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Volumn 39, Issue 13, 2011, Pages 5658-5668

Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; MESSENGER RNA; MICRORNA; RNA INDUCED SILENCING COMPLEX; SMALL UNTRANSLATED RNA; TRANSFER RNA; UNTRANSLATED RNA;

EID: 80052191259     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr110     Document Type: Article
Times cited : (69)

References (48)
  • 1
    • 60149088848 scopus 로고    scopus 로고
    • Origins and mechanisms of miRNAs and siRNAs
    • Carthew, R.W. and Sontheimer, E.J. (2009) Origins and mechanisms of miRNAs and siRNAs. Cell, 136, 642-655.
    • (2009) Cell , vol.136 , pp. 642-655
    • Carthew, R.W.1    Sontheimer, E.J.2
  • 2
    • 34447102459 scopus 로고    scopus 로고
    • Molecular Basis for Target RNA Recognition and Cleavage by Human RISC
    • DOI 10.1016/j.cell.2007.04.037, PII S0092867407005831
    • Ameres, S.L., Martinez, J. and Schroeder, R. (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell, 130, 101-112. (Pubitemid 47031315)
    • (2007) Cell , vol.130 , Issue.1 , pp. 101-112
    • Ameres, S.L.1    Martinez, J.2    Schroeder, R.3
  • 3
    • 0037144457 scopus 로고    scopus 로고
    • Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA
    • Llave, C., Xie, Z., Kasschau, K.D. and Carrington, J.C. (2002) Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 297, 2053-2056.
    • (2002) Science , vol.297 , pp. 2053-2056
    • Llave, C.1    Xie, Z.2    Kasschau, K.D.3    Carrington, J.C.4
  • 4
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 5
    • 0037134020 scopus 로고    scopus 로고
    • A system for stable expression of short interfering RNAs in mammalian cells
    • DOI 10.1126/science.1068999
    • Brummelkamp, T.R., Bernards, R. and Agami, R. (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science, 296, 550-553. (Pubitemid 34408678)
    • (2002) Science , vol.296 , Issue.5567 , pp. 550-553
    • Brummelkamp, T.R.1    Bernards, R.2    Agami, R.3
  • 6
    • 0037173613 scopus 로고    scopus 로고
    • Short interfering RNA confers intracellular antiviral immunity in human cells
    • DOI 10.1038/nature00873
    • Gitlin, L., Karelsky, S. and Andino, R. (2002) Short interfering RNA confers intracellular antiviral immunity in human cells. Nature, 418, 430-434. (Pubitemid 34826844)
    • (2002) Nature , vol.418 , Issue.6896 , pp. 430-434
    • Gitlin, L.1    Karelsky, S.2    Andino, R.3
  • 7
    • 24044548350 scopus 로고    scopus 로고
    • Tolerated wobble mutations in siRNAs decrease specificity, but can enhance activity in vivo
    • DOI 10.1093/nar/gki785
    • Holen, T., Moe, S.E., Sorbo, J.G., Meza, T.J., Ottersen, O.P. and Klungland, A. (2005) Tolerated wobble mutations in siRNAs decrease specificity, but can enhance activity in vivo. Nucleic Acids Res., 33, 4704-4710. (Pubitemid 41418872)
    • (2005) Nucleic Acids Research , vol.33 , Issue.15 , pp. 4704-4710
    • Holen, T.1    Moe, S.E.2    Sorbo, J.G.3    Meza, T.J.4    Ottersen, O.P.5    Klungland, A.6
  • 8
    • 0037440005 scopus 로고    scopus 로고
    • Tolerance for mutations and chemical modifications in a siRNA
    • DOI 10.1093/nar/gkg147
    • Amarzguioui, M., Holen, T., Babaie, E. and Prydz, H. (2003) Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res., 31, 589-595. (Pubitemid 36175948)
    • (2003) Nucleic Acids Research , vol.31 , Issue.2 , pp. 589-595
    • Amarzguioui, M.1    Holen, T.2    Babaie, E.3    Prydz, H.4
  • 9
    • 0035856381 scopus 로고    scopus 로고
    • Short 5′-phosphorylated double-stranded RNAs induce RNA interference in Drosophila
    • DOI 10.1016/S0960-9822(01)00541-3
    • Boutla, A., Delidakis, C., Livadaras, I., Tsagris, M. and Tabler, M. (2001) Short 50-phosphorylated double-stranded RNAs induce RNA interference in Drosophila. Curr. Biol., 11, 1776-1780. (Pubitemid 33092166)
    • (2001) Current Biology , vol.11 , Issue.22 , pp. 1776-1780
    • Boutla, A.1    Delidakis, C.2    Livadaras, I.3    Tsagris, M.4    Tabler, M.5
  • 10
    • 0037089135 scopus 로고    scopus 로고
    • Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor
    • Holen, T., Amarzguioui, M., Wiiger, M.T., Babaie, E. and Prydz, H. (2002) Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor. Nucleic Acids Res., 30, 1757-1766. (Pubitemid 34679753)
    • (2002) Nucleic Acids Research , vol.30 , Issue.8 , pp. 1757-1766
    • Holen, T.1    Amarzguioui, M.2    Wiiger, M.T.3    Babaie, E.4    Prydz, H.5
  • 11
    • 0142173075 scopus 로고    scopus 로고
    • Small RNAs with imperfect match to endogenous mRNA repress translation. Implications for off-target activity of small inhibitory RNA in mammalian cells
    • DOI 10.1074/jbc.M307089200
    • Saxena, S., Jonsson, Z.O. and Dutta, A. (2003) Small RNAs with imperfect match to endogenous mRNA repress translation. Implications for off-target activity of small inhibitory RNA in mammalian cells. J. Biol. Chem., 278, 44312-44319. (Pubitemid 37377177)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.45 , pp. 44312-44319
    • Saxena, S.1    Jonsson, Z.O.2    Dutta, A.3
  • 12
    • 4444363152 scopus 로고    scopus 로고
    • MicroRNA control of PHABULOSA in leaf development: Importance of pairing to the microRNA 5′ region
    • DOI 10.1038/sj.emboj.7600340
    • Mallory, A.C., Reinhart, B.J., Jones-Rhoades, M.W., Tang, G., Zamore, P.D., Barton, M.K. and Bartel, D.P. (2004) MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 50 region. EMBO J., 23, 3356-3364. (Pubitemid 39209159)
    • (2004) EMBO Journal , vol.23 , Issue.16 , pp. 3356-3364
    • Mallory, A.C.1    Reinhart, B.J.2    Jones-Rhoades, M.W.3    Tang, G.4    Zamore, P.D.5    Barton, M.K.6    Bartel, D.P.7
  • 13
    • 77950952075 scopus 로고    scopus 로고
    • MicroRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis
    • Beauclair, L., Yu, A. and Bouche, N. (2010) MicroRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis. Plant J., 62, 454-462.
    • (2010) Plant J. , vol.62 , pp. 454-462
    • Beauclair, L.1    Yu, A.2    Bouche, N.3
  • 14
    • 84860209234 scopus 로고    scopus 로고
    • New insights into miR398 functions in Arabidopsis
    • Bouche, N. (2010) New insights into miR398 functions in Arabidopsis. Plant Signal Behav., 5, 684-686.
    • (2010) Plant Signal Behav. , vol.5 , pp. 684-686
    • Bouche, N.1
  • 16
    • 2142654329 scopus 로고    scopus 로고
    • MicroRNA-Directed Cleavage of HOXB8 mRNA
    • DOI 10.1126/science.1097434
    • Yekta, S., Shih, I.H. and Bartel, D.P. (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science, 304, 594-596. (Pubitemid 38541919)
    • (2004) Science , vol.304 , Issue.5670 , pp. 594-596
    • Yekta, S.1    Shih, I.-H.2    Bartel, D.P.3
  • 17
    • 77955492563 scopus 로고    scopus 로고
    • Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases
    • Karginov, F.V., Cheloufi, S., Chong, M.M., Stark, A., Smith, A.D. and Hannon, G.J. (2010) Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Mol. Cell, 38, 781-788.
    • (2010) Mol. Cell , vol.38 , pp. 781-788
    • Karginov, F.V.1    Cheloufi, S.2    Chong, M.M.3    Stark, A.4    Smith, A.D.5    Hannon, G.J.6
  • 18
    • 77955475953 scopus 로고    scopus 로고
    • Expanding the microRNA targeting code: Functional sites with centered pairing
    • Shin, C., Nam, J.W., Farh, K.K., Chiang, H.R., Shkumatava, A. and Bartel, D.P. (2010) Expanding the microRNA targeting code: functional sites with centered pairing. Mol. Cell, 38, 789-802.
    • (2010) Mol. Cell , vol.38 , pp. 789-802
    • Shin, C.1    Nam, J.W.2    Farh, K.K.3    Chiang, H.R.4    Shkumatava, A.5    Bartel, D.P.6
  • 19
    • 43449091567 scopus 로고    scopus 로고
    • Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome
    • Addo-Quaye, C., Eshoo, T.W., Bartel, D.P. and Axtell, M.J. (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr. Biol., 18, 758-762.
    • (2008) Curr. Biol. , vol.18 , pp. 758-762
    • Addo-Quaye, C.1    Eshoo, T.W.2    Bartel, D.P.3    Axtell, M.J.4
  • 21
    • 13444306641 scopus 로고    scopus 로고
    • NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • DOI 10.1093/nar/gki025
    • Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33, D501-504. (Pubitemid 40207924)
    • (2005) Nucleic Acids Research , vol.33
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 22
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
    • (2009) Genome Biol. , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 23
    • 2342626647 scopus 로고    scopus 로고
    • 2+-dependent endonuclease
    • DOI 10.1016/j.cub.2004.03.008, PII S0960982204001769
    • Schwarz, D.S., Tomari, Y. and Zamore, P.D. (2004) The RNA-induced silencing complex is a Mg2+-dependent endonuclease. Curr. Biol., 14, 787-791. (Pubitemid 38583713)
    • (2004) Current Biology , vol.14 , Issue.9 , pp. 787-791
    • Schwarz, D.S.1    Tomari, Y.2    Zamore, P.D.3
  • 24
    • 77956034926 scopus 로고    scopus 로고
    • Novel endoribonucleases as central players in various pathways of eukaryotic RNA metabolism
    • Tomecki, R. and Dziembowski, A. (2010) Novel endoribonucleases as central players in various pathways of eukaryotic RNA metabolism. RNA, 16, 1692-1724.
    • (2010) RNA , vol.16 , pp. 1692-1724
    • Tomecki, R.1    Dziembowski, A.2
  • 25
    • 34147223557 scopus 로고    scopus 로고
    • A+U-rich instability elements differentially activate 5′-3′ and 3′-5′ mRNA decay
    • DOI 10.1128/MCB.01445-06
    • Murray, E.L. and Schoenberg, D.R. (2007) A+U-rich instability elements differentially activate 50-30 and 30-50 mRNA decay. Mol. Cell Biol., 27, 2791-2799. (Pubitemid 46581295)
    • (2007) Molecular and Cellular Biology , vol.27 , Issue.8 , pp. 2791-2799
    • Murray, E.L.1    Schoenberg, D.R.2
  • 26
    • 65249141709 scopus 로고    scopus 로고
    • Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells
    • Sharova, L.V., Sharov, A.A., Nedorezov, T., Piao, Y., Shaik, N. and Ko, M.S. (2009) Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. DNA Res., 16, 45-58.
    • (2009) DNA Res. , vol.16 , pp. 45-58
    • Sharova, L.V.1    Sharov, A.A.2    Nedorezov, T.3    Piao, Y.4    Shaik, N.5    Ko, M.S.6
  • 27
    • 72749089855 scopus 로고    scopus 로고
    • A novel class of small RNAs: TRNA-derived RNA fragments (tRFs)
    • Lee, Y.S., Shibata, Y., Malhotra, A. and Dutta, A. (2009) A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev., 23, 2639-2649.
    • (2009) Genes Dev. , vol.23 , pp. 2639-2649
    • Lee, Y.S.1    Shibata, Y.2    Malhotra, A.3    Dutta, A.4
  • 29
    • 2342481623 scopus 로고    scopus 로고
    • Recent advances in X-chromosome inactivation
    • DOI 10.1016/j.ceb.2004.03.005, PII S0955067404000432
    • Heard, E. (2004) Recent advances in X-chromosome inactivation. Curr. Opin. Cell Biol., 16, 247-255. (Pubitemid 38610404)
    • (2004) Current Opinion in Cell Biology , vol.16 , Issue.3 , pp. 247-255
    • Heard, E.1
  • 30
    • 71549169628 scopus 로고    scopus 로고
    • Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs
    • Cole, C., Sobala, A., Lu, C., Thatcher, S.R., Bowman, A., Brown, J.W., Green, P.J., Barton, G.J. and Hutvagner, G. (2009) Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA, 15, 2147-2160.
    • (2009) RNA , vol.15 , pp. 2147-2160
    • Cole, C.1    Sobala, A.2    Lu, C.3    Thatcher, S.R.4    Bowman, A.5    Brown, J.W.6    Green, P.J.7    Barton, G.J.8    Hutvagner, G.9
  • 33
    • 0035803583 scopus 로고    scopus 로고
    • Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate
    • DOI 10.1093/emboj/20.23.6877
    • Elbashir, S.M., Martinez, J., Patkaniowska, A., Lendeckel, W. and Tuschl, T. (2001) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J., 20, 6877-6888. (Pubitemid 33134217)
    • (2001) EMBO Journal , vol.20 , Issue.23 , pp. 6877-6888
    • Elbashir, S.M.1    Martinez, J.2    Patkaniowska, A.3    Lendeckel, W.4    Tuschl, T.5
  • 37
  • 38
    • 56349113455 scopus 로고    scopus 로고
    • 30 end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA
    • Wilusz, J.E., Freier, S.M. and Spector, D.L. (2008) 30 end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell, 135, 919-932.
    • (2008) Cell , vol.135 , pp. 919-932
    • Wilusz, J.E.1    Freier, S.M.2    Spector, D.L.3
  • 39
    • 54449101066 scopus 로고    scopus 로고
    • Separate cis-trans pathways post-transcriptionally regulate murine CD154 (CD40 ligand) expression: A novel function for CA repeats in the 30-untranslated region
    • Hamilton, B.J., Wang, X.W., Collins, J., Bloch, D., Bergeron, A., Henry, B., Terry, B.M., Zan, M., Mouland, A.J. and Rigby, W.F. (2008) Separate cis-trans pathways post-transcriptionally regulate murine CD154 (CD40 ligand) expression: a novel function for CA repeats in the 30-untranslated region. J. Biol. Chem., 283, 25606-25616.
    • (2008) J. Biol. Chem. , vol.283 , pp. 25606-25616
    • Hamilton, B.J.1    Wang, X.W.2    Collins, J.3    Bloch, D.4    Bergeron, A.5    Henry, B.6    Terry, B.M.7    Zan, M.8    Mouland, A.J.9    Rigby, W.F.10
  • 40
    • 0037217365 scopus 로고    scopus 로고
    • HnRNP L stimulates splicing of the eNOS gene by binding to variable-length CA repeats
    • DOI 10.1038/nsb875
    • Hui, J., Stangl, K., Lane, W.S. and Bindereif, A. (2003) HnRNP L stimulates splicing of the eNOS gene by binding to variable-length CA repeats. Nat. Struct. Biol., 10, 33-37. (Pubitemid 36034174)
    • (2003) Nature Structural Biology , vol.10 , Issue.1 , pp. 33-37
    • Hui, J.1    Stangl, K.2    Lane, W.S.3    Bindereiff, A.4
  • 42
    • 33344476794 scopus 로고    scopus 로고
    • Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA
    • DOI 10.1261/rna.2305406
    • Kadaba, S., Wang, X. and Anderson, J.T. (2006) Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5 S rRNA. RNA, 12, 508-521. (Pubitemid 43290877)
    • (2006) RNA , vol.12 , Issue.3 , pp. 508-521
    • Kadaba, S.1    Wang, X.2    Anderson, J.T.3
  • 43
    • 33745116597 scopus 로고    scopus 로고
    • Polyadenylation of ribosomal RNA in human cells
    • DOI 10.1093/nar/gkl357
    • Slomovic, S., Laufer, D., Geiger, D. and Schuster, G. (2006) Polyadenylation of ribosomal RNA in human cells. Nucleic Acids Res., 34, 2966-2975. (Pubitemid 44540424)
    • (2006) Nucleic Acids Research , vol.34 , Issue.10 , pp. 2966-2975
    • Slomovic, S.1    Laufer, D.2    Geiger, D.3    Schuster, G.4
  • 46
    • 0033981301 scopus 로고    scopus 로고
    • Yeast exosome mutants accumulate 3'-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs
    • DOI 10.1128/MCB.20.2.441-452.2000
    • van Hoof, A., Lennertz, P. and Parker, R. (2000) Yeast exosome mutants accumulate 30-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol. Cell Biol., 20, 441-452. (Pubitemid 30023085)
    • (2000) Molecular and Cellular Biology , vol.20 , Issue.2 , pp. 441-452
    • Van Hoof, A.1    Lennertz, P.2    Parker, R.3
  • 47
  • 48
    • 32544459316 scopus 로고    scopus 로고
    • Control of mRNA stability in eukaryotes
    • Newbury, S.F. (2006) Control of mRNA stability in eukaryotes. Biochem. Soc. Trans., 34, 30-34. (Pubitemid 43235526)
    • (2006) Biochemical Society Transactions , vol.34 , Issue.1 , pp. 30-34
    • Newbury, S.F.1


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