title: Cis-acting influences on Alu RNA levels.
abstract: The human short interspersed repeated element (SINE), Alu, amplifies through a poorly understood RNA-mediated mechanism, termed retroposition. There are over one million copies of Alu per haploid human genome. The copies show some internal variations in sequence and are very heterogeneous in chromosomal environment. However, very few Alu elements actively amplify. The amplification rate has decreased greatly in the last 40 million years. Factors influencing Alu transcription would directly affect an element's retroposition capability. Therefore, we evaluated several features that might influence expression from individual Alu elements. The influence of various internal sequence variations and 3' unique flanks on full-length Alu RNA steady-state levels was determined. Alu subfamily diagnostic mutations do not significantly alter the amount of Alu RNA observed. However, sequences containing random mutations throughout the right half of selected genomic Alu elements altered Alu RNA steady-state levels in cultured cells. In addition, sequence variations at the 3' unique end of the transcript also significantly altered the Alu RNA levels. In general, sequence mutations and 3' end sequences contribute to Alu RNA levels, suggesting that the master Alu element(s) have a multitude of individual differences that collectively gives them a selective advantage over other Alu elements.
authors.affiliation: Tulane Cancer Center, SL-66, and Department of Environmental Health Sciences, Tulane University-Health Sciences Center, 1430 Tulane Avenue, New Orleans, LA 70112, USA.
authors.forename: C
authors.initials: C
authors.lastname: Alemán
authors.forename: A M
authors.initials: AM
authors.lastname: Roy-Engel
authors.forename: T H
authors.initials: TH
authors.lastname: Shaikh
authors.forename: P L
authors.initials: PL
authors.lastname: Deininger
mesh_terms: D016475:3T3 Cells; D020087:Alu Elements / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D015152:Blotting, Northern; D002460:Cell Line; D004274:DNA, Recombinant; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D005786:Gene Expression Regulation; D006367:HeLa Cells; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D016296:Mutagenesis; D009154:Mutation; D010957:Plasmids / Q000235:genetics; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D020871:RNA Stability; D012689:Sequence Homology, Nucleic Acid; D014407:Tumor Cells, Cultured
chemical_list: D004274:DNA, Recombinant; D012313:RNA