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Volumn 20, Issue 2, 2010, Pages 149-155

Genomic gems: SINE RNAs regulate mRNA production

Author keywords

[No Author keywords available]

Indexed keywords

GROWTH HORMONE; MESSENGER RNA; RNA POLYMERASE II;

EID: 77952238354     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2010.01.004     Document Type: Review
Times cited : (96)

References (63)
  • 1
    • 33747881750 scopus 로고    scopus 로고
    • The general transcription machinery and general cofactors
    • Thomas M.C., Chiang C.M. The general transcription machinery and general cofactors. Crit Rev Biochem Mol Biol 2006, 41:105-178.
    • (2006) Crit Rev Biochem Mol Biol , vol.41 , pp. 105-178
    • Thomas, M.C.1    Chiang, C.M.2
  • 2
    • 0842265974 scopus 로고    scopus 로고
    • Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors
    • Kadonaga J.T. Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell 2004, 116:247-257.
    • (2004) Cell , vol.116 , pp. 247-257
    • Kadonaga, J.T.1
  • 3
    • 33847070442 scopus 로고    scopus 로고
    • The role of chromatin during transcription
    • Li B., Carey M., Workman J.L. The role of chromatin during transcription. Cell 2007, 128:707-719.
    • (2007) Cell , vol.128 , pp. 707-719
    • Li, B.1    Carey, M.2    Workman, J.L.3
  • 4
    • 0034912714 scopus 로고    scopus 로고
    • Transcriptional coactivator complexes
    • Naar A.M., Lemon B.D., Tjian R. Transcriptional coactivator complexes. Annu Rev Biochem 2001, 70:475-501.
    • (2001) Annu Rev Biochem , vol.70 , pp. 475-501
    • Naar, A.M.1    Lemon, B.D.2    Tjian, R.3
  • 5
    • 60149110358 scopus 로고    scopus 로고
    • Pre-mRNA processing reaches back to transcription and ahead to translation
    • Moore M.J., Proudfoot N.J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 2009, 136:688-700.
    • (2009) Cell , vol.136 , pp. 688-700
    • Moore, M.J.1    Proudfoot, N.J.2
  • 7
    • 33748303049 scopus 로고    scopus 로고
    • Non-coding-RNA regulators of RNA polymerase II transcription
    • Goodrich J.A., Kugel J.F. Non-coding-RNA regulators of RNA polymerase II transcription. Nat Rev Mol Cell Biol 2006, 7:612-616.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 612-616
    • Goodrich, J.A.1    Kugel, J.F.2
  • 10
    • 28844473478 scopus 로고    scopus 로고
    • Short retroposons in eukaryotic genomes
    • Kramerov D.A., Vassetzky N.S. Short retroposons in eukaryotic genomes. Int Rev Cytol 2005, 247:165-221.
    • (2005) Int Rev Cytol , vol.247 , pp. 165-221
    • Kramerov, D.A.1    Vassetzky, N.S.2
  • 13
    • 33644503176 scopus 로고    scopus 로고
    • A large family of ancient repeat elements in the human genome is under strong selection
    • Kamal M., Xie X., Lander E.S. A large family of ancient repeat elements in the human genome is under strong selection. Proc Natl Acad Sci USA 2006, 103:2740-2745.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 2740-2745
    • Kamal, M.1    Xie, X.2    Lander, E.S.3
  • 14
    • 33745620751 scopus 로고    scopus 로고
    • Functional noncoding sequences derived from SINEs in the mammalian genome
    • Nishihara H., Smit A.F., Okada N. Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res 2006, 16:864-874.
    • (2006) Genome Res , vol.16 , pp. 864-874
    • Nishihara, H.1    Smit, A.F.2    Okada, N.3
  • 15
    • 0030115346 scopus 로고    scopus 로고
    • A swine SINE (PRE-1 sequence) distribution in swine-related animal species and its phylogenetic analysis in swine genome
    • Yasue H., Wada Y. A swine SINE (PRE-1 sequence) distribution in swine-related animal species and its phylogenetic analysis in swine genome. Anim Genet 1996, 27:95-98.
    • (1996) Anim Genet , vol.27 , pp. 95-98
    • Yasue, H.1    Wada, Y.2
  • 16
    • 0032777627 scopus 로고    scopus 로고
    • Genetic relationships among hippopotamus, whales, and bovine based on SINE insertion analysis
    • Nomura O., Yasue H. Genetic relationships among hippopotamus, whales, and bovine based on SINE insertion analysis. Mamm Genome 1999, 10:526-527.
    • (1999) Mamm Genome , vol.10 , pp. 526-527
    • Nomura, O.1    Yasue, H.2
  • 17
    • 0027205382 scopus 로고
    • Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution
    • Murata S., Takasaki N., Saitoh M., Okada N. Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proc Natl Acad Sci USA 1993, 90:6995-6999.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 6995-6999
    • Murata, S.1    Takasaki, N.2    Saitoh, M.3    Okada, N.4
  • 18
    • 0035206024 scopus 로고    scopus 로고
    • Transcriptional activation of short interspersed elements by DNA-damaging agents
    • Rudin C.M., Thompson C.B. Transcriptional activation of short interspersed elements by DNA-damaging agents. Genes Chromosomes Cancer 2001, 30:64-71.
    • (2001) Genes Chromosomes Cancer , vol.30 , pp. 64-71
    • Rudin, C.M.1    Thompson, C.B.2
  • 19
    • 0032735573 scopus 로고    scopus 로고
    • Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo
    • Li T., Spearow J., Rubin C.M., Schmid C.W. Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo. Gene 1999, 239:367-372.
    • (1999) Gene , vol.239 , pp. 367-372
    • Li, T.1    Spearow, J.2    Rubin, C.M.3    Schmid, C.W.4
  • 20
    • 0033567043 scopus 로고    scopus 로고
    • Silk worm Bm1 SINE RNA increases following cellular insults
    • Kimura R.H., Choudary P.V., Schmid C.W. Silk worm Bm1 SINE RNA increases following cellular insults. Nucleic Acids Res 1999, 27:3380-3387.
    • (1999) Nucleic Acids Res , vol.27 , pp. 3380-3387
    • Kimura, R.H.1    Choudary, P.V.2    Schmid, C.W.3
  • 21
    • 22244473932 scopus 로고    scopus 로고
    • 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
    • Schutz E., Urnovitz H.B., Iakoubov L., Schulz-Schaeffer W., Wemheuer W., Brenig B. 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 Diagn Lab Immunol 2005, 12:814-820.
    • (2005) Clin Diagn Lab Immunol , vol.12 , pp. 814-820
    • Schutz, E.1    Urnovitz, H.B.2    Iakoubov, L.3    Schulz-Schaeffer, W.4    Wemheuer, W.5    Brenig, B.6
  • 22
    • 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., Schmid C.W. Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res 1995, 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
  • 23
    • 34249937354 scopus 로고    scopus 로고
    • Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
    • Lowe C.B., Bejerano G., Haussler D. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci USA 2007, 104:8005-8010.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 8005-8010
    • Lowe, C.B.1    Bejerano, G.2    Haussler, D.3
  • 24
    • 57049092878 scopus 로고    scopus 로고
    • The take and give between retrotransposable elements and their hosts
    • Beauregard A., Curcio M.J., Belfort M. The take and give between retrotransposable elements and their hosts. Annu Rev Genet 2008, 42:587-617.
    • (2008) Annu Rev Genet , vol.42 , pp. 587-617
    • Beauregard, A.1    Curcio, M.J.2    Belfort, M.3
  • 26
    • 47049122843 scopus 로고    scopus 로고
    • Alu element-mediated gene silencing
    • Chen L.L., DeCerbo J.N., Carmichael G.G. Alu element-mediated gene silencing. EMBO J 2008, 27:1694-1705.
    • (2008) EMBO J , vol.27 , pp. 1694-1705
    • Chen, L.L.1    DeCerbo, J.N.2    Carmichael, G.G.3
  • 29
    • 0026697046 scopus 로고
    • The herpes simplex virus immediate-early protein ICP27 stimulates the transcription of cellular Alu repeated sequences by increasing the activity of transcription factor TFIIIC
    • Jang K.L., Latchman D.S. The herpes simplex virus immediate-early protein ICP27 stimulates the transcription of cellular Alu repeated sequences by increasing the activity of transcription factor TFIIIC. Biochem J 1992, 284:667-673.
    • (1992) Biochem J , vol.284 , pp. 667-673
    • Jang, K.L.1    Latchman, D.S.2
  • 30
    • 0022779283 scopus 로고
    • Induction of specific transcription by RNA polymerase III in transformed cells
    • Carey M.F., Singh K., Botchan M., Cozzarelli N.R. Induction of specific transcription by RNA polymerase III in transformed cells. Mol Cell Biol 1986, 6:3068-3076.
    • (1986) Mol Cell Biol , vol.6 , pp. 3068-3076
    • Carey, M.F.1    Singh, K.2    Botchan, M.3    Cozzarelli, N.R.4
  • 31
    • 0025886657 scopus 로고
    • Alu RNA secondary structure consists of two independent 7 SL RNA-like folding units
    • Sinnett D., Richer C., Deragon J.M., Labuda D. Alu RNA secondary structure consists of two independent 7 SL RNA-like folding units. J Biol Chem 1991, 266:8675-8678.
    • (1991) J Biol Chem , vol.266 , pp. 8675-8678
    • Sinnett, D.1    Richer, C.2    Deragon, J.M.3    Labuda, D.4
  • 32
    • 0026091135 scopus 로고
    • The subset of mouse B1 (Alu-equivalent) sequences expressed as small processed cytoplasmic transcripts
    • Maraia R.J. The subset of mouse B1 (Alu-equivalent) sequences expressed as small processed cytoplasmic transcripts. Nucleic Acids Res 1991, 19:5695-5702.
    • (1991) Nucleic Acids Res , vol.19 , pp. 5695-5702
    • Maraia, R.J.1
  • 33
    • 0022388991 scopus 로고
    • Repeat sequence families derived from mammalian tRNA genes
    • Daniels G.R., Deininger P.L. Repeat sequence families derived from mammalian tRNA genes. Nature 1985, 317:819-822.
    • (1985) Nature , vol.317 , pp. 819-822
    • Daniels, G.R.1    Deininger, P.L.2
  • 34
    • 0032531815 scopus 로고    scopus 로고
    • Does SINE evolution preclude Alu function?
    • Schmid C.W. Does SINE evolution preclude Alu function?. Nucleic Acids Res 1998, 26:4541-4550.
    • (1998) Nucleic Acids Res , vol.26 , pp. 4541-4550
    • Schmid, C.W.1
  • 35
    • 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., Kugel J.F. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat Struct Mol Biol 2004, 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
  • 38
    • 33947721021 scopus 로고    scopus 로고
    • Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription
    • Espinoza C.A., Goodrich J.A., Kugel J.F. Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription. RNA 2007, 13:583-596.
    • (2007) RNA , vol.13 , pp. 583-596
    • Espinoza, C.A.1    Goodrich, J.A.2    Kugel, J.F.3
  • 39
    • 65249158053 scopus 로고    scopus 로고
    • B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes
    • Yakovchuk P., Goodrich J.A., Kugel J.F. B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc Natl Acad Sci USA 2009, 106:5569-5574.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 5569-5574
    • Yakovchuk, P.1    Goodrich, J.A.2    Kugel, J.F.3
  • 40
    • 73549120620 scopus 로고    scopus 로고
    • TFIIF facilitates dissociation of RNA polymerase II from non-coding RNAs that lack a repression domain
    • Wagner S.D., Kugel J.F., Goodrich J.A. TFIIF facilitates dissociation of RNA polymerase II from non-coding RNAs that lack a repression domain. Mol Cell Biol 2010, 30:91-97.
    • (2010) Mol Cell Biol , vol.30 , pp. 91-97
    • Wagner, S.D.1    Kugel, J.F.2    Goodrich, J.A.3
  • 42
    • 0347125202 scopus 로고    scopus 로고
    • AluGene: a database of Alu elements incorporated within protein-coding genes
    • Dagan T., Sorek R., Sharon E., Ast G., Graur D. AluGene: a database of Alu elements incorporated within protein-coding genes. Nucleic Acids Res 2004, 32:D489-492.
    • (2004) Nucleic Acids Res , vol.32
    • Dagan, T.1    Sorek, R.2    Sharon, E.3    Ast, G.4    Graur, D.5
  • 43
    • 44649199179 scopus 로고    scopus 로고
    • Boundaries. Boundaries. Boundaries???
    • Lunyak V.V. Boundaries. Boundaries. Boundaries???. Curr Opin Cell Biol 2008, 20:281-287.
    • (2008) Curr Opin Cell Biol , vol.20 , pp. 281-287
    • Lunyak, V.V.1
  • 45
    • 1642473041 scopus 로고    scopus 로고
    • How prevalent is functional alternative splicing in the human genome?
    • Sorek R., Shamir R., Ast G. How prevalent is functional alternative splicing in the human genome?. Trends Genet 2004, 20:68-71.
    • (2004) Trends Genet , vol.20 , pp. 68-71
    • Sorek, R.1    Shamir, R.2    Ast, G.3
  • 46
    • 2342437120 scopus 로고    scopus 로고
    • Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition
    • Grover D., Mukerji M., Bhatnagar P., Kannan K., Brahmachari S.K. Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition. Bioinformatics 2004, 20:813-817.
    • (2004) Bioinformatics , vol.20 , pp. 813-817
    • Grover, D.1    Mukerji, M.2    Bhatnagar, P.3    Kannan, K.4    Brahmachari, S.K.5
  • 48
    • 34748869000 scopus 로고    scopus 로고
    • Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome
    • Sela N., Mersch B., Gal-Mark N., Lev-Maor G., Hotz-Wagenblatt A., Ast G. Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol 2007, 8:R127.
    • (2007) Genome Biol , vol.8
    • Sela, N.1    Mersch, B.2    Gal-Mark, N.3    Lev-Maor, G.4    Hotz-Wagenblatt, A.5    Ast, G.6
  • 49
    • 0036064148 scopus 로고    scopus 로고
    • Alu-containing exons are alternatively spliced
    • Sorek R., Ast G., Graur D. Alu-containing exons are alternatively spliced. Genome Res 2002, 12(7):1060-1067.
    • (2002) Genome Res , vol.12 , Issue.7 , pp. 1060-1067
    • Sorek, R.1    Ast, G.2    Graur, D.3
  • 50
    • 43249117483 scopus 로고    scopus 로고
    • Multifactorial interplay controls the splicing profile of Alu-derived exons
    • Ram O., Schwartz S., Ast G. Multifactorial interplay controls the splicing profile of Alu-derived exons. Mol Cell Biol 2008, 28:3513-3525.
    • (2008) Mol Cell Biol , vol.28 , pp. 3513-3525
    • Ram, O.1    Schwartz, S.2    Ast, G.3
  • 51
    • 41849135100 scopus 로고    scopus 로고
    • Alternative splicing of Alu exons-two arms are better than one
    • Gal-Mark N., Schwartz S., Ast G. Alternative splicing of Alu exons-two arms are better than one. Nucleic Acids Res 2008, 36:2012-2023.
    • (2008) Nucleic Acids Res , vol.36 , pp. 2012-2023
    • Gal-Mark, N.1    Schwartz, S.2    Ast, G.3
  • 52
    • 0028356158 scopus 로고
    • Alu sequences in the coding regions of mRNA: a source of protein variability
    • Makalowski W., Mitchell G.A., Labuda D. Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet 1994, 10:188-193.
    • (1994) Trends Genet , vol.10 , pp. 188-193
    • Makalowski, W.1    Mitchell, G.A.2    Labuda, D.3
  • 53
    • 63549096870 scopus 로고    scopus 로고
    • Alu exonization events reveal features required for precise recognition of exons by the splicing machinery
    • Schwartz S., Gal-Mark N., Kfir N., Oren R., Kim E., Ast G. Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Comput Biol 2009, 5:e1000300.
    • (2009) PLoS Comput Biol , vol.5
    • Schwartz, S.1    Gal-Mark, N.2    Kfir, N.3    Oren, R.4    Kim, E.5    Ast, G.6
  • 54
    • 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., Ast G. The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons. Science 2003, 300:1288-1291.
    • (2003) Science , vol.300 , pp. 1288-1291
    • Lev-Maor, G.1    Sorek, R.2    Shomron, N.3    Ast, G.4
  • 55
    • 0031003879 scopus 로고    scopus 로고
    • Editing of glutamate receptor B subunit ion channel RNAs by four alternatively spliced DRADA2 double-stranded RNA adenosine deaminases
    • Lai F., Chen C.X., Carter K.C., Nishikura K. Editing of glutamate receptor B subunit ion channel RNAs by four alternatively spliced DRADA2 double-stranded RNA adenosine deaminases. Mol Cell Biol 1997, 17:2413-2424.
    • (1997) Mol Cell Biol , vol.17 , pp. 2413-2424
    • Lai, F.1    Chen, C.X.2    Carter, K.C.3    Nishikura, K.4
  • 57
    • 12344300804 scopus 로고    scopus 로고
    • Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome
    • Athanasiadis A., Rich A., Maas S. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol 2004, 2:e391.
    • (2004) PLoS Biol , vol.2
    • Athanasiadis, A.1    Rich, A.2    Maas, S.3
  • 60
    • 0034507456 scopus 로고    scopus 로고
    • Functions and mechanisms of RNA editing
    • Gott J.M., Emeson R.B. Functions and mechanisms of RNA editing. Annu Rev Genet 2000, 34:499-531.
    • (2000) Annu Rev Genet , vol.34 , pp. 499-531
    • Gott, J.M.1    Emeson, R.B.2
  • 61
    • 50349089199 scopus 로고    scopus 로고
    • Beyond DNA: RNA editing and steps toward Alu exonization in primates
    • Moller-Krull M., Zemann A., Roos C., Brosius J., Schmitz J. Beyond DNA: RNA editing and steps toward Alu exonization in primates. J Mol Biol 2008, 382:601-609.
    • (2008) J Mol Biol , vol.382 , pp. 601-609
    • Moller-Krull, M.1    Zemann, A.2    Roos, C.3    Brosius, J.4    Schmitz, J.5
  • 63
    • 0033529064 scopus 로고    scopus 로고
    • Regulation of alternative splicing by RNA editing
    • Rueter S.M., Dawson T.R., Emeson R.B. Regulation of alternative splicing by RNA editing. Nature 1999, 399:75-80.
    • (1999) Nature , vol.399 , pp. 75-80
    • Rueter, S.M.1    Dawson, T.R.2    Emeson, R.B.3


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