Home LiteratureArticle Details
PMID: 17020921 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Review

Alu elements as regulators of gene expression.

Nucleic acids research ·Vol. 34 ·No. 19 ·2006-00-00 ·Pages 5491-7

Häsler J, Strub K

Abstract

Alu elements are the most abundant repetitive elements in the human genome; they emerged 65 million years ago from a 5' to 3' fusion of the 7SL RNA gene and amplified throughout the human genome by retrotransposition to reach the present number of more than one million copies. Over the last years, several lines of evidence demonstrated that these elements modulate gene expression at the post-transcriptional level in at least three independent manners. They have been shown to be involved in alternative splicing, RNA editing and translation regulation. These findings highlight how the genome adapted to these repetitive elements by assigning them important functions in regulation of gene expression. Alu elements should therefore be considered as a large reservoir of potential regulatory functions that have been actively participating in primate evolution.

MeSH Terms
Alu Elements Base Sequence Gene Expression Regulation Molecular Sequence Data Protein Biosynthesis RNA/chemistry RNA Editing RNA Splicing
Chemicals
RNA
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Häsler Julien
Université de Genève, Katharina Strub, Département de Biologie Cellulaire, 30 quai Ernest Ansermet, 1211 GENEVE 4, Switzerland.
Strub Katharina
References (70)
70 references, click to expand
  1. Origin of the Alu family: a family of Alu-like monomers gave birth to the left and the right arms of the Alu elements.
    Nucleic Acids Res. 1992 Jul 11;20(13):3397-401 PMID: 1378589
  2. On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA".
    Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10706-10 PMID: 1279691
  3. Alu transcripts: cytoplasmic localisation and regulation by DNA methylation.
    Nucleic Acids Res. 1994 Mar 25;22(6):1087-95 PMID: 7512262
  4. Alu sequences in the coding regions of mRNA: a source of protein variability.
    Trends Genet. 1994 Jun;10(6):188-93 PMID: 8073532
  5. Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts.
    Nucleic Acids Res. 1995 May 25;23(10):1758-65 PMID: 7784180
  6. The SRP9/14 subunit of the signal recognition particle (SRP) is present in more than 20-fold excess over SRP in primate cells and exists primarily free but also in complex with small cytoplasmic Alu RNAs.
    Mol Biol Cell. 1995 Apr;6(4):471-84 PMID: 7542942
  7. Splice-mediated insertion of an Alu sequence in the COL4A3 mRNA causing autosomal recessive Alport syndrome.
    Hum Mol Genet. 1995 Apr;4(4):675-9 PMID: 7633417
  8. The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons.
    Science. 2003 May 23;300(5623):1288-91 PMID: 12764196
  9. LINE-mediated retrotransposition of marked Alu sequences.
    Nat Genet. 2003 Sep;35(1):41-8 PMID: 12897783
  10. Partial deficiency of the C-terminal-domain phosphatase of RNA polymerase II is associated with congenital cataracts facial dysmorphism neuropathy syndrome.
    Nat Genet. 2003 Oct;35(2):185-9 PMID: 14517542
  11. Mechanisms of alternative pre-messenger RNA splicing.
    Annu Rev Biochem. 2003;72:291-336 PMID: 12626338
  12. Liver disintegration in the mouse embryo caused by deficiency in the RNA-editing enzyme ADAR1.
    J Biol Chem. 2004 Feb 6;279(6):4894-902 PMID: 14615479
  13. Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons.
    Mol Cell. 2004 Apr 23;14(2):221-31 PMID: 15099521
  14. LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression?
    Bioessays. 2005 Aug;27(8):775-84 PMID: 16015595
  15. Exonization of AluYa5 in the human ACE gene requires mutations in both 3' and 5' splice sites and is facilitated by a conserved splicing enhancer.
    Nucleic Acids Res. 2005;33(12):3897-906 PMID: 16027113
  16. Identification of splicing silencers and enhancers in sense Alus: a role for pseudoacceptors in splice site repression.
    Mol Cell Biol. 2005 Aug;25(16):6912-20 PMID: 16055705
  17. ADAR gene family and A-to-I RNA editing: diverse roles in posttranscriptional gene regulation.
    Prog Nucleic Acid Res Mol Biol. 2005;79:299-338 PMID: 16096031
  18. Extensive adenosine-to-inosine editing detected in Alu repeats of antisense RNAs reveals scarcity of sense-antisense duplex formation.
    FEBS Lett. 2006 Apr 17;580(9):2301-5 PMID: 16574103
  19. Alu RNP and Alu RNA regulate translation initiation in vitro.
    Nucleic Acids Res. 2006;34(8):2374-85 PMID: 16682445
  20. LINE FUSION GENES: a database of LINE expression in human genes.
    BMC Genomics. 2006;7:139 PMID: 16756682
  21. The frequency and position of Alu repeats in cDNAs, as determined by database searching.
    Genomics. 1995 Jun 10;27(3):544-8 PMID: 7558040
  22. The role of RNA editing in controlling glutamate receptor channel properties.
    J Neurochem. 1996 Jan;66(1):1-5 PMID: 8522940
  23. Distinct transcription start sites generate two forms of BRCA1 mRNA.
    Hum Mol Genet. 1995 Dec;4(12):2259-64 PMID: 8634696
  24. Monomeric scAlu and nascent dimeric Alu RNAs induced by adenovirus are assembled into SRP9/14-containing RNPs in HeLa cells.
    Nucleic Acids Res. 1996 Nov 1;24(21):4165-70 PMID: 8932367
  25. Complete genomic sequence and analysis of 117 kb of human DNA containing the gene BRCA1.
    Genome Res. 1996 Nov;6(11):1029-49 PMID: 8938427
  26. The SRP9/14 subunit of the human signal recognition particle binds to a variety of Alu-like RNAs and with higher affinity than its mouse homolog.
    Nucleic Acids Res. 1997 Jan 15;25(2):318-26 PMID: 9016560
  27. Editing of glutamate receptor B subunit ion channel RNAs by four alternatively spliced DRADA2 double-stranded RNA adenosine deaminases.
    Mol Cell Biol. 1997 May;17(5):2413-24 PMID: 9111310
  28. Regulation of serotonin-2C receptor G-protein coupling by RNA editing.
    Nature. 1997 May 15;387(6630):303-8 PMID: 9153397
  29. Complex regulation of the BRCA1 gene.
    J Biol Chem. 1997 Aug 22;272(34):20994-7 PMID: 9261099
  30. Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase PKR.
    Mol Cell Biol. 1998 Jan;18(1):58-68 PMID: 9418853
  31. Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA.
    EMBO J. 1998 Feb 16;17(4):1120-7 PMID: 9463389
  32. Control of genes by mammalian retroposons.
    Int Rev Cytol. 1999;186:1-48 PMID: 9770296
  33. A mutation (IVS8+0.6kbdelTC) creating a new donor splice site activates a cryptic exon in an Alu-element in intron 8 of the human beta-glucuronidase gene.
    Hum Genet. 1998 Dec;103(6):686-93 PMID: 9921904
  34. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.
    PLoS Biol. 2004 Dec;2(12):e391 PMID: 15534692
  35. Is abundant A-to-I RNA editing primate-specific?
    Trends Genet. 2005 Feb;21(2):77-81 PMID: 15661352
  36. Alu-SINE exonization: en route to protein-coding function.
    Mol Biol Evol. 2005 Aug;22(8):1702-11 PMID: 15901843
  37. Analysis of transcription factors binding to the human 7SL RNA gene promoter.
    Biochem Cell Biol. 1999;77(5):431-8 PMID: 10593606
  38. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity.
    Cell. 2000 Jun 9;101(6):671-84 PMID: 10892653
  39. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2.
    Nature. 2000 Jul 6;406(6791):78-81 PMID: 10894545
  40. The 3' UTR of human MnSOD mRNA hybridizes to a small cytoplasmic RNA and inhibits gene expression.
    Biochem Biophys Res Commun. 2000 Aug 11;274(3):641-8 PMID: 10924331
  41. A-to-I pre-mRNA editing in Drosophila is primarily involved in adult nervous system function and integrity.
    Cell. 2000 Aug 18;102(4):437-49 PMID: 10966106
  42. Structure and assembly of the Alu domain of the mammalian signal recognition particle.
    Nature. 2000 Nov 9;408(6809):167-73 PMID: 11089964
  43. Initial sequencing and analysis of the human genome.
    Nature. 2001 Feb 15;409(6822):860-921 PMID: 11237011
  44. Hierarchical assembly of the Alu domain of the mammalian signal recognition particle.
    RNA. 2001 May;7(5):731-40 PMID: 11350037
  45. Repetitive elements in the 5' untranslated region of a human zinc-finger gene modulate transcription and translation efficiency.
    Genomics. 2001 Aug;76(1-3):110-6 PMID: 11549323
  46. Differential stress induction of individual Alu loci: implications for transcription and retrotransposition.
    Gene. 2001 Oct 3;276(1-2):135-41 PMID: 11591480
  47. Transposable elements are found in a large number of human protein-coding genes.
    Trends Genet. 2001 Nov;17(11):619-21 PMID: 11672845
  48. Alu elements in human growth hormone receptor gene 5' untranslated region exons.
    J Mol Endocrinol. 2001 Dec;27(3):357-66 PMID: 11719288
  49. A genomic view of alternative splicing.
    Nat Genet. 2002 Jan;30(1):13-9 PMID: 11753382
  50. Alu repeats and human genomic diversity.
    Nat Rev Genet. 2002 May;3(5):370-9 PMID: 11988762
  51. Altered editing of serotonin 2C receptor pre-mRNA in the prefrontal cortex of depressed suicide victims.
    Neuron. 2002 Apr 25;34(3):349-56 PMID: 11988167
  52. Structural determinants of BRCA1 translational regulation.
    J Biol Chem. 2002 May 10;277(19):17349-58 PMID: 11877386
  53. Alu-containing exons are alternatively spliced.
    Genome Res. 2002 Jul;12(7):1060-7 PMID: 12097342
  54. Selective stimulation of translational expression by Alu RNA.
    Nucleic Acids Res. 2002 Jul 15;30(14):3253-61 PMID: 12136107
  55. RNA editing by adenosine deaminases generates RNA and protein diversity.
    Biochimie. 2002 Aug;84(8):791-803 PMID: 12457566
  56. Conservation of human alternative splice events in mouse.
    Nucleic Acids Res. 2003 May 15;31(10):2544-52 PMID: 12736303
  57. Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes.
    BMC Genomics. 2006;7:133 PMID: 16740159
  58. Alu elements within human mRNAs are probable microRNA targets.
    Trends Genet. 2006 Oct;22(10):532-6 PMID: 16914224
  59. RNA editing level in the mouse is determined by the genomic repeat repertoire.
    RNA. 2006 Oct;12(10):1802-9 PMID: 16940548
  60. PKR; a sentinel kinase for cellular stress.
    Oncogene. 1999 Nov 1;18(45):6112-20 PMID: 10557102
  61. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements.
    Gene. 1999 Sep 30;238(1):115-34 PMID: 10570990
  62. Systematic identification of abundant A-to-I editing sites in the human transcriptome.
    Nat Biotechnol. 2004 Aug;22(8):1001-5 PMID: 15258596
  63. From "junk" to gene: curriculum vitae of a primate receptor isoform gene.
    J Mol Biol. 2004 Aug 20;341(4):883-6 PMID: 15328599
  64. Widespread RNA editing of embedded alu elements in the human transcriptome.
    Genome Res. 2004 Sep;14(9):1719-25 PMID: 15342557
  65. Selfish DNA: the ultimate parasite.
    Nature. 1980 Apr 17;284(5757):604-7 PMID: 7366731
  66. Selfish DNA.
    Nature. 1980 Dec 25;288(5792):645-6 PMID: 7453798
  67. Structure, polymorphism, and novel repeated DNA elements revealed by a complete sequence of the human alpha-fetoprotein gene.
    Biochemistry. 1987 Mar 10;26(5):1332-43 PMID: 2436661
  68. Alu RNA secondary structure consists of two independent 7 SL RNA-like folding units.
    J Biol Chem. 1991 May 15;266(14):8675-8 PMID: 1709156
  69. Binding sites of the 9- and 14-kilodalton heterodimeric protein subunit of the signal recognition particle (SRP) are contained exclusively in the Alu domain of SRP RNA and contain a sequence motif that is conserved in evolution.
    Mol Cell Biol. 1991 Aug;11(8):3949-59 PMID: 1712900
  70. Fusion of a free left Alu monomer and a free right Alu monomer at the origin of the Alu family in the primate genomes.
    Nucleic Acids Res. 1992 Feb 11;20(3):487-93 PMID: 1741283
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
Published
2006-00-00
Epub
2006-00-04
Pages
5491-7
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1636486
Subset
IM
Corrections
ErratumIn
-
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com