to Ps. mevalonii HL. Peptide identities of 87.4% and 54.3% respectively were observed. Southern analysis of 29 strains of laboratory mice and of Mus spretus revealed a total of about 25 kb of hybridizing fragments and three polymorphic fragments in both EcoRI and Hin-dIII digestions. The mouse HL locus (Hmgcl) was localized on Chromosome (Chr) 4: Pmv-19-12.6 +/- 3.6 cM-Hmgcl-7.3 +/- 2.3 cM-Xmv-8-1.5 +/- 1.0 cM-Gpd-1. The human HL locus (HMGCL) was mapped to distal Chr 1p by analysis of a human-hamster hybrid cell panel and by in situ hybridization.

Amino Acid Sequence↗
PubMed1992

Linkage mapping by simultaneous screening of multiple polymorphic loci using Alu oligonucleotide-directed PCR.

We present the use of our recently described multiple-loci polymorphic DNA markers ("alumorphs") for linkage mapping of the human genome. By using the polymerase chain reaction (PCR) with an Alu-specific primer we could reveal, in a single experiment, up to 20 genomic polymorphisms seen as the presence or absence of amplified DNA fragments originating from genomic segments flanked by Alu repeats. Using this approach we examined genomic DNA samples from two families with a history of pseudovitamin D-deficiency rickets (PDDR), an autosomal recessive disorder. An indication of linkage with the PDDR phenotype was found for one of the polymorphic bands, denoted 30A. A significant linkage [logarithm-of-odds (lod) score greater than 3.0] was obtained between this polymorphism and a number of chromosome 12q markers tightly linked to PDDR. The 30A band specifically hybridized to DNA digests from hybrid cell lines carrying a human chromosome 12, thus independently assigning the 30A marker to this chromosome. Since Alu elements are ubiquitous in human DNA, the use of alternative Alu-specific primers, which reveal different sets of Alu-flanked loci, should provide an efficient and rapid approach to human genetic mapping.

Base Sequence↗
PubMed1992

Single-strand conformational polymorphisms (SSCP): detection of useful polymorphisms at the dystrophin locus.

We searched for DNA polymorphisms in seven amplified fragments of the dystrophin gene. Three fragments exhibited variable mobilities during nondenaturing strand-separating gel electrophoresis (SSGE). These variants were due to single base changes (three transversions and one transition). Three were intronic (upstream from exons 17, 15, and 48) and one was in exon 48. The frequencies of these sequence variants were determined in a sample of 54 normal X chromosomes of Caucasian origin. One of these DNA polymorphisms was observed in every 650 bp tested and the average heterozygosity was 0.05% per base pair (0.08% if exons were excluded). Such a detection density and the fact that single-strand conformational polymorphisms do not depend on the presence of any specific sequence makes them especially valuable as genetic markers. In the dystrophin locus this approach could allow simultaneous detection of frequent deletions.

DNA, Single-Stranded↗
PubMedDate not supplied

Neutral polymorphisms in the deletion-prone regions of the dystrophin gene.

The single-strand conformational polymorphism technique was used to search for neutral polymorphisms in 18 PCR-amplified dystrophin gene fragments. Out of the seven polymorphisms (six intronic and one exonic) detected in Caucasians, one was absent from the Oriental population. Significant differences in allele frequencies between the two populations were observed for three of the intronic polymorphisms. In Caucasians, one variant position occurred per 728 bp of the total DNA or one per 483 bp of the intronic sequence; the corresponding average heterozygosities were 0.04 and 0.06%, respectively.

Alleles↗