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Batzer and Deininger 2002 Nature Reviews Genetics

Batzer and Deininger 2002 Nature Reviews Genetics - REVIEWS...

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370 | MAY 2002 | VOLUME 3 www.nature.com/reviews/genetics R E V I E W S The role of mobile elements in the shaping of eukary- otic genomes is becoming more and more recognized. Mobile elements make up over 45% of the human genome. These elements continue to amplify and, as a result of negative effects of their transposition, they contribute to a notable number of human diseases. All eukaryotic genomes contain mobile elements, although the proportion and activity of the classes of elements varies widely between genomes. Mobile ele- ments are important in insertional mutagenesis and unequal homologous recombination events. They use extensive cellular resources in their replication, expres- sion and amplification. There is considerable debate as to whether they are primarily an intracellular plague that attacks the host genome and exploits cellular resources, or whether they are tolerated because of their occasional positive influences in genome evolu- tion. The recent completion of the draft sequence of the human genome provides an unprecedented opportunity to assess the biological properties of Alu repeats and the influence that they have had on the architechture of the human genome. Here, we present an overview of the biology and the impact of Alu repeats — the largest family of mobile elements in the human genome. Discovery and origin of Alu elements The term ‘repetitive element’ describes various DNA sequences that are present in multiple copies in the genomes in which they reside. Repetitive elements can be subdivided into those that are tandemly arrayed (for example, MICROSATELLITES , MINISATELLITES and telomeres) or interspersed (for example, mobile elements and processed PSEUDOGENES ). Interspersed elements can be subdivided on the basis of size, with short interspersed elements (SINEs) being less than 500 bp long 1–4 . Alu SINEs were identified originally almost 30 years ago as a component in human DNA RENATURATION CURVES 5,6 . The name ‘Alu elements’ was given to these repeated sequences as members of this family of repeats contain a recognition site for the restriction enzyme Alu I (REF. 5) . Subsequent detailed analyses of this portion of the renaturation curves led to sequence analysis of individual Alu elements. They were initially cloned using linkers with Bam HI restric- tion endonuclease sites that resulted in the generation of Bam-linked ubiquitous repeat (BLUR) clones 7,8 . Full-length Alu elements are ~300 bp long and are commonly found in introns, 3 untranslated regions of genes and intergenic genomic regions (BOX 1) . Initial estimates indicated that these mobile elements were present in the human genome at an extremely high copy number (~500,000 copies) 7 . Recently, a detailed analysis of the draft sequence of the human genome has shown that, out of more than one mil- lion copies, Alu elements are the most abundant SINEs, which makes them the most abundant of all mobile elements in the human genome 9 . Because of ALU REPEATS AND HUMAN GENOMIC DIVERSITY Mark A. Batzer* and Prescott L. Deininger ‡§
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