Abstract
The Alu Yb-lineage is a 'young' primarily human-specific group of short interspersed element (SINE) subfamilies that have integrated throughout the human genome. In this study, we have computationally screened the draft sequence of the human genome for Alu Yb-lineage subfamily members present on autosomal chromosomes. A total of 1,733 Yb Alu subfamily members have integrated into human autosomes. The average ages of Yb-lineage subfamilies, Yb7, Yb8 and Yb9, are estimated as 4.81, 2.39 and 2.32 million years, respectively. In order to determine the contribution of the Alu Yb-lineage to human genomic diversity, 1,202 loci were analysed using polymerase chain reaction (PCR)-based assays, which amplify the genomic regions containing individual Yb-lineage subfamily members. Approximately 20 per cent of the Yb-lineage Alu elements are polymorphic for insertion presence/absence in the human genome. Fewer than 0.5 per cent of the Yb loci also demonstrate insertions at orthologous positions in non-human primate genomes. Genomic sequencing of these unusual loci demonstrates that each of the orthologous loci from non-human primate genomes contains older Y, Sg and Sx Alu family members that have been altered, through various mechanisms, into Yb8 sequences. These data suggest that Alu Yb-lineage subfamily members are largely restricted to the human genome. The high copy number, level of insertion polymorphism and estimated age indicate that members of the Alu Yb elements will be useful in a wide range of genetic analyses.
Highlights
Short interspersed elements (SINEs) are a class of retroelements that are typically less than 500 nucleotides long and lack open reading frames (ORFs).[1,2,3,4,5] Alu elements are dimeric, primate-specific short interspersed element (SINE) that have reached a copy number in excess of one million in the human genome.[6]
A total of 1,733 Yb-lineage Alu elements were detected within autosomal chromosomes (Table 1)
With the addition of 118 subfamily elements previously found on the sex chromosomes, 1,851 Yb elements have been recovered from the human draft sequence.[21]
Summary
Short interspersed elements (SINEs) are a class of retroelements that are typically less than 500 nucleotides long and lack open reading frames (ORFs).[1,2,3,4,5] Alu elements are dimeric, primate-specific SINEs that have reached a copy number in excess of one million in the human genome.[6]. Since Alu elements first appeared in the primate genome, their amplification rate has fluctuated and is thought to be currently 100-fold slower than the peak rate 40 million years ago.[13,14]
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