메뉴 건너뛰기




Volumn 5, Issue , 2014, Pages

Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide- induced inflammatory response in human monocytes

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM LIPOPOLYSACCHARIDE; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN L; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERLEUKIN 1BETA; INTERLEUKIN 8; LOCKED NUCLEIC ACID; LONG UNTRANSLATED RNA; MESSENGER RNA; TUMOR NECROSIS FACTOR ALPHA; LIPOPOLYSACCHARIDE; RNA;

EID: 84902286789     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms4979     Document Type: Article
Times cited : (255)

References (46)
  • 1
    • 77955751471 scopus 로고    scopus 로고
    • Identification of LPS-inducible genes downregulated by ubiquinone in human THP-1 monocytes
    • Schmelzer, C. & Döring, F. Identification of LPS-inducible genes downregulated by ubiquinone in human THP-1 monocytes. Biofactors 36, 222-228 (2010).
    • (2010) Biofactors , vol.36 , pp. 222-228
    • Schmelzer, C.1    Döring, F.2
  • 3
    • 0034307661 scopus 로고    scopus 로고
    • Comprehensive gene expression profile of LPS-stimulated human monocytes by SAGE
    • Suzuki, T. et al. Comprehensive gene expression profile of LPS-stimulated human monocytes by SAGE. Blood 96, 2584-2591 (2000).
    • (2000) Blood , vol.96 , pp. 2584-2591
    • Suzuki, T.1
  • 4
    • 84865757142 scopus 로고    scopus 로고
    • Landscape of transcription in human cells
    • Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101-108 (2012).
    • (2012) Nature , vol.489 , pp. 101-108
    • Djebali, S.1
  • 6
    • 62249133709 scopus 로고    scopus 로고
    • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    • Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227 (2009).
    • (2009) Nature , vol.458 , pp. 223-227
    • Guttman, M.1
  • 7
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili, M. N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).
    • (2011) Genes Dev. , vol.25 , pp. 1915-1927
    • Cabili, M.N.1
  • 8
    • 84865727393 scopus 로고    scopus 로고
    • The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
    • Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775-1789 (2012).
    • (2012) Genome Res. , vol.22 , pp. 1775-1789
    • Derrien, T.1
  • 10
    • 75649139134 scopus 로고    scopus 로고
    • Physiological and pathological roles for MicroRNAs in the immune system
    • O'Connell, R. M., Rao, D. S., Chaudhuri, A. A. & Baltimore, D. Physiological and pathological roles for microRNAs in the immune system. Nat. Rev. Immunol. 10, 111-122 (2010).
    • (2010) Nat. Rev. Immunol. , vol.10 , pp. 111-122
    • O'Connell, R.M.1    Rao, D.S.2    Chaudhuri, A.A.3    Baltimore, D.4
  • 11
    • 45549103746 scopus 로고    scopus 로고
    • MicroRNAs and the immune response
    • Lindsay, M. A. microRNAs and the immune response. Trends Immunol. 29, 343-351 (2008).
    • (2008) Trends Immunol. , vol.29 , pp. 343-351
    • Lindsay, M.A.1
  • 12
    • 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
  • 13
    • 77952399594 scopus 로고    scopus 로고
    • Transcription: Enhancers make non-coding RNA
    • Ren, B. Transcription: enhancers make non-coding RNA. Nature 465, 173-174 (2010).
    • (2010) Nature , vol.465 , pp. 173-174
    • Ren, B.1
  • 14
    • 84870182699 scopus 로고    scopus 로고
    • Noncoding transcription at enhancers: General principles and functional models
    • Natoli, G. & Andrau, J.-C. Noncoding transcription at enhancers: general principles and functional models. Annu. Rev. Genet. 46, 1-19 (2012).
    • (2012) Annu. Rev. Genet. , vol.46 , pp. 1-19
    • Natoli, G.1    Andrau, J.-C.2
  • 15
    • 77952908743 scopus 로고    scopus 로고
    • A large fraction of extragenic RNA pol II transcription sites overlap enhancers
    • De Santa, F. et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 8, e1000384 (2010).
    • (2010) PLoS Biol. , vol.8
    • De Santa, F.1
  • 16
    • 80053590671 scopus 로고    scopus 로고
    • A global clustering algorithm to identify long intergenic non-coding RNA-with applications in mouse macrophages
    • Garmire, L. X. et al. A global clustering algorithm to identify long intergenic non-coding RNA-with applications in mouse macrophages. PLoS ONE 6, e24051 (2011).
    • (2011) PLoS ONE , vol.6
    • Garmire, L.X.1
  • 17
    • 84888232130 scopus 로고    scopus 로고
    • Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs
    • Marques, A. C. et al. Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs. Genome Biol. 14, R131 (2013).
    • (2013) Genome Biol. , vol.14
    • Marques, A.C.1
  • 18
    • 77952367798 scopus 로고    scopus 로고
    • Widespread transcription at neuronal activity-regulated enhancers
    • Kim, T.-K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182-187 (2010).
    • (2010) Nature , vol.465 , pp. 182-187
    • Kim, T.-K.1
  • 19
    • 84880748598 scopus 로고    scopus 로고
    • A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics
    • Rapicavoli, N. A. et al. A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. eLife 2, e00762 (2013).
    • (2013) ELife , vol.2
    • Rapicavoli, N.A.1
  • 20
    • 84881478367 scopus 로고    scopus 로고
    • A long noncoding RNA mediates both activation and repression of immune response genes
    • Carpenter, S. et al. A long noncoding RNA mediates both activation and repression of immune response genes. Science 341, 789-792 (2013).
    • (2013) Science , vol.341 , pp. 789-792
    • Carpenter, S.1
  • 21
    • 84892923750 scopus 로고    scopus 로고
    • The long noncoding RNA THRIL regulates TNFa expression through its interaction with hnRNPL
    • Li, Z. et al. The long noncoding RNA THRIL regulates TNFa expression through its interaction with hnRNPL. Proc. Natl Acad. Sci. USA 21, 1002-1007 (2014).
    • (2014) Proc. Natl Acad. Sci. USA , vol.21 , pp. 1002-1007
    • Li, Z.1
  • 22
    • 84874235143 scopus 로고    scopus 로고
    • Conservation and divergence in the transcriptional programs of the human and mouse immune systems
    • Shay, T. et al. Conservation and divergence in the transcriptional programs of the human and mouse immune systems. Proc. Natl Acad. Sci. USA 110, 2946-2951 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 2946-2951
    • Shay, T.1
  • 23
    • 84864629645 scopus 로고    scopus 로고
    • Rapid turnover of long noncoding RNAs and the evolution of gene expression
    • Kutter, C. et al. Rapid turnover of long noncoding RNAs and the evolution of gene expression. PLoS Genet. 8, e1002841 (2012).
    • (2012) PLoS Genet. , vol.8
    • Kutter, C.1
  • 24
    • 57149096220 scopus 로고    scopus 로고
    • Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding
    • Robertson, A. G. et al. Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res. 18, 1906-1917 (2008).
    • (2008) Genome Res. , vol.18 , pp. 1906-1917
    • Robertson, A.G.1
  • 25
    • 57849140661 scopus 로고    scopus 로고
    • Divergent transcription from active promoters
    • Seila, A. C. et al. Divergent transcription from active promoters. Science 322, 1849-1851 (2008).
    • (2008) Science , vol.322 , pp. 1849-1851
    • Seila, A.C.1
  • 26
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848 (2008).
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 27
    • 84880968176 scopus 로고    scopus 로고
    • GAT: A simulation framework for testing the association of genomic intervals
    • Heger, A., Webber, C., Goodson, M., Ponting, C. P. & Lunter, G. GAT: a simulation framework for testing the association of genomic intervals. Bioinformatics 29, 2046-2048 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 2046-2048
    • Heger, A.1    Webber, C.2    Goodson, M.3    Ponting, C.P.4    Lunter, G.5
  • 28
    • 84864545087 scopus 로고    scopus 로고
    • Treating inflammation by blocking interleukin-1 in a broad spectrum of diseases
    • Dinarello, C. A., Simon, A. & van der Meer, J. W. M. Treating inflammation by blocking interleukin-1 in a broad spectrum of diseases. Nat. Rev. Drug Discov. 11, 633-652 (2012).
    • (2012) Nat. Rev. Drug Discov. , vol.11 , pp. 633-652
    • Dinarello, C.A.1    Simon, A.2    Van Der-Meer, J.W.M.3
  • 29
    • 11844305963 scopus 로고    scopus 로고
    • Attenuation of murine collagen-induced arthritis by a novel, potent, selective small molecule inhibitor of IκB kinase 2, TPCA-1 (2-[(aminocarbonyl)amino]-5-(4-fluorophenyl)-3-thiophenecarboxamide), occurs via reduction of proinflammatory cytokines and antigen-induced T cell proliferation
    • DOI 10.1124/jpet.104.074484
    • Podolin, P. L. et al. Attenuation of murine collagen-induced arthritis by a novel, potent, selective small molecule inhibitor of IkappaB Kinase 2, TPCA-1 (2-[(aminocarbonyl)amino]-5-(4-fluorophenyl)-3-thiophenecarboxamide), occurs via reduction of proinflammatory cytokines and antigen-induced T cell Proliferation. J. Pharmacol. Exp. Ther. 312, 373-381 (2005). (Pubitemid 40096491)
    • (2005) Journal of Pharmacology and Experimental Therapeutics , vol.312 , Issue.1 , pp. 373-381
    • Podolin, P.L.1    Callahan, J.F.2    Bolognese, B.J.3    Li, Y.H.4    Carlson, K.5    Davis, T.G.6    Mellor, G.W.7    Evans, C.8    Roshak, A.K.9
  • 30
    • 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
  • 31
    • 84879695128 scopus 로고    scopus 로고
    • Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation
    • Li, W. et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498, 516-520 (2013).
    • (2013) Nature , vol.498 , pp. 516-520
    • Li, W.1
  • 32
    • 84879694221 scopus 로고    scopus 로고
    • Rev-erbs repress macrophage gene expression by inhibiting enhancer-directed transcription
    • Lam, M. T. Y. et al. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 498, 511-515 (2013).
    • (2013) Nature , vol.498 , pp. 511-515
    • Lam, M.T.Y.1
  • 33
    • 77955323879 scopus 로고    scopus 로고
    • A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response
    • Huarte, M. et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142, 409-419 (2010).
    • (2010) Cell , vol.142 , pp. 409-419
    • Huarte, M.1
  • 34
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of LincRNAs
    • Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of LincRNAs. Nat. Biotechnol. 28, 503-510 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 503-510
    • Guttman, M.1
  • 35
    • 79952186298 scopus 로고    scopus 로고
    • MicroRNAs: The fine-tuners of toll-like receptor signalling
    • O'Neill, L. A., Sheedy, F. J. & McCoy, C. E. MicroRNAs: the fine-tuners of Toll-like receptor signalling. Nat. Rev. Immunol. 11, 163-175 (2011).
    • (2011) Nat. Rev. Immunol. , vol.11 , pp. 163-175
    • O'Neill, L.A.1    Sheedy, F.J.2    McCoy, C.E.3
  • 36
    • 84881526410 scopus 로고    scopus 로고
    • Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription
    • Kaikkonen, M. U. et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol. Cell 51, 310-325 (2013).
    • (2013) Mol. Cell , vol.51 , pp. 310-325
    • Kaikkonen, M.U.1
  • 37
    • 65549104157 scopus 로고    scopus 로고
    • Histone modifications at human enhancers reflect global cell-type-specific gene expression
    • Heintzman, N. D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108-112 (2009).
    • (2009) Nature , vol.459 , pp. 108-112
    • Heintzman, N.D.1
  • 38
    • 81055126951 scopus 로고    scopus 로고
    • Discovery of active enhancers through bidirectional expression of short transcripts
    • Melgar, M. F., Collins, F. S. & Sethupathy, P. Discovery of active enhancers through bidirectional expression of short transcripts. Genome Biol. 12, R113 (2011).
    • (2011) Genome Biol. , vol.12
    • Melgar, M.F.1    Collins, F.S.2    Sethupathy, P.3
  • 39
    • 84857066786 scopus 로고    scopus 로고
    • Modular regulatory principles of large non-coding RNAs
    • Guttman, M. & Rinn, J. L. Modular regulatory principles of large non-coding RNAs. Nature 482, 339-346 (2012).
    • (2012) Nature , vol.482 , pp. 339-346
    • Guttman, M.1    Rinn, J.L.2
  • 40
    • 84873456575 scopus 로고    scopus 로고
    • ERNAs are required for p53-dependent enhancer activity and gene transcription
    • Melo, C. A. et al. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol. Cell 49, 524-535 (2013).
    • (2013) Mol. Cell , vol.49 , pp. 524-535
    • Melo, C.A.1
  • 41
    • 81055157096 scopus 로고    scopus 로고
    • The emerging role of interleukin-1b in autoinflammatory diseases
    • Lane, T. & Lachmann, H. J. The emerging role of interleukin-1b in autoinflammatory diseases. Curr. Allergy Asthma Rep. 11, 361-368 (2011).
    • (2011) Curr. Allergy Asthma Rep. , vol.11 , pp. 361-368
    • Lane, T.1    Lachmann, H.J.2
  • 42
    • 77954638595 scopus 로고    scopus 로고
    • Effects of formoterol and salmeterol on cytokine release from monocyte-derived macrophages
    • Donnelly, L. E., Tudhope, S. J., Fenwick, P. S. & Barnes, P. J. Effects of formoterol and salmeterol on cytokine release from monocyte-derived macrophages. Eur. Respir. J. 36, 178-186 (2010).
    • (2010) Eur. Respir. J. , vol.36 , pp. 178-186
    • Donnelly, L.E.1    Tudhope, S.J.2    Fenwick, P.S.3    Barnes, P.J.4
  • 43
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-seq
    • Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 44
    • 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
    • Kong, L.1
  • 45
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
    • (2010) Genome Biol. , vol.11
    • Anders, S.1    Huber, W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.