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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Alu Elements

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Disease relevance of Alu Elements


High impact information on Alu Elements

  • We show that CCFDN is caused by a single-nucleotide substitution in an antisense Alu element in intron 6 of CTDP1 (encoding the protein phosphatase FCP1, an essential component of the eukaryotic transcription machinery), resulting in a rare mechanism of aberrant splicing and an Alu insertion in the processed mRNA [6].
  • Between these two segments the human sex chromosomes differ by the insertion of an Alu element on the Y chromosome [7].
  • Why then does RNA polymerase III transcribe the few 7SL genes so efficiently, while transcripts from the far more abundant Alu elements are not readily detectable [8]?
  • We find that a human 7SL gene and a synthetic Alu sequence derived from it are expressed 50-100-fold more efficiently in vitro than either a representative Alu element or two 7SL pseudogenes [8].
  • The sequences encoding the NGF receptor were molecularly cloned using the human Alu repetitive sequence as a probe [9].

Biological context of Alu Elements


Associations of Alu Elements with chemical compounds


Gene context of Alu Elements

  • Genomic analyses revealed that the breaks were close to Alu elements in intron 16 of MORF and intron 2 of CBP and that duplications had occurred near the breakpoints [19].
  • This function is carried out by the Alu domain, which consists of two proteins, SRP9 and SRP14, and the portion of SRP (7SL) RNA which is homologous to the Alu family of repetitive sequences [20].
  • The recombination site in the GPA gene was confirmed to be within an Alu repetitive sequence [21].
  • Unlike previously reported large germline deletions in BRCA1, neither breakpoint resides within an Alu element [22].
  • A significant lack of Alu elements was observed across the major and minor breakpoint cluster regions of BCR and across a 25-kb region showing a high frequency of breakage in ABL1 [23].

Analytical, diagnostic and therapeutic context of Alu Elements

  • PRINS harbors two Alu elements, it is transcribed by RNA polymerase II, and it is expressed at different levels in various human tissues [24].
  • Sequence analysis of the deletions showed that the 5' breakpoints occurred at different sites in the same Alu element in intron 15, while the 3' breakpoints were located in different Alu repeats in intron 17 [25].
  • Long-distance PCR amplified the genomic junction region, which involved the fusion of the 3' portion of an Alu element in intron 6 of MLL with the 5' portion of an Alu element in intron 7 of CBL [26].


  1. Adenovirus type 2 preferentially stimulates polymerase III transcription of Alu elements by relieving repression: a potential role for chromatin. Russanova, V.R., Driscoll, C.T., Howard, B.H. Mol. Cell. Biol. (1995) [Pubmed]
  2. Structure and expression of the c-sis gene and its relationship to sporadic meningiomas. Smidt, M., Dumanski, J.P., Collins, V.P., Ratner, L. Cancer Res. (1991) [Pubmed]
  3. Insertion of Alu element responsible for acute intermittent porphyria. Mustajoki, S., Ahola, H., Mustajoki, P., Kauppinen, R. Hum. Mutat. (1999) [Pubmed]
  4. Structure of DNA near long tandem arrays of alpha satellite DNA at the centromere of human chromosome 7. Wevrick, R., Willard, V.P., Willard, H.F. Genomics (1992) [Pubmed]
  5. Partially unspliced and fully spliced ELF3 mRNA, including a new Alu element in human breast cancer. Kaplan, M.H., Wang, X.P., Xu, H.P., Dosik, M.H. Breast Cancer Res. Treat. (2004) [Pubmed]
  6. Partial deficiency of the C-terminal-domain phosphatase of RNA polymerase II is associated with congenital cataracts facial dysmorphism neuropathy syndrome. Varon, R., Gooding, R., Steglich, C., Marns, L., Tang, H., Angelicheva, D., Yong, K.K., Ambrugger, P., Reinhold, A., Morar, B., Baas, F., Kwa, M., Tournev, I., Guerguelcheva, V., Kremensky, I., Lochmüller, H., Müllner-Eidenböck, A., Merlini, L., Neumann, L., Bürger, J., Walter, M., Swoboda, K., Thomas, P.K., von Moers, A., Risch, N., Kalaydjieva, L. Nat. Genet. (2003) [Pubmed]
  7. Population structure of the human pseudoautosomal boundary. Ellis, N., Taylor, A., Bengtsson, B.O., Kidd, J., Rogers, J., Goodfellow, P. Nature (1990) [Pubmed]
  8. Upstream sequences modulate the internal promoter of the human 7SL RNA gene. Ullu, E., Weiner, A.M. Nature (1985) [Pubmed]
  9. Gene transfer and molecular cloning of the human NGF receptor. Chao, M.V., Bothwell, M.A., Ross, A.H., Koprowski, H., Lanahan, A.A., Buck, C.R., Sehgal, A. Science (1986) [Pubmed]
  10. Chromosomal translocation mechanisms at intronic alu elements in mammalian cells. Elliott, B., Richardson, C., Jasin, M. Mol. Cell (2005) [Pubmed]
  11. DNA methylation in the Alu sequences of diploid and haploid primary human cells. Kochanek, S., Renz, D., Doerfler, W. EMBO J. (1993) [Pubmed]
  12. The polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome. Economou, E.P., Bergen, A.W., Warren, A.C., Antonarakis, S.E. Proc. Natl. Acad. Sci. U.S.A. (1990) [Pubmed]
  13. Distinctive sequence organization and functional programming of an Alu repeat promoter. Perez-Stable, C., Ayres, T.M., Shen, C.K. Proc. Natl. Acad. Sci. U.S.A. (1984) [Pubmed]
  14. Splice-mediated insertion of an Alu sequence inactivates ornithine delta-aminotransferase: a role for Alu elements in human mutation. Mitchell, G.A., Labuda, D., Fontaine, G., Saudubray, J.M., Bonnefont, J.P., Lyonnet, S., Brody, L.C., Steel, G., Obie, C., Valle, D. Proc. Natl. Acad. Sci. U.S.A. (1991) [Pubmed]
  15. Alu elements support independent origin of prosimian, platyrrhine, and catarrhine Mhc-DRB genes. Kriener, K., O'hUigin, C., Klein, J. Genome Res. (2000) [Pubmed]
  16. Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells. Kondo, Y., Issa, J.P. J. Biol. Chem. (2003) [Pubmed]
  17. Molecular analysis of DNA junctions produced by illegitimate recombination in human cells. Stary, A., Sarasin, A. Nucleic Acids Res. (1992) [Pubmed]
  18. Rat prostatic steroid binding protein: characterisation of the Alu element upstream of the C3 genes. Hurst, H.C., Parker, M.G. Nucleic Acids Res. (1984) [Pubmed]
  19. Fusion of the MORF and CBP genes in acute myeloid leukemia with the t(10;16)(q22;p13). Panagopoulos, I., Fioretos, T., Isaksson, M., Samuelsson, U., Billström, R., Strömbeck, B., Mitelman, F., Johansson, B. Hum. Mol. Genet. (2001) [Pubmed]
  20. Assembly of the Alu domain of the signal recognition particle (SRP): dimerization of the two protein components is required for efficient binding to SRP RNA. Strub, K., Walter, P. Mol. Cell. Biol. (1990) [Pubmed]
  21. Glycophorin B and glycophorin E genes arose from the glycophorin A ancestral gene via two duplications during primate evolution. Rearden, A., Magnet, A., Kudo, S., Fukuda, M. J. Biol. Chem. (1993) [Pubmed]
  22. Complex germline rearrangement of BRCA1 associated with breast and ovarian cancer. Payne, S.R., Newman, B., King, M.C. Genes Chromosomes Cancer (2000) [Pubmed]
  23. Nonrandom distribution of interspersed repeat elements in the BCR and ABL1 genes and its relation to breakpoint cluster regions. Jeffs, A.R., Wells, E., Morris, C.M. Genes Chromosomes Cancer (2001) [Pubmed]
  24. Identification and characterization of a novel, psoriasis susceptibility-related noncoding RNA gene, PRINS. Sonkoly, E., Bata-Csorgo, Z., Pivarcsi, A., Polyanka, H., Kenderessy-Szabo, A., Molnar, G., Szentpali, K., Bari, L., Megyeri, K., Mandi, Y., Dobozy, A., Kemeny, L., Szell, M. J. Biol. Chem. (2005) [Pubmed]
  25. Identification of Alu-mediated deletions in the Fanconi anemia gene FAA. Levran, O., Doggett, N.A., Auerbach, A.D. Hum. Mutat. (1998) [Pubmed]
  26. Identification of CBL, a proto-oncogene at 11q23.3, as a novel MLL fusion partner in a patient with de novo acute myeloid leukemia. Fu, J.F., Hsu, J.J., Tang, T.C., Shih, L.Y. Genes Chromosomes Cancer (2003) [Pubmed]
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