메뉴 건너뛰기




Volumn 2, Issue DEC, 2014, Pages

Uncovering RNA editing sites in long non-coding RNAs

Author keywords

A to I editing; LncRNA; Long non coding RNA; NcRNA; RNA editing; RNA Seq; Transcriptome

Indexed keywords

CODES (SYMBOLS); GENE EXPRESSION; GENE EXPRESSION REGULATION; GENES; RNA;

EID: 84994614739     PISSN: None     EISSN: 22964185     Source Type: Journal    
DOI: 10.3389/fbioe.2014.00064     Document Type: Article
Times cited : (41)

References (27)
  • 1
    • 84879692466 scopus 로고    scopus 로고
    • Comparative analysis of RNA sequencing methods for degraded or low-input samples
    • Adiconis, X., Borges-Rivera, D., Satija, R., Deluca, D. S., Busby, M. A., Berlin, A. M., et al. (2013). Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat. Methods 10, 623-629. doi: 10.1038/nmeth.2483
    • (2013) Nat. Methods , vol.10 , pp. 623-629
    • Adiconis, X.1    Borges-Rivera, D.2    Satija, R.3    Deluca, D.S.4    Busby, M.A.5    Berlin, A.M.6
  • 2
    • 84895535383 scopus 로고    scopus 로고
    • A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes
    • Bazak, L., Haviv, A., Barak, M., Jacob-Hirsch, J., Deng, P., Zhang, R., et al. (2014). A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes. Genome Res. 24, 365-376. doi:10.1101/gr.164749.113
    • (2014) Genome Res , vol.24 , pp. 365-376
    • Bazak, L.1    Haviv, A.2    Barak, M.3    Jacob-Hirsch, J.4    Deng, P.5    Zhang, R.6
  • 3
    • 23044437498 scopus 로고    scopus 로고
    • RNA meets chromatin
    • Bernstein, E., and Allis, C. D. (2005). RNA meets chromatin. Genes Dev 19, 1635-1655. doi:10.1101/gad.1324305
    • (2005) Genes Dev , vol.19 , pp. 1635-1655
    • Bernstein, E.1    Allis, C.D.2
  • 4
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Consortium, E. P. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74. doi:10.1038/nature11247
    • (2012) Nature , vol.489 , pp. 57-74
    • Consortium, E.P.1
  • 5
    • 84905509806 scopus 로고    scopus 로고
    • Long intergenic non-coding RNAs (LincRNAs) identified by RNA-seq in breast cancer
    • Ding, X., Zhu, L., Ji, T., Zhang, X., Wang, F., Gan, S., et al. (2014). Long intergenic non-coding RNAs (LincRNAs) identified by RNA-seq in breast cancer. PLoS ONE 9:e103270. doi:10.1371/journal.pone.0103270
    • (2014) PLoS ONE , vol.9
    • Ding, X.1    Zhu, L.2    Ji, T.3    Zhang, X.4    Wang, F.5    Gan, S.6
  • 8
    • 84888861753 scopus 로고    scopus 로고
    • Systematic evaluation of spliced alignment programs for RNA-seq data
    • Engstrom, P. G., Steijger, T., Sipos, B., Grant, G. R., Kahles, A., Alioto, T., et al. (2013). Systematic evaluation of spliced alignment programs for RNA-seq data. Nat. Methods 10, 1185-1191. doi:10.1038/nmeth.2722
    • (2013) Nat. Methods , vol.10 , pp. 1185-1191
    • Engstrom, P.G.1    Steijger, T.2    Sipos, B.3    Grant, G.R.4    Kahles, A.5    Alioto, T.6
  • 9
    • 84890559595 scopus 로고    scopus 로고
    • Long non-coding RNAs: new players in cell differentiation and development
    • Fatica, A., and Bozzoni, I. (2014). Long non-coding RNAs: new players in cell differentiation and development. Nat. Rev. Genet. 15, 7-21. doi:10.1038/nrg3606
    • (2014) Nat. Rev. Genet , vol.15 , pp. 7-21
    • Fatica, A.1    Bozzoni, I.2
  • 10
    • 84855255195 scopus 로고    scopus 로고
    • ADARs: allies or enemies? The importance of A-to-I RNA editing in human disease: from cancer to HIV-1
    • Gallo, A., and Locatelli, F. (2011). ADARs: allies or enemies? The importance of A-to-I RNA editing in human disease: from cancer to HIV-1. Biol. Rev. Camb. Philos. Soc. 87, 95-110. doi:10.1111/j.1469-185X.2011.00186.x
    • (2011) Biol. Rev. Camb. Philos. Soc , vol.87 , pp. 95-110
    • Gallo, A.1    Locatelli, F.2
  • 11
    • 84865760395 scopus 로고    scopus 로고
    • GENCODE: the reference human genome annotation for the ENCODE project
    • Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., et al. (2012). GENCODE: the reference human genome annotation for the ENCODE project. Genome Res. 22, 1760-1774. doi:10.1101/gr.135350.111
    • (2012) Genome Res , vol.22 , pp. 1760-1774
    • Harrow, J.1    Frankish, A.2    Gonzalez, J.M.3    Tapanari, E.4    Diekhans, M.5    Kokocinski, F.6
  • 12
    • 70449953975 scopus 로고    scopus 로고
    • The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs
    • Jacquier, A. (2009). The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat. Rev. Genet. 10, 833-844. doi:10.1038/nrg2683
    • (2009) Nat. Rev. Genet , vol.10 , pp. 833-844
    • Jacquier, A.1
  • 13
    • 3543004084 scopus 로고    scopus 로고
    • Systematic identification of abundant A-to-I editing sites in the human transcriptome
    • Levanon, E. Y., Eisenberg, E., Yelin, R., Nemzer, S., Hallegger, M., Shemesh, R., et al. (2004). Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat. Biotechnol. 22, 1001-1005. doi:10.1038/nbt996
    • (2004) Nat. Biotechnol , vol.22 , pp. 1001-1005
    • Levanon, E.Y.1    Eisenberg, E.2    Yelin, R.3    Nemzer, S.4    Hallegger, M.5    Shemesh, R.6
  • 14
    • 84880917068 scopus 로고    scopus 로고
    • PIWI-interacting RNAs: from generation to transgenerational epigenetics
    • Luteijn, M. J., and Ketting, R. F. (2013). PIWI-interacting RNAs: from generation to transgenerational epigenetics. Nat. Rev. Genet. 14, 523-534. doi:10.1038/nrg3495
    • (2013) Nat. Rev. Genet , vol.14 , pp. 523-534
    • Luteijn, M.J.1    Ketting, R.F.2
  • 15
    • 84867537101 scopus 로고    scopus 로고
    • A-to-I editing of protein coding and noncoding RNAs
    • Mallela, A., and Nishikura, K. (2012). A-to-I editing of protein coding and noncoding RNAs. Crit. Rev. Biochem. Mol. Biol. 47, 493-501. doi:10.3109/10409238.2012.714350
    • (2012) Crit. Rev. Biochem. Mol. Biol , vol.47 , pp. 493-501
    • Mallela, A.1    Nishikura, K.2
  • 16
    • 77952293063 scopus 로고    scopus 로고
    • Functions and regulation of RNA editing by ADAR deaminases
    • Nishikura, K. (2010). Functions and regulation of RNA editing by ADAR deaminases. Annu. Rev. Biochem. 79, 321-349. doi:10.1146/annurev-biochem-060208-105251
    • (2010) Annu. Rev. Biochem , vol.79 , pp. 321-349
    • Nishikura, K.1
  • 17
    • 65649126066 scopus 로고    scopus 로고
    • Transcript length bias in RNA-seq data confounds systems biology
    • Oshlack, A., and Wakefield, M. J. (2009). Transcript length bias in RNA-seq data confounds systems biology. Biol. Direct 4, 14. doi:10.1186/1745-6150-4-14
    • (2009) Biol. Direct , vol.4 , pp. 14
    • Oshlack, A.1    Wakefield, M.J.2
  • 18
    • 77955812141 scopus 로고    scopus 로고
    • Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing
    • Picardi, E., Horner, D. S., Chiara, M., Schiavon, R., Valle, G., and Pesole, G. (2010). Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing. Nucleic Acids Res. 38, 4755-4767. doi:10.1093/nar/gkq202
    • (2010) Nucleic Acids Res , vol.38 , pp. 4755-4767
    • Picardi, E.1    Horner, D.S.2    Chiara, M.3    Schiavon, R.4    Valle, G.5    Pesole, G.6
  • 19
    • 84880213242 scopus 로고    scopus 로고
    • REDItools: high-throughput RNA editing detection made easy
    • Picardi, E., and Pesole, G. (2013). REDItools: high-throughput RNA editing detection made easy. Bioinformatics 29, 1813-1814. doi:10.1093/bioinformatics/btt287
    • (2013) Bioinformatics , vol.29 , pp. 1813-1814
    • Picardi, E.1    Pesole, G.2
  • 20
    • 77953747443 scopus 로고    scopus 로고
    • Proteome diversification by adenosine to inosine RNA editing
    • Pullirsch, D., and Jantsch, M. F. (2010). Proteome diversification by adenosine to inosine RNA editing. RNA Biol. 7, 205-212. doi:10.4161/rna.7.2.11286
    • (2010) RNA Biol , vol.7 , pp. 205-212
    • Pullirsch, D.1    Jantsch, M.F.2
  • 21
    • 84891797364 scopus 로고    scopus 로고
    • RADAR: a rigorously annotated database of A-to-I RNA editing
    • Ramaswami, G., and Li, J. B. (2014). RADAR: a rigorously annotated database of A-to-I RNA editing. Nucleic Acids Res. 42, D109-D113. doi:10.1093/nar/gkt996
    • (2014) Nucleic Acids Res , vol.42 , pp. D109-D113
    • Ramaswami, G.1    Li, J.B.2
  • 22
    • 84861970552 scopus 로고    scopus 로고
    • Accurate identification of human Alu and non-Alu RNA editing sites
    • Ramaswami, G., Lin, W., Piskol, R., Tan, M. H., Davis, C., and Li, J. B. (2012). Accurate identification of human Alu and non-Alu RNA editing sites. Nat. Methods 9, 579-581. doi:10.1038/nmeth.1982
    • (2012) Nat. Methods , vol.9 , pp. 579-581
    • Ramaswami, G.1    Lin, W.2    Piskol, R.3    Tan, M.H.4    Davis, C.5    Li, J.B.6
  • 23
    • 84881341209 scopus 로고    scopus 로고
    • The ADAR protein family
    • Savva, Y. A., Rieder, L. E., and Reenan, R. A. (2012). The ADAR protein family. Genome Biol. 13, 252. doi:10.1186/gb-2012-13-12-252
    • (2012) Genome Biol , vol.13 , pp. 252
    • Savva, Y.A.1    Rieder, L.E.2    Reenan, R.A.3
  • 24
    • 79957840356 scopus 로고    scopus 로고
    • Long noncoding RNAs and human disease
    • Wapinski, O., and Chang, H. Y. (2011). Long noncoding RNAs and human disease. Trends Cell Biol 21, 354-361. doi:10.1016/j.tcb.2011.04.001
    • (2011) Trends Cell Biol , vol.21 , pp. 354-361
    • Wapinski, O.1    Chang, H.Y.2
  • 25
    • 68349090253 scopus 로고    scopus 로고
    • Regulation of the mammalian epigenome by long noncoding RNAs
    • Whitehead, J., Pandey, G. K., and Kanduri, C. (2009). Regulation of the mammalian epigenome by long noncoding RNAs. Biochim Biophys Acta 1790, 936-947. doi:10.1016/j.bbagen.2008.10.007
    • (2009) Biochim Biophys Acta , vol.1790 , pp. 936-947
    • Whitehead, J.1    Pandey, G.K.2    Kanduri, C.3
  • 26
    • 77951820899 scopus 로고    scopus 로고
    • Fast and SNP-tolerant detection of complex variants and splicing in short reads
    • Wu, T. D., and Nacu, S. (2011). Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26, 873-881. doi:10.1093/bioinformatics/btq057
    • (2011) Bioinformatics , vol.26 , pp. 873-881
    • Wu, T.D.1    Nacu, S.2
  • 27
    • 84891798006 scopus 로고    scopus 로고
    • NONCODEv4: exploring the world of long non-coding RNA genes
    • Xie, C., Yuan, J., Li, H., Li, M., Zhao, G., Bu, D., et al. (2014). NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res. 42, D98-D103. doi:10.1093/nar/gkt1222
    • (2014) Nucleic Acids Res , vol.42 , pp. D98-D103
    • Xie, C.1    Yuan, J.2    Li, H.3    Li, M.4    Zhao, G.5    Bu, D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.