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Volumn 5, Issue 3, 2013, Pages 839-848

Mapping of mitochondrial RNA-protein interactions by digital rnase footprinting

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MITOCHONDRIAL RNA; RIBONUCLEASE; RIBOSOME RNA; RNA BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSFER RNA; RNA; RNA, MITOCHONDRIAL;

EID: 84887610980     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2013.09.036     Document Type: Article
Times cited : (39)

References (37)
  • 2
    • 85046980054 scopus 로고    scopus 로고
    • Involvement of human ELAC2 gene product in 3' end processing of mitochondrial tRNAs
    • Brzezniak L.K., Bijata M., Szczesny R.J., Stepien P.P. Involvement of human ELAC2 gene product in 3' end processing of mitochondrial tRNAs. RNA Biol. 2011, 8:616-626.
    • (2011) RNA Biol. , vol.8 , pp. 616-626
    • Brzezniak, L.K.1    Bijata, M.2    Szczesny, R.J.3    Stepien, P.P.4
  • 4
    • 58149189877 scopus 로고    scopus 로고
    • GtRNAdb: a database of transfer RNA genes detected in genomic sequence
    • Database issue
    • Chan P.P.P., Lowe T.M.T. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009, 37(Database issue):D93-D97.
    • (2009) Nucleic Acids Res. , vol.37
    • Chan, P.P.P.1    Lowe, T.M.T.2
  • 5
    • 77954199175 scopus 로고    scopus 로고
    • A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data
    • Chen X., Hoffman M.M., Bilmes J.A., Hesselberth J.R., Noble W.S. A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. Bioinformatics 2010, 26:i334-i342.
    • (2010) Bioinformatics , vol.26
    • Chen, X.1    Hoffman, M.M.2    Bilmes, J.A.3    Hesselberth, J.R.4    Noble, W.S.5
  • 7
    • 84857198283 scopus 로고    scopus 로고
    • Modular recognition of nucleic acids by PUF, TALE and PPR proteins
    • Filipovska A., Rackham O. Modular recognition of nucleic acids by PUF, TALE and PPR proteins. Mol. Biosyst. 2012, 8:699-708.
    • (2012) Mol. Biosyst. , vol.8 , pp. 699-708
    • Filipovska, A.1    Rackham, O.2
  • 12
    • 54549088876 scopus 로고    scopus 로고
    • RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme
    • Holzmann J., Frank P., Löffler E., Bennett K.L., Gerner C., Rossmanith W. RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme. Cell 2008, 135:462-474.
    • (2008) Cell , vol.135 , pp. 462-474
    • Holzmann, J.1    Frank, P.2    Löffler, E.3    Bennett, K.L.4    Gerner, C.5    Rossmanith, W.6
  • 13
    • 38949118287 scopus 로고    scopus 로고
    • Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection
    • Jia W., Higgs P.G. Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection. Mol. Biol. Evol. 2008, 25:339-351.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 339-351
    • Jia, W.1    Higgs, P.G.2
  • 14
    • 42449139620 scopus 로고    scopus 로고
    • Lack of secondary structure characterizes the 5' ends of mammalian mitochondrial mRNAs
    • Jones C.N., Wilkinson K.A., Hung K.T., Weeks K.M., Spremulli L.L. Lack of secondary structure characterizes the 5' ends of mammalian mitochondrial mRNAs. RNA 2008, 14:862-871.
    • (2008) RNA , vol.14 , pp. 862-871
    • Jones, C.N.1    Wilkinson, K.A.2    Hung, K.T.3    Weeks, K.M.4    Spremulli, L.L.5
  • 15
    • 33846611978 scopus 로고    scopus 로고
    • TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences
    • Karpenahalli M.R., Lupas A.N., Söding J. TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences. BMC Bioinformatics 2007, 8:2.
    • (2007) BMC Bioinformatics , vol.8 , pp. 2
    • Karpenahalli, M.R.1    Lupas, A.N.2    Söding, J.3
  • 17
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B.B., Trapnell C.C., Pop M.M., Salzberg S.L.S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10:R25.
    • (2009) Genome Biol. , vol.10
    • Langmead, B.B.1    Trapnell, C.C.2    Pop, M.M.3    Salzberg, S.L.S.4
  • 21
    • 0019423857 scopus 로고
    • Distinctive features of the 5'-terminal sequences of the human mitochondrial mRNAs
    • Montoya J., Ojala D., Attardi G. Distinctive features of the 5'-terminal sequences of the human mitochondrial mRNAs. Nature 1981, 290:465-470.
    • (1981) Nature , vol.290 , pp. 465-470
    • Montoya, J.1    Ojala, D.2    Attardi, G.3
  • 22
    • 72149090954 scopus 로고    scopus 로고
    • A simple cipher governs DNA recognition by TAL effectors
    • Moscou M.J., Bogdanove A.J. A simple cipher governs DNA recognition by TAL effectors. Science 2009, 326:1501.
    • (2009) Science , vol.326 , pp. 1501
    • Moscou, M.J.1    Bogdanove, A.J.2
  • 23
    • 0019444843 scopus 로고
    • TRNA punctuation model of RNA processing in human mitochondria
    • Ojala D., Montoya J., Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature 1981, 290:470-474.
    • (1981) Nature , vol.290 , pp. 470-474
    • Ojala, D.1    Montoya, J.2    Attardi, G.3
  • 24
    • 44949098384 scopus 로고    scopus 로고
    • Improved northern blot method for enhanced detection of small RNA
    • Pall G.S., Hamilton A.J. Improved northern blot method for enhanced detection of small RNA. Nat. Protoc. 2008, 3:1077-1084.
    • (2008) Nat. Protoc. , vol.3 , pp. 1077-1084
    • Pall, G.S.1    Hamilton, A.J.2
  • 25
    • 84864293617 scopus 로고    scopus 로고
    • The role of mammalian PPR domain proteins in the regulation of mitochondrial gene expression
    • Rackham O., Filipovska A. The role of mammalian PPR domain proteins in the regulation of mitochondrial gene expression. Biochim. Biophys. Acta 2012, 1819:1008-1016.
    • (2012) Biochim. Biophys. Acta , vol.1819 , pp. 1008-1016
    • Rackham, O.1    Filipovska, A.2
  • 27
    • 81755161589 scopus 로고    scopus 로고
    • Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins
    • Rackham O., Shearwood A.-M.J., Mercer T.R., Davies S.M.K., Mattick J.S., Filipovska A. Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins. RNA 2011, 17:2085-2093.
    • (2011) RNA , vol.17 , pp. 2085-2093
    • Rackham, O.1    Shearwood, A.-M.J.2    Mercer, T.R.3    Davies, S.M.K.4    Mattick, J.S.5    Filipovska, A.6
  • 28
    • 84867571779 scopus 로고    scopus 로고
    • The human mitochondrial transcriptome and the RNA-binding proteins that regulate its expression
    • Rackham O., Mercer T.R., Filipovska A. The human mitochondrial transcriptome and the RNA-binding proteins that regulate its expression. Wiley Interdiscip Rev RNA 2012, 3:675-695.
    • (2012) Wiley Interdiscip Rev RNA , vol.3 , pp. 675-695
    • Rackham, O.1    Mercer, T.R.2    Filipovska, A.3
  • 29
    • 84860147226 scopus 로고    scopus 로고
    • Short non-coding RNA fragments accumulating in chloroplasts: footprints of RNA binding proteins?
    • Ruwe H., Schmitz-Linneweber C. Short non-coding RNA fragments accumulating in chloroplasts: footprints of RNA binding proteins?. Nucleic Acids Res. 2012, 40:3106-3116.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 3106-3116
    • Ruwe, H.1    Schmitz-Linneweber, C.2
  • 30
    • 56549095978 scopus 로고    scopus 로고
    • Pentatricopeptide repeat proteins: a socket set for organelle gene expression
    • Schmitz-Linneweber C., Small I. Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci. 2008, 13:663-670.
    • (2008) Trends Plant Sci. , vol.13 , pp. 663-670
    • Schmitz-Linneweber, C.1    Small, I.2
  • 32
    • 80054692304 scopus 로고    scopus 로고
    • The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser
    • Simone D., Calabrese F.M., Lang M., Gasparre G., Attimonelli M. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. BMC Genomics 2011, 12:517.
    • (2011) BMC Genomics , vol.12 , pp. 517
    • Simone, D.1    Calabrese, F.M.2    Lang, M.3    Gasparre, G.4    Attimonelli, M.5
  • 33
    • 0035980117 scopus 로고    scopus 로고
    • Proteomic analysis of the mammalian mitochondrial ribosome. Identification of protein components in the 28S small subunit
    • Suzuki T., Terasaki M., Takemoto-Hori C., Hanada T., Ueda T., Wada A., Watanabe K. Proteomic analysis of the mammalian mitochondrial ribosome. Identification of protein components in the 28S small subunit. J.Biol. Chem. 2001, 276:33181-33195.
    • (2001) J.Biol. Chem. , vol.276 , pp. 33181-33195
    • Suzuki, T.1    Terasaki, M.2    Takemoto-Hori, C.3    Hanada, T.4    Ueda, T.5    Wada, A.6    Watanabe, K.7
  • 34
    • 0035877697 scopus 로고    scopus 로고
    • Structural compensation for the deficit of rRNA with proteins in the mammalian mitochondrial ribosome. Systematic analysis of protein components of the large ribosomal subunit from mammalian mitochondria
    • Suzuki T., Terasaki M., Takemoto-Hori C., Hanada T., Ueda T., Wada A., Watanabe K. Structural compensation for the deficit of rRNA with proteins in the mammalian mitochondrial ribosome. Systematic analysis of protein components of the large ribosomal subunit from mammalian mitochondria. J.Biol. Chem. 2001, 276:21724-21736.
    • (2001) J.Biol. Chem. , vol.276 , pp. 21724-21736
    • Suzuki, T.1    Terasaki, M.2    Takemoto-Hori, C.3    Hanada, T.4    Ueda, T.5    Wada, A.6    Watanabe, K.7
  • 35
    • 80755169463 scopus 로고    scopus 로고
    • Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases
    • Suzuki T., Nagao A., Suzuki T. Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases. Annu. Rev. Genet. 2011, 45:299-329.
    • (2011) Annu. Rev. Genet. , vol.45 , pp. 299-329
    • Suzuki, T.1    Nagao, A.2    Suzuki, T.3
  • 36
    • 0037162703 scopus 로고    scopus 로고
    • Modular recognition of RNA by a human pumilio-homology domain
    • Wang X., McLachlan J., Zamore P.D., Hall T.M. Modular recognition of RNA by a human pumilio-homology domain. Cell 2002, 110:501-512.
    • (2002) Cell , vol.110 , pp. 501-512
    • Wang, X.1    McLachlan, J.2    Zamore, P.D.3    Hall, T.M.4
  • 37
    • 84860153569 scopus 로고    scopus 로고
    • Protein-mediated protection as the predominant mechanism for defining processed mRNA termini in land plant chloroplasts
    • Zhelyazkova P., Hammani K., Rojas M., Voelker R., Vargas-Suárez M., Börner T., Barkan A. Protein-mediated protection as the predominant mechanism for defining processed mRNA termini in land plant chloroplasts. Nucleic Acids Res. 2012, 40:3092-3105.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 3092-3105
    • Zhelyazkova, P.1    Hammani, K.2    Rojas, M.3    Voelker, R.4    Vargas-Suárez, M.5    Börner, T.6    Barkan, A.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.