Young human Alu subfamilies have diagnostic mutations compared to most Alu repeats and can be identified by specific oligonucleotide hybridization probes and primers. Unlike the great majority of Alus, these subfamilies are enriched for recently transposed members. Also, unlike most Alus, one or more source genes coding for new members is transcribed into 300 nt poly A plus and 120 nt poly A minus RNAs. Based on these advances, we may now ultimately learn how so many alus accumulated within the human genome. Concerning transposition, goals are to learn the activity of these subfamilies, where new members are inserted and the consequences of Alu insertion polymorphisms. Other goals are to learn the function of the Alu transcripts, whether the regulated expression of distinct Alu source genes determine their transpositional activity and to isolate the active source genes. PCR amplification using flanking single copy primers will test the frequency of polymorphism of individual cloned members of these subfamilies and identify especially active sequence variants corresponding to unusually active source genes (Aim 1A). Structural comparisons of these loci will show whether Alu insertions promote rearrangements in flanking sequences. Subsidiary issues concern Alu mobility. In situ hybridization to metaphase chromosomes using probes corresponding to these subfamilies will test specific models explaining how Alus concentrate at R bands (Aim 1B). Exploiting the availability of Alu primers specific to young subfamilies, Alu polymorphism of total human DNA will be surveyed by several PCR approaches (Aim 1C). Predicted 3' extensions of these highly specific primers will be used to isolate candidate Alu source genes by anchor and inverse PCR. cDNA sequencing and other structural studies will determine the relationship between the 300 nt and 120 nt transcripts, the number of transcriptionally active genes and whether transcriptional activity of distinct Alu genes correlates with their relative transpositional activity (Aim 2A). The relationship of the Alu transcripts to 7S L RNA, a structural homologue, will be tested by comparing the regulated transcription of Alu and 7S L RNAs (Aim 2B) and learning which SRP proteins bind the Alu transcripts in vivo (Aim 2C). An in vitro system will be developed to determine whether the 120 nt transcript results from processing of 300 nt transcripts or from different transcriptional termination (Aim 2D).
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