Nucleic Acids Research, 2000, Vol. 28, No. 23 4755-4761
© 2000 Oxford University Press
Cis-acting influences on Alu RNA levels
1Tulane Cancer Center, SL-66, and Department of Environmental Health Sciences, Tulane University–Health Sciences Center, 1430 Tulane Avenue, New Orleans, LA 70112, USA, 2Department of Biochemistry and Molecular Biology, Louisiana State University–Health Sciences Center, New Orleans, LA, USA and 3Laboratory of Molecular Genetics, Alton Oschner Medical Foundation, New Orleans, LA 70121, USA
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.
* To whom correspondence should be addressed at: Tulane Cancer Center, Tulane University–Medical Center, 1430 Tulane Avenue, SL-66, New Orleans, LA 70112, USA. Tel: +1 504 988 6385; Fax: +1 504 588 5516; Email: pdeinin{at}tulane.edu Present addresses: Claudina Alemán, Laboratory of Cell Biology, NCI/NIH Building 37/Room 1A09, Bethesda, MD 20892, USA Tamim H. Shaikh, Division of Human Genetics and Molecular Biology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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