Abstract
Elucidation of complete nucleotide sequence of the human has revealed that coding sequences that store the information needed to synthesize functional proteins, occupy only 2% of the genomic region. The remaining 98%, barring few regulatory sequences, has been referred to as non-functional or junk DNA and consists of many kinds of repeat elements. In fact, human genome is the most repeat rich genome sequenced so far, in which more than half of the region is occupied by such sequences. Determination of significance of these repeats in the human genome has become the focus of many studies all over the world, especially after genome sequencing did not reveal any significant difference in coding regions between lower eukaryotes and human. In this article, we have focused on Alu repeats that are primate specific elements with many interesting biological properties. Moreover, these are the repeats with highest copy number in the human genome. We have highlighted different facets of their interaction with the genome and changing paradigms regarding their role in genome organization.
Similar content being viewed by others
References
F. Antequera A. Bird (1993) ArticleTitleNumber of CpG islands and genes in human and mouse Proc. Natl. Acad. Sci. USA 90 11995–11999 Occurrence Handle1:CAS:528:DyaK2cXntVKmuw%3D%3D Occurrence Handle7505451
S.S. Arcot T.H. Shaikh J. Kim L. Bennett M. Alegria-Hartman (1995a) ArticleTitleSequence diversity and chromosomal distribution of “young” Alu repeats Gene 163 273–278 Occurrence Handle10.1016/0378-1119(95)00317-Y Occurrence Handle1:CAS:528:DyaK2MXosVOgsL0%3D
S.S. Arcot Z. Wang J.L. Weber P.L. Deininger M.A. Batzer (1995b) ArticleTitleAlu repeats: a source for the genesis of primate microsatellites Genomics 29 136–144 Occurrence Handle10.1006/geno.1995.1224 Occurrence Handle1:CAS:528:DyaK2MXotF2htbc%3D
P. Arnaud C. Goubely T. Pelissier J.M. Deragon (2000) ArticleTitleSINE retroposons can be used in vivo as nucleation centers for de novo methylation Mol. Cell Biol. 20 3434–3441 Occurrence Handle10.1128/MCB.20.10.3434-3441.2000 Occurrence Handle1:CAS:528:DC%2BD3cXivFyhtrk%3D Occurrence Handle10779333
V. Babich N. Aksenov V. Alexeenko S.L. Oei G. Buchlow (1999) ArticleTitleAssociation of some potential hormone response elements in human genes with the Alu family repeats Gene 239 341–349 Occurrence Handle10.1016/S0378-1119(99)00391-1 Occurrence Handle1:CAS:528:DyaK1MXntVSntrs%3D Occurrence Handle10548736
A.D. Bailey C.K. Shen (1993) ArticleTitleSequential insertion of Alu family repeats into specific genomic sites of higher primates Proc. Natl. Acad. Sci. USA 90 7205–7209 Occurrence Handle1:CAS:528:DyaK3sXlsFeiu7c%3D Occurrence Handle8394013
W.J. Bailey D.H. Fitch D.A. Tagle J. Czelusniak J.L. Slightom (1991) ArticleTitleMolecular evolution of the psi eta-globin gene locus: gibbon phylogeny and the hominoid slowdown Mol. Biol. Evol. 8 155–184 Occurrence Handle1:CAS:528:DyaK3MXks1Grsbs%3D Occurrence Handle2046542
M.A. Batzer P.L. Deininger (2002) ArticleTitleAlu repeats and human genomic diversity Nat. Rev. Genet. 3 370–379 Occurrence Handle10.1038/nrg798 Occurrence Handle1:CAS:528:DC%2BD38Xjs1yhtbg%3D Occurrence Handle11988762
M.A. Batzer C.M. Rubin U. Hellmann-Blumberg M. Alegria-Hartman E.P. Leeflang (1995) ArticleTitleDispersion and insertion polymorphism in two small subfamilies of recently amplified human Alu repeats J. Mol. Biol. 247 418–427 Occurrence Handle10.1006/jmbi.1994.0150 Occurrence Handle1:CAS:528:DyaK2MXkvFSlt7c%3D Occurrence Handle7714898
M.A. Batzer P.L. Deininger U. Hellmann-Blumberg J. Jurka D. Labuda (1996) ArticleTitleStandardized nomenclature for Alu repeats J. Mol. Evol. 42 3–6 Occurrence Handle1:CAS:528:DyaK28XntFOntA%3D%3D Occurrence Handle8576960
A.P. Bird (1980) ArticleTitleDNA methylation and the frequency of CpG in animal DNA Nucleic Acids Res. 8 1499–1504 Occurrence Handle1:CAS:528:DyaL3cXktVantb8%3D Occurrence Handle6253938
J.D. Boeke (1997) ArticleTitleLINEs and Alus–the polyA connection Nat. Genet. 16 6–7 Occurrence Handle10.1038/ng0597-6 Occurrence Handle1:CAS:528:DyaK2sXivFKhs7Y%3D Occurrence Handle9140383
S.K. Brahmachari G. Meera P.S. Sarkar P. Balagurumoorthy J. Tripathi (1995) ArticleTitleSimple repetitive sequences in the genome: structure and functional significance Electrophoresis 16 1705–1714 Occurrence Handle10.1002/elps.11501601283 Occurrence Handle1:CAS:528:DyaK2MXovV2lt7w%3D Occurrence Handle8582360
A.T. Brini G.M. Lee J.P. Kinet (1993) ArticleTitleInvolvement of Alu sequences in the cell-specific regulation of transcription of the gamma chain of Fc and T cell receptors J. Biol. Chem. 268 1355–1361 Occurrence Handle1:CAS:528:DyaK3sXpsFCqtQ%3D%3D Occurrence Handle8419337
R.J. Britten (1994) ArticleTitleEvidence that most human Alu sequences were inserted in a process that ceased about 30 million years ago Proc. Natl. Acad. Sci. USA 91 6148–6150 Occurrence Handle1:CAS:528:DyaK2cXksl2hu7Y%3D Occurrence Handle8016128
J. Brosius (1991) ArticleTitleRetroposons–seeds of evolution Science 251 753 Occurrence Handle1:STN:280:By6C3MfgtFU%3D Occurrence Handle1990437
J. Brosius (1999) ArticleTitleRNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements Gene 238 115–134 Occurrence Handle10.1016/S0378-1119(99)00227-9 Occurrence Handle1:CAS:528:DyaK1MXntFKnurY%3D Occurrence Handle10570990
E. Brownell Mittereder N. N.R. Rice (1989) ArticleTitleA human rel proto-oncogene cDNA containing an Alu fragment as a potential coding exon Oncogene 4 935–942 Occurrence Handle1:CAS:528:DyaK3cXhslegsr0%3D Occurrence Handle2666912
V. Campuzano L. Montermini M.D. Molto L. Pianese M. Cossee (1996) ArticleTitleFriedreich’s ataxia: autosomal recessive disease caused by an intronic GAA triplet repeat expansion Science 271 1423–1427 Occurrence Handle1:CAS:528:DyaK28XhsFegtbk%3D Occurrence Handle8596916
C. Chauhan D. Dash D. Grover J. Rajamani M. Mukerji (2002) ArticleTitleOrigin and instability of GAA repeats: insights from Alu elements J. Biomol. Struct. Dyn. 20 253–263 Occurrence Handle1:CAS:528:DC%2BD38Xos1Ckt7g%3D Occurrence Handle12354077
S.J. Chen Z. Chen M.P. Font L. d’Auriol C.J. Larsen (1989) ArticleTitleStructural alterations of the BCR and ABL genes in Ph1 positive acute leukemias with rearrangements in the BCR gene first intron: further evidence implicating Alu sequences in the chromosome translocation Nucleic Acids Res. 17 7631–7642 Occurrence Handle1:CAS:528:DyaL1MXmt1KnsLw%3D Occurrence Handle2678002
M. Conrad S.K. Brahmachari V. Sasisekharan (1986) ArticleTitleDNA structural variability as a factor in gene expression and evolution Biosystems 19 123–126 Occurrence Handle10.1016/0303-2647(86)90024-9 Occurrence Handle1:CAS:528:DyaL28XlsVOmsLY%3D Occurrence Handle3730535
D.N. Cooper H. Youssoufian (1988) ArticleTitleThe CpG dinucleotide and human genetic disease Hum. Genet. 78 151–155 Occurrence Handle1:CAS:528:DyaL1cXhs1amtrc%3D Occurrence Handle3338800
P.L. Deininger M.A. Batzer (1999) ArticleTitleAlu repeats and human disease Mol. Genet. Metab. 67 183–193 Occurrence Handle10.1006/mgme.1999.2864 Occurrence Handle1:CAS:528:DyaK1MXjvFWrtr4%3D Occurrence Handle10381326
S. Delgado M. Gomez A. Bird F. Antequera (1998) ArticleTitleInitiation of DNA replication at CpG islands in mammalian chromosomes EMBO J. 17 2426–2435 Occurrence Handle10.1093/emboj/17.8.2426 Occurrence Handle1:CAS:528:DyaK1cXivFOmt74%3D Occurrence Handle9545253
M. Dewannieux C. Esnault T. Heidmann (2003) ArticleTitleLINE-mediated retrotransposition of marked Alu sequences Nat. Genet. 35 41–48 Occurrence Handle10.1038/ng1223 Occurrence Handle1:CAS:528:DC%2BD3sXmslemu70%3D Occurrence Handle12897783
E.P. Economou A.W. Bergen A.C. Warren S.E. Antonarakis (1990) ArticleTitleThe polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome Proc. Natl. Acad. Sci. USA 87 2951–2954 Occurrence Handle1:CAS:528:DyaK3cXktFykt7k%3D Occurrence Handle2326257
E.W. Englander B.H. Howard (1995) ArticleTitleNucleosome positioning by human Alu elements in chromatin J. Biol. Chem. 270 10091–10096 Occurrence Handle1:CAS:528:DyaK2MXltlWns7Y%3D Occurrence Handle7730313
E.W. Englander A.P. Wolffe B.H. Howard (1993) ArticleTitleNucleosome interactions with a human Alu element. Transcriptional repression and effects of template methylation J. Biol. Chem. 268 19565–19573 Occurrence Handle1:CAS:528:DyaK3sXltFSntb8%3D Occurrence Handle8366099
T.G. Fanning M.F. Singer (1987) ArticleTitleLINE-1: a mammalian transposable element Biochim. Biophys. Acta 910 203–212 Occurrence Handle1:CAS:528:DyaL1cXjt1OgtA%3D%3D Occurrence Handle2445384
Q. Feng J.V. Moran H.H. Kazazian SuffixJr. J.D. Boeke (1996) ArticleTitleHuman L1 retrotransposon encodes a conserved endonuclease required for retrotransposition Cell 87 905–916 Occurrence Handle10.1016/S0092-8674(00)81997-2 Occurrence Handle1:CAS:528:DyaK28Xntlyru78%3D Occurrence Handle8945517
A.J. Fornace SuffixJr. J.B. Mitchell (1986) ArticleTitleInduction of B2 RNA polymerase III transcription by heat shock: enrichment for heat shock induced sequences in rodent cells by hybridization subtraction Nucleic Acids Res. 14 5793–5811 Occurrence Handle1:CAS:528:DyaL28Xls1KjtLg%3D Occurrence Handle2426659
D. Fornasari E. Battaglioli A. Flora S. Terzano F. Clementi (1997) ArticleTitleStructural and functional characterization of the human alpha3 nicotinic subunit gene promoter Mol. Pharmacol. 51 250–261 Occurrence Handle1:CAS:528:DyaK2sXhtlWms7k%3D Occurrence Handle9203630
M. Gardiner-Garden M. Frommer (1987) ArticleTitleCpG islands in vertebrate genomes J. Mol. Biol. 196 261–282 Occurrence Handle1:CAS:528:DyaL2sXlt1ygsrc%3D Occurrence Handle3656447
D. Gebow N. Miselis H.L. Liber (2000) ArticleTitleHomologous and nonhomologous recombination resulting in deletion: effects of p53 status, microhomology, and repetitive DNA length and orientation Mol. Cell Biol. 20 4028–4035 Occurrence Handle10.1128/MCB.20.11.4028-4035.2000 Occurrence Handle1:CAS:528:DC%2BD3cXjt1Cmtr4%3D Occurrence Handle10805745
N. Gharani D.M. Waterworth S. Batty D. White C. Gilling-Smith (1997) ArticleTitleAssociation of the steroid synthesis gene CYP11a with polycystic ovary syndrome and hyperandrogenism Hum. Mol. Genet. 6 397–402 Occurrence Handle10.1093/hmg/6.3.397 Occurrence Handle1:CAS:528:DyaK2sXhvFKlsbc%3D Occurrence Handle9147642
J.M. Greally (2002) ArticleTitleShort interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome Proc. Natl. Acad. Sci. USA 99 327–332 Occurrence Handle10.1073/pnas.012539199 Occurrence Handle1:CAS:528:DC%2BD38Xlt1Clsw%3D%3D Occurrence Handle11756672
D. Grover P.P. Majumder C.B. Rao S.K. Brahmachari M. Mukerji (2003) ArticleTitleNonrandom distribution of alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22 Mol. Biol. Evol. 20 1420–1424 Occurrence Handle1:CAS:528:DC%2BD3sXntlantL0%3D Occurrence Handle12832639
Grover, D., M. Mukerji, P. Bhatnagar, K. Kannan & S.K. Brahmachari, 2004. Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition. Bioinformatics
J.E. Hambor J. Mennone M.E. Coon J.H. Hanke P. Kavathas (1993) ArticleTitleIdentification and characterization of an Alu-containing, T-cell-specific enhancer located in the last intron of the human CD8 alpha gene Mol. Cell Biol. 13 7056–7070 Occurrence Handle1:CAS:528:DyaK2cXisV2hug%3D%3D Occurrence Handle8413295
H.K. Hamdi H. Nishio J. Tavis R. Zielinski A. Dugaiczyk (2000) ArticleTitleAlu-mediated phylogenetic novelties in gene regulation and development J. Mol. Biol. 299 931–939 Occurrence Handle10.1006/jmbi.2000.3795 Occurrence Handle1:CAS:528:DC%2BD3cXjvVSrsr8%3D Occurrence Handle10843848
K.N. Hogeveen M. Talikka G.L. Hammond (2001) ArticleTitleHuman sex hormone-binding globulin promoter activity is influenced by a (TAAAA)n repeat element within an Alu sequence J. Biol. Chem. 276 36383–36390 Occurrence Handle10.1074/jbc.M104681200 Occurrence Handle1:CAS:528:DC%2BD3MXnt1yrsbY%3D Occurrence Handle11473114
C.M. Houck F.P. Rinehart C.W. Schmid (1979) ArticleTitleA ubiquitous family of repeated DNA sequences in the human genome J. Mol. Biol. 132 289–306 Occurrence Handle10.1016/0022-2836(79)90261-4 Occurrence Handle1:CAS:528:DyaE1MXlslantLk%3D Occurrence Handle533893
P. Jagadeeswaran B.G. Forget S.M. Weissman (1981) ArticleTitleShort interspersed repetitive DNA elements in eucaryotes: transposable DNA elements generated by reverse transcription of RNA pol III transcripts? Cell 26 141–142 Occurrence Handle10.1016/0092-8674(81)90296-8 Occurrence Handle1:CAS:528:DyaL38XivFarsw%3D%3D Occurrence Handle6277493
A.R. Jeffs S.M. Benjes T.L. Smith S.J. Sowerby C.M. Morris (1998) ArticleTitleThe BCR gene recombines preferentially with Alu elements in complex BCR-ABL translocations of chronic myeloid leukaemia Hum. Mol. Genet. 7 767–776 Occurrence Handle10.1093/hmg/7.5.767 Occurrence Handle1:CAS:528:DyaK1cXjsVaksrs%3D Occurrence Handle9536079
P.A. Jones D. Takai (2001) ArticleTitleThe role of DNA methylation in mammalian epigenetics Science 293 1068–1070 Occurrence Handle10.1126/science.1063852 Occurrence Handle1:CAS:528:DC%2BD3MXmtVWlsbY%3D Occurrence Handle11498573
P.A. Jones W.M. Rideout SuffixIII J.C. Shen C.H. Spruck Y.C. Tsai (1992) ArticleTitleMethylation, mutation and cancer Bioessays 14 33–36 Occurrence Handle1:CAS:528:DyaK38XhslWiurg%3D Occurrence Handle1546979
P.L. Jones G.J. Veenstra P.A. Wade D. Vermaak S.U. Kass (1998) ArticleTitleMethylated DNA and MeCP2 recruit histone deacetylase to repress transcription Nat. Genet. 19 187–191 Occurrence Handle10.1038/561 Occurrence Handle1:CAS:528:DyaK1cXls1Cqsbg%3D Occurrence Handle9620779
J. Jurka (1997) ArticleTitleSequence patterns indicate an enzymatic involvement in integration of mammalian retroposons Proc. Natl. Acad. Sci. USA 94 1872–1877 Occurrence Handle10.1073/pnas.94.5.1872 Occurrence Handle1:CAS:528:DyaK2sXhslaqtLo%3D Occurrence Handle9050872
J. Jurka C. Pethiyagoda (1995) ArticleTitleSimple repetitive DNA sequences from primates: compilation and analysis J. Mol. Evol. 40 120–126 Occurrence Handle10.1007/BF00167107 Occurrence Handle1:CAS:528:DyaK2MXjsVyksb4%3D Occurrence Handle7699718
V. Kapitonov J. Jurka (1996) ArticleTitleThe age of Alu subfamilies J. Mol. Evol. 42 59–65 Occurrence Handle10.1007/BF00163212 Occurrence Handle1:CAS:528:DyaK28XntFOmtg%3D%3D Occurrence Handle8576965
D.D. Kim T.T. Kim T. Walsh Y. Kobayashi T.C. Matise (2004) ArticleTitleWidespread RNA editing of embedded alu elements in the human transcriptome Genome Res. 14 1719–1725 Occurrence Handle10.1101/gr.2855504 Occurrence Handle1:CAS:528:DC%2BD2cXnsFGjsb8%3D Occurrence Handle15342557
B. Knebelmann L. Forestier L. Drouot S. Quinones C. Chuet (1995) ArticleTitleSplice-mediated insertion of an Alu sequence in the COL4A3 mRNA causing autosomal recessive Alport syndrome Hum. Mol. Genet. 4 675–679 Occurrence Handle1:CAS:528:DyaK2MXltlSju7k%3D Occurrence Handle7633417
J.R. Korenberg M.C. Rykowski (1988) ArticleTitleHuman genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands Cell 53 391–400 Occurrence Handle10.1016/0092-8674(88)90159-6 Occurrence Handle1:CAS:528:DyaL1cXktlejtbw%3D Occurrence Handle3365767
J. Kreahling B.R. Graveley (2004) ArticleTitleThe origins and implications of Aluternative splicing Trends Genet. 20 1–4 Occurrence Handle10.1016/j.tig.2003.11.001 Occurrence Handle1:CAS:528:DC%2BD3sXpvFyrsb8%3D Occurrence Handle14698612
E.S. Lander L.M. Linton B. Birren C. Nusbaum M.C. Zody (2001) ArticleTitleInitial sequencing and analysis of the human genome Nature 409 860–921 Occurrence Handle10.1038/35057062 Occurrence Handle1:CAS:528:DC%2BD3MXhsFCjtLc%3D Occurrence Handle11237011
F. Larsen G. Gundersen R. Lopez H. Prydz (1992) ArticleTitleCpG islands as gene markers in the human genome Genomics 13 1095–1107 Occurrence Handle10.1016/0888-7543(92)90024-M Occurrence Handle1:CAS:528:DyaK3sXhs1aitL0%3D Occurrence Handle1505946
E.P. Leeflang I.N. Chesnokov C.W. Schmid (1993) ArticleTitleMobility of short interspersed repeats within the chimpanzee lineage J. Mol. Evol. 37 566–572 Occurrence Handle1:CAS:528:DyaK2cXkslWnsQ%3D%3D Occurrence Handle8114109
E.Y. Levanon E. Eisenberg R. Yelin S. Nemzer M. Hallegger (2004) ArticleTitleSystematic identification of abundant A-to-I editing sites in the human transcriptome Nat. Biotechnol. 22 1001–1005 Occurrence Handle10.1038/nbt996 Occurrence Handle1:CAS:528:DC%2BD2cXmtFWru7w%3D Occurrence Handle15258596
V.G. Levitsky O.A. Podkolodnaya N.A. Kolchanov N.L. Podkolodny (2001a) ArticleTitleNucleosome formation potential of eukaryotic DNA: calculation and promoters analysis Bioinformatics 17 998–1010 Occurrence Handle1:CAS:528:DC%2BD38XisFKqsQ%3D%3D
V.G. Levitsky O.A. Podkolodnaya N.A. Kolchanov N.L. Podkolodny (2001b) ArticleTitleNucleosome formation potential of exons, introns, and Alu repeats Bioinformatics 17 1062–1064 Occurrence Handle1:CAS:528:DC%2BD38XisFOjsw%3D%3D
E. Li C. Beard R. Jaenisch (1993) ArticleTitleRole for DNA methylation in genomic imprinting Nature 366 362–365 Occurrence Handle1:CAS:528:DyaK2cXlsFCm Occurrence Handle8247133
W.M. Liu W.M. Chu P.V. Choudary C.W. Schmid (1995) ArticleTitleCell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts Nucleic Acids Res. 23 1758–1765 Occurrence Handle1:CAS:528:DyaK2MXmsVOksL0%3D Occurrence Handle7784180
K.S. Lobachev J.E. Stenger O.G. Kozyreva J. Jurka D.A. Gordenin (2000) ArticleTitleInverted Alu repeats unstable in yeast are excluded from the human genome EMBO J. 19 3822–3830 Occurrence Handle10.1093/emboj/19.14.3822 Occurrence Handle1:CAS:528:DC%2BD3cXmtlegsLk%3D Occurrence Handle10899135
D.D. Luan M.H. Korman J.L. Jakubczak T.H. Eickbush (1993) ArticleTitleReverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition Cell 72 595–605 Occurrence Handle10.1016/0092-8674(93)90078-5 Occurrence Handle1:CAS:528:DyaK3sXhs1ansrc%3D Occurrence Handle7679954
M. Ludwig K.D. Wohn W.D. Schleuning K. Olek (1992) ArticleTitleAllelic dimorphism in the human tissue-type plasminogen activator (TPA) gene as a result of an Alu insertion/deletion event Hum. Genet. 88 388–392 Occurrence Handle1:CAS:528:DyaK38XisV2ksrw%3D Occurrence Handle1346771
W. Makalowski (2003) ArticleTitleGenomics. Not junk after all Science 300 1246–1247 Occurrence Handle10.1126/science.1085690 Occurrence Handle1:CAS:528:DC%2BD3sXlt1Sjsrw%3D Occurrence Handle12764185
S.L. Mathias A.F. Scott H.H. Kazazian SuffixJr. J.D. Boeke A. Gabriel (1991) ArticleTitleReverse transcriptase encoded by a human transposable element Science 254 1808–1810 Occurrence Handle1:CAS:528:DyaK38XhtVSlsrs%3D Occurrence Handle1722352
G.S. McHaffie S.H. Ralston (1995) ArticleTitleOrigin of a negative calcium response element in an ALU-repeat: implications for regulation of gene expression by extracellular calcium Bone 17 11–14 Occurrence Handle10.1016/8756-3282(95)00131-V Occurrence Handle1:CAS:528:DyaK2MXnt1Omu7k%3D Occurrence Handle7577152
A.J. Mighell A.F. Markham P.A. Robinson (1997) ArticleTitleAlu sequences FEBS Lett. 417 1–5 Occurrence Handle10.1016/S0014-5793(97)01259-3 Occurrence Handle1:CAS:528:DyaK2sXntVOhs7c%3D Occurrence Handle9395063
G.A. Mitchell D. Labuda G. Fontaine J.M. Saudubray J.P. Bonnefont (1991) ArticleTitleSplice-mediated insertion of an Alu sequence inactivates ornithine delta-aminotransferase: a role for Alu elements in human mutation Proc. Natl. Acad. Sci. USA 88 815–819 Occurrence Handle1:CAS:528:DyaK3MXhtFKhsr4%3D Occurrence Handle1992472
R.K. Moyzis D.C. Torney J. Meyne J.M. Buckingham J.R. Wu (1989) ArticleTitleThe distribution of interspersed repetitive DNA sequences in the human genome Genomics 4 273–289 Occurrence Handle10.1016/0888-7543(89)90331-5 Occurrence Handle1:CAS:528:DyaL1MXktVWrtLY%3D Occurrence Handle2714792
X. Nan H.H. Ng C.A. Johnson C.D. Laherty B.M. Turner (1998) ArticleTitleTranscriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex Nature 393 386–389 Occurrence Handle1:CAS:528:DyaK1cXjsFKgurc%3D Occurrence Handle9620804
A. Nekrutenko W.H. Li (2001) ArticleTitleTransposable elements are found in a large number of human protein-coding genes Trends Genet. 17 619–621 Occurrence Handle10.1016/S0168-9525(01)02445-3 Occurrence Handle1:CAS:528:DC%2BD3MXnslemtL8%3D Occurrence Handle11672845
T. Niu X. Chen X. Xu (2002) ArticleTitleAngiotensin converting enzyme gene insertion/deletion polymorphism and cardiovascular disease: therapeutic implications Drugs 62 977–993 Occurrence Handle10.2165/00003495-200262070-00001 Occurrence Handle1:CAS:528:DC%2BD38XksVKqs7Y%3D Occurrence Handle11985486
J. Norris D. Fan C. Aleman J.R. Marks P.A. Futreal (1995) ArticleTitleIdentification of a new subclass of Alu DNA repeats which can function as estrogen receptor-dependent transcriptional enhancers J. Biol. Chem. 270 22777–22782 Occurrence Handle1:CAS:528:DyaK2MXosFOqurg%3D Occurrence Handle7559405
S.L. Oei V.S. Babich V.I. Kazakov N.M. Usmanova A.V. Kropotov (2004) ArticleTitleClusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters Genomics 83 873–882 Occurrence Handle10.1016/j.ygeno.2003.11.001 Occurrence Handle1:CAS:528:DC%2BD2cXivFGnsr0%3D Occurrence Handle15081116
S. Ohno T. Yomo (1991) ArticleTitleThe grammatical rule for all DNA: junk and coding sequences Electrophoresis 12 103–108 Occurrence Handle10.1002/elps.1150120203 Occurrence Handle1:CAS:528:DyaK3MXktVantLc%3D Occurrence Handle2040257
Y. Ohshima Y. Gotoh (1987) ArticleTitleSignals for the selection of a splice site in pre-mRNA. Computer analysis of splice junction sequences and like sequences J. Mol. Biol. 195 247–259 Occurrence Handle10.1016/0022-2836(87)90647-4 Occurrence Handle1:STN:280:BieD3M7isVU%3D Occurrence Handle3656413
L.E. Orgel F.H. Crick C. Sapienza (1980) ArticleTitleSelfish DNA Nature 288 645–646 Occurrence Handle10.1038/288645a0 Occurrence Handle1:STN:280:Bi6D1MfpsVI%3D Occurrence Handle7453798
M.A. Pasha A.P. Khan R. Kumar R.B. Ram S.K. Grover (2002) ArticleTitleVariations in angiotensin-converting enzyme gene insertion/deletion polymorphism in Indian populations of different ethnic origins J. Biosci. 27 67–70 Occurrence Handle1:CAS:528:DC%2BD38Xjt1Ciu74%3D Occurrence Handle11927778
C. Perez-Stable C.K. Shen (1986) ArticleTitleCompetitive and cooperative functioning of the anterior and posterior promoter elements of an Alu family repeat Mol. Cell Biol. 6 2041–2052 Occurrence Handle1:CAS:528:DyaL28XksFGmsL8%3D Occurrence Handle3023916
A.G. Polson P.F. Crain S.C. Pomerantz J.A. McCloskey B.L. Bass (1991) ArticleTitleThe mechanism of adenosine to inosine conversion by the double-stranded RNA unwinding/modifying activity: a high-performance liquid chromatography-mass spectrometry analysis Biochemistry 30 11507–11514 Occurrence Handle10.1021/bi00113a004 Occurrence Handle1:CAS:528:DyaK3MXmslCns7g%3D Occurrence Handle1747369
C.G. Proud (1995) ArticleTitlePKR: a new name and new roles Trends Biochem. Sci. 20 241–246 Occurrence Handle10.1016/S0968-0004(00)89025-8 Occurrence Handle1:CAS:528:DyaK2MXmtlaqu7w%3D Occurrence Handle7631421
Y. Quentin (1994a) ArticleTitleA master sequence related to a free left Alu monomer (FLAM) at the origin of the B1 family in rodent genomes Nucleic Acids Res. 22 2222–2227 Occurrence Handle1:CAS:528:DyaK2cXltVWjsLs%3D
Y. Quentin (1994b) ArticleTitleEmergence of master sequences in families of retroposons derived from 7sl RNA Genetica 93 203–215 Occurrence Handle10.1007/BF01435252 Occurrence Handle1:CAS:528:DyaK2MXislOmtr4%3D
M.J. Rieder S.L. Taylor A.G. Clark D.A. Nickerson (1999) ArticleTitleSequence variation in the human angiotensin converting enzyme Nat. Genet. 22 59–62 Occurrence Handle10.1038/8760 Occurrence Handle1:CAS:528:DyaK1MXjtVags7g%3D Occurrence Handle10319862
J. Rogers (1983) ArticleTitleRetroposons defined Nature 301 460 Occurrence Handle10.1038/301460e0 Occurrence Handle1:STN:280:BiyC3MrjtVA%3D Occurrence Handle6185851
C.M. Rubin C.A. VandeVoort R.L. Teplitz C.W. Schmid (1994) ArticleTitleAlu repeated DNAs are differentially methylated in primate germ cells Nucleic Acids Res. 22 5121–5127 Occurrence Handle1:CAS:528:DyaK2MXisl2msL8%3D Occurrence Handle7800508
N.S. Rudiger N. Gregersen M.C. Kielland-Brandt (1995) ArticleTitleOne short well conserved region of Alu-sequences is involved in human gene rearrangements and has homology with prokaryotic chi Nucleic Acids Res. 23 256–260 Occurrence Handle1:STN:280:ByqC28nmsVI%3D Occurrence Handle7862530
C. Schmid R. Maraia (1992) ArticleTitleTranscriptional regulation and transpositional selection of active SINE sequences Curr. Opin. Genet. Dev. 2 874–882 Occurrence Handle10.1016/S0959-437X(05)80110-8 Occurrence Handle1:CAS:528:DyaK3sXktVWktLY%3D Occurrence Handle1335809
C.W. Schmid (1991) ArticleTitleHuman Alu subfamilies and their methylation revealed by blot hybridization Nucleic Acids Res. 19 5613–5617 Occurrence Handle1:CAS:528:DyaK3MXmslans7o%3D Occurrence Handle1945838
C.W. Schmid (1996) ArticleTitleAlu: structure, origin, evolution, significance and function of one-tenth of human DNA Prog. Nucleic Acid Res. Mol. Biol. 53 283–319 Occurrence Handle1:CAS:528:DyaK28XktlCms70%3D Occurrence Handle8650306
M.R. Shen M.A. Batzer P.L. Deininger (1991) ArticleTitleEvolution of the master Alu gene(s) J. Mol. Evol. 33 311–320 Occurrence Handle1:CAS:528:DyaK3MXmtVShs7w%3D Occurrence Handle1774786
M.R. Shen J. Brosius P.L. Deininger (1997) ArticleTitleBC1 RNA, the transcript from a master gene for ID element amplification, is able to prime its own reverse transcription Nucleic Acids Res. 25 1641–1648 Occurrence Handle1:CAS:528:DyaK2sXjt1amtL8%3D Occurrence Handle9092674
D. Sinnett C. Richer J.M. Deragon D. Labuda (1992) ArticleTitleAlu RNA transcripts in human embryonal carcinoma cells. Model of post-transcriptional selection of master sequences J. Mol. Biol. 226 689–706 Occurrence Handle10.1016/0022-2836(92)90626-U Occurrence Handle1:CAS:528:DyaK3sXltFSnsL4%3D Occurrence Handle1507221
V. Slagel E. Flemington V. Traina-Dorge H. Bradshaw P. Deininger (1987) ArticleTitleClustering and subfamily relationships of the Alu family in the human genome Mol. Biol. Evol. 4 19–29 Occurrence Handle1:CAS:528:DyaL2sXhtlaktrk%3D Occurrence Handle3128713
R. Sorek G. Ast D. Graur (2002) ArticleTitleAlu-containing exons are alternatively spliced Genome Res. 12 1060–1067 Occurrence Handle10.1101/gr.229302 Occurrence Handle1:CAS:528:DC%2BD38XlsVWgsr8%3D Occurrence Handle12097342
J.E. Stenger K.S. Lobachev D. Gordenin T.A. Darden J. Jurka (2001) ArticleTitleBiased distribution of inverted and direct Alus in the human genome: implications for insertion, exclusion, and genome stability Genome Res. 11 12–27 Occurrence Handle10.1101/gr.158801 Occurrence Handle1:CAS:528:DC%2BD3MXmsVCktw%3D%3D Occurrence Handle11156612
Z. Szabo S.A. Levi-Minzi A.M. Christiano C. Struminger M. Stoneking (1999) ArticleTitleSequential loss of two neighboring exons of the tropoelastin gene during primate evolution J. Mol. Evol. 49 664–671 Occurrence Handle1:CAS:528:DyaK1MXnsVajtro%3D Occurrence Handle10552047
D. Takai P.A. Jones (2003) ArticleTitleThe CpG island searcher: a new WWW resource In Silico. Biol. 3 235–240 Occurrence Handle1:CAS:528:DC%2BD3sXovFCqtbc%3D Occurrence Handle12954087
L.A. Tonkin L. Saccomanno D.P. Morse T. Brodigan M. Krause (2002) ArticleTitleRNA editing by ADARs is important for normal behavior in Caenorhabditis elegans EMBO J. 21 6025–6035 Occurrence Handle10.1093/emboj/cdf607 Occurrence Handle1:CAS:528:DC%2BD38XptFOrtrk%3D Occurrence Handle12426375
E.N. Trifonov (1997) ArticleTitle[Genetic level of DNA sequences is determined by superposition of many codes] Mol. Biol. (Mosk.) 31 759–767 Occurrence Handle1:STN:280:ByiH2Mzis1Q%3D
E. Ullu C. Tschudi (1984) ArticleTitleAlu sequences are processed 7SL RNA genes Nature 312 171–172 Occurrence Handle1:CAS:528:DyaL2MXktVymtw%3D%3D Occurrence Handle6209580
G. Vansant W.F. Reynolds (1995) ArticleTitleThe consensus sequence of a major Alu subfamily contains a functional retinoic acid response element Proc. Natl. Acad. Sci. USA 92 8229–8233 Occurrence Handle1:CAS:528:DyaK2MXnvVymt7w%3D Occurrence Handle7667273
R. Vervoort R. Gitzelmann W. Lissens I. Liebaers (1998) ArticleTitleA 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. 103 686–693 Occurrence Handle10.1007/s004390050892 Occurrence Handle1:CAS:528:DyaK1cXnvFSjurk%3D Occurrence Handle9921904
A.S. Waldman R.M. Liskay (1988) ArticleTitleDependence of intrachromosomal recombination in mammalian cells on uninterrupted homology Mol. Cell Biol. 8 5350–5357 Occurrence Handle1:CAS:528:DyaL1MXhvFemsQ%3D%3D Occurrence Handle2854196
M.R. Wallace L.B. Andersen A.M. Saulino P.E. Gregory T.W. Glover (1991) ArticleTitleA de novo Alu insertion results in neurofibromatosis type 1 Nature 353 864–866 Occurrence Handle10.1038/353864a0 Occurrence Handle1:CAS:528:DyaK3MXmslansrs%3D Occurrence Handle1719426
H. Watanabe A. Fujiyama M. Hattori T.D. Taylor A. Toyoda (2004) ArticleTitleDNA sequence and comparative analysis of chimpanzee chromosome 22 Nature 429 382–388 Occurrence Handle10.1038/nature02564 Occurrence Handle1:CAS:528:DC%2BD2cXkt1OnsLo%3D Occurrence Handle15164055
A.M. Weiner P.L. Deininger A. Efstratiadis (1986) ArticleTitleNonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information Annu. Rev. Biochem. 55 631–661 Occurrence Handle10.1146/annurev.bi.55.070186.003215 Occurrence Handle1:CAS:528:DyaL28Xlt1ygtbY%3D Occurrence Handle2427017
P. Yi W. Zhang Z. Zhai L. Miao Y. Wang (2003) ArticleTitleBcl-rambo beta, a special splicing variant with an insertion of an Alu-like cassette, promotes etoposide- and Taxol-induced cell death FEBS Lett. 534 61–68 Occurrence Handle10.1016/S0014-5793(02)03778-X Occurrence Handle1:CAS:528:DC%2BD3sXjt1Sktg%3D%3D Occurrence Handle12527362
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Grover, D., Kannan, K., Brahmachari, S.K. et al. ALU-ring elements in the primate genomes. Genetica 124, 273–289 (2005). https://doi.org/10.1007/s10709-005-3086-8
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/s10709-005-3086-8