Repeat Length Variation Research Articles

Repeat length variation in the dopamine D4 receptor gene shows no evidence of association with schizophrenia.

The D4 receptor has been shown to exist in several allelic forms (Van Tol et al., Nature 358:149-152, 1992) reflecting variation in the number of 48 base-pair sequence repeats in the putative cytoplasmic loop. We report a comparison of repeat length variation between schizophrenic patients and controls. Our sample of 106 unrelated schizophrenic cases and 119 controls showed no significant differences in allele or genotype distribution between patients and controls. In particular, we were unable to support the previous observation of an excess of 4-repeat homozygotes in patients.

Characterization of nuclear ribosomal DNA (rDNA) in Gaeumannomyces graminis and correlation of rDNA variation with G. graminis varieties

Analysis of nuclear ribosomal(r) RNA genes in Gaeumannomyces graminis has revealed two levels of variation: one allowed identification of G. gramminis varieties and the other enabled discrimination between isolates within varieties. The three varieties, G. graminis var. graminis (Ggg), var. avenae (Gga) and var. tritici (Ggt) could be differentiated based on the size of an EcoR I fragment, a Hind III-EcoR I fragment and a Hind III-Pst I fragment from the 26S rRNA coding region. Within the collection of isolates identified as Ggt on morphological criteria, three subgroups (T1, T2 and T3) could be distinguished based on the size of the three fragment types from the 26S rRNA coding region. The sizes of the three fragment types also distinguish Ggg, Gga and Ggt (subgroup T1). Ggt (subgroup T2) possesses large amounts of the Hind III-Pst I fragment that is typical of Gga and trace amount of the Hind III-Pst I fragment characteristic of Ggt (subgroup T1). Ggt (subgroup T3) possesses all the three fragments that marked Gga and none of Ggt (subgroup T1). All isolates in T2 and T3 were pathogenic to wheat, oats and bentgrass. Isolates within each variety could be differentiated by restriction site differences in the intergenic spacer region and by variation in repeat length.

Ribosomal DNA variation and its phylogenetic implication in the genusBrachypodium (Poaceae)

The structure of ribosomal DNA ofBrachypodium and several other grass species was investigated using a heterologous rDNA probe from wheat. Several different rDNA families were present among perennial and annual species within the genus. In contrast to the annual species the perennial species exhibited a very low degree of repeat length variation. An extra Eco RI site and a Hin dIII site were observed in the IGS, which distinguishedBrachypodium from other grass genera. The restriction fragment length polymorphism and length variation of the repeat units have taxonomic value withinBrachypodium and are correlated with the classification ofBrachypodium derived from other data.

Molecular analysis of late onset Huntington's disease.

Late onset Huntington's disease is characterised by onset of symptoms after the age of 50 and is usually associated with a milder course. We have analysed the CAG trinucleotide repeat within the HD gene in 133 late onset patients from 107 extended families. The median upper allele size for the CAG repeat was 42 with a range of 38 to 48 repeats. A significant negative correlation (r = -0.29, p = 0.001) was found between the length of repeat and age of onset for the total cohort. However, for persons with age of onset greater than 60, no significant correlation was found. In addition, no significant correlation was found between age of onset and size of the lower allele and the sex of the affected parent or grandparent. There was no preponderance of maternal descent for late onset cases in this series. This study shows that variation in repeat length only accounts for approximately 7% of the variation in age of onset for persons beyond the age of 50 and clearly shows how with increasing onset age the effect of the repeat length on this onset age seems to diminish.

Targeting of the creatine kinase M gene in embryonic stem cells using isogenic and nonisogenic vectors.

Replacement vectors with genomic DNA originating from different mouse strains were used to introduce site-specific mutations into the creatine kinase M (CKM) gene of mouse embryonic stem (ES) cells. Here we demonstrate that in mouse strain 129-derived ES cells, the gene is at least 25-fold more efficiently targeted with an isogenic, 129-derived vector (129-pRV8.3) than with a nonisogenic, BALB/c-specific vector (BALB/c-pRV8.3). The two targeting constructs were identical except for allelic differences which were typed by partial sequencing. These included base pair mismatches (2%) and a polymorphic [GTC]-repeat length variation. Both in separate transfections as well as in cotransfections with mixed vectors, homologous disruption of the CKM gene resulted uniquely from the 129-isogenic DNA. Our data confirm earlier observations on requirements for homologous recombination in pro- and eukaryotic systems and indicate that targeting of the CKM locus is highly sensitive to small sequence differences between cognate segments in the endogenous and incoming DNA.

5S ribosomal gene variation in the soybean and its progenitor

The soybean, Glycine max and its wild progenitor, Glycine soja, have been surveyed for repeat length variation for the nuclearly encoded 5S ribosomal RNA genes. There is little variation among the 33 accessions assayed, with a common repeat length of 345 bases being typical of both taxa. A 334 base size variant was encountered in individuals from two populations of G. soja from China. The low level of variability is in marked contrast to the variation observed within and between the species of the perennial subgenus Glycine.

Ribosomal gene variation in soybean (Glycine) and its relatives

The genes encoding the 18S∶25S ribosomal RNA gene repeat in soybean (Glycine max) and its relatives in the genus Glycine are surveyed for variation in repeat length and restriction enzyme site locations. Within the wild species of subgenus Glycine, considerable differences in repeat size occur, with a maximum observed in G. falcata. Repeat length and site polymorphisms occur in several species, but within individual plants only single repeat types are observed. The rDNA of the cultivated soybean and its wild progenitor, G. soja are identical at the level of this study, and no variation is found in over 40 accessions of the two species. Data from rDNA mapping studies are congruent with those of previous biosystematic studies, and in some instances give evidence of divergences not seen with other approaches.

The organization and genetics of rDNA length variants in peas

There is extensive repeat length variation in pea rDNA. Many lines of pea have more than one repeat length class, and those with two rDNA repeat length classes are the most common. No interspersion of rDNA repeat length classes has been found. The rDNA length classes show simple Mendelian inheritance. Length variation of pea rDNA is organized between long tandem arrays of rDNA repeat. Studies of trisomies have shown that rDNA length class dosage correlates with chromosome dosage.

Analysis of recombinant DNA clones of the endogenous BALB/c murine leukemia virus WN1802N: variation in long terminal repeat length.

We analyzed 15 recombinant DNA clones of the unintegrated closed circular DNA intermediate of the BALB/c endogenous ecotropic murine leukemia virus WN1802N. Thirteen of these clones had an insert which corresponded to the complete murine leukemia virus genome. Of these, six contained a single long terminal repeat (LTR) and seven contained two LTRs. The viral genomes in nine clones had an LTR of 520 base pairs (bp), one had an LTR of 570 bp, three had an LTR of 600 bp, and one had an LTR of 670 bp. Restriction endonuclease analysis demonstrated that the size variability resides in the U3 region. Seven of eight clones which yielded infectious virus by DNA transfection had the 520-bp LTR, and the other had a 600-bp LTR. More detailed examination of plasmid subclones of three isolates with different-sized LTRs revealed that the approximate position which varies in the U3 region corresponds to the 72-bp repeat region of Moloney sarcoma virus. Possible consequences of these variations are discussed.

Length and sequence heterogeneity of the histone gene repeat unit of the sea urchin, S. purpuratus

Histone gene repeats in S. purpuratus are shown to be of variable length and sequence. Two recombinant plasmids containing the full-length 6.3 kb histone repeat unit are found to differ in length at two sites in the repeating structure and in the occurrence of two restriction enzyme recognition sites. Variation in repeat length is also demonstrated in the unfractionated DNA of five sea urchins and in a sample of DNA enriched for histone gene sequences by density gradient methods. The repeats in each individual are of a very limited number of major classes, which may differ from one another in overall length or in distribution and presence of particular restriction enzyme sites. Variations are found to occur at many regions of the repeat; some have been mapped specifically to spacer regions. Repeats may differ dramatically from individual to individual since there is no one type of repeat class common to all, although the absolute length differences of the repeats that are found are small.

The length of nucleosome-associated DNA is the same in both transcribed and nontranscribed regions of chromatin.

THE fundamental structural unit of chromatin is a nucleoprotein complex containing two molecules each of the histones H2A, H2B, H3 and H4 in association with approximately 200 base pairs of DNA (for review see ref. 1). At least 85% of nuclear DNA is organised in these chromatin subunits or nucleosomes2, and it has been shown that both transcribed3–8 and nontranscribed9–12 DNA sequences are arranged in nucleosomes. The length of DNA in the nucleosome repeat unit varies between organisms and even between cell types in the same organism1. The origin of this variation in repeat length, ranging from 160 to 240 base pairs per nucleosome, is unknown. However, there is a general correlation between repeat lengths and transcriptional activity : transcriptionally active cells have shorter nucleosome repeat lengths than less active cells13. Thus, it has been suggested that the nucleosome repeat length of transcribed DNA may be different from that of nontranscribed sequences, thereby implicating nucleosome oranisation in gene regulation14. We report here that both transcribed and nontranscribed DNA sequences are organised in nucleosomes with the same repeat lengths.

The nucleotide sequence of oocyte 5S DNA in xenopus laevis. I. The AT-rich spacer

The primary sequence of the principal spacer region in X. laevis oocyte 5S DNA has been determined. The spacer is AT-rich and comprises half or more of each repeating unit. The sequence is internally repetitious; most of it can be represented by the following set of oligonucleotides: CAA C AGTTTTCAA AA GGTTTG C AA G TTTTT(T) The spacer, which varies in length from about 360 to 570 or more nucleotides, can be subdivided into a region (A 2) which is variable in length in different repeating units, flanked by regions (A 1, A 3, B 1) which are relatively constant in length. The A 2 region consists, on the average, of 5–6 tandem copies of the oligonucleotide CAAAGTTT-GAGTTTT; variation in the redundancy of this oligonucleotide accounts for much of the repeat length variation in the genomic 5S DNA. Most copies of this oligonucleotide are identical, although several differing by 1 or 2 nucleotides have been detected in plasmid-cloned 5S DNA fragments. Regions A 1 and A 3 comprise a linear array of similar, but not identical, oligonucleotides; most repeating units contain very similar A 1 and A 3 sequences. Region B 1 is a sequence of 49 nucleotides immediately adjacent to the 5′ terminus of the 5S rRNA sequence. It is GC-rich, much less repetitive than the remainder of the spacer and contains several palindromes, but no regions of dyad symmetry. This sequence is identical in all six of the single cloned repeating units of 5S DNA analyzed.