Research on a highly repetitive family of genetic elements of mammals was continued. Alu sequences are small transposed elements endogenous to the human genome. Nearly one million dispersed copies constitute 5% of the genetic material. Although function is unknown, the propensity of Alu elements for mobility and recombination has caused genetic variability and multiple heritable disorders in humans by both RNA- and DNA-mediated mutations. Germline and fetal-specific expression of RNA from a specific subset of these elements suggests their involvement in normal development. The regulated expression of Alu and its mouse homologue B1 involves multiple levels of control. Examination of activities that positively and negatively influence their expression increased our insight into the transcriptional regulation and propensity for transposition of these elements. Protein factors that interact with these DNA elements to regulate their expression, as well as proteins that modulate the metabolism of their RNA products were characterized. The chromosomal location of the sequences that encode human scAlu RNA were mapped by northern analysis of rodent x human somatic hybrids. The exact sequences were determined from scalu CDNA clones. Further characterization of a scalu RNA-binding protein included its localization to a specific human chromosome by a functional mapping approach. We identified a conserved, sequence-specific motif in scB1/Alu RNA important for binding. Homology of scB1 and scAlu RNAs was established by comparing these transcripts with respect to subcellular distribution, copy number, secondary structure, post-transcriptional processing and ability to bind to a specific protein. The positive effects of fetal serum on levels of scB1 RNA in mouse NIH 3T3 cells were studied. Effects of cis-acting control elements and trans-acting factors on B1-Alu gene transcription was continued. A fascile assay that utilizes immobilized transcription complexes improved the resolution and interpretability of these analyses.
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