Analysis of the human Alu Ya-lineage.
The Alu Ya-lineage is a group of related, short interspersed elements (SINEs) found in primates. This lineage includes subfamilies Ya1-Ya5, Ya5a2 and others. Some of these subfamilies are still actively mobilizing in the human genome. We have analyzed 2482 elements that reside in the human genome draft sequence and focused our analyses on the 2318 human autosomal Ya Alu elements. A total of 1470 autosomal loci were subjected to polymerase chain reaction (PCR)-based assays that allow analysis of individual Ya-lineage Alu elements. About 22% (313/1452) of the Ya-lineage Alu elements were polymorphic for the insertion presence on human autosomes. Less than 0.01% (5/1452) of the Ya-lineage loci analyzed displayed insertions in orthologous loci in non-human primate genomes. DNA sequence analysis of the orthologous inserts showed that the orthologous loci contained older pre-existing Y, Sc or Sq Alu subfamily elements that were the result of parallel forward insertions or involved in gene conversion events in the human lineage. This study is the largest analysis of a group of "young", evolutionarily related human subfamilies. The size, evolutionary age and variable allele insertion frequencies of several of these subfamilies makes members of the Ya-lineage useful tools for human population studies and primate phylogenetics.
Otieno
Anthony C
AC
Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Microsystems, Louisiana State University, 202 Life Sciences Building, Baton Rouge 70803, USA.
Carter
Anthony B
AB
Hedges
Dale J
DJ
Walker
Jerilyn A
JA
Ray
David A
DA
Garber
Randall K
RK
Anders
Bridget A
BA
Stoilova
Nadica
N
Laborde
Meredith E
ME
Fowlkes
Justin D
JD
Huang
Cheney H
CH
Perodeau
Benjamin
B
Batzer
Mark A
MA
D020087:Alu Elements; D000818:Animals; D002460:Cell Line; D002877:Chromosomes, Human; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D005785:Gene Conversion; D015894:Genome, Human; D006801:Humans; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA