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Volumn 7, Issue , 2016, Pages

A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; LONG UNTRANSLATED RNA NORAD; MESSENGER RNA; PUMILIO PROTEIN PUM1; PUMILIO PROTEIN PUM2; RNA BINDING PROTEIN; UNCLASSIFIED DRUG; NORAD LONG NON-CODING RNA, HUMAN; PUM1 PROTEIN, HUMAN; PUM2 PROTEIN, HUMAN;

EID: 84978865101     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms12209     Document Type: Article
Times cited : (179)

References (50)
  • 1
    • 84879987789 scopus 로고    scopus 로고
    • LincRNAs: Genomics, evolution, and mechanisms
    • Ulitsky, I. & Bartel, D. P. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26-46 (2013).
    • (2013) Cell , vol.154 , pp. 26-46
    • Ulitsky, I.1    Bartel, D.P.2
  • 2
    • 79957840356 scopus 로고    scopus 로고
    • Long noncoding RNAs and human disease
    • Wapinski, O. & Chang, H. Y. Long noncoding RNAs and human disease. Trends Cell Biol. 21, 354-361 (2011).
    • (2011) Trends Cell Biol. , vol.21 , pp. 354-361
    • Wapinski, O.1    Chang, H.Y.2
  • 3
    • 84861904178 scopus 로고    scopus 로고
    • Genome regulation by long noncoding RNAs
    • Rinn, J. L. & Chang, H. Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 81, 145-166 (2012).
    • (2012) Annu. Rev. Biochem. , vol.81 , pp. 145-166
    • Rinn, J.L.1    Chang, H.Y.2
  • 4
    • 84875177348 scopus 로고    scopus 로고
    • X-inactivation, imprinting, and long noncoding RNAs in health and disease
    • Lee, J. T. & Bartolomei, M. S. X-inactivation, imprinting, and long noncoding RNAs in health and disease. Cell 152, 1308-1323 (2013).
    • (2013) Cell , vol.152 , pp. 1308-1323
    • Lee, J.T.1    Bartolomei, M.S.2
  • 5
    • 84869088820 scopus 로고    scopus 로고
    • Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat
    • Carrieri, C. et al. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491, 454-457 (2012).
    • (2012) Nature , vol.491 , pp. 454-457
    • Carrieri, C.1
  • 6
    • 79951495822 scopus 로고    scopus 로고
    • LncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 30 UTRs via Alu elements
    • Gong, C. & Maquat, L. E. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 30 UTRs via Alu elements. Nature 470, 284-288 (2011).
    • (2011) Nature , vol.470 , pp. 284-288
    • Gong, C.1    Maquat, L.E.2
  • 7
    • 84875369248 scopus 로고    scopus 로고
    • Circular RNAs are a large class of animal RNAs with regulatory potency
    • Memczak, S. et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333-338 (2013).
    • (2013) Nature , vol.495 , pp. 333-338
    • Memczak, S.1
  • 8
    • 84875372911 scopus 로고    scopus 로고
    • Natural RNA circles function as efficient microRNA sponges
    • Hansen, T. B. et al. Natural RNA circles function as efficient microRNA sponges. Nature 495, 384-388 (2013).
    • (2013) Nature , vol.495 , pp. 384-388
    • Hansen, T.B.1
  • 9
    • 84956906428 scopus 로고    scopus 로고
    • Expanded identification and characterization of mammalian circular RNAs
    • Guo, J. U., Agarwal, V., Guo, H. & Bartel, D. P. Expanded identification and characterization of mammalian circular RNAs. Genome Biol. 15, 409 (2014).
    • (2014) Genome Biol. , vol.15 , pp. 409
    • Guo, J.U.1    Agarwal, V.2    Guo, H.3    Bartel, D.P.4
  • 10
    • 0142119568 scopus 로고    scopus 로고
    • The PUF family of RNA-binding proteins: Does evolutionarily conserved structure equal conserved function?
    • Spassov, D. S. & Jurecic, R. The PUF family of RNA-binding proteins: does evolutionarily conserved structure equal conserved function? IUBMB Life 55, 359-366 (2003).
    • (2003) IUBMB Life , vol.55 , pp. 359-366
    • Spassov, D.S.1    Jurecic, R.2
  • 11
    • 84904460276 scopus 로고    scopus 로고
    • The RNA binding domain of Pumilio antagonizes poly-adenosine binding protein and accelerates deadenylation
    • Weidmann, C. A. et al. The RNA binding domain of Pumilio antagonizes poly-adenosine binding protein and accelerates deadenylation. RNA 20, 1298-1319 (2014).
    • (2014) RNA , vol.20 , pp. 1298-1319
    • Weidmann, C.A.1
  • 12
    • 0032857210 scopus 로고    scopus 로고
    • The Drosophila pumilio gene encodes two functional protein isoforms that play multiple roles in germline development, gonadogenesis, oogenesis and embryogenesis
    • Parisi, M. & Lin, H. The Drosophila pumilio gene encodes two functional protein isoforms that play multiple roles in germline development, gonadogenesis, oogenesis and embryogenesis. Genetics 153, 235-250 (1999).
    • (1999) Genetics , vol.153 , pp. 235-250
    • Parisi, M.1    Lin, H.2
  • 13
    • 8844253301 scopus 로고    scopus 로고
    • The translational repressor Pumilio regulates presynaptic morphology and controls postsynaptic accumulation of translation factor eIF-4E
    • Menon, K. P. et al. The translational repressor Pumilio regulates presynaptic morphology and controls postsynaptic accumulation of translation factor eIF-4E. Neuron 44, 663-676 (2004).
    • (2004) Neuron , vol.44 , pp. 663-676
    • Menon, K.P.1
  • 14
    • 52349122355 scopus 로고    scopus 로고
    • Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system
    • Galgano, A. et al. Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PloS ONE 3, e3164 (2008).
    • (2008) PloS ONE , vol.3
    • Galgano, A.1
  • 15
    • 33745791191 scopus 로고    scopus 로고
    • Dendritic localization of the translational repressor Pumilio 2 and its contribution to dendritic stress granules
    • Vessey, J. P. et al. Dendritic localization of the translational repressor Pumilio 2 and its contribution to dendritic stress granules. J. Neurosci. 26, 6496-6508 (2006).
    • (2006) J. Neurosci. , vol.26 , pp. 6496-6508
    • Vessey, J.P.1
  • 16
    • 37749015690 scopus 로고    scopus 로고
    • Conserved regulation of MAP kinase expression by PUF RNA-binding proteins
    • Lee, M. H. et al. Conserved regulation of MAP kinase expression by PUF RNA-binding proteins. PLoS Genet. 3, e233 (2007).
    • (2007) PLoS Genet. , vol.3 , pp. e233
    • Lee, M.H.1
  • 17
    • 0037457894 scopus 로고    scopus 로고
    • Human Pumilio-2 is expressed in embryonic stem cells and germ cells and interacts with DAZ (Deleted in AZoospermia) and DAZ-like proteins
    • Moore, F. L. et al. Human Pumilio-2 is expressed in embryonic stem cells and germ cells and interacts with DAZ (Deleted in AZoospermia) and DAZ-like proteins. Proc. Natl Acad. Sci. USA 100, 538-543 (2003).
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 538-543
    • Moore, F.L.1
  • 18
    • 84954399183 scopus 로고    scopus 로고
    • Noncoding RNA NORAD regulates genomic stability by sequestering PUMILIO proteins
    • Lee, S. et al. Noncoding RNA NORAD regulates genomic stability by sequestering PUMILIO proteins. Cell 164, 69-80 (2016).
    • (2016) Cell , vol.164 , pp. 69-80
    • Lee, S.1
  • 19
    • 53349161901 scopus 로고    scopus 로고
    • Imaging individual mRNA molecules using multiple singly labeled probes
    • Raj, A. et al. Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods 5, 877-879 (2008).
    • (2008) Nat. Methods , vol.5 , pp. 877-879
    • Raj, A.1
  • 20
    • 84929705123 scopus 로고    scopus 로고
    • Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species
    • Hezroni, H. et al. Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. Cell Rep. 11, 1110-1122 (2015).
    • (2015) Cell Rep. , vol.11 , pp. 1110-1122
    • Hezroni, H.1
  • 21
    • 84876020023 scopus 로고    scopus 로고
    • CPAT: Coding-potential assessment tool using an alignment-free logistic regression model
    • Wang, L. et al. CPAT: coding-potential assessment tool using an alignment-free logistic regression model. Nucleic Acids Res. 41, e74 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. e74
    • Wang, L.1
  • 22
    • 34547582418 scopus 로고    scopus 로고
    • CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine
    • Kong, L. et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 35, W345-W349 (2007).
    • (2007) Nucleic Acids Res. , vol.35 , pp. W345-W349
    • Kong, L.1
  • 23
    • 81055155799 scopus 로고    scopus 로고
    • Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    • Ingolia, N. T., Lareau, L. F. & Weissman, J. S. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147, 789-802 (2011).
    • (2011) Cell , vol.147 , pp. 789-802
    • Ingolia, N.T.1    Lareau, L.F.2    Weissman, J.S.3
  • 24
    • 84920944681 scopus 로고    scopus 로고
    • Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation
    • Rubio, C. A. et al. Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation. Genome Biol. 15, 476 (2014).
    • (2014) Genome Biol. , vol.15 , pp. 476
    • Rubio, C.A.1
  • 25
    • 84922489184 scopus 로고    scopus 로고
    • Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes
    • Ingolia, N. T. et al. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep. 8, 1365-1379 (2014).
    • (2014) Cell Rep. , vol.8 , pp. 1365-1379
    • Ingolia, N.T.1
  • 26
    • 84922394487 scopus 로고    scopus 로고
    • MRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues
    • Eichhorn, S. W. et al. mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol. Cell 56, 104-115 (2014).
    • (2014) Mol. Cell , vol.56 , pp. 104-115
    • Eichhorn, S.W.1
  • 27
    • 84907221438 scopus 로고    scopus 로고
    • RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer
    • Wolfe, A. L. et al. RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. Nature 513, 65-70 (2014).
    • (2014) Nature , vol.513 , pp. 65-70
    • Wolfe, A.L.1
  • 28
    • 84879969127 scopus 로고    scopus 로고
    • Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins
    • Guttman, M. et al. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell 154, 240-251 (2013).
    • (2013) Cell , vol.154 , pp. 240-251
    • Guttman, M.1
  • 29
    • 33646272409 scopus 로고    scopus 로고
    • Identification and classification of conserved RNA secondary structures in the human genome
    • Pedersen, J. S. et al. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput. Biol. 2, e33 (2006).
    • (2006) PLoS Comput. Biol. , vol.2 , pp. e33
    • Pedersen, J.S.1
  • 30
    • 77950920903 scopus 로고    scopus 로고
    • Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
    • Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129-141 (2010).
    • (2010) Cell , vol.141 , pp. 129-141
    • Hafner, M.1
  • 31
    • 84867832074 scopus 로고    scopus 로고
    • Human Pumilio proteins recruit multiple deadenylases to efficiently repress messenger RNAs
    • Van Etten, J. et al. Human Pumilio proteins recruit multiple deadenylases to efficiently repress messenger RNAs. J. Biol. Chem. 287, 36370-36383 (2012).
    • (2012) J. Biol. Chem. , vol.287 , pp. 36370-36383
    • Van Etten, J.1
  • 32
    • 84946197772 scopus 로고    scopus 로고
    • Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation
    • Gaidatzis, D., Burger, L., Florescu, M. & Stadler, M. B. Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation. Nat. Biotechnol. 33, 722-729 (2015).
    • (2015) Nat. Biotechnol. , vol.33 , pp. 722-729
    • Gaidatzis, D.1    Burger, L.2    Florescu, M.3    Stadler, M.B.4
  • 33
    • 84896120165 scopus 로고    scopus 로고
    • Genetic exploration of the exit from self-renewal using haploid embryonic stem cells
    • Leeb, M. et al. Genetic exploration of the exit from self-renewal using haploid embryonic stem cells. Cell Stem Cell 14, 385-393 (2014).
    • (2014) Cell Stem Cell , vol.14 , pp. 385-393
    • Leeb, M.1
  • 34
    • 76649122816 scopus 로고    scopus 로고
    • Expander: From expression microarrays to networks and functions
    • Ulitsky, I. et al. Expander: from expression microarrays to networks and functions. Nat. Protoc. 5, 303-322 (2010).
    • (2010) Nat. Protoc. , vol.5 , pp. 303-322
    • Ulitsky, I.1
  • 35
    • 62549134121 scopus 로고    scopus 로고
    • Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    • Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218-223 (2009).
    • (2009) Science , vol.324 , pp. 218-223
    • Ingolia, N.T.1    Ghaemmaghami, S.2    Newman, J.R.3    Weissman, J.S.4
  • 36
    • 0037082158 scopus 로고    scopus 로고
    • High-level and high-throughput recombinant protein production by transient transfection of suspensiongrowing human 293-EBNA1 cells
    • Durocher, Y., Perret, S. & Kamen, A. High-level and high-throughput recombinant protein production by transient transfection of suspensiongrowing human 293-EBNA1 cells. Nucleic Acids Res. 30, E9 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. E9
    • Durocher, Y.1    Perret, S.2    Kamen, A.3
  • 37
    • 84908337188 scopus 로고    scopus 로고
    • A novel function of human Pumilio proteins in cytoplasmic sensing of viral infection
    • Narita, R. et al. A novel function of human Pumilio proteins in cytoplasmic sensing of viral infection. PLoS Pathog. 10, e1004417 (2014).
    • (2014) PLoS Pathog. , vol.10
    • Narita, R.1
  • 38
    • 84874297756 scopus 로고    scopus 로고
    • Selective serotonin reuptake inhibitors (SSRIs) inhibit insulin secretion and action in pancreatic beta cells
    • Isaac, R. et al. Selective serotonin reuptake inhibitors (SSRIs) inhibit insulin secretion and action in pancreatic beta cells. J Biol. Chem. 288, 5682-5693 (2013).
    • (2013) J Biol. Chem. , vol.288 , pp. 5682-5693
    • Isaac, R.1
  • 39
    • 84865379361 scopus 로고    scopus 로고
    • LincRNA-p21 suppresses target mRNA translation
    • Yoon, J. H. et al. LincRNA-p21 suppresses target mRNA translation. Mol. Cell 47, 648-655 (2012).
    • (2012) Mol. Cell , vol.47 , pp. 648-655
    • Yoon, J.H.1
  • 40
    • 77955644289 scopus 로고    scopus 로고
    • Mammalian microRNAs predominantly act to decrease target mRNA levels
    • Guo, H., Ingolia, N. T., Weissman, J. S. & Bartel, D. P. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466, 835-840 (2010).
    • (2010) Nature , vol.466 , pp. 835-840
    • Guo, H.1    Ingolia, N.T.2    Weissman, J.S.3    Bartel, D.P.4
  • 41
    • 84871809302 scopus 로고    scopus 로고
    • STAR: Ultrafast universal RNA-seq aligner
    • Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 15-21
    • Dobin, A.1
  • 42
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq - A Python framework to work with high-throughput sequencing data
    • Anders, S., Pyl, P. T. & Huber, W. HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2015).
    • (2015) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 43
    • 84885087303 scopus 로고    scopus 로고
    • A guide to design and optimization of reporter assays for 30 untranslated region mediated regulation of mammalian messenger RNAs
    • Van Etten, J., Schagat, T. L. & Goldstrohm, A. C. A guide to design and optimization of reporter assays for 30 untranslated region mediated regulation of mammalian messenger RNAs. Methods 63, 110-118 (2013).
    • (2013) Methods , vol.63 , pp. 110-118
    • Van Etten, J.1    Schagat, T.L.2    Goldstrohm, A.C.3
  • 44
    • 84880617636 scopus 로고    scopus 로고
    • WEB-based GEne SeT Analysis Toolkit (WebGestalt): Update 2013
    • Wang, J., Duncan, D., Shi, Z. & Zhang, B. WEB-based GEne SeT Analysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res. 41, W77-W83 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. W77-W83
    • Wang, J.1    Duncan, D.2    Shi, Z.3    Zhang, B.4
  • 45
    • 84897406127 scopus 로고    scopus 로고
    • A promoter-level mammalian expression atlas
    • The FANTOM5 Consortium. A promoter-level mammalian expression atlas. Nature 507, 462-470 (2014).
    • (2014) Nature , vol.507 , pp. 462-470
    • The FANTOM5 Consortium1
  • 46
    • 84861903786 scopus 로고    scopus 로고
    • A quantitative atlas of polyadenylation in five mammals
    • Derti, A. et al. A quantitative atlas of polyadenylation in five mammals. Genome Res. 22, 1173-1183 (2012).
    • (2012) Genome Res. , vol.22 , pp. 1173-1183
    • Derti, A.1
  • 47
    • 79959446962 scopus 로고    scopus 로고
    • PhyloCSF: A comparative genomics method to distinguish protein coding and non-coding regions
    • Lin, M. F., Jungreis, I. & Kellis, M. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics 27, i275-i282 (2011).
    • (2011) Bioinformatics , vol.27 , pp. i275-i282
    • Lin, M.F.1    Jungreis, I.2    Kellis, M.3
  • 48
    • 0033990061 scopus 로고    scopus 로고
    • Flexible sequence similarity searching with the FASTA3 program package
    • Pearson, W. R. Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol. 132, 185-219 (2000).
    • (2000) Methods Mol. Biol. , vol.132 , pp. 185-219
    • Pearson, W.R.1
  • 49
    • 80051786284 scopus 로고    scopus 로고
    • PARalyzer: Definition of RNA binding sites from PAR-CLIP short-read sequence data
    • Corcoran, D. L. et al. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol. 12, R79 (2011).
    • (2011) Genome Biol. , vol.12 , pp. R79
    • Corcoran, D.L.1
  • 50
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R. & Siepel, A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 20, 110-121 (2010).
    • (2010) Genome Res. , vol.20 , pp. 110-121
    • Pollard, K.S.1    Hubisz, M.J.2    Rosenbloom, K.R.3    Siepel, A.4


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