Isolation of clones on chromosome 7 that contain recognition sites for rare-cutting enzymes by oligonucleotide hybridization

Application of Alu-splice PCR on chromosome 21: DSCR1 and Intersectin

Down syndrome (DS) is a major cause of mental retardation and congenital heart defects, with an overall incidence of one in 700 live births. DS is caused by increases in the amounts of a number of normal gene products, the exact number and identity of which are presently unknown. Elucidating the molecular basis of DS relies on the identification of the gene products whose augmentation by 50% or more causes symptoms of the disease. With the aim of contributing to the transcriptional map of human chromosome 21 and to identify new genes with potential involvement in DS, we developed a technique to isolate expressed sequences called Alu-splice PCR, which is very simple to perform and is independent of gene expression patterns. Putative exons are PCR amplified in genomic DNA by virtue of their proximity to Alu repeats using primers designed from splice-site consensus sequences in combination with specific Alu repeat primers. The Alu repeats, which are repetitive DNA elements found exclusively and at high frequency in the genomes of primates, impart the human specificity to the method. The splice-site consensus sequences were used to direct primers to exon boundaries. Using the Alu-splice technique, we have identified at least three new genes. We trapped an exon of DSCR1 (Down Syndrome Candidate Region 1) and two different exons of a gene called human Intersectin (ITSN). Presently, we are working with another novel trapped exon to identify the corresponding gene. The major advantage of Alu-splice PCR is that the technique can be readily established in any laboratory which has the basic facilities for molecular biology because no specialised materials or expertise is required.

Hybridization of the variable number of tandem repeat core oligonucleotide GNNGTGGG to 350 cosmids from chromosome 7

An efficient method using short oligonucleotides is described for the isolation of minisatellite markers of the type variable number of tandem repeats (VNTR). It is used to screen 350 cosmids from chromosome 7 for the presence of such potentially polymorphic DNA segments. From the number of hybridization signals to chromosome 7 cosmids, I estimate the human genome to have at least about 15000 VNTR loci containing minisatellite core sequences, which is well above previous estimates.

Screening cosmid libraries with oligonucleotides corresponding to splice-site consensus sequences

To facilitate the identification of genes within genomic DNA, we have developed a method based on the use of short oligonucleotides designed from the consensus sequences of splice sites. We describe here the hybridization and washing conditions under which such oligonucleotides can be used to screen cosmid libraries. We confirm the presence of genes within cosmids identified by screening with one oligonucleotide by showing that DNA isolated from such cosmids will hybridize to another splice-site oligonucleotide.

Oligonucleotides as short as 7-mers can be used for PCR amplification

Amplification of DNA sequences using the polymerase chain reaction (PCR) requires as primers two oligonucleotides, which are carefully designed for length and G/C content. Such primers are generally between 18 and 30 bases long so that the primer sequences can amplify a unique sequence in the target genome; they should possess a minimal degree of secondary structure. We have tested the minimum length of G/C-rich and palindromic oligonucleotides to be used as primers in PCR. Oligonucleotides with sequences corresponding to the recognition sites of rare restriction enzymes were used on the DNA of vector constructs as model template DNA. Surprisingly, we found specific amplification with a low background over a wide range of temperatures for oligonucleotides as short as 7 nucleotides. This findings contradicts the previously reported empirical relationship between oligonucleotide length and ability to trigger amplification and points to the complex relationship between thermodynamic and kinetic criteria in relation to PCR. This technique should lead to new application in the cloning and screening of complex genomes.

Leukaemic T cells from patients with chronic lymphocytic leukaemia of T-cell origin respond to Staphylococcus aureus enterotoxin superantigens

We investigated the in vitro responsiveness of peripheral blood lymphocytes from two patients with T-cell chronic lymphocytic leukaemia (T-CLL) to Staphylococcus aureus enterotoxin (SE) superantigens. T-cell receptor (TcR) alpha beta (V beta 7.1)-expressing CD4+ leukaemic T cells from patient HE (white blood cell count 480,000/microliters) proliferated in response to SEA and, only at 1000-fold higher concentrations, to SEB, SED, and SEE. CD4+CD8+ TcR alpha beta (V beta 12.1)-expressing leukaemic T cells from patient KO (white blood cell count 120,000/microliters) were activated by SEB but not by the other tested SEs. In both instances, the activation of leukaemic T cells by SE was dependent on the presence of HLA-DR+ cells. Southern blot analysis of TcR beta gene rearrangement confirmed that the proliferating cells were derived from the leukaemic T-cell clone and not from contaminating normal T cells. These data indicate that leukaemic T cells from patients with T-CLL exert a clonally variable responsiveness to SE superantigens. We conclude that recognition of specific antigen and subsequent signal transduction can be initiated via the TcR of leukaemic T-CLL cells.

On the essence of "meaningless" simple repetitive DNA in eukaryote genomes

Various kinds of simple tandemly repetitive DNA sequences are abundantly interspersed in the genomes of practically all eukaryotic species studied. The comparatively elevated mutation rates of simple repeat blocks result in highly polymorphic and therefore extremely informative investigation systems for studies on forensic, ecological and genetic relationship questions. Recently the techniques for analyzing simple repeats have achieved great effectivity and simplicity. Beyond their utility as tools for differentiation and individualization, certain of these repeated elements harbor quite unexpected qualities which may be discussed in the context of their biological meaning. i) A specific subset of simple (cac)n or (gtg)n repeats is expressed in mature mRNA and total cellular RNA. ii) Despite the apparently high mutation rate certain (gt)n or mixed (gt)n/(ga)m stretches of intronic simple repeats are preserved in immunologically relevant genes for at least 70 x 10(6) years and they bind nuclear protein molecules with high affinities. Consequently in addition to their tool character, the biological aspects of simple repeated DNA should be taken into consideration.

Simple repeats are not found more abundantly at G/C-rich regions

Three hundred and fifty cosmids from chromosome 7, previously analyzed for the presence of rare-cutting restriction enzyme sites, were analyzed for the presence of microsatellite sequences [(CA)n or (CT)n repeats]. Of these, 147 cosmids were found to contain at least one (CA)n repeat unit and 51 cosmids contained at least one (CT)n repeat unit. No evidence was found for the prevalence of microsatellite repeat units in the vicinity of rare-cutter restriction enzyme sites.