메뉴 건너뛰기




Volumn 42, Issue 12, 2014, Pages 7981-7996

Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PRIMER RNA; RNA; RNA LIGASE; VIRUS RNA;

EID: 84903954670     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku424     Document Type: Article
Times cited : (21)

References (50)
  • 1
    • 35348962397 scopus 로고    scopus 로고
    • Kaposi's sarcoma-associated herpesvirus
    • Knipe, D.M., Howley, P.M., Griffin, D.E., Lamb, R.A., Martin, M.A., Roizman, B., Straus, S.E. (eds) Lippincott, Williams & Wilkins, Philadelphia
    • Ganem, D. (2007) Kaposi's sarcoma-associated herpesvirus. In: Knipe, D.M., Howley, P.M., Griffin, D.E., Lamb, R.A., Martin, M.A., Roizman, B., Straus, S.E. (eds), Fields Virology. Lippincott, Williams & Wilkins, Philadelphia, Vol. 5th, pp. 2847-2888.
    • (2007) Fields Virology , vol.5 , pp. 2847-2888
    • Ganem, D.1
  • 3
    • 17244375710 scopus 로고    scopus 로고
    • Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells
    • Cai, X., Lu, S., Zhang, Z., Gonzalez, C.M., Damania, B., Cullen, B.R. (2005) Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells. Proc. Natl. Acad. Sci. U. S. A., 102, 5570-5575.
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 5570-5575
    • Cai, X.1    Lu, S.2    Zhang, Z.3    Gonzalez, C.M.4    Damania, B.5    Cullen, B.R.6
  • 4
    • 21644438873 scopus 로고    scopus 로고
    • Cloning and identification of a microRNA cluster within the latency-associated region of Kaposi's sarcoma-associated herpesvirus
    • Samols, M.A., Hu, J., Skalsky, R.L., Renne, R. (2005) Cloning and identification of a microRNA cluster within the latency-associated region of Kaposi's sarcoma-associated herpesvirus. J. Virol., 79, 9301-9305.
    • (2005) J. Virol. , vol.79 , pp. 9301-9305
    • Samols, M.A.1    Hu, J.2    Skalsky, R.L.3    Renne, R.4
  • 5
    • 33144466305 scopus 로고    scopus 로고
    • Transcriptional origin of Kaposi's sarcoma-associated herpesvirus microRNAs
    • Cai, X., Cullen, B.R. (2006) Transcriptional origin of Kaposi's sarcoma-associated herpesvirus microRNAs. J. Virol., 80, 2234-2242.
    • (2006) J. Virol. , vol.80 , pp. 2234-2242
    • Cai, X.1    Cullen, B.R.2
  • 6
    • 77955098309 scopus 로고    scopus 로고
    • Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs
    • Lin, Y.-T., Kincaid, R.P., Arasappan, D., Dowd, S.E., Hunicke-Smith, S.P., Sullivan, C.S. (2010) Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs. RNA N. Y. N, 16, 1540-1558.
    • (2010) RNA N. Y. N , vol.16 , pp. 1540-1558
    • Lin, Y.-T.1    Kincaid, R.P.2    Arasappan, D.3    Dowd, S.E.4    Hunicke-Smith, S.P.5    Sullivan, C.S.6
  • 7
    • 84869216658 scopus 로고    scopus 로고
    • MiRNAs and usRNAs discovered in Kaposi's sarcoma-associated herpesvirus virions
    • Lin, X., Li, X., Liang, D., Lan, K. (2012) miRNAs and usRNAs discovered in Kaposi's sarcoma-associated herpesvirus virions. J. Virol., 86, 12717-12730.
    • (2012) J. Virol. , vol.86 , pp. 12717-12730
    • Lin, X.1    Li, X.2    Liang, D.3    Lan, K.4
  • 8
    • 84865114128 scopus 로고    scopus 로고
    • Kaposi's sarcoma-associated herpesvirus microRNAs
    • Gottwein, E. (2012) Kaposi's sarcoma-associated herpesvirus microRNAs. Front. Microbiol., 3, 165.
    • (2012) Front. Microbiol. , vol.3 , pp. 165
    • Gottwein, E.1
  • 9
    • 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
  • 11
    • 55049119136 scopus 로고    scopus 로고
    • Posttranscriptional regulation of miRNAs harboring conserved terminal loops
    • Michlewski, G., Guil, S., Semple, C.A., Cáceres, J.F. (2008) Posttranscriptional regulation of miRNAs harboring conserved terminal loops. Mol. Cell, 32, 383-393.
    • (2008) Mol. Cell , vol.32 , pp. 383-393
    • Michlewski, G.1    Guil, S.2    Semple, C.A.3    Cáceres, J.F.4
  • 13
    • 23044502585 scopus 로고    scopus 로고
    • Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences
    • Zeng, Y., Cullen, B.R. (2005) Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences. J. Biol. Chem., 280, 27595-27603.
    • (2005) J. Biol. Chem. , vol.280 , pp. 27595-27603
    • Zeng, Y.1    Cullen, B.R.2
  • 14
    • 78649870594 scopus 로고    scopus 로고
    • The terminal loop region controls microRNA processing by Drosha and Dicer
    • Zhang, X., Zeng, Y. (2010) The terminal loop region controls microRNA processing by Drosha and Dicer. Nucleic Acids Res., 38, 7689-7697.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 7689-7697
    • Zhang, X.1    Zeng, Y.2
  • 16
    • 84859967050 scopus 로고    scopus 로고
    • Pri-miR-17-92a transcript folds into a tertiary structure and autoregulates its processing
    • Chakraborty, S., Mehtab, S., Patwardhan, A., Krishnan, Y. (2012) Pri-miR-17-92a transcript folds into a tertiary structure and autoregulates its processing. RNA N. Y. N, 18, 1014-1028.
    • (2012) RNA N. Y. N , vol.18 , pp. 1014-1028
    • Chakraborty, S.1    Mehtab, S.2    Patwardhan, A.3    Krishnan, Y.4
  • 18
    • 16244412610 scopus 로고    scopus 로고
    • RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)
    • Merino, E.J., Wilkinson, K.A., Coughlan, J.L., Weeks, K.M. (2005) RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc., 127, 4223-4231.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 4223-4231
    • Merino, E.J.1    Wilkinson, K.A.2    Coughlan, J.L.3    Weeks, K.M.4
  • 20
    • 77954573536 scopus 로고    scopus 로고
    • Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay
    • Dölken, L., Malterer, G., Erhard, F., Kothe, S., Friedel, C.C., Suffert, G., Marcinowski, L., Motsch, N., Barth, S., Beitzinger, M. et al. (2010) Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay. Cell Host Microbe., 7, 324-334.
    • (2010) Cell Host Microbe. , vol.7 , pp. 324-334
    • Dölken, L.1    Malterer, G.2    Erhard, F.3    Kothe, S.4    Friedel, C.C.5    Suffert, G.6    Marcinowski, L.7    Motsch, N.8    Barth, S.9    Beitzinger, M.10
  • 22
    • 36849029340 scopus 로고    scopus 로고
    • Identification of virally encoded microRNAs
    • Pfeffer, S. (2007) Identification of virally encoded microRNAs. Methods Enzymol., 427, 51-63.
    • (2007) Methods Enzymol. , vol.427 , pp. 51-63
    • Pfeffer, S.1
  • 26
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M., 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
  • 27
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A.R., Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinforma. Oxf. Engl., 26, 841-842.
    • (2010) Bioinforma. Oxf. Engl. , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 29
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar, R., Domrachev, M., Lash, A.E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 30
    • 84857097117 scopus 로고    scopus 로고
    • Small RNA deep sequencing identifies microRNAs and other small noncoding RNAs from human herpesvirus 6B
    • Tuddenham, L., Jung, J.S., Chane-Woon-Ming, B., Dölken, L., Pfeffer, S. (2012) Small RNA deep sequencing identifies microRNAs and other small noncoding RNAs from human herpesvirus 6B. J. Virol., 86, 1638-1649.
    • (2012) J. Virol. , vol.86 , pp. 1638-1649
    • Tuddenham, L.1    Jung, J.S.2    Chane-Woon-Ming, B.3    Dölken, L.4    Pfeffer, S.5
  • 31
    • 34247162792 scopus 로고    scopus 로고
    • A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry
    • Mortimer, S.A., Weeks, K.M. (2007) A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J. Am. Chem. Soc., 129, 4144-4145.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 4144-4145
    • Mortimer, S.A.1    Weeks, K.M.2
  • 32
    • 70349145411 scopus 로고    scopus 로고
    • Time-resolved RNA SHAPE chemistry: Quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution
    • Mortimer, S.A., Weeks, K.M. (2009) Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution. Nat. Protoc., 4, 1413-1421.
    • (2009) Nat. Protoc. , vol.4 , pp. 1413-1421
    • Mortimer, S.A.1    Weeks, K.M.2
  • 33
    • 84888416888 scopus 로고    scopus 로고
    • SHAPE analysis of the 5' end of the Mason-Pfizer monkey virus (MPMV) genomic RNA reveals structural elements required for genome dimerization
    • Aktar, S.J., Jabeen, A., Ali, L.M., Vivet-Boudou, V., Marquet, R., Rizvi, T.A. (2013) SHAPE analysis of the 5' end of the Mason-Pfizer monkey virus (MPMV) genomic RNA reveals structural elements required for genome dimerization. RNA N. Y. N, 19, 1648-1658.
    • (2013) RNA N. Y. N , vol.19 , pp. 1648-1658
    • Aktar, S.J.1    Jabeen, A.2    Ali, L.M.3    Vivet-Boudou, V.4    Marquet, R.5    Rizvi, T.A.6
  • 34
    • 52949152433 scopus 로고    scopus 로고
    • ShapeFinder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis
    • Vasa, S.M., Guex, N., Wilkinson, K.A., Weeks, K.M., Giddings, M.C. (2008) ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA N. Y. N, 14, 1979-1990.
    • (2008) RNA N. Y. N , vol.14 , pp. 1979-1990
    • Vasa, S.M.1    Guex, N.2    Wilkinson, K.A.3    Weeks, K.M.4    Giddings, M.C.5
  • 36
    • 77949447172 scopus 로고    scopus 로고
    • RNAstructure: Software for RNA secondary structure prediction and analysis
    • Reuter, J.S., Mathews, D.H. (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformat., 11, 129.
    • (2010) BMC Bioinformat. , vol.11 , pp. 129
    • Reuter, J.S.1    Mathews, D.H.2
  • 37
    • 77955405123 scopus 로고    scopus 로고
    • Assemble: An interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
    • Jossinet, F., Ludwig, T.E., Westhof, E. (2010) Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinforma. Oxf. Engl., 26, 2057-2059.
    • (2010) Bioinforma. Oxf. Engl. , vol.26 , pp. 2057-2059
    • Jossinet, F.1    Ludwig, T.E.2    Westhof, E.3
  • 38
    • 73849149037 scopus 로고    scopus 로고
    • In-depth analysis of Kaposi's sarcoma-associated herpesvirus microRNA expression provides insights into the mammalian microRNA-processing machinery
    • Umbach, J.L., Cullen, B.R. (2010) In-depth analysis of Kaposi's sarcoma-associated herpesvirus microRNA expression provides insights into the mammalian microRNA-processing machinery. J. Virol., 84, 695-703.
    • (2010) J. Virol. , vol.84 , pp. 695-703
    • Umbach, J.L.1    Cullen, B.R.2
  • 40
    • 72849117513 scopus 로고    scopus 로고
    • Characterization of viral and human RNAs smaller than canonical MicroRNAs
    • Li, Z., Kim, S.W., Lin, Y., Moore, P.S., Chang, Y., John, B. (2009) Characterization of viral and human RNAs smaller than canonical MicroRNAs. J. Virol., 83, 12751-12758.
    • (2009) J. Virol. , vol.83 , pp. 12751-12758
    • Li, Z.1    Kim, S.W.2    Lin, Y.3    Moore, P.S.4    Chang, Y.5    John, B.6
  • 41
    • 84886251526 scopus 로고    scopus 로고
    • Kaposi's sarcoma-associated herpesvirus microRNA single-nucleotide polymorphisms identified in clinical samples can affect microRNA processing, level of expression, and silencing activity
    • Han, S.-J., Marshall, V., Barsov, E., Quinones, O., Ray, A., Labo, N., Trivett, M., Ott, D., Renne, R., Whitby, D. (2013) Kaposi's sarcoma-associated herpesvirus microRNA single-nucleotide polymorphisms identified in clinical samples can affect microRNA processing, level of expression, and silencing activity. J. Virol., 87, 12237-12248.
    • (2013) J. Virol. , vol.87 , pp. 12237-12248
    • Han, S.-J.1    Marshall, V.2    Barsov, E.3    Quinones, O.4    Ray, A.5    Labo, N.6    Trivett, M.7    Ott, D.8    Renne, R.9    Whitby, D.10
  • 43
    • 12544255565 scopus 로고    scopus 로고
    • Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha
    • Zeng, Y., Yi, R., Cullen, B.R. (2005) Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J., 24, 138-148.
    • (2005) EMBO J. , vol.24 , pp. 138-148
    • Zeng, Y.1    Yi, R.2    Cullen, B.R.3
  • 44
    • 84874086395 scopus 로고    scopus 로고
    • Beyond secondary structure: Primary-sequence determinants license pri-miRNA hairpins for processing
    • Auyeung, V.C., Ulitsky, I., McGeary, S.E., Bartel, D.P. (2013) Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell, 152, 844-858.
    • (2013) Cell , vol.152 , pp. 844-858
    • Auyeung, V.C.1    Ulitsky, I.2    McGeary, S.E.3    Bartel, D.P.4
  • 45
    • 84868153864 scopus 로고    scopus 로고
    • Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs
    • Heo, I., Ha, M., Lim, J., Yoon, M.-J., Park, J.-E., Kwon, S.C., Chang, H., Kim, V.N. (2012) Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs. Cell, 151, 521-532.
    • (2012) Cell , vol.151 , pp. 521-532
    • Heo, I.1    Ha, M.2    Lim, J.3    Yoon, M.-J.4    Park, J.-E.5    Kwon, S.C.6    Chang, H.7    Kim, V.N.8
  • 46
    • 33646721162 scopus 로고    scopus 로고
    • A novel assay for viral microRNA function identifies a single nucleotide polymorphism that affects Drosha processing
    • Gottwein, E., Cai, X., Cullen, B.R. (2006) A novel assay for viral microRNA function identifies a single nucleotide polymorphism that affects Drosha processing. J. Virol., 80, 5321-5326.
    • (2006) J. Virol. , vol.80 , pp. 5321-5326
    • Gottwein, E.1    Cai, X.2    Cullen, B.R.3
  • 47
    • 80655149142 scopus 로고    scopus 로고
    • Drosha processing controls the specificity and efficiency of global microRNA expression
    • Feng, Y., Zhang, X., Song, Q., Li, T., Zeng, Y. (2011) Drosha processing controls the specificity and efficiency of global microRNA expression. Biochim. Biophys. Acta, 1809, 700-707.
    • (2011) Biochim. Biophys. Acta , vol.1809 , pp. 700-707
    • Feng, Y.1    Zhang, X.2    Song, Q.3    Li, T.4    Zeng, Y.5
  • 50
    • 33846945735 scopus 로고    scopus 로고
    • Processing of intronic microRNAs
    • Kim, Y.-K., Kim, V.N. (2007) Processing of intronic microRNAs. EMBO J., 26, 775-783.
    • (2007) EMBO J. , vol.26 , pp. 775-783
    • Kim, Y.-K.1    Kim, V.N.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.