Diagnostic applications of repetitive DNA sequences

Human tumor necrosis factor receptor p75/80 (CD120b) gene structure and promoter characterization

Tumor necrosis factor receptor p75 (TNF-R p75) is a 75-kDa type I transmembrane protein expressed predominantly on cells of hematopoietic lineage. TNF-R p75 belongs to the TNF receptor superfamily characterized by cysteine-rich extracellular regions composed of three to six disulfide-linked domains. In the present report we have characterized, for the first time, the complete gene structure for human TNF-R p75, which spans approximately 43 kbp. The gene consists of 10 exons (ranging from 34 base pairs to 2.5 kilobase pairs) and nine introns (343 base pairs to 19 kilobase pairs). Consensus elements for transcription factors involved in T cell development and activation were noted in the 5'-flanking region including T cell factor-1, Ikaros, AP-1, CK-2, interleukin-6 receptor E (IL-6RE), ISRE, GAS, NF-kappaB, and Sp1. The unusual (GATA)n and (GAA)(GGA) repeats found within intron 1 may prove useful for further genome analysis within the 1p36 chromosomal locus. Characterization of the human TNF-R p75 gene structure will permit further assessment of its involvement in normal hematopoietic cell development and function, autoimmune disease, and nonrandom translocations in hematopoietic malignancies.

Selected di- and tetranucleotide microsatellites from chromosomes 7, 12, 14, and Y in various Eurasian populations

Microsatellite polymorphisms of nine Eurasian populations (> 1200 chromosomes) were analyzed for the following loci: i) intronic (gt)n stretches of three T cell receptor (TCR) B loci on chromosome 7 (TCRBV6S1, TCRBV6S3, TCRBV6S7); ii) an intergenic (gt)n repeat in the region between the TCRDV3 and TCRAJ61 elements on chromosome 14; iii) two tetranucleotide simple repeats (D12S66, D12S67), not linked to known genes on chromosome 12; iv) a Y-chromosomal (gata)n polymorphism (DYS19). In general, allele frequencies and heterozygosity rates were similar, but specific alleles were missing in one or more populations. Distinct DYS19 alleles predominated in particular cohorts. Different allele frequencies were observed for the TCR loci in European and Asian populations. Tetranucleotide polymorphisms were distributed normally, whereas TCR alleles displayed bimodal frequency profiles. For TCRBV6S1 and TCRBV6S7, this profile reflects a diallelic protein polymorphism that correlates exactly with the length of the intronic repeats.

Towards covering immunological genes with highly informative markers: a trans-species approach

To establish a highly informative screening system for immunologically relevant genes ("immunoprinting") we co-amplified via polymerase chain reaction (PCR) polymorphic exons plus adjacent intronic simple repetitive dinucleotide stretches in the T-cell receptor (Tcr) Vb6 and Major Histocompatibility Complex (MHC)-DRB loci in man and several ungulate species. In both gene families the basic structure of the simple repeat was found to be preserved for more than 70 x 10(6) years in all investigated species. The simple repeats exhibit extensive length variability. Distinct exon sequences are correlated with a defined repeat length and substructure. In addition, PCR and the oligonucleotides for typing were applicable to a broad range of species from different mammalian orders. Multiplex PCR of different members of the Tcr Vb6 family and MHC-DRB resulted in a complex pattern similar to an oligolocus fingerprint. Hence immunoprinting can be employed for searching for associations of immunologically relevant genes with diseases even across species barriers.

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.