Nucleic Acids Research, Vol 26, Issue 20 4541-4550, Copyright © 1998 by Oxford University Press
CW Schmid
The evolution, mobility and deleterious genetic effects of human Alus are
fairly well understood. The complexity of regulated transcriptional
expression of Alus is becoming apparent and insight into the mechanism of
retrotransposition is emerging. Unresolved questions concern why mobile,
highly repetitive short interspersed elements (SINEs) have been tolerated
throughout evolution and why and how families of such sequences are
periodically replaced. Either certain SINEs are more successful genomic
parasites or positive selection drives their relative success and genomic
maintenance. A complete understanding of the evolutionary dynamics and
significance of SINEs requires determining whether or not they have a
function(s). Recent evidence suggests two possibilities, one concerning DNA
and the other RNA. Dispersed Alus exhibit remarkable tissue-specific
differences in the level of their 5-methylcytosine content. Differences in
Alu methylation in the male and female germlines suggest that Alu DNA may
be involved in either the unique chromatin organization of sperm or
signaling events in the early embryo. Alu RNA is increased by cellular
insults and stimulates protein synthesis by inhibiting PKR, the eIF2 kinase
that is regulated by double-stranded RNA. PKR serves other roles
potentially linking Alu RNA to a variety of vital cell functions. Since
Alus have appeared only recently within the primate lineage, this proposal
provokes the challenging question of how Alu RNA could have possibly
assumed a significant role in cell physiology.
REVIEWS
Does SINE evolution preclude Alu function?
Section of Molecular and Cellular Biology and Department of Chemistry, University of California at Davis, Davis, CA 95616, USA. cwschmid@ucdavis.edu
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  T. Mourier and E. Willerslev Retrotransposons and non-protein coding RNAs Brief Funct Genomic Proteomic, November 1, 2009; 8(6): 493 - 501. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Farcas, E. Schneider, K. Frauenknecht, I. Kondova, R. Bontrop, J. Bohl, B. Navarro, M. Metzler, H. Zischler, U. Zechner, et al. Differences in DNA Methylation Patterns and Expression of the CCRK Gene in Human and Nonhuman Primate Cortices Mol. Biol. Evol., June 1, 2009; 26(6): 1379 - 1389. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. A. Ray, C. Feschotte, H. J.T. Pagan, J. D. Smith, E. J. Pritham, P. Arensburger, P. W. Atkinson, and N. L. Craig Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus Genome Res., May 1, 2008; 18(5): 717 - 728. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Rodriguez, L. Vives, M. Jorda, C. Morales, M. Munoz, E. Vendrell, and M. A. Peinado Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells Nucleic Acids Res., February 11, 2008; 36(3): 770 - 784. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H.-R. Wang, C.-Y. Hsieh, Y.-C. Twu, and L.-C. Yu Expression of the Human Sda -1,4-N-Acetylgalactosaminyltransferase II Gene is Dependent on the Promoter Methylation Status Glycobiology, January 1, 2008; 18(1): 104 - 113. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Cardelli, F. Marchegiani, L. Cavallone, F. Olivieri, S. Giovagnetti, E. Mugianesi, R. Moresi, R. Lisa, and C. Franceschi A Polymorphism of the YTHDF2 Gene (1p35) Located in an Alu-Rich Genomic Domain Is Associated With Human Longevity. J. Gerontol. A Biol. Sci. Med. Sci., June 1, 2006; 61(6): 547 - 556. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B S Nunez, P M Piermarini, A N Evans, and S L Applebaum Cloning and characterization of cDNAs encoding steroidogenic acute regulatory protein from freshwater stingrays (Potamotrygon spp.) J. Mol. Endocrinol., December 1, 2005; 35(3): 557 - 569. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Wang and E. F. Kirkness Short interspersed elements (SINEs) are a major source of canine genomic diversity Genome Res., December 1, 2005; 15(12): 1798 - 1808. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. A. Onafuwa-Nuga, S. R. King, and A. Telesnitsky Nonrandom Packaging of Host RNAs in Moloney Murine Leukemia Virus J. Virol., November 1, 2005; 79(21): 13528 - 13537. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. N. van de Lagemaat, L. Gagnier, P. Medstrand, and D. L. Mager Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates Genome Res., September 1, 2005; 15(9): 1243 - 1249. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Goodison, J. Yuan, D. Sloan, R. Kim, C. Li, N. C. Popescu, and V. Urquidi The RhoGAP Protein DLC-1 Functions as a Metastasis Suppressor in Breast Cancer Cells Cancer Res., July 15, 2005; 65(14): 6042 - 6053. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Schutz, H. B. Urnovitz, L. Iakoubov, W. Schulz-Schaeffer, W. Wemheuer, and B. Brenig Bov-tA Short Interspersed Nucleotide Element Sequences in Circulating Nucleic Acids from Sera of Cattle with Bovine Spongiform Encephalopathy (BSE) and Sera of Cattle Exposed to BSE Clin. Vaccine Immunol., July 1, 2005; 12(7): 814 - 820. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. K. Gogolevskaya, A. P. Koval, and D. A. Kramerov Evolutionary History of 4.5SH RNA Mol. Biol. Evol., July 1, 2005; 22(7): 1546 - 1554. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Pelissier, C. Bousquet-Antonelli, L. Lavie, and J.-M. Deragon Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana Nucleic Acids Res., July 28, 2004; 32(13): 3957 - 3966. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. T. Nishant, H. Ravishankar, and M. R. S. Rao Characterization of a Mouse Recombination Hot Spot Locus Encoding a Novel Non-Protein-Coding RNA Mol. Cell. Biol., June 15, 2004; 24(12): 5620 - 5634. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Hedges, P. A. Callinan, R. Cordaux, J. Xing, E. Barnes, and M. A. Batzer Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages Genome Res., June 1, 2004; 14(6): 1068 - 1075. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. S. Yang, M. R. H. Estecio, K. Doshi, Y. Kondo, E. H. Tajara, and J.-P. J. Issa A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements Nucleic Acids Res., February 18, 2004; 32(3): e38 - e38. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Jurka, O. Kohany, A. Pavlicek, V. V. Kapitonov, and M. V. Jurka Duplication, coclustering, and selection of human Alu retrotransposons PNAS, February 3, 2004; 101(5): 1268 - 1272. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Doerwald, C. Onnekink, S. T. van Genesen, W. W. de Jong, and N. H. Lubsen Translational Thermotolerance Provided by Small Heat Shock Proteins Is Limited to Cap-dependent Initiation and Inhibited by 2-Aminopurine J. Biol. Chem., December 12, 2003; 278(50): 49743 - 49750. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Hisano, H. Ohta, Y. Nishimune, and M. Nozaki Methylation of CpG dinucleotides in the open reading frame of a testicular germ cell-specific intronless gene, Tact1/Actl7b, represses its expression in somatic cells Nucleic Acids Res., August 15, 2003; 31(16): 4797 - 4804. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Morgan, D. Conklin, A. J. Pawson, R. Sellar, T. R. Ott, and R. P. Millar A Transcriptionally Active Human Type II Gonadotropin-Releasing Hormone Receptor Gene Homolog Overlaps Two Genes in the Antisense Orientation on Chromosome 1q.12 Endocrinology, February 1, 2003; 144(2): 423 - 436. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. L. Deininger and M. A. Batzer Mammalian Retroelements Genome Res., October 1, 2002; 12(10): 1455 - 1465. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Medstrand, L. N. van de Lagemaat, and D. L. Mager Retroelement Distributions in the Human Genome: Variations Associated With Age and Proximity to Genes Genome Res., October 1, 2002; 12(10): 1483 - 1495. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-H. Chou, T. Hayakawa, S. Diaz, M. Krings, E. Indriati, M. Leakey, S. Paabo, Y. Satta, N. Takahata, and A. Varki Inactivation of CMP-N-acetylneuraminic acid hydroxylase occurred prior to brain expansion during human evolution PNAS, September 3, 2002; 99(18): 11736 - 11741. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Takai and P. A. Jones Comprehensive analysis of CpG islands in human chromosomes 21 and 22 PNAS, March 19, 2002; 99(6): 3740 - 3745. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Nussbaum, S. Gunnery, and M. B. Mathews The 3'-untranslated regions of cytoskeletal muscle mRNAs inhibit translation by activating the double-stranded RNA-dependent protein kinase PKR Nucleic Acids Res., March 1, 2002; 30(5): 1205 - 1212. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Ogiwara, M. Miya, K. Ohshima, and N. Okada V-SINEs: A New Superfamily of Vertebrate SINEs That Are Widespread in Vertebrate Genomes and Retain a Strongly Conserved Segment within Each Repetitive Unit Genome Res., February 1, 2002; 12(2): 316 - 324. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Hayakawa, Y. Satta, P. Gagneux, A. Varki, and N. Takahata Alu-mediated inactivation of the human CMP- N-acetylneuraminic acid hydroxylase gene PNAS, September 13, 2001; (2001) 191268198. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. D. Makova, M. Ramsay, T. Jenkins, and W.-H. Li Human DNA Sequence Variation in a 6.6-kb Region Containing the Melanocortin 1 Receptor Promoter Genetics, July 1, 2001; 158(3): 1253 - 1268. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. O. Stuart, K. T. Bush, and S. K. Nigam Changes in global gene expression patterns during development and maturation of the rat kidney PNAS, April 25, 2001; (2001) 91110798. [Abstract] [Full Text]
|
|
|
|
 |
|
 Y. V. B. K. Subrahmanyam, S. Yamaga, Y. Prashar, H. H. Lee, N. P. Hoe, Y. Kluger, M. Gerstein, J. D. Goguen, P. E. Newburger, and S. M. Weissman RNA expression patterns change dramatically in human neutrophils exposed to bacteria Blood, April 15, 2001; 97(8): 2457 - 2468. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Gemund, C. Ramu, B. Altenberg-Greulich, and T. J. Gibson Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries Nucleic Acids Res., March 15, 2001; 29(6): 1272 - 1277. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Liang, H. Igarashi, T. Tsuzuki, Y. Nakabeppu, M. Sekiguchi, K. S. Kasprzak, and Y.-H. Shiao Presence of Potential Nickel-Responsive Element(s) in the Mouse MTH1 Promoter Ann. Clin. Lab. Sci., January 1, 2001; 31(1): 91 - 98. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. A. Rojas, A. Vazquez-Tello, G. Ferbeyre, F. Venanzetti, L. Bachmann, B. Paquin, V. Sbordoni, and R. Cedergren Hammerhead-mediated processing of satellite pDo500 family transcripts from Dolichopoda cave crickets Nucleic Acids Res., October 15, 2000; 28(20): 4037 - 4043. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T.-H. Li, C. Kim, C. M. Rubin, and C. W. Schmid K562 cells implicate increased chromatin accessibility in Alu transcriptional activation Nucleic Acids Res., August 15, 2000; 28(16): 3031 - 3039. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Greally Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome PNAS, January 8, 2002; 99(1): 327 - 332. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. O. Stuart, K. T. Bush, and S. K. Nigam Changes in global gene expression patterns during development and maturation of the rat kidney PNAS, May 8, 2001; 98(10): 5649 - 5654. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Hayakawa, Y. Satta, P. Gagneux, A. Varki, and N. Takahata Alu-mediated inactivation of the human CMP- N-acetylneuraminic acid hydroxylase gene PNAS, September 25, 2001; 98(20): 11399 - 11404. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Pavlicek, J. Paces, D. Elleder, and J. Hejnar Processed Pseudogenes of Human Endogenous Retroviruses Generated by LINEs: Their Integration, Stability, and Distribution Genome Res., March 1, 2002; 12(3): 391 - 399. [Abstract] [Full Text] [PDF]
|
|