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Volumn 88, Issue 1, 2013, Pages 19-29

Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs

Author keywords

Boundary; Methylation; PiRNA; TFIIIC; Transposable element

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR III; TRANSCRIPTION FACTOR IIIC; UNCLASSIFIED DRUG;

EID: 84877910548     PISSN: 13417568     EISSN: 18805779     Source Type: Journal    
DOI: 10.1266/ggs.88.19     Document Type: Review
Times cited : (53)

References (118)
  • 1
    • 0021810791 scopus 로고
    • Transcription, processing and nuclear transport of a B1 Alu RNA species complementary to an intron of the murine alpha-fetoprotein gene
    • Adeniyi-Jones, S., and Zasloff, M. (1985) Transcription, processing and nuclear transport of a B1 Alu RNA species complementary to an intron of the murine alpha-fetoprotein gene. Nature 317, 81-84.
    • (1985) Nature , vol.317 , pp. 81-84
    • Adeniyi-Jones, S.1    Zasloff, M.2
  • 2
    • 4344579113 scopus 로고    scopus 로고
    • The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock
    • Allen, T. A., Von Kaenel, S., Goodrich, J. A., and Kugel, J. F. (2004) The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat. Struct. Mol. Biol. 11, 816-821.
    • (2004) Nat. Struct. Mol. Biol , vol.11 , pp. 816-821
    • Allen, T.A.1    von Kaenel, S.2    Goodrich, J.A.3    Kugel, J.F.4
  • 3
    • 17144380460 scopus 로고    scopus 로고
    • Functional roles of 3'-terminal structures of template RNA during in vivo retrotransposition of non-LTR retrotransposon, R1Bm
    • Anzai, T., Osanai, M., Hamada, M., and Fujiwara, H. (2005) Functional roles of 3'-terminal structures of template RNA during in vivo retrotransposition of non-LTR retrotransposon, R1Bm. Nucleic Acids Res. 33, 1993-2002.
    • (2005) Nucleic Acids Res , vol.33 , pp. 1993-2002
    • Anzai, T.1    Osanai, M.2    Hamada, M.3    Fujiwara, H.4
  • 4
    • 46149115158 scopus 로고    scopus 로고
    • Virus infection induces NFkappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression
    • Apostolou, E., and Thanos, D. (2008) Virus infection induces NFkappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression. Cell 134, 85-96.
    • (2008) Cell , vol.134 , pp. 85-96
    • Apostolou, E.1    Thanos, D.2
  • 5
    • 34248160438 scopus 로고    scopus 로고
    • Developmentally regulated piRNA clusters implicate MILI in transposon control
    • Aravin, A. A., Sachidanandam, R., Girard, A., Fejes-Toth, K., and Hannon, G. J. (2007) Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316, 744-747.
    • (2007) Science , vol.316 , pp. 744-747
    • Aravin, A.A.1    Sachidanandam, R.2    Girard, A.3    Fejes-Toth, K.4    Hannon, G.J.5
  • 6
    • 12344300804 scopus 로고    scopus 로고
    • Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome
    • Athanasiadis, A., Rich, A., and Maas, S. (2004) Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol. 2, e391.
    • (2004) PLoS Biol , vol.2
    • Athanasiadis, A.1    Rich, A.2    Maas, S.3
  • 7
    • 0024245366 scopus 로고
    • Small B2 RNAs in mouse oocytes, embryos, and somatic tissues
    • Bachvarova, R. (1988) Small B2 RNAs in mouse oocytes, embryos, and somatic tissues. Dev. Biol. 130, 513-523.
    • (1988) Dev. Biol , vol.130 , pp. 513-523
    • Bachvarova, R.1
  • 9
    • 0025063806 scopus 로고
    • DNA methylation inhibits transcription by RNA polymerase III of a tRNA gene, but not of a 5S rRNA gene
    • Besser, D., Gotz, F., Schulze-Forster, K., Wagner, H., Kroger, H., and Simon, D. (1990) DNA methylation inhibits transcription by RNA polymerase III of a tRNA gene, but not of a 5S rRNA gene. FEBS Lett. 269, 358-362.
    • (1990) FEBS Lett , vol.269 , pp. 358-362
    • Besser, D.1    Gotz, F.2    Schulze-Forster, K.3    Wagner, H.4    Kroger, H.5    Simon, D.6
  • 10
    • 79957660882 scopus 로고    scopus 로고
    • Human nucleosomes: Special role of CG dinucleotides and Alunucleosomes
    • Bettecken, T., Frenkel, Z. M., and Trifonov, E. N. (2011) Human nucleosomes: special role of CG dinucleotides and Alunucleosomes. BMC Genomics 12, 273.
    • (2011) BMC Genomics , vol.12 , pp. 273
    • Bettecken, T.1    Frenkel, Z.M.2    Trifonov, E.N.3
  • 11
    • 0036144048 scopus 로고    scopus 로고
    • DNA methylation patterns and epigenetic memory
    • Bird, A. (2002) DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6-21.
    • (2002) Genes Dev , vol.16 , pp. 6-21
    • Bird, A.1
  • 13
    • 4544223707 scopus 로고    scopus 로고
    • Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L
    • Bourc'his, D., and Bestor, T. H. (2004) Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431, 96-99.
    • (2004) Nature , vol.431 , pp. 96-99
    • Bourc'his, D.1    Bestor, T.H.2
  • 14
    • 0029796901 scopus 로고    scopus 로고
    • DNA sequence insertion and evolutionary variation in gene regulation
    • Britten, R. J. (1996) DNA sequence insertion and evolutionary variation in gene regulation. Proc. Natl. Acad. Sci. USA 93, 9374-9377.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 9374-9377
    • Britten, R.J.1
  • 16
    • 0031982714 scopus 로고    scopus 로고
    • Potential Alu function: Regulation of the activity of double-stranded RNA-activated kinase PKR
    • Chu, W. M., Ballard, R., Carpick, B. W., Williams, B. R., and Schmid, C. W. (1998) Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase PKR. Mol. Cell. Biol. 18, 58-68.
    • (1998) Mol. Cell. Biol , vol.18 , pp. 58-68
    • Chu, W.M.1    Ballard, R.2    Carpick, B.W.3    Williams, B.R.4    Schmid, C.W.5
  • 18
    • 0032559061 scopus 로고    scopus 로고
    • Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure
    • Cost, G. J., and Boeke, J. D. (1998) Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure. Biochemistry 37, 18081-18093.
    • (1998) Biochemistry , vol.37 , pp. 18081-18093
    • Cost, G.J.1    Boeke, J.D.2
  • 19
    • 0022388991 scopus 로고
    • Repeat sequence families derived from mammalian tRNA genes
    • Daniels, G. R., and Deininger, P. L. (1985) Repeat sequence families derived from mammalian tRNA genes. Nature 317, 819-822.
    • (1985) Nature , vol.317 , pp. 819-822
    • Daniels, G.R.1    Deininger, P.L.2
  • 20
    • 0036796354 scopus 로고    scopus 로고
    • Mammalian retroelements
    • Deininger, P. L., and Batzer, M. A. (2002) Mammalian retroelements. Genome Res. 12, 1455-1465.
    • (2002) Genome Res , vol.12 , pp. 1455-1465
    • Deininger, P.L.1    Batzer, M.A.2
  • 21
    • 0019868389 scopus 로고
    • Base sequence studies of 300 nucleotide renatured repeated human DNA clones
    • Deininger, P. L., Jolly, D. J., Rubin, C. M., Friedmann, T., and Schmid, C. W. (1981) Base sequence studies of 300 nucleotide renatured repeated human DNA clones. J. Mol. Biol. 151, 17-33.
    • (1981) J. Mol. Biol , vol.151 , pp. 17-33
    • Deininger, P.L.1    Jolly, D.J.2    Rubin, C.M.3    Friedmann, T.4    Schmid, C.W.5
  • 24
    • 18844365062 scopus 로고    scopus 로고
    • L1-mediated retrotransposition of murine B1 and B2 SINEs recapitulated in cultured cells
    • Dewannieux, M., and Heidmann, T. (2005) L1-mediated retrotransposition of murine B1 and B2 SINEs recapitulated in cultured cells. J. Mol. Biol. 349, 241-247.
    • (2005) J. Mol. Biol , vol.349 , pp. 241-247
    • Dewannieux, M.1    Heidmann, T.2
  • 25
    • 0041353551 scopus 로고    scopus 로고
    • LINEmediated retrotransposition of marked Alu sequences
    • Dewannieux, M., Esnault, C., and Heidmann, T. (2003) LINEmediated retrotransposition of marked Alu sequences. Nat. Genet. 35, 41-48.
    • (2003) Nat. Genet , vol.35 , pp. 41-48
    • Dewannieux, M.1    Esnault, C.2    Heidmann, T.3
  • 26
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., and Ren, B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376-380.
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1    Selvaraj, S.2    Yue, F.3    Kim, A.4    Li, Y.5    Shen, Y.6    Hu, M.7    Liu, J.S.8    Ren, B.9
  • 27
    • 0018894384 scopus 로고
    • Selfish genes, the phenotype paradigm and genome evolution
    • Doolittle, W. F., and Sapienza, C. (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284, 601-603.
    • (1980) Nature , vol.284 , pp. 601-603
    • Doolittle, W.F.1    Sapienza, C.2
  • 29
    • 0028951144 scopus 로고
    • Nucleosome positioning by human Alu elements in chromatin
    • Englander, E. W., and Howard, B. H. (1995) Nucleosome positioning by human Alu elements in chromatin. J. Biol. Chem. 270, 10091-10096.
    • (1995) J. Biol. Chem , vol.270 , pp. 10091-10096
    • Englander, E.W.1    Howard, B.H.2
  • 30
    • 0027304429 scopus 로고
    • Nucleosome interactions with a human Alu element. Transcriptional repression and effects of template methylation
    • Englander, E. W., Wolffe, A. P., and Howard, B. H. (1993) Nucleosome interactions with a human Alu element. Transcriptional repression and effects of template methylation. J. Biol. Chem. 268, 19565-19573.
    • (1993) J. Biol. Chem , vol.268 , pp. 19565-19573
    • Englander, E.W.1    Wolffe, A.P.2    Howard, B.H.3
  • 32
  • 33
    • 42349096534 scopus 로고    scopus 로고
    • Transposable elements and the evolution of regulatory networks
    • Feschotte, C. (2008) Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet. 9, 397-405.
    • (2008) Nat. Rev. Genet , vol.9 , pp. 397-405
    • Feschotte, C.1
  • 34
    • 0023056872 scopus 로고
    • Induction of B2 RNA polymerase III transcription by heat shock: Enrichment for heat shock induced sequences in rodent cells by hybridization subtraction
    • Fornace, A. J. Jr., and Mitchell, J. B. (1986) Induction 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.
    • (1986) Nucleic Acids Res , vol.14 , pp. 5793-5811
    • Fornace Jr., A.J.1    Mitchell, J.B.2
  • 35
    • 0035967858 scopus 로고    scopus 로고
    • The RNA polymerase III transcription apparatus
    • Geiduschek, E. P., and Kassavetis, G. A. (2001) The RNA polymerase III transcription apparatus. J. Mol. Biol. 310, 1-26.
    • (2001) J. Mol. Biol , vol.310 , pp. 1-26
    • Geiduschek, E.P.1    Kassavetis, G.A.2
  • 36
    • 33646145936 scopus 로고    scopus 로고
    • Do transposable elements really contribute to proteomes?
    • Gotea, V., and Makalowski, W. (2006) Do transposable elements really contribute to proteomes? Trends Genet. 22, 260-267.
    • (2006) Trends Genet , vol.22 , pp. 260-267
    • Gotea, V.1    Makalowski, W.2
  • 39
    • 33846021959 scopus 로고    scopus 로고
    • Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts
    • Ichiyanagi, K., Nakajima, R., Kajikawa, M., and Okada, N. (2007) Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts. Genome Res. 17, 33-41.
    • (2007) Genome Res , vol.17 , pp. 33-41
    • Ichiyanagi, K.1    Nakajima, R.2    Kajikawa, M.3    Okada, N.4
  • 41
    • 84877892296 scopus 로고    scopus 로고
    • Small RNAs and regulation of transposons in plants
    • Ito, H. (2013) Small RNAs and regulation of transposons in plants. Genes Genet. Syst. 88, 3-7.
    • (2013) Genes Genet. Syst , vol.88 , pp. 3-7
    • Ito, H.1
  • 42
    • 0019869111 scopus 로고
    • Short interspersed repetitive DNA elements in eucaryotes: Transposable DNA elements generated by reverse transcription of RNA pol III transcripts?
    • Jagadeeswaran, P., Forget, B. G., and Weissman, S. M. (1981) Short interspersed repetitive DNA elements in eucaryotes: transposable DNA elements generated by reverse transcription of RNA pol III transcripts? Cell 26, 141-142.
    • (1981) Cell , vol.26 , pp. 141-142
    • Jagadeeswaran, P.1    Forget, B.G.2    Weissman, S.M.3
  • 43
    • 0031055331 scopus 로고    scopus 로고
    • Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons
    • Jurka, J. (1997) Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. USA 94, 1872-1877.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 1872-1877
    • Jurka, J.1
  • 45
    • 0036849412 scopus 로고    scopus 로고
    • LINEs mobilize SINEs in the eel through a shared 3' sequence
    • Kajikawa, M., and Okada, N. (2002) LINEs mobilize SINEs in the eel through a shared 3' sequence. Cell 111, 433-444.
    • (2002) Cell , vol.111 , pp. 433-444
    • Kajikawa, M.1    Okada, N.2
  • 46
    • 0038709269 scopus 로고    scopus 로고
    • A novel class of SINE elements derived from 5S rRNA
    • Kapitonov, V. V., and Jurka, J. (2003) A novel class of SINE elements derived from 5S rRNA. Mol. Biol. Evol. 20, 694-702.
    • (2003) Mol. Biol. Evol , vol.20 , pp. 694-702
    • Kapitonov, V.V.1    Jurka, J.2
  • 47
    • 0021882531 scopus 로고
    • Repetitive sequence transcripts and U1 RNA in mouse oocytes and eggs
    • Kaplan, G., Jelinek, W. R., and Bachvarova, R. (1985) Repetitive sequence transcripts and U1 RNA in mouse oocytes and eggs. Dev. Biol. 109, 15-24.
    • (1985) Dev. Biol , vol.109 , pp. 15-24
    • Kaplan, G.1    Jelinek, W.R.2    Bachvarova, R.3
  • 48
    • 79957844585 scopus 로고    scopus 로고
    • DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs
    • Karimi, M. M., Goyal, P., Maksakova, I. A., Bilenky, M., Leung, D., Tang, J. X., Shinkai, Y., Mager, D. L., Jones, S., Hirst, M., et al. (2011) DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell 8, 676-687.
    • (2011) Cell Stem Cell , vol.8 , pp. 676-687
    • Karimi, M.M.1    Goyal, P.2    Maksakova, I.A.3    Bilenky, M.4    Leung, D.5    Tang, J.X.6    Shinkai, Y.7    Mager, D.L.8    Jones, S.9    Hirst, M.10
  • 50
    • 0027474543 scopus 로고
    • DNA methylation in the Alu sequences of diploid and haploid primary human cells
    • Kochanek, S., Renz, D., and Doerfler, W. (1993) DNA methylation in the Alu sequences of diploid and haploid primary human cells. EMBO J. 12, 1141-1151.
    • (1993) EMBO J , vol.12 , pp. 1141-1151
    • Kochanek, S.1    Renz, D.2    Doerfler, W.3
  • 51
    • 0042346386 scopus 로고    scopus 로고
    • Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells
    • Kondo, Y., and Issa, J. P. (2003) Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells. J. Biol. Chem. 278, 27658-27662.
    • (2003) J. Biol. Chem , vol.278 , pp. 27658-27662
    • Kondo, Y.1    Issa, J.P.2
  • 52
    • 0023946286 scopus 로고
    • Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands
    • Korenberg, J. R., and Rykowski, M. C. (1988) Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands. Cell 53, 391-400.
    • (1988) Cell , vol.53 , pp. 391-400
    • Korenberg, J.R.1    Rykowski, M.C.2
  • 53
    • 0018432209 scopus 로고
    • Long double-stranded sequences (dsRNA-B) of nuclear pre-mRNA consist of a few highly abundant classes of sequences: Evidence from DNA cloning experiments
    • Kramerov, D. A., Grigoryan, A. A., Ryskov, A. P., and Georgiev, G. P. (1979) Long double-stranded sequences (dsRNA-B) of nuclear pre-mRNA consist of a few highly abundant classes of sequences: evidence from DNA cloning experiments. Nucleic Acids Res. 6, 697-713.
    • (1979) Nucleic Acids Res , vol.6 , pp. 697-713
    • Kramerov, D.A.1    Grigoryan, A.A.2    Ryskov, A.P.3    Georgiev, G.P.4
  • 56
    • 0038701605 scopus 로고    scopus 로고
    • The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons
    • Lev-Maor, G., Sorek, R., Shomron, N., and Ast, G. (2003) The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science 300, 1288-1291.
    • (2003) Science , vol.300 , pp. 1288-1291
    • Lev-Maor, G.1    Sorek, R.2    Shomron, N.3    Ast, G.4
  • 58
    • 0032735573 scopus 로고    scopus 로고
    • Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo
    • Li, T., Spearow, J., Rubin, C. M., and Schmid, C. W. (1999) Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo. Gene 239, 367-372.
    • (1999) Gene , vol.239 , pp. 367-372
    • Li, T.1    Spearow, J.2    Rubin, C.M.3    Schmid, C.W.4
  • 60
    • 0027251502 scopus 로고
    • Proposed roles for DNA methylation in Alu transcriptional repression and mutational inactivation
    • Liu, W. M., and Schmid, C. W. (1993) Proposed roles for DNA methylation in Alu transcriptional repression and mutational inactivation. Nucleic Acids Res. 21, 1351-1359.
    • (1993) Nucleic Acids Res , vol.21 , pp. 1351-1359
    • Liu, W.M.1    Schmid, C.W.2
  • 61
    • 0029030242 scopus 로고
    • Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts
    • Liu, W. M., Chu, W. M., Choudary, P. V., and Schmid, C. W. (1995) Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res. 23, 1758-1765.
    • (1995) Nucleic Acids Res , vol.23 , pp. 1758-1765
    • Liu, W.M.1    Chu, W.M.2    Choudary, P.V.3    Schmid, C.W.4
  • 62
    • 0027450385 scopus 로고
    • Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition
    • Luan, D. D., Korman, M. H., Jakubczak, J. L., and Eickbush, T. H. (1993) Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72, 595-605.
    • (1993) Cell , vol.72 , pp. 595-605
    • Luan, D.D.1    Korman, M.H.2    Jakubczak, J.L.3    Eickbush, T.H.4
  • 63
    • 80053990356 scopus 로고    scopus 로고
    • Genomic relationship between SINE retrotransposons, Pol III-Pol II transcription, and chromatin organization: The journey from junk to jewel
    • Lunyak, V. V., and Atallah, M. (2011) Genomic relationship between SINE retrotransposons, Pol III-Pol II transcription, and chromatin organization: the journey from junk to jewel. Biochem. Cell Biol. 89, 495-504.
    • (2011) Biochem. Cell Biol , vol.89 , pp. 495-504
    • Lunyak, V.V.1    Atallah, M.2
  • 67
    • 0036798062 scopus 로고    scopus 로고
    • Retroelement Distributions In the Human Genome: Variations Associated With Age and Proximity to Genes
    • Medstrand, P., van de Lagemaat, L. N., and Mager, D. L. (2002) Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Res. 12, 1483-1495.
    • (2002) Genome Res , vol.12 , pp. 1483-1495
    • Medstrand, P.1    van de Lagemaat, L.N.2    Mager, D.L.3
  • 70
    • 77951962545 scopus 로고    scopus 로고
    • Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells
    • Moqtaderi, Z., Wang, J., Raha, D., White, R. J., Snyder, M., Weng, Z., and Struhl, K. (2010) Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat. Struct. Mol. Biol. 17, 635-640.
    • (2010) Nat. Struct. Mol. Biol , vol.17 , pp. 635-640
    • Moqtaderi, Z.1    Wang, J.2    Raha, D.3    White, R.J.4    Snyder, M.5    Weng, Z.6    Struhl, K.7
  • 73
    • 33745620751 scopus 로고    scopus 로고
    • Functional noncoding sequences derived from SINEs in the mammalian genome
    • Nishihara, H., Smit, A. F., and Okada, N. (2006) Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res. 16, 864-874.
    • (2006) Genome Res , vol.16 , pp. 864-874
    • Nishihara, H.1    Smit, A.F.2    Okada, N.3
  • 74
    • 33646912186 scopus 로고    scopus 로고
    • A role for TFIIIC transcription factor complex in genome organization
    • Noma, K., Cam, H. P., Maraia, R. J., and Grewal, S. I. (2006) A role for TFIIIC transcription factor complex in genome organization. Cell 125, 859-872.
    • (2006) Cell , vol.125 , pp. 859-872
    • Noma, K.1    Cam, H.P.2    Maraia, R.J.3    Grewal, S.I.4
  • 75
    • 1842665155 scopus 로고    scopus 로고
    • Clusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters
    • Oei, S. L., Babich, V. S., Kazakov, V. I., Usmanova, N. M., Kropotov, A. V., and Tomilin, N. V. (2004) Clusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters. Genomics 83, 873-882.
    • (2004) Genomics , vol.83 , pp. 873-882
    • Oei, S.L.1    Babich, V.S.2    Kazakov, V.I.3    Usmanova, N.M.4    Kropotov, A.V.5    Tomilin, N.V.6
  • 77
    • 0015271630 scopus 로고
    • So much "junk" DNA in our genome
    • Ohno, S. (1972) So much "junk" DNA in our genome. Brookhaven Symp. Biol. 23, 366-370.
    • (1972) Brookhaven Symp. Biol , vol.23 , pp. 366-370
    • Ohno, S.1
  • 78
    • 23844437243 scopus 로고    scopus 로고
    • SINEs and LINEs: Symbionts of eukaryotic genomes with a common tail
    • Ohshima, K., and Okada, N. (2005) SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet. Genome Res. 110, 475-490.
    • (2005) Cytogenet. Genome Res , vol.110 , pp. 475-490
    • Ohshima, K.1    Okada, N.2
  • 79
    • 0029927086 scopus 로고    scopus 로고
    • The 3' ends of tRNA-derived short interspersed repetitive elements are derived from the 3' ends of long interspersed repetitive elements
    • 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. Mol. Cell. Biol. 16, 3756-3764.
    • (1996) Mol. Cell. Biol , vol.16 , pp. 3756-3764
    • Ohshima, K.1    Hamada, M.2    Terai, Y.3    Okada, N.4
  • 80
    • 1542682570 scopus 로고    scopus 로고
    • Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates
    • Ohshima, K., Hattori, M., Yada, T., Gojobori, T., Sakaki, Y., and Okada, N. (2003) Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol. 4, R74.
    • (2003) Genome Biol , vol.4
    • Ohshima, K.1    Hattori, M.2    Yada, T.3    Gojobori, T.4    Sakaki, Y.5    Okada, N.6
  • 82
    • 77954693443 scopus 로고    scopus 로고
    • Emergence of mammals by emergency: Exaptation
    • Okada, N., Sasaki, T., Shimogori, T., and Nishihara, H. (2010) Emergence of mammals by emergency: exaptation. Genes Cells 15, 801-812.
    • (2010) Genes Cells , vol.15 , pp. 801-812
    • Okada, N.1    Sasaki, T.2    Shimogori, T.3    Nishihara, H.4
  • 84
    • 0018857680 scopus 로고
    • Selfish DNA: The ultimate parasite
    • Orgel, L. E., and Crick, F. H. (1980) Selfish DNA: the ultimate parasite. Nature 284, 604-607.
    • (1980) Nature , vol.284 , pp. 604-607
    • Orgel, L.E.1    Crick, F.H.2
  • 85
    • 0023046916 scopus 로고
    • Transcriptional inactivity of Alu repeats in HeLa cells
    • Paulson, K. E., and Schmid, C. W. (1986) Transcriptional inactivity of Alu repeats in HeLa cells. Nucleic Acids Res. 14, 6145-6158.
    • (1986) Nucleic Acids Res , vol.14 , pp. 6145-6158
    • Paulson, K.E.1    Schmid, C.W.2
  • 86
    • 67549119096 scopus 로고    scopus 로고
    • CTCF: Master weaver of the genome
    • Phillips, J. E., and Corces, V. G. (2009) CTCF: master weaver of the genome. Cell 137, 1194-1211.
    • (2009) Cell , vol.137 , pp. 1194-1211
    • Phillips, J.E.1    Corces, V.G.2
  • 87
    • 0029999154 scopus 로고    scopus 로고
    • An Alu element in the myeloperoxidase promoter contains a composite SP1-thyroid hormone-retinoic acid response element
    • Piedrafita, F. J., Molander, R. B., Vansant, G., Orlova, E. A., Pfahl, M., and Reynolds, W. F. (1996) An Alu element in the myeloperoxidase promoter contains a composite SP1-thyroid hormone-retinoic acid response element. J. Biol. Chem. 271, 14412-14420.
    • (1996) J. Biol. Chem , vol.271 , pp. 14412-14420
    • Piedrafita, F.J.1    Molander, R.B.2    Vansant, G.3    Orlova, E.A.4    Pfahl, M.5    Reynolds, W.F.6
  • 88
    • 33746377600 scopus 로고    scopus 로고
    • Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes
    • Polak, P., and Domany, E. (2006) Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics 7, 133.
    • (2006) BMC Genomics , vol.7 , pp. 133
    • Polak, P.1    Domany, E.2
  • 89
    • 0035839126 scopus 로고    scopus 로고
    • Epigenetic reprogramming in mammalian development
    • Reik, W., Dean, W., and Walter, J. (2001) Epigenetic reprogramming in mammalian development. Science 293, 1089-1093.
    • (2001) Science , vol.293 , pp. 1089-1093
    • Reik, W.1    Dean, W.2    Walter, J.3
  • 90
    • 40349112875 scopus 로고    scopus 로고
    • Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo
    • Roman, A. C., Benitez, D. A., Carvajal-Gonzalez, J. M., and Fernandez-Salguero, P. M. (2008) Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo. Proc. Natl. Acad. Sci. USA 105, 1632-1637.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 1632-1637
    • Roman, A.C.1    Benitez, D.A.2    Carvajal-Gonzalez, J.M.3    Fernandez-Salguero, P.M.4
  • 92
    • 0018896269 scopus 로고
    • Partial nucleotide sequence of the 300-nucleotide interspersed repeated human DNA sequences
    • Rubin, C. M., Houck, C. M., Deininger, P. L., Friedmann, T., and Schmid, C. W. (1980) Partial nucleotide sequence of the 300-nucleotide interspersed repeated human DNA sequences. Nature 284, 372-374.
    • (1980) Nature , vol.284 , pp. 372-374
    • Rubin, C.M.1    Houck, C.M.2    Deininger, P.L.3    Friedmann, T.4    Schmid, C.W.5
  • 93
    • 84877898486 scopus 로고    scopus 로고
    • The epigenetic regulation of transposable elements by PIWI-interacting RNAs in Drosophila
    • Saito, K. (2013) The epigenetic regulation of transposable elements by PIWI-interacting RNAs in Drosophila. Genes Genet. Syst. 88, 9-17.
    • (2013) Genes Genet. Syst , vol.88 , pp. 9-17
    • Saito, K.1
  • 94
    • 0022315823 scopus 로고
    • Rodent type 2 Alu family, rat identifier sequence, rabbit C family, and bovine or goat 73-bp repeat may have evolved from tRNA genes
    • Sakamoto, K., and Okada, N. (1985) Rodent type 2 Alu family, rat identifier sequence, rabbit C family, and bovine or goat 73-bp repeat may have evolved from tRNA genes. J. Mol. Evol. 22, 134-140.
    • (1985) J. Mol. Evol , vol.22 , pp. 134-140
    • Sakamoto, K.1    Okada, N.2
  • 95
    • 35948981635 scopus 로고    scopus 로고
    • Ancient Exaptation of a CORE-SINE Retroposon Into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene
    • Santangelo, A. M., de Souza, F. S., Franchini, L. F., Bumaschny, V. F., Low, M. J., and Rubinstein, M. (2007) Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene. PLoS Genet. 3, 1813-1826.
    • (2007) PLoS Genet , vol.3 , pp. 1813-1826
    • Santangelo, A.M.1    de Souza, F.S.2    Franchini, L.F.3    Bumaschny, V.F.4    Low, M.J.5    Rubinstein, M.6
  • 96
    • 38349100549 scopus 로고    scopus 로고
    • Epigenetic events in mammalian germ-cell development: Reprogramming and beyond
    • Sasaki, H., and Matsui, Y. (2008) Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat. Rev. Genet. 9, 129-140.
    • (2008) Nat. Rev. Genet , vol.9 , pp. 129-140
    • Sasaki, H.1    Matsui, Y.2
  • 98
    • 0032531815 scopus 로고    scopus 로고
    • Does SINE evolution preclude Alu function?
    • Schmid, C. W. (1998) Does SINE evolution preclude Alu function? Nucleic Acids Res. 26, 4541-4550.
    • (1998) Nucleic Acids Res , vol.26 , pp. 4541-4550
    • Schmid, C.W.1
  • 100
    • 0037108150 scopus 로고    scopus 로고
    • Recruitment of RNA polymerase III to its target promoters
    • Schramm, L., and Hernandez, N. (2002) Recruitment of RNA polymerase III to its target promoters. Genes Dev. 16, 2593-2620.
    • (2002) Genes Dev , vol.16 , pp. 2593-2620
    • Schramm, L.1    Hernandez, N.2
  • 101
    • 0020332775 scopus 로고
    • Highly repeated sequences in mammalian genomes
    • Singer, M. F. (1982) Highly repeated sequences in mammalian genomes. Int. Rev. Cytol. 76, 67-112.
    • (1982) Int. Rev. Cytol , vol.76 , pp. 67-112
    • Singer, M.F.1
  • 102
    • 79953089167 scopus 로고    scopus 로고
    • PIWIinteracting small RNAs: The vanguard of genome defence
    • Siomi, M. C., Sato, K., Pezic, D., and Aravin, A. A. (2011) PIWIinteracting small RNAs: the vanguard of genome defence. Nat. Rev. Mol. Cell Biol. 12, 246-258.
    • (2011) Nat. Rev. Mol. Cell Biol , vol.12 , pp. 246-258
    • Siomi, M.C.1    Sato, K.2    Pezic, D.3    Aravin, A.A.4
  • 103
    • 64249139170 scopus 로고    scopus 로고
    • Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution
    • Solovei, I., Kreysing, M., Lanctot, C., Kosem, S., Peichl, L., Cremer, T., Guck, J., and Joffe, B. (2009) Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution. Cell 137, 356-368.
    • (2009) Cell , vol.137 , pp. 356-368
    • Solovei, I.1    Kreysing, M.2    Lanctot, C.3    Kosem, S.4    Peichl, L.5    Cremer, T.6    Guck, J.7    Joffe, B.8
  • 104
    • 0036064148 scopus 로고    scopus 로고
    • Alu-containing exons are alternatively spliced
    • Sorek, R., Ast, G., and Graur, D. (2002) Alu-containing exons are alternatively spliced. Genome Res. 12, 1060-1067.
    • (2002) Genome Res , vol.12 , pp. 1060-1067
    • Sorek, R.1    Ast, G.2    Graur, D.3
  • 105
    • 77952121837 scopus 로고    scopus 로고
    • Effects of Alu elements on global nucleosome positioning in the human genome
    • Tanaka, Y., Yamashita, R., Suzuki, Y., and Nakai, K. (2010) Effects of Alu elements on global nucleosome positioning in the human genome. BMC Genomics 11, 309.
    • (2010) BMC Genomics , vol.11 , pp. 309
    • Tanaka, Y.1    Yamashita, R.2    Suzuki, Y.3    Nakai, K.4
  • 106
    • 82955188747 scopus 로고    scopus 로고
    • A mammalian conserved element derived from SINE displays enhancer properties recapitulating Satb2 expression in early-born callosal projection neurons
    • Tashiro, K., Teissier, A., Kobayashi, N., Nakanishi, A., Sasaki, T., Yan, K., Tarabykin, V., Vigier, L., Sumiyama, K., Hirakawa, M., et al. (2011) A mammalian conserved element derived from SINE displays enhancer properties recapitulating Satb2 expression in early-born callosal projection neurons. PLoS One 6, e28497.
    • (2011) PLoS One , vol.6
    • Tashiro, K.1    Teissier, A.2    Kobayashi, N.3    Nakanishi, A.4    Sasaki, T.5    Yan, K.6    Tarabykin, V.7    Vigier, L.8    Sumiyama, K.9    Hirakawa, M.10
  • 107
    • 74549153240 scopus 로고    scopus 로고
    • Alu and B1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes
    • Tsirigos, A., and Rigoutsos, I. (2009) Alu and B1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes. PLoS Comput. Biol. 5, e1000610.
    • (2009) PLoS Comput. Biol , vol.5
    • Tsirigos, A.1    Rigoutsos, I.2
  • 108
  • 109
    • 0021127698 scopus 로고
    • Alu sequences are processed 7SL RNA genes
    • Ullu, E., and Tschudi, C. (1984) Alu sequences are processed 7SL RNA genes. Nature 312, 171-172.
    • (1984) Nature , vol.312 , pp. 171-172
    • Ullu, E.1    Tschudi, C.2
  • 110
    • 0029153564 scopus 로고
    • The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element
    • Vansant, G., and Reynolds, W. F. (1995) The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element. Proc. Natl. Acad. Sci. USA 92, 8229-8233.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 8229-8233
    • Vansant, G.1    Reynolds, W.F.2
  • 111
    • 84876581626 scopus 로고    scopus 로고
    • SINEBase: A database and tool for SINE analysis
    • Vassetzky, N. S., and Kramerov, D. A. (2013) SINEBase: a database and tool for SINE analysis. Nucleic Acids Res. 41, D83-D89.
    • (2013) Nucleic Acids Res , vol.41
    • Vassetzky, N.S.1    Kramerov, D.A.2
  • 112
    • 0031662164 scopus 로고    scopus 로고
    • Transcription of IAP endogenous retroviruses is constrained by cytosine methylation
    • Walsh, C. P., Chaillet, J. R., and Bestor, T. H. (1998) Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 20, 116-117.
    • (1998) Nat. Genet , vol.20 , pp. 116-117
    • Walsh, C.P.1    Chaillet, J.R.2    Bestor, T.H.3
  • 116
    • 0019186902 scopus 로고
    • An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome
    • Weiner, A. M. (1980) An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell 22, 209-218.
    • (1980) Cell , vol.22 , pp. 209-218
    • Weiner, A.M.1
  • 118
    • 59349083791 scopus 로고    scopus 로고
    • Methylation and deamination of CpGs generate p53-binding sites on a genomic scale
    • Zemojtel, T., Kielbasa, S. M., Arndt, P. F., Chung, H. R., and Vingron, M. (2009) Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends Genet. 25, 63-66.
    • (2009) Trends Genet , vol.25 , pp. 63-66
    • Zemojtel, T.1    Kielbasa, S.M.2    Arndt, P.F.3    Chung, H.R.4    Vingron, M.5


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