메뉴 건너뛰기




Volumn 16, Issue 6, 2016, Pages 1588-1603

Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DINUCLEOTIDE; DOXYCYCLINE; INITIATION FACTOR 4A; INITIATION FACTOR 4A3; MESSENGER RNA; NUCLEAR PROTEIN; RIBOSOME PROTEIN; RNA BINDING PROTEIN; RNA BINDING PROTEIN SERINE RICH DOMAIN 1; SMALL INTERFERING RNA; TRANSCRIPTOME; UNCLASSIFIED DRUG; UPFRAMESHIFT PROTEIN 3B; RIBONUCLEOPROTEIN; RNA PRECURSOR;

EID: 84979763375     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2016.06.096     Document Type: Article
Times cited : (57)

References (61)
  • 4
    • 84980360970 scopus 로고    scopus 로고
    • Intranuclear binding in space and time of exon junction complex and NXF1 to premRNPs/mRNPs in vivo
    • Björk, P., Persson, J.O., Wieslander, L., Intranuclear binding in space and time of exon junction complex and NXF1 to premRNPs/mRNPs in vivo. J. Cell Biol. 211 (2015), 63–75.
    • (2015) J. Cell Biol. , vol.211 , pp. 63-75
    • Björk, P.1    Persson, J.O.2    Wieslander, L.3
  • 6
    • 33747182255 scopus 로고    scopus 로고
    • The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA
    • Bono, F., Ebert, J., Lorentzen, E., Conti, E., The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA. Cell 126 (2006), 713–725.
    • (2006) Cell , vol.126 , pp. 713-725
    • Bono, F.1    Ebert, J.2    Lorentzen, E.3    Conti, E.4
  • 13
    • 4043118349 scopus 로고    scopus 로고
    • Association of the breast cancer protein MLN51 with the exon junction complex via its speckle localizer and RNA binding module
    • Degot, S., Le Hir, H., Alpy, F., Kedinger, V., Stoll, I., Wendling, C., Seraphin, B., Rio, M.C., Tomasetto, C., Association of the breast cancer protein MLN51 with the exon junction complex via its speckle localizer and RNA binding module. J. Biol. Chem. 279 (2004), 33702–33715.
    • (2004) J. Biol. Chem. , vol.279 , pp. 33702-33715
    • Degot, S.1    Le Hir, H.2    Alpy, F.3    Kedinger, V.4    Stoll, I.5    Wendling, C.6    Seraphin, B.7    Rio, M.C.8    Tomasetto, C.9
  • 15
    • 84891687767 scopus 로고    scopus 로고
    • Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs
    • Friedersdorf, M.B., Keene, J.D., Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs. Genome Biol., 15, 2014, R2.
    • (2014) Genome Biol. , vol.15 , pp. R2
    • Friedersdorf, M.B.1    Keene, J.D.2
  • 16
    • 25844512736 scopus 로고    scopus 로고
    • Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements
    • Gehring, N.H., Kunz, J.B., Neu-Yilik, G., Breit, S., Viegas, M.H., Hentze, M.W., Kulozik, A.E., Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements. Mol. Cell 20 (2005), 65–75.
    • (2005) Mol. Cell , vol.20 , pp. 65-75
    • Gehring, N.H.1    Kunz, J.B.2    Neu-Yilik, G.3    Breit, S.4    Viegas, M.H.5    Hentze, M.W.6    Kulozik, A.E.7
  • 17
    • 66249134562 scopus 로고    scopus 로고
    • The hierarchy of exon-junction complex assembly by the spliceosome explains key features of mammalian nonsense-mediated mRNA decay
    • Gehring, N.H., Lamprinaki, S., Hentze, M.W., Kulozik, A.E., The hierarchy of exon-junction complex assembly by the spliceosome explains key features of mammalian nonsense-mediated mRNA decay. PLoS Biol., 7, 2009, e1000120.
    • (2009) PLoS Biol. , vol.7 , pp. e1000120
    • Gehring, N.H.1    Lamprinaki, S.2    Hentze, M.W.3    Kulozik, A.E.4
  • 18
    • 65249119729 scopus 로고    scopus 로고
    • Disassembly of exon junction complexes by PYM
    • Gehring, N.H., Lamprinaki, S., Kulozik, A.E., Hentze, M.W., Disassembly of exon junction complexes by PYM. Cell 137 (2009), 536–548.
    • (2009) Cell , vol.137 , pp. 536-548
    • Gehring, N.H.1    Lamprinaki, S.2    Kulozik, A.E.3    Hentze, M.W.4
  • 19
    • 2342439151 scopus 로고    scopus 로고
    • Splicing of oskar RNA in the nucleus is coupled to its cytoplasmic localization
    • Hachet, O., Ephrussi, A., Splicing of oskar RNA in the nucleus is coupled to its cytoplasmic localization. Nature 428 (2004), 959–963.
    • (2004) Nature , vol.428 , pp. 959-963
    • Hachet, O.1    Ephrussi, A.2
  • 20
    • 84893743482 scopus 로고    scopus 로고
    • De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function
    • Han, A., Stoilov, P., Linares, A.J., Zhou, Y., Fu, X.D., Black, D.L., De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function. PLoS Comput. Biol., 10, 2014, e1003442.
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003442
    • Han, A.1    Stoilov, P.2    Linares, A.J.3    Zhou, Y.4    Fu, X.D.5    Black, D.L.6
  • 22
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    • Huang, W., Sherman, B.T., Lempicki, R.A., Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37 (2009), 1–13.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1-13
    • Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 25
    • 0035823150 scopus 로고    scopus 로고
    • Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex
    • Kim, V.N., Kataoka, N., Dreyfuss, G., Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex. Science 293 (2001), 1832–1836.
    • (2001) Science , vol.293 , pp. 1832-1836
    • Kim, V.N.1    Kataoka, N.2    Dreyfuss, G.3
  • 27
    • 0034672093 scopus 로고    scopus 로고
    • The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions
    • Le Hir, H., Izaurralde, E., Maquat, L.E., Moore, M.J., The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J. 19 (2000), 6860–6869.
    • (2000) EMBO J. , vol.19 , pp. 6860-6869
    • Le Hir, H.1    Izaurralde, E.2    Maquat, L.E.3    Moore, M.J.4
  • 28
    • 0035801373 scopus 로고    scopus 로고
    • The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay
    • Le Hir, H., Gatfield, D., Izaurralde, E., Moore, M.J., The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J. 20 (2001), 4987–4997.
    • (2001) EMBO J. , vol.20 , pp. 4987-4997
    • Le Hir, H.1    Gatfield, D.2    Izaurralde, E.3    Moore, M.J.4
  • 29
    • 0033575702 scopus 로고    scopus 로고
    • Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing
    • Mayeda, A., Badolato, J., Kobayashi, R., Zhang, M.Q., Gardiner, E.M., Krainer, A.R., Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing. EMBO J. 18 (1999), 4560–4570.
    • (1999) EMBO J. , vol.18 , pp. 4560-4570
    • Mayeda, A.1    Badolato, J.2    Kobayashi, R.3    Zhang, M.Q.4    Gardiner, E.M.5    Krainer, A.R.6
  • 30
    • 48149095822 scopus 로고    scopus 로고
    • Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense?
    • McGlincy, N.J., Smith, C.W., Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense?. Trends Biochem. Sci. 33 (2008), 385–393.
    • (2008) Trends Biochem. Sci. , vol.33 , pp. 385-393
    • McGlincy, N.J.1    Smith, C.W.2
  • 32
    • 6944256813 scopus 로고    scopus 로고
    • Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise
    • Mendell, J.T., Sharifi, N.A., Meyers, J.L., Martinez-Murillo, F., Dietz, H.C., Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet. 36 (2004), 1073–1078.
    • (2004) Nat. Genet. , vol.36 , pp. 1073-1078
    • Mendell, J.T.1    Sharifi, N.A.2    Meyers, J.L.3    Martinez-Murillo, F.4    Dietz, H.C.5
  • 33
    • 0033761629 scopus 로고    scopus 로고
    • Synthesis of the translational apparatus is regulated at the translational level
    • Meyuhas, O., Synthesis of the translational apparatus is regulated at the translational level. Eur. J. Biochem. 267 (2000), 6321–6330.
    • (2000) Eur. J. Biochem. , vol.267 , pp. 6321-6330
    • Meyuhas, O.1
  • 36
    • 84861323734 scopus 로고    scopus 로고
    • The structure of the ASAP core complex reveals the existence of a Pinin-containing PSAP complex
    • Murachelli, A.G., Ebert, J., Basquin, C., Le Hir, H., Conti, E., The structure of the ASAP core complex reveals the existence of a Pinin-containing PSAP complex. Nat. Struct. Mol. Biol. 19 (2012), 378–386.
    • (2012) Nat. Struct. Mol. Biol. , vol.19 , pp. 378-386
    • Murachelli, A.G.1    Ebert, J.2    Basquin, C.3    Le Hir, H.4    Conti, E.5
  • 37
    • 0942268832 scopus 로고    scopus 로고
    • Splicing enhances translation in mammalian cells: an additional function of the exon junction complex
    • Nott, A., Le Hir, H., Moore, M.J., Splicing enhances translation in mammalian cells: an additional function of the exon junction complex. Genes Dev. 18 (2004), 210–222.
    • (2004) Genes Dev. , vol.18 , pp. 210-222
    • Nott, A.1    Le Hir, H.2    Moore, M.J.3
  • 38
    • 1442354190 scopus 로고    scopus 로고
    • An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay
    • Palacios, I.M., Gatfield, D., St Johnston, D., Izaurralde, E., An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay. Nature 427 (2004), 753–757.
    • (2004) Nature , vol.427 , pp. 753-757
    • Palacios, I.M.1    Gatfield, D.2    St Johnston, D.3    Izaurralde, E.4
  • 40
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson, M.D., McCarthy, D.J., Smyth, G.K., edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26 (2010), 139–140.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 42
    • 33745150462 scopus 로고    scopus 로고
    • Ribosomal protein S6 phosphorylation: from protein synthesis to cell size
    • Ruvinsky, I., Meyuhas, O., Ribosomal protein S6 phosphorylation: from protein synthesis to cell size. Trends Biochem. Sci. 31 (2006), 342–348.
    • (2006) Trends Biochem. Sci. , vol.31 , pp. 342-348
    • Ruvinsky, I.1    Meyuhas, O.2
  • 43
    • 46149112362 scopus 로고    scopus 로고
    • Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay
    • Saltzman, A.L., Kim, Y.K., Pan, Q., Fagnani, M.M., Maquat, L.E., Blencowe, B.J., Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol. Cell. Biol. 28 (2008), 4320–4330.
    • (2008) Mol. Cell. Biol. , vol.28 , pp. 4320-4330
    • Saltzman, A.L.1    Kim, Y.K.2    Pan, Q.3    Fagnani, M.M.4    Maquat, L.E.5    Blencowe, B.J.6
  • 46
    • 84899493057 scopus 로고    scopus 로고
    • ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
    • Shen, L., Shao, N., Liu, X., Nestler, E., ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics, 15, 2014, 284.
    • (2014) BMC Genomics , vol.15 , pp. 284
    • Shen, L.1    Shao, N.2    Liu, X.3    Nestler, E.4
  • 47
    • 1842577707 scopus 로고    scopus 로고
    • eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay
    • Shibuya, T., Tange, T.O., Sonenberg, N., Moore, M.J., eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay. Nat. Struct. Mol. Biol. 11 (2004), 346–351.
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 346-351
    • Shibuya, T.1    Tange, T.O.2    Sonenberg, N.3    Moore, M.J.4
  • 49
    • 84892728434 scopus 로고    scopus 로고
    • Sequencing depth and coverage: key considerations in genomic analyses
    • Sims, D., Sudbery, I., Ilott, N.E., Heger, A., Ponting, C.P., Sequencing depth and coverage: key considerations in genomic analyses. Nat. Rev. Genet. 15 (2014), 121–132.
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 121-132
    • Sims, D.1    Sudbery, I.2    Ilott, N.E.3    Heger, A.4    Ponting, C.P.5
  • 50
    • 84869090905 scopus 로고    scopus 로고
    • The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus
    • Singh, G., Kucukural, A., Cenik, C., Leszyk, J.D., Shaffer, S.A., Weng, Z., Moore, M.J., The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell 151 (2012), 750–764.
    • (2012) Cell , vol.151 , pp. 750-764
    • Singh, G.1    Kucukural, A.2    Cenik, C.3    Leszyk, J.D.4    Shaffer, S.A.5    Weng, Z.6    Moore, M.J.7
  • 51
    • 32344437827 scopus 로고    scopus 로고
    • Novel modes of splicing repression by PTB
    • Spellman, R., Smith, C.W., Novel modes of splicing repression by PTB. Trends Biochem. Sci. 31 (2006), 73–76.
    • (2006) Trends Biochem. Sci. , vol.31 , pp. 73-76
    • Spellman, R.1    Smith, C.W.2
  • 52
    • 84936744064 scopus 로고    scopus 로고
    • Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
    • Sugimoto, Y., König, J., Hussain, S., Zupan, B., Curk, T., Frye, M., Ule, J., Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol., 13, 2012, R67.
    • (2012) Genome Biol. , vol.13 , pp. R67
    • Sugimoto, Y.1    König, J.2    Hussain, S.3    Zupan, B.4    Curk, T.5    Frye, M.6    Ule, J.7
  • 53
    • 0035794679 scopus 로고    scopus 로고
    • SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs
    • Sureau, A., Gattoni, R., Dooghe, Y., Stévenin, J., Soret, J., SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs. EMBO J. 20 (2001), 1785–1796.
    • (2001) EMBO J. , vol.20 , pp. 1785-1796
    • Sureau, A.1    Gattoni, R.2    Dooghe, Y.3    Stévenin, J.4    Soret, J.5
  • 54
    • 28344456363 scopus 로고    scopus 로고
    • Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core
    • Tange, T.O., Shibuya, T., Jurica, M.S., Moore, M.J., Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core. RNA 11 (2005), 1869–1883.
    • (2005) RNA , vol.11 , pp. 1869-1883
    • Tange, T.O.1    Shibuya, T.2    Jurica, M.S.3    Moore, M.J.4
  • 55
    • 84873828345 scopus 로고    scopus 로고
    • Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability
    • Tani, H., Imamachi, N., Salam, K.A., Mizutani, R., Ijiri, K., Irie, T., Yada, T., Suzuki, Y., Akimitsu, N., Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability. RNA Biol. 9 (2012), 1370–1379.
    • (2012) RNA Biol. , vol.9 , pp. 1370-1379
    • Tani, H.1    Imamachi, N.2    Salam, K.A.3    Mizutani, R.4    Ijiri, K.5    Irie, T.6    Yada, T.7    Suzuki, Y.8    Akimitsu, N.9
  • 56
    • 84875634162 scopus 로고    scopus 로고
    • Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
    • Thorvaldsdóttir, H., Robinson, J.T., Mesirov, J.P., Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14 (2013), 178–192.
    • (2013) Brief. Bioinform. , vol.14 , pp. 178-192
    • Thorvaldsdóttir, H.1    Robinson, J.T.2    Mesirov, J.P.3
  • 57
    • 84996555435 scopus 로고    scopus 로고
    • Transcriptome-wide modulation of splicing by the exon junction complex
    • Wang, Z., Murigneux, V., Le Hir, H., Transcriptome-wide modulation of splicing by the exon junction complex. Genome Biol., 15, 2014, 551.
    • (2014) Genome Biol. , vol.15 , pp. 551
    • Wang, Z.1    Murigneux, V.2    Le Hir, H.3
  • 58
    • 32044454232 scopus 로고    scopus 로고
    • hUPF2 silencing identifies physiologic substrates of mammalian nonsense-mediated mRNA decay
    • Wittmann, J., Hol, E.M., Jäck, H.M., hUPF2 silencing identifies physiologic substrates of mammalian nonsense-mediated mRNA decay. Mol. Cell. Biol. 26 (2006), 1272–1287.
    • (2006) Mol. Cell. Biol. , vol.26 , pp. 1272-1287
    • Wittmann, J.1    Hol, E.M.2    Jäck, H.M.3
  • 59
    • 72149117411 scopus 로고    scopus 로고
    • Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping
    • Xue, Y., Zhou, Y., Wu, T., Zhu, T., Ji, X., Kwon, Y.S., Zhang, C., Yeo, G., Black, D.L., Sun, H., et al. Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol. Cell 36 (2009), 996–1006.
    • (2009) Mol. Cell , vol.36 , pp. 996-1006
    • Xue, Y.1    Zhou, Y.2    Wu, T.3    Zhu, T.4    Ji, X.5    Kwon, Y.S.6    Zhang, C.7    Yeo, G.8    Black, D.L.9    Sun, H.10
  • 60
    • 59649107040 scopus 로고    scopus 로고
    • An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells
    • Yeo, G.W., Coufal, N.G., Liang, T.Y., Peng, G.E., Fu, X.D., Gage, F.H., An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat. Struct. Mol. Biol. 16 (2009), 130–137.
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 130-137
    • Yeo, G.W.1    Coufal, N.G.2    Liang, T.Y.3    Peng, G.E.4    Fu, X.D.5    Gage, F.H.6
  • 61
    • 81755172088 scopus 로고    scopus 로고
    • Autoregulation of the nonsense-mediated mRNA decay pathway in human cells
    • Yepiskoposyan, H., Aeschimann, F., Nilsson, D., Okoniewski, M., Mühlemann, O., Autoregulation of the nonsense-mediated mRNA decay pathway in human cells. RNA 17 (2011), 2108–2118.
    • (2011) RNA , vol.17 , pp. 2108-2118
    • Yepiskoposyan, H.1    Aeschimann, F.2    Nilsson, D.3    Okoniewski, M.4    Mühlemann, O.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.