메뉴 건너뛰기




Volumn 44, Issue 16, 2016, Pages

Illumina-based RiboMethSeq approach for mapping of 2′-O-Me residues in RNA

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL RNA; RIBOSOME RNA; NUCLEOTIDE; OLIGONUCLEOTIDE; SMALL NUCLEOLAR RNA;

EID: 84988959155     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw547     Document Type: Article
Times cited : (165)

References (51)
  • 3
    • 0029855867 scopus 로고    scopus 로고
    • A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus
    • Tycowski, K.T., Smith, C.M., Shu, M.D. and Steitz, J.A. (1996) A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus. Proc. Natl. Acad. Sci. U.S.A., 93, 14480-14485.
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 14480-14485
    • Tycowski, K.T.1    Smith, C.M.2    Shu, M.D.3    Steitz, J.A.4
  • 4
    • 0032214692 scopus 로고    scopus 로고
    • Modification of U6 spliceosomal RNA is guided by other small RNAs
    • Tycowski, K.T., You, Z.H., Graham, P.J. and Steitz, J.A. (1998) Modification of U6 spliceosomal RNA is guided by other small RNAs. Mol. Cell, 2, 629-638.
    • (1998) Mol. Cell , vol.2 , pp. 629-638
    • Tycowski, K.T.1    You, Z.H.2    Graham, P.J.3    Steitz, J.A.4
  • 5
    • 77953656943 scopus 로고    scopus 로고
    • TRNA stabilization by modified nucleotides
    • Motorin, Y. and Helm, M. (2010) tRNA stabilization by modified nucleotides. Biochemistry, 49, 4934-4944.
    • (2010) Biochemistry , vol.49 , pp. 4934-4944
    • Motorin, Y.1    Helm, M.2
  • 6
    • 77951181044 scopus 로고    scopus 로고
    • Regulation of pre-mRNA splicing in Xenopus oocytes by targeted 2′-O-methylation
    • Ge, J., Liu, H. and Yu, Y.-T. (2010) Regulation of pre-mRNA splicing in Xenopus oocytes by targeted 2′-O-methylation. RNA, 16, 1078-1085.
    • (2010) RNA , vol.16 , pp. 1078-1085
    • Ge, J.1    Liu, H.2    Yu, Y.-T.3
  • 7
    • 84862803181 scopus 로고    scopus 로고
    • Regulation of small RNA stability: Methylation and beyond
    • Ji, L. and Chen, X. (2012) Regulation of small RNA stability: methylation and beyond. Cell Res., 22, 624-636.
    • (2012) Cell Res. , vol.22 , pp. 624-636
    • Ji, L.1    Chen, X.2
  • 8
    • 37749034810 scopus 로고    scopus 로고
    • Targeted pre-mRNA modification for gene silencing and regulation
    • Zhao, X. and Yu, Y.-T. (2008) Targeted pre-mRNA modification for gene silencing and regulation. Nat. Methods, 5, 95-100.
    • (2008) Nat. Methods , vol.5 , pp. 95-100
    • Zhao, X.1    Yu, Y.-T.2
  • 10
    • 84941995713 scopus 로고    scopus 로고
    • 2′-O-methylation within bacterial RNA acts as suppressor of TLR7/TLR8 activation in human innate immune cells
    • Rimbach, K., Kaiser, S., Helm, M., Dalpke, A.H. and Eigenbrod, T. (2015) 2′-O-Methylation within Bacterial RNA Acts as Suppressor of TLR7/TLR8 Activation in Human Innate Immune Cells. J. Innate Immun., 7, 482-493.
    • (2015) J. Innate Immun. , vol.7 , pp. 482-493
    • Rimbach, K.1    Kaiser, S.2    Helm, M.3    Dalpke, A.H.4    Eigenbrod, T.5
  • 12
    • 0032126521 scopus 로고    scopus 로고
    • Cap ribose methylation of c-mos mRNA stimulates translation and oocyte maturation in Xenopus laevis
    • Kuge, H., Brownlee, G.G., Gershon, P.D. and Richter, J.D. (1998) Cap ribose methylation of c-mos mRNA stimulates translation and oocyte maturation in Xenopus laevis. Nucleic Acids Res., 26, 3208-3214.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 3208-3214
    • Kuge, H.1    Brownlee, G.G.2    Gershon, P.D.3    Richter, J.D.4
  • 13
    • 70350289940 scopus 로고    scopus 로고
    • Ribose 2′-O methylation of the vesicular stomatitis virus mRNA cap precedes and facilitates subsequent guanine-N-7 methylation by the large polymerase protein
    • Rahmeh, A.A., Li, J., Kranzusch, P.J. and Whelan, S.P.J. (2009) Ribose 2′-O methylation of the vesicular stomatitis virus mRNA cap precedes and facilitates subsequent guanine-N-7 methylation by the large polymerase protein. J. Virol., 83, 11043-11050.
    • (2009) J. Virol. , vol.83 , pp. 11043-11050
    • Rahmeh, A.A.1    Li, J.2    Kranzusch, P.J.3    Whelan, S.P.J.4
  • 14
  • 15
    • 0027536869 scopus 로고
    • Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly
    • Tollervey, D., Lehtonen, H., Jansen, R., Kern, H. and Hurt, E.C. (1993) Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly. Cell, 72, 443-457.
    • (1993) Cell , vol.72 , pp. 443-457
    • Tollervey, D.1    Lehtonen, H.2    Jansen, R.3    Kern, H.4    Hurt, E.C.5
  • 16
    • 0031758488 scopus 로고    scopus 로고
    • Birth of the snoRNPs: The evolution of the modification-guide snoRNAs
    • Lafontaine, D.L. and Tollervey, D. (1998) Birth of the snoRNPs: the evolution of the modification-guide snoRNAs. Trends Biochem. Sci., 23, 383-388.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 383-388
    • Lafontaine, D.L.1    Tollervey, D.2
  • 17
    • 0030963268 scopus 로고    scopus 로고
    • Function and synthesis of small nucleolar RNAs
    • Tollervey, D. and Kiss, T. (1997) Function and synthesis of small nucleolar RNAs. Curr. Opin. Cell Biol., 9, 337-342.
    • (1997) Curr. Opin. Cell Biol. , vol.9 , pp. 337-342
    • Tollervey, D.1    Kiss, T.2
  • 18
    • 0036206498 scopus 로고    scopus 로고
    • Identification and characterization of tRNA (Gm18) methyltransferase from Thermus thermophilus HB8: Domain structure and conserved amino acid sequence motifs
    • Hori, H., Suzuki, T., Sugawara, K., Inoue, Y., Shibata, T., Kuramitsu, S., Yokoyama, S., Oshima, T. and Watanabe, K. (2002) Identification and characterization of tRNA (Gm18) methyltransferase from Thermus thermophilus HB8: domain structure and conserved amino acid sequence motifs. Genes Cells Devoted Mol. Cell. Mech., 7, 259-272.
    • (2002) Genes Cells Devoted Mol. Cell. Mech. , vol.7 , pp. 259-272
    • Hori, H.1    Suzuki, T.2    Sugawara, K.3    Inoue, Y.4    Shibata, T.5    Kuramitsu, S.6    Yokoyama, S.7    Oshima, T.8    Watanabe, K.9
  • 19
    • 1842404152 scopus 로고    scopus 로고
    • The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for tRNA (Gm18) 2′-O-methyltransferase activity
    • Persson, B.C., Jager, G. and Gustafsson, C. (1997) The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for tRNA (Gm18) 2′-O-methyltransferase activity. Nucleic Acids Res., 25, 4093-4097.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4093-4097
    • Persson, B.C.1    Jager, G.2    Gustafsson, C.3
  • 20
    • 0141869105 scopus 로고    scopus 로고
    • Functional requirement for symmetric assembly of archaeal box C/D small ribonucleoprotein particles
    • Rashid, R., Aittaleb, M., Chen, Q., Spiegel, K., Demeler, B. and Li, H. (2003) Functional requirement for symmetric assembly of archaeal box C/D small ribonucleoprotein particles. J. Mol. Biol., 333, 295-306.
    • (2003) J. Mol. Biol. , vol.333 , pp. 295-306
    • Rashid, R.1    Aittaleb, M.2    Chen, Q.3    Spiegel, K.4    Demeler, B.5    Li, H.6
  • 21
    • 0043026864 scopus 로고    scopus 로고
    • Efficient RNA 2′-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C/D RNPs
    • Tran, E.J., Zhang, X. and Maxwell, E.S. (2003) Efficient RNA 2′-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C/D RNPs. EMBO J., 22, 3930-3940.
    • (2003) EMBO J. , vol.22 , pp. 3930-3940
    • Tran, E.J.1    Zhang, X.2    Maxwell, E.S.3
  • 22
    • 0035723065 scopus 로고    scopus 로고
    • Mapping 2′-O-methyl groups in ribosomal RNA
    • Maden, B.E. (2001) Mapping 2′-O-methyl groups in ribosomal RNA. Methods (San Diego, Calif), 25, 374-382.
    • (2001) Methods (San Diego, Calif , vol.25 , pp. 374-382
    • Maden, B.E.1
  • 23
    • 0028949935 scopus 로고
    • Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA
    • Maden, B.E., Corbett, M.E., Heeney, P.A., Pugh, K. and Ajuh, P.M. (1995) Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA. Biochimie, 77, 22-29.
    • (1995) Biochimie , vol.77 , pp. 22-29
    • Maden, B.E.1    Corbett, M.E.2    Heeney, P.A.3    Pugh, K.4    Ajuh, P.M.5
  • 24
    • 84869025816 scopus 로고    scopus 로고
    • RTL-P: A sensitive approach for detecting sites of 2′-O-methylation in RNA molecules
    • Dong, Z.-W., Shao, P., Diao, L.-T., Zhou, H., Yu, C.-H. and Qu, L.-H. (2012) RTL-P: a sensitive approach for detecting sites of 2′-O-methylation in RNA molecules. Nucleic Acids Res., 40, e157.
    • (2012) Nucleic Acids Res. , vol.40 , pp. e157
    • Dong, Z.-W.1    Shao, P.2    Diao, L.-T.3    Zhou, H.4    Yu, C.-H.5    Qu, L.-H.6
  • 25
    • 84939504193 scopus 로고    scopus 로고
    • C/D box sRNA-guided 2′-O-methylation patterns of archaeal rRNA molecules
    • Dennis, P.P., Tripp, V., Lui, L., Lowe, T. and Randau, L. (2015) C/D box sRNA-guided 2′-O-methylation patterns of archaeal rRNA molecules. BMC Genomics, 16, 632.
    • (2015) BMC Genomics , vol.16 , pp. 632
    • Dennis, P.P.1    Tripp, V.2    Lui, L.3    Lowe, T.4    Randau, L.5
  • 27
    • 84879642219 scopus 로고    scopus 로고
    • Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs
    • Edelheit, S., Schwartz, S., Mumbach, M.R., Wurtzel, O. and Sorek, R. (2013) Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs. PLoS Genet., 9, e1003602.
    • (2013) PLoS Genet. , vol.9 , pp. e1003602
    • Edelheit, S.1    Schwartz, S.2    Mumbach, M.R.3    Wurtzel, O.4    Sorek, R.5
  • 28
    • 84888791449 scopus 로고    scopus 로고
    • Characterizing 5-methylcytosine in the mammalian epitranscriptome
    • Hussain, S., Aleksic, J., Blanco, S., Dietmann, S. and Frye, M. (2013) Characterizing 5-methylcytosine in the mammalian epitranscriptome. Genome Biol., 14, 215.
    • (2013) Genome Biol. , vol.14 , pp. 215
    • Hussain, S.1    Aleksic, J.2    Blanco, S.3    Dietmann, S.4    Frye, M.5
  • 32
    • 84872032385 scopus 로고    scopus 로고
    • Transcriptome-wide mapping of N (6)-methyladenosine by m (6)A-seq based on immunocapturing and massively parallel sequencing
    • Dominissini, D., Moshitch-Moshkovitz, S., Salmon-Divon, M., Amariglio, N. and Rechavi, G. (2013) Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing. Nat. Protoc., 8, 176-189.
    • (2013) Nat. Protoc. , vol.8 , pp. 176-189
    • Dominissini, D.1    Moshitch-Moshkovitz, S.2    Salmon-Divon, M.3    Amariglio, N.4    Rechavi, G.5
  • 33
    • 84922180958 scopus 로고    scopus 로고
    • Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells
    • Carlile, T.M., Rojas-Duran, M.F., Zinshteyn, B., Shin, H., Bartoli, K.M. and Gilbert, W.V. (2014) Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature, 515, 143-146.
    • (2014) Nature , vol.515 , pp. 143-146
    • Carlile, T.M.1    Rojas-Duran, M.F.2    Zinshteyn, B.3    Shin, H.4    Bartoli, K.M.5    Gilbert, W.V.6
  • 34
    • 84908626586 scopus 로고    scopus 로고
    • Transcriptome-wide mapping of pseudouridines: Pseudouridine synthases modify specific mRNAs in S. Cerevisiae
    • Lovejoy, A.F., Riordan, D.P. and Brown, P.O. (2014) Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae. PLoS One, 9, e110799.
    • (2014) PLoS One , vol.9 , pp. e110799
    • Lovejoy, A.F.1    Riordan, D.P.2    Brown, P.O.3
  • 38
    • 84957828213 scopus 로고    scopus 로고
    • Transcriptome-wide mapping reveals reversible and dynamic N (1)-methyladenosine methylome
    • Li, X., Xiong, X., Wang, K., Wang, L., Shu, X., Ma, S. and Yi, C. (2016) Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome. Nat. Chem. Biol., 12, 311-316.
    • (2016) Nat. Chem. Biol. , vol.12 , pp. 311-316
    • Li, X.1    Xiong, X.2    Wang, K.3    Wang, L.4    Shu, X.5    Ma, S.6    Yi, C.7
  • 41
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for Illumina sequence data
    • Bolger, A.M., Lohse, M. and Usadel, B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114-2120.
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 42
  • 43
    • 0025683270 scopus 로고
    • Preparation and enzymatic hydrolysis of DNA and RNA for mass spectrometry
    • Crain, P.F. (1990) Preparation and enzymatic hydrolysis of DNA and RNA for mass spectrometry. Methods Enzymol., 193, 782-790.
    • (1990) Methods Enzymol. , vol.193 , pp. 782-790
    • Crain, P.F.1
  • 44
    • 84962421726 scopus 로고    scopus 로고
    • Analysis of RNA modifications by liquid chromatography-tandem mass spectrometry
    • Thuring, K., Schmid, K., Keller, P. and Helm, M. (2016) Analysis of RNA modifications by liquid chromatography-tandem mass spectrometry. Methods, doi:10.1016/j.ymeth.2016.03.019.
    • (2016) Methods
    • Thuring, K.1    Schmid, K.2    Keller, P.3    Helm, M.4
  • 45
    • 0019467224 scopus 로고
    • 5′-Terminal sequences of eucaryotic mRNA can be cloned with high efficiency
    • Land, H., Grez, M., Hauser, H., Lindenmaier, W. and Schutz, G. (1981) 5′-Terminal sequences of eucaryotic mRNA can be cloned with high efficiency. Nucleic Acids Res., 9, 2251-2266.
    • (1981) Nucleic Acids Res. , vol.9 , pp. 2251-2266
    • Land, H.1    Grez, M.2    Hauser, H.3    Lindenmaier, W.4    Schutz, G.5
  • 46
    • 79959203991 scopus 로고    scopus 로고
    • Novel methods for rRNA removal and directional, ligation-free RNA-seq library preparation
    • Sooknanan, R., Pease, J. and Doyle, K. (2010) Novel methods for rRNA removal and directional, ligation-free RNA-seq library preparation. Nat. Methods, 7, http://www.nature.com/nmeth/journal/v7/n10/pdf/nmeth.f.313.pdf.
    • (2010) Nat. Methods , vol.7
    • Sooknanan, R.1    Pease, J.2    Doyle, K.3
  • 47
    • 0020491299 scopus 로고
    • Changes of post-transcriptional modification of wye base in tumor-specific tRNAPhe
    • Kuchino, Y., Borek, E., Grunberger, D., Mushinski, J.F. and Nishimura, S. (1982) Changes of post-transcriptional modification of wye base in tumor-specific tRNAPhe. Nucleic Acids Res., 10, 6421-6432.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 6421-6432
    • Kuchino, Y.1    Borek, E.2    Grunberger, D.3    Mushinski, J.F.4    Nishimura, S.5
  • 48
    • 0028923456 scopus 로고
    • Highly specific and efficient cleavage of squid tRNA(Lys) catalyzed by magnesium ions
    • Matsuo, M., Yokogawa, T., Nishikawa, K., Watanabe, K. and Okada, N. (1995) Highly specific and efficient cleavage of squid tRNA(Lys) catalyzed by magnesium ions. J. Biol. Chem., 270, 10097-10104.
    • (1995) J. Biol. Chem. , vol.270 , pp. 10097-10104
    • Matsuo, M.1    Yokogawa, T.2    Nishikawa, K.3    Watanabe, K.4    Okada, N.5
  • 49
    • 84899586607 scopus 로고    scopus 로고
    • The dynamic epitranscriptome: N6-methyladenosine and gene expression control
    • Meyer, K.D. and Jaffrey, S.R. (2014) The dynamic epitranscriptome: N6-methyladenosine and gene expression control. Nat. Rev. Mol. Cell Biol., 15, 313-326.
    • (2014) Nat. Rev. Mol. Cell Biol. , vol.15 , pp. 313-326
    • Meyer, K.D.1    Jaffrey, S.R.2
  • 50
    • 84255209216 scopus 로고    scopus 로고
    • Cellular dynamics of RNA modification
    • Yi, C. and Pan, T. (2011) Cellular dynamics of RNA modification. Acc. Chem. Res., 44, 1380-1388.
    • (2011) Acc. Chem. Res. , vol.44 , pp. 1380-1388
    • Yi, C.1    Pan, T.2
  • 51
    • 84919384495 scopus 로고    scopus 로고
    • Nutritional status modulates box C/D snoRNP biogenesis by regulated subcellular relocalization of the R2TP complex
    • Kakihara, Y., Makhnevych, T., Zhao, L., Tang, W. and Houry, W.A. (2014) Nutritional status modulates box C/D snoRNP biogenesis by regulated subcellular relocalization of the R2TP complex. Genome Biol., 15, 404.
    • (2014) Genome Biol. , vol.15 , pp. 404
    • Kakihara, Y.1    Makhnevych, T.2    Zhao, L.3    Tang, W.4    Houry, W.A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.