Report of a critical recombination further narrowing the TSC1 region.

A large tuberous sclerosis multigenerational family segregating with markers on chromosome 9q from the TSC1 region was studied with a new highly polymorphic marker (designated A6) from the region. A critical affected person showed recombination with the marker, eliminating approximately 100 kilobases from the telomeric end of the critical region, which contains three genes and three to four additional exons for which the associated genes have not been delineated. This information serves to further the search for the TSC1 gene.     

A recombination event in the closely linked plasminogen and apolipoprotein(a) gene loci

Genetic studies as well as in situ hybridisation data have strongly demonstrated that the genes coding for apoprotein(a) and plasminogen are linked and localised to chromosome 6 at band 6q26-27. We describe in this report the presence of a recombination event in a region of approximately 50 kb of DNA separating the two genes. The recombination was found in an Italian family, in which a mutation affecting both plasminogen plasma level and activity of plasminogen activity has been detected. Polymerase chain reaction and sequencing analysis showed the presence of a mutation different from those previouly reported in two Japanese families.     

Identification of a preferred region for recombination and mutation in HIV-1 gag

We designed a cell culture-based system to test the hypothesis that recombination events during HIV-1 replication would be more frequent near the dimerization initiation sequence (DIS). A 459-bp region spanning the DIS through the 5'-end of gag was sequenced and analyzed to determine the frequency and distribution of crossover sites. We found a strong preference for recombination events occurring within a 112-nt-long region encompassing the gag AUG (64% of crossovers occurred in this region, compared to 10-14% in surrounding regions with similar lengths). Surprisingly, the region immediately surrounding the DIS was not a preferred site of recombination. Analysis of recombination events using RNA templates transcribed in vitro revealed a preference for crossover sites at the start of the gag coding region, similar to that observed in cell culture. This recombinogenic region was unusually G-rich and promoted extensive pausing by RT in vitro. Template features that induce RT pausing very likely contribute to the observed template switching events in gag during minus-strand synthesis. The region in gag that was a preferred site for recombination also had an approximately 2-fold higher mutation frequency compared to the rest of the region sequenced, but mutations were no more common in recombinant compared to non-recombinant clones, suggesting that recombination events were not mutagenic.     

Linkage disequilibrium and recombination make a telomeric site for the Huntington''s disease gene unlikely.

In a Scottish family in which Huntington's disease (HD) was segregating, recombination was observed between the D4S115/S111 and D4S43/S95 loci, with the HD gene associated with the more proximal D4S43/S95 locus. Analysis of linkage disequilibrium in Scottish families showed significant non-random association between the HD gene and alleles at the D4S95 and D4S98 loci. This adds to previous evidence that the HD locus is not sited at the telomere of chromosome 4.     

Molecular characterization of a new deletion of the GBA1 gene due to an inter Alu recombination event

Gaucher disease is the most frequent lysosomal storage disorder due to the autosomal recessive deficiency of acid β-glucosidase. More than 300 mutations in the GBA1 gene have been described. However only one large deletion of the GBA1 gene has been reported to date. Here, using a combination of different experimental approaches including PCR, sequencing and Southern blot analysis, we describe the identification and characterization of a new large deletion of the GBA1 gene due to an inter Alu recombination event.     

Mutations in the NHLRC1 gene are the common cause for Lafora disease in the Japanese population

Lafora disease (LD) is a rare autosomal recessive genetic disorder characterized by epilepsy, myoclonus, and progressive neurological deterioration. LD is caused by mutations in the EMP2A gene encoding a protein phosphatase. A second gene for LD, termed NHLRC1 and encoding a putative E3 ubiquitin ligase, was recently identified on chromosome 6p22. The LD is relatively common in southern Europe, the Middle East, and Southeast Asia. A few sporadic cases with typical LD phenotype have been reported from Japan; however, our earlier study failed to find EPM2A mutations in four Japanese families with LD. We recruited four new families from Japan and searched for mutations in EPM2A . All eight families were also screened for NHLRC1 mutations. We found five independent families having novel mutations in NHLRC1. Identified mutations include five missense mutations (p.I153M, p.C160R, p.W219R, p.D245N, and p.R253K) and a deletion mutation (c.897insA; p.S299fs13). We also found a family with a ten base pair deletion (c.822-832del10) in the coding region of EPM2A. In two families, no EPM2A or NHLRC1 mutation was found. Our study, in addition to documenting the genetic and molecular heterogeneity observed for LD, suggests that mutations in the NHLRC1 gene may be a common cause of LD in the Japanese population.     

The Lafora disease gene product laforin interacts with HIRIP5, a phylogenetically conserved protein containing a NifU-like domain

Lafora disease is an autosomal recessive type of progressive myoclonus epilepsy caused by mutations in the EPM2A gene. The EPM2A gene-encoded protein laforin is a dual-specificity phosphatase that associates with polyribosomes. Because the cellular functions of laforin are largely unknown, we used the yeast-two hybrid system to screen for protein(s) that interact with laforin. We found that laforin interacts with a phylogenetically conserved protein HIRIP5 that harbors a NifU-like domain. Both in vitro and in vivo assay have shown that the interaction is specific and that laforin probably uses its N-terminal CBD-4 domain to interact with the C-terminal NifU-like domain of the HIRIP5 protein. HIRIP5 encodes a cytosolic protein and is expressed ubiquitously, perhaps reflecting a house-keeping function. The presence of a NifU-like domain in the HIRIP5 protein raises an interesting possibility that it may be involved in iron homeostasis. Although the significance of the interaction between HIRIP5 and laforin proteins is not yet fully known, because laforin dephosphorylated HIRIP5 in vitro, HIRIP5 promises to be an interesting laforin-binding partner and would contribute to the understanding of the molecular pathology of Lafora disease.     

Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster

The Pc locus of sorghum (Sorghum bicolor) determines dominant sensitivity to a host-selective toxin produced by the fungal pathogen Periconia circinata. The Pc region was cloned by a map-based approach and found to contain three tandemly repeated genes with the structures of nucleotide binding site–leucine-rich repeat (NBS–LRR) disease resistance genes. Thirteen independent Pc-to-pc mutations were analyzed, and each was found to remove all or part of the central gene of the threesome. Hence, this central gene is Pc. Most Pc-to-pc mutations were associated with unequal recombination. Eight recombination events were localized to different sites in a 560-bp region within the ~3.7-kb NBS–LRR genes. Because any unequal recombination located within the flanking NBS–LRR genes would have removed Pc, the clustering of cross-over events within a 560-bp segment indicates that a site-directed recombination process exists that specifically targets unequal events to generate LRR diversity in NBS–LRR loci.     

Lafora disease: a case report, pathologic and genetic study

A 19-year-old male patient presented with progressive myoclonic seizures and speech disorder. The patient had photosensitivity, a few episodes of sudden transient blindness, and infrequent complex visual auras, dysarthria and mild ataxia, frequent myoclonic jerks prominently in the legs and severe dementia. Microscopic examination of the axillary skin biopsy revealed periodic acid-Schiff positive inclusion bodies in abluminal side of the apocrine sweat gland acini. Molecular screening showed a homozygous R241X mutation in EPM2A. Genotyping helps in the correct diagnosis of the Lafora disease (LD), which may be difficult to diagnose based on the available histopathological testing only. Our study is an effort to determine the distribution of mutations in LD patients in our region.     

Bias of the estimated recombination fraction and lod score due to an association between a disease gene a marker gene

An association between a recessive disease gene and a biallelic codominant linked marker is shown to induce some bias in the estimation of the recombination fraction by the lod score method. We demonstrate that ignoring the association may lead to an underestimate of the true recombination fraction and the lod score.     

A clustering of RNA recombination sites adjacent to a hypervariable region of the peplomer gene of murine coronavirus

Coronaviruses undergo RNA recombination at a very high frequency. To understand the mechanism of recombination in murine coronavirus, we have performed RNA sequencing of viral genomic RNA to determine the precise sites of recombination in a series of recombinants which have crossovers within the gene encoding the peplomer protein. We found that all of the recombination sites are clustered within a region of 278 nucleotides in the 5'-half of the gene. This region in which all of the crossovers occurred represents a small fraction of the distance between the two selection markers used for the isolation of these recombinant viruses. This result suggests that this region may be a preferred site for RNA recombination. The crossover sites are located within and immediately adjacent to a hypervariable area of the gene. This area has undergone deletions of varying sizes in several virus strains which have been passaged either in vivo or in vitro. These results suggest that a similar RNA structure may be involved in the occurrence of both recombination and deletion events.     

Complementarity-determining region (CDR) implantation: a theme of recombination.

A novel technology in the area of antibody engineering has been developed which allows for the creation of new types of antibody molecules. It is called complementarity-determining region (CDR) implantation and permits the random combination of CDR sequences formed in vivo into a single master framework. Thus, totally new gene combinations can be produced and used in selection processes. The result is a genetic variability which is extremely large, even exceeding the natural variability found in the immune system. In this commentary, CDR implantation is presented and the technology is discussed.