Short Interspersed Elements (SINEs)

Carl W Schmid, University of California, Davis, California, USA
Carol M Rubin, University of California, Davis, California, USA

Published online: September 2005

DOI: 10.1038/npg.els.0005325

Abstract

Short interspersed elements (SINEs) are highly repetitive sequences that retrotranspose into eukaryotic DNA through intermediates transcribed by RNA polymerase III (pol III). In many species, SINEs are a ubiquitously dispersed feature of the whole genome, often constituting a significant (∼10%) mass fraction of total DNA. SINEs cause mutations both by their retrotransposition within genes and by unequal recombination, and are widely considered to be examples of ‘selfish’ or ‘parasitic’ DNA.

Keywords: SINEs; Alu; retrotransposition; transposons; selfish DNA

Figure 1.

Interspersed repeat structure. (a) The primate Alu left and right monomers are shown relative to their ancestor, 7SL. The two monomers are linked by a short AT‐rich region. Only the left monomer contains functional A and B boxes that are essential for RNA polymerase III transcription. The right monomer contains an additional 31 nucleotides of 7SL sequence not found in the left monomer (numbering is approximate). (b) Structure of the tRNA‐related rodent B2 SINE. The ancestor of the B2 tRNA‐related portion is lysine tRNA. Other species contain SINEs derived from glycine or arginine tRNAs that have similar structures (see Okada and Ohshima, ).
close

References

Deininger PL and Batzer MA (1999) Alu repeats and human disease. Molecular Genetics and Metabolism 67: 183–193.

Deininger PL, Sherry ST, Risch G, et al. (1997) Interspersed repeat insertion polymorphisms for studies of human molecular anthropology. In: Papiha SS, Deka R and Chakraboorty R (eds.) Genomic Diversity: Applications in Human Population Genetics, chap. 14, pp. 201–212. New York, NY: Kluwer Academic.

Howard BH and Sakamoto K (1990) Alu interspersed repeats: selfish DNA or a functional gene family? New Biologist 2: 759–770.

Jurka J (1997) Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proceedings of the National Academy of Sciences of the United States of America 94: 1872–1877.

Jurka J, Zietkiewicz E and Labuda D (1995) Ubiquitous mammalian‐wide interspersed repeats (MIRs) are molecular fossils from the mesozoic era. Nucleic Acids Research 23: 170–175.

Kimura RH, Choudary PV and Schmid CW (1999) Silk worm Bm1 SINE RNA increases following cellular insults. Nucleic Acids Research 27: 3380–3387.

Labuda D, Zietkiewicz E and Mitchell GA (1995) Alu elements as a source of genomic variation: deleterious effects and evolutionary novelties. In: Maraia RJ (ed.) The Impact of Short Interspersed Elements (SINEs) on the Host Genome, chap. 1, pp. 1–24. Austin, TX, USA: RG Landes Co.

Lander ES, Linton LM, Birrin B, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.

Li T, Spearow J, Rubin CM and Schmid CW (1999) Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo. Gene 239: 367–372.

Makalowski W (1995) SINEs as a genomic scrap yard: an essay on genomic evolution. In: Maraia RJ (ed.) The Impact of Short Interspersed Elements (SINEs) on the Host Genome, chap. 5, pp. 81–104. Austin, TX, USA: RG Landes Co.

Ohshima K, Hamada M, Terai Y and Okada N (1996) The 3′ ends of tRNA‐derived short interspersed repetitive elements are derived from the 3′ ends of long interspersed repetitive elements. Molecular and Cell Biology 16: 3756–3764.

Okada N and Hamada M (1997) The 3′ ends of tRNA‐derived SINEs originated from the 3′ ends of LINEs: a new example from the bovine genome. Journal of Molecular Evolution 44(supplement 1): S52–S56.

Okada N, Hamada M, Ogiwara I and Ohshima K (1997) SINEs and LINEs share common 3′ sequences: a review. Gene 205: 229–243.

Okada N and Ohshima K (1995) Evolution of tRNA derived SINEs. In: Maraia RJ (ed.) The Impact of Short Interspersed Elements (SINEs) on the Host Genome, chap. 4, pp. 61–80. Austin, Texas, USA: RG Landes Co.

Schmid CW (1996) Alu: structure, origin, evolution, significance and function of one‐tenth of human DNA. Progress in Nucleic Acid Research and Molecular Biology 53: 283–319.

Schmid CW (1998) Does SINE evolution preclude Alu function? Nucleic Acids Research 26: 4541–4550.

Smit AF and Riggs AD (1995) MIRs are classic, tRNA‐derived SINEs that amplified before the mammalian radiation. Nucleic Acids Research 23: 98–102.

Stoneking M, Fontius JJ, Clifford SL, et al. (1997) Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Research 11: 1061–1071.

Related Sub-Topics:

DNA Structure and Function | Chromosomes and Chromatin Modifications | Nucleic Acid Structure | Evolution of Coding and Functional Modules | Mutational Mechanisms of Genetic Disease | DNA Damage and Repair | Replication and Recombination | Gene and Genome Structure and Organisation
Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

Article Title: Short Interspersed Elements (SINEs)
 
How to Cite close
Schmid, Carl W, and Rubin, Carol M(Sep 2005) Short Interspersed Elements (SINEs). In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005325]