ABSTRACT
The recently inserted subfamilies of Alu retroposons (Ya5/8 and Yb8) are composed of approximately 2000 elements. We have screened a human chromosome 19-specific cosmid library for the presence of Ya5/8 and Yb8 Alu family members. This analysis resulted in the identification of 12 Ya5/8 Alu family members and 15 Yb8 Alu family members from human chromosome 19. The total number of Ya5/8 and Yb8 Alu family members located on human chromosome 19 does not differ from that expected based upon random integration of Alu repeats within the human genome. The distribution of both subfamilies of Alu elements along human chromosome 19 also appears to be random. DNA sequence analysis of the individual Alu elements revealed a low level of random mutations within both subfamilies of Alu elements consistent with their recent evolutionary origin. Oligonucleotide primers complementary to the flanking unique sequences adjacent to each Alu element were used in polymerase chain reaction assays to determine the phylogenetic distribution and human genomic variation associated with each Alu family member. All of the chromosome 19-specific Ya5/8 and Yb8 Alu family members were restricted to the human genome and absent from orthologous positions within the genomes of several non-human primates. Three of the Yb8 Alu family members were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. The polymorphic Alu elements will be useful tools for the study of human population genetics.
Subject(s)
Chromosomes, Human, Pair 19/genetics , Repetitive Sequences, Nucleic Acid/genetics , Retroelements/genetics , Animals , Base Sequence , Cell Line , Cloning, Molecular , Cosmids/genetics , Evolution, Molecular , Gene Library , Humans , Molecular Sequence Data , Mutation/genetics , Phylogeny , Polymerase Chain Reaction , Polymorphism, Genetic/genetics , Primates , Sequence Alignment , Sequence Analysis, DNAABSTRACT
Usher syndrome type 1C (USH1C) occurs in a small population of Acadian descendants from southwestern Louisiana. Linkage and linkage disequilibrium analyses localize USH1C to chromosome 11p between markers D11S1397 and D11S1888, an interval of less than 680 kb. Here, we refine the USH1C linkage to a region less than 400 kb, between genetic markers D11S1397 and D11S1890. Using 17 genetic markers from this interval, we have isolated a contiguous set of 60 bacterial artificial chromosomes (BACs) that span the USH1C critical region. Exon trapping of BAC clones from this region resulted in the recovery of an exon of the nuclear EF-hand acidic (NEFA) gene. However, DNA sequence analysis of the NEFA cDNA from lymphocytes of affected individuals provided no evidence of mutation, making structural mutations in the NEFA protein unlikely as the cellular cause of Acadian Usher syndrome.
