Otieno AC, Carter AB, Hedges DJ, Walker JA, Ray DA, Garber RK, Anders BA, Stoilova N, Laborde ME, Fowlkes JD, Huang CH, Perodeau B, and Batzer MA¹.

Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Microsystems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.

¹ Corresponding author.
E-MAIL:   mbatzer@lsu.edu   FAX:   (225) 578-7113.

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. PMID: 15313610 [PubMed] 

SINEs ( short interspersed element ) are ancient retrotransposons, comprising over 10 % of the human genone by weight. SINEs synthesize noncoding RNA species by means of RNA polymerase III. Alu and B2 are SINEs and may have important functions as a source of new genes, new promoters, and new regulators during the course of evolution. Subfamilies of Alu are currently being used as probes of splicing and to detect the structural differences between the human and other primate genomes. The noncoding functions of B2 RNA and other SINE RNAs in mice are now under investigation as gene regulators (see References, below)..

1. Ferrigno O, Virolle T, Djabari Z, Ortonne J-P, White RJ, and Aberdam D, "Transposable B2 SINE elements can provide mobile RNA polymerase II promoters", Nature Genetics, vol. 28,  no. 1, pp. 77-81 (May, 2001). (doi:10.1038/88306 ).

2.  Sorek R, Lev-Maor G, Reznick M, Dagan T, Belinky F, Graur D, and Ast G, "Minimal conditions for exonization of intronic sequences: 5' splice site formation in Alu exons", Mol. Cell vol. 14, no. 2, pp. 221-231 (April, 2004).

3. Allen TA, Von Kaenel S, Goodrich JA, and Kugel JF, "The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock", Nature Structural and Molecular Biology, Published online: 08 August 2004; | doi:10.1038/nsmb813

4. Espinoza CA, Allen TA, Hieb AR, Kugel JF, and Goodrich JA, "B2 RNA binds directly to RNA polymerase II to repress transcript synthesis",  Nature Structural and Molecular Biology, Published online: 08 August 2004; | doi:10.1038/nsmb812

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