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The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.
Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.
Alu Repeats: Tools for Genomics and Modes of Evolution
Mark A. Batzer, David H. Kass, Michelle Alegria-Hartman, and Prescott L. Deininger
Human Genome Center, L-452, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94550. Department of Biochemistry, Louisiana State University Medical Center, 1901 Perdido St., New Orleans, LA 70112.
There are over 500,000 Alu repeats dispersed throughout the human genome in a semirandom manner. Alu elements serve as priming sites for the amplification of unique DNA sequenceS located between Alu repeats that reside in relatively close proximity in a process termed inter-Alu Polymerase Chain Reaction (PCR). Physical mapping of the human genome involves a variety of complex hybridization based procedures. Some of these procedures rely upon the ability to separate human clones derived from human/rodent hybrid cell lines from those that contain background rodent derived DNA sequences. The ability to block the repetitive element (Alu repeat) portion of inter-Alu PCR products derived from a variety of complex sources is also crucial for the isolation of unique DNA sequences. We have constructed a new consensus Alu repeat probe (pPD39) designed for these purposes.
The Alu family of repeats can be divided into distinct subfamilies based upon specific diagnostic mutations. Older subfamilies of Alu repeats are more prevalent, while the more recent subfamilies have fewer copies. Many of the younger Alu elements are absent from the orthologous loci of non-human primates indicating that they arose in recent evolutionary history by retroposition, the predominant mode of Short INterspersed Element (SINE) amplification. PCR analysis of one young Alu subfamily (Sb2) member located on human chromosome 19 within the Low Density Lipoprotein Receptor (LDLR) gene revealed the presence of this element at orthologous positions within the genomes of a number of non-human primates. Analysis of the 5' and 3' flanking DNA sequences surrounding this Alu repeat showed that mutations had occurred at a neutral rate, in contrast to a higher degree of variation within the Alu sequence. The nucleotide sequence of the Alu repeat corresponded to an older Primate-Specific (PS) subfamily member within all of the non-human primate genomes. The alteration of this Alu sequence from one of the oldest to one of the youngest Alu subfamilies apparently occurred by a gene conversion event. Although gene conversions of Alu repeats are rare events, these data suggest that such events do occur, and contribute to the evolution of SlNEs.
This work was supported in part by grants from the U.S. Department of Energy (LDRD 94-LW-103) to M.A.B. and National Institutes of Health (ROl HG 00770) to P.L.D.and by Lawrence Livermore National Laboratory under the auspices of the U.S. Department of Energy contract no.W-7405-ENG-48.