메뉴 건너뛰기




Volumn 31, Issue 5, 2015, Pages 239-251

The Landscape of long noncoding RNA classification

Author keywords

Annotation of long non coding RNAs; Classification of long non coding RNAs; Function of long non coding RNAs; LincRNA; LncRNA; Long non coding RNA; Systems biology; Transcriptome; VlincRNA

Indexed keywords

LONG UNTRANSLATED RNA; MESSENGER RNA; TRANSCRIPTOME;

EID: 84928761213     PISSN: 01689525     EISSN: 13624555     Source Type: Journal    
DOI: 10.1016/j.tig.2015.03.007     Document Type: Review
Times cited : (974)

References (170)
  • 1
    • 0037012881 scopus 로고    scopus 로고
    • Large-scale transcriptional activity in chromosomes 21 and 22
    • Kapranov P., et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 2002, 296:916-919.
    • (2002) Science , vol.296 , pp. 916-919
    • Kapranov, P.1
  • 2
    • 0142104045 scopus 로고    scopus 로고
    • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
    • Okazaki Y., et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002, 420:563-573.
    • (2002) Nature , vol.420 , pp. 563-573
    • Okazaki, Y.1
  • 3
    • 84865757142 scopus 로고    scopus 로고
    • Landscape of transcription in human cells
    • Djebali S., et al. Landscape of transcription in human cells. Nature 2012, 489:101-108.
    • (2012) Nature , vol.489 , pp. 101-108
    • Djebali, S.1
  • 4
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Bernstein B.E., et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Bernstein, B.E.1
  • 5
    • 78650292831 scopus 로고    scopus 로고
    • The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA
    • Kapranov P., et al. The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA. BMC Biol. 2010, 8:149.
    • (2010) BMC Biol. , vol.8 , pp. 149
    • Kapranov, P.1
  • 6
    • 84906281802 scopus 로고    scopus 로고
    • Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease
    • Clark B.S., Blackshaw S. Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease. Front. Genet. 2014, 5:164.
    • (2014) Front. Genet. , vol.5 , pp. 164
    • Clark, B.S.1    Blackshaw, S.2
  • 7
    • 79953888460 scopus 로고    scopus 로고
    • The functional role of long non-coding RNA in human carcinomas
    • Gibb E.A., et al. The functional role of long non-coding RNA in human carcinomas. Mol. Cancer 2011, 10:38.
    • (2011) Mol. Cancer , vol.10 , pp. 38
    • Gibb, E.A.1
  • 8
    • 84885682654 scopus 로고    scopus 로고
    • Long non-coding RNAs: novel targets for nervous system disease diagnosis and therapy
    • Qureshi I.A., Mehler M.F. Long non-coding RNAs: novel targets for nervous system disease diagnosis and therapy. Neurotherapeutics 2013, 10:632-646.
    • (2013) Neurotherapeutics , vol.10 , pp. 632-646
    • Qureshi, I.A.1    Mehler, M.F.2
  • 9
    • 84871018923 scopus 로고    scopus 로고
    • Perspectives of long non-coding RNAs in cancer diagnostics
    • Reis E.M., Verjovski-Almeida S. Perspectives of long non-coding RNAs in cancer diagnostics. Front. Genet. 2012, 3:32.
    • (2012) Front. Genet. , vol.3 , pp. 32
    • Reis, E.M.1    Verjovski-Almeida, S.2
  • 10
    • 84866247939 scopus 로고    scopus 로고
    • Genomic "dark matter" in prostate cancer: exploring the clinical utility of ncRNA as biomarkers
    • Vergara I.A., et al. Genomic "dark matter" in prostate cancer: exploring the clinical utility of ncRNA as biomarkers. Front. Genet. 2012, 3:23.
    • (2012) Front. Genet. , vol.3 , pp. 23
    • Vergara, I.A.1
  • 11
    • 84880652927 scopus 로고    scopus 로고
    • Targeting long non-coding RNA to therapeutically upregulate gene expression
    • Wahlestedt C. Targeting long non-coding RNA to therapeutically upregulate gene expression. Nat. Rev. Drug Discov. 2013, 12:433-446.
    • (2013) Nat. Rev. Drug Discov. , vol.12 , pp. 433-446
    • Wahlestedt, C.1
  • 12
    • 84902161967 scopus 로고    scopus 로고
    • Dark matter RNA illuminates the puzzle of genome-wide association studies
    • St Laurent G., et al. Dark matter RNA illuminates the puzzle of genome-wide association studies. BMC Med. 2014, 12:97.
    • (2014) BMC Med. , vol.12 , pp. 97
    • St Laurent, G.1
  • 13
    • 84879153972 scopus 로고    scopus 로고
    • The dark matter rises: the expanding world of regulatory RNAs
    • Clark M.B., et al. The dark matter rises: the expanding world of regulatory RNAs. Essays Biochem. 2013, 54:1-16.
    • (2013) Essays Biochem. , vol.54 , pp. 1-16
    • Clark, M.B.1
  • 14
    • 84901298360 scopus 로고    scopus 로고
    • Epigenetic regulation by heritable RNA
    • Liebers R., et al. Epigenetic regulation by heritable RNA. PLoS Genet. 2014, 10:e1004296.
    • (2014) PLoS Genet. , vol.10 , pp. e1004296
    • Liebers, R.1
  • 15
    • 84906095861 scopus 로고    scopus 로고
    • The RNA-centred view of the synapse: non-coding RNAs and synaptic plasticity
    • Smalheiser N.R. The RNA-centred view of the synapse: non-coding RNAs and synaptic plasticity. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2014, 369.
    • (2014) Philos. Trans. R. Soc. Lond. B: Biol. Sci. , pp. 369
    • Smalheiser, N.R.1
  • 16
    • 0025943108 scopus 로고
    • If genes just make proteins and our proteins are the same, then why are we so different?
    • Penman S. If genes just make proteins and our proteins are the same, then why are we so different?. J. Cell. Biochem. 1991, 47:95-98.
    • (1991) J. Cell. Biochem. , vol.47 , pp. 95-98
    • Penman, S.1
  • 17
    • 0019886314 scopus 로고
    • A general function of noncoding polynucleotide sequences. Mass binding of transconformational proteins
    • Zuckerkandl E. A general function of noncoding polynucleotide sequences. Mass binding of transconformational proteins. Mol. Biol. Rep. 1981, 7:149-158.
    • (1981) Mol. Biol. Rep. , vol.7 , pp. 149-158
    • Zuckerkandl, E.1
  • 18
    • 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 2009, 458:223-227.
    • (2009) Nature , vol.458 , pp. 223-227
    • Guttman, M.1
  • 19
    • 67650921949 scopus 로고    scopus 로고
    • Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
    • Khalil A.M., et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:11667-11672.
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 11667-11672
    • Khalil, A.M.1
  • 20
    • 84903817064 scopus 로고    scopus 로고
    • The ways of action of long non-coding RNAs in cytoplasm and nucleus
    • Zhang K., et al. The ways of action of long non-coding RNAs in cytoplasm and nucleus. Gene 2014, 547:1-9.
    • (2014) Gene , vol.547 , pp. 1-9
    • Zhang, K.1
  • 21
    • 84870238817 scopus 로고    scopus 로고
    • Dark matter RNA: existence, function, and controversy
    • Kapranov P., St Laurent G. Dark matter RNA: existence, function, and controversy. Front. Genet. 2012, 3:60.
    • (2012) Front. Genet. , vol.3 , pp. 60
    • Kapranov, P.1    St Laurent, G.2
  • 22
    • 65649092633 scopus 로고    scopus 로고
    • The genetic signatures of noncoding RNAs
    • Mattick J.S. The genetic signatures of noncoding RNAs. PLoS Genet. 2009, 5:e1000459.
    • (2009) PLoS Genet. , vol.5 , pp. e1000459
    • Mattick, J.S.1
  • 24
    • 36049020719 scopus 로고    scopus 로고
    • Noncoding RNAs: couplers of analog and digital information in nervous system function?
    • St Laurent G., Wahlestedt C. Noncoding RNAs: couplers of analog and digital information in nervous system function?. Trends Neurosci. 2007, 30:612-621.
    • (2007) Trends Neurosci. , vol.30 , pp. 612-621
    • St Laurent, G.1    Wahlestedt, C.2
  • 25
    • 84897406127 scopus 로고    scopus 로고
    • A promoter-level mammalian expression atlas
    • FANTOM Consortium and the RIKEN PMI and CLST (DGT)
    • A promoter-level mammalian expression atlas. Nature 2014, 507:462-470. FANTOM Consortium and the RIKEN PMI and CLST (DGT).
    • (2014) Nature , vol.507 , pp. 462-470
  • 26
    • 84878682420 scopus 로고    scopus 로고
    • The Genotype-Tissue Expression (GTEx) project
    • Lonsdale J., et al. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 2013, 45:580-585.
    • (2013) Nat. Genet. , vol.45 , pp. 580-585
    • Lonsdale, J.1
  • 27
    • 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. 2010, 28:503-510.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 503-510
    • Guttman, M.1
  • 28
    • 84899076976 scopus 로고    scopus 로고
    • Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein coding RNAs
    • Hackermuller J., et al. Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein coding RNAs. Genome Biol. 2014, 15:R48.
    • (2014) Genome Biol. , vol.15 , pp. R48
    • Hackermuller, J.1
  • 29
    • 84880335244 scopus 로고    scopus 로고
    • VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer
    • St Laurent G., et al. VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer. Genome Biol. 2013, 14:R73.
    • (2013) Genome Biol. , vol.14 , pp. R73
    • St Laurent, G.1
  • 30
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell C., et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 2012, 7:562-578.
    • (2012) Nat. Protoc. , vol.7 , pp. 562-578
    • Trapnell, C.1
  • 31
    • 84899623353 scopus 로고    scopus 로고
    • Genome-guided transcript assembly by integrative analysis of RNA sequence data
    • Boley N., et al. Genome-guided transcript assembly by integrative analysis of RNA sequence data. Nat. Biotechnol. 2014, 32:341-346.
    • (2014) Nat. Biotechnol. , vol.32 , pp. 341-346
    • Boley, N.1
  • 32
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst J., et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011, 473:43-49.
    • (2011) Nature , vol.473 , pp. 43-49
    • Ernst, J.1
  • 33
    • 84865760395 scopus 로고    scopus 로고
    • GENCODE: the reference human genome annotation for The ENCODE Project
    • Harrow J., et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012, 22:1760-1774.
    • (2012) Genome Res. , vol.22 , pp. 1760-1774
    • Harrow, J.1
  • 34
    • 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. 2011, 25:1915-1927.
    • (2011) Genes Dev. , vol.25 , pp. 1915-1927
    • Cabili, M.N.1
  • 35
    • 77955110979 scopus 로고    scopus 로고
    • Genome-wide computational identification and manual annotation of human long noncoding RNA genes
    • Jia H., et al. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA 2010, 16:1478-1487.
    • (2010) RNA , vol.16 , pp. 1478-1487
    • Jia, H.1
  • 36
    • 78651325932 scopus 로고    scopus 로고
    • LncRNAdb: a reference database for long noncoding RNAs
    • Amaral P.P., et al. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res. 2011, 39:D146-D151.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D146-D151
    • Amaral, P.P.1
  • 37
    • 84946086288 scopus 로고    scopus 로고
    • An update on LNCipedia: a database for annotated human lncRNA sequences
    • Volders P.J., et al. An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Res. 2015, 43:D174-D180.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D174-D180
    • Volders, P.J.1
  • 38
    • 34250160256 scopus 로고    scopus 로고
    • RNA maps reveal new RNA classes and a possible function for pervasive transcription
    • Kapranov P., et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316:1484-1488.
    • (2007) Science , vol.316 , pp. 1484-1488
    • Kapranov, P.1
  • 39
    • 80053045739 scopus 로고    scopus 로고
    • Molecular mechanisms of long noncoding RNAs
    • Wang K.C., Chang H.Y. Molecular mechanisms of long noncoding RNAs. Mol. Cell 2011, 43:904-914.
    • (2011) Mol. Cell , vol.43 , pp. 904-914
    • Wang, K.C.1    Chang, H.Y.2
  • 40
    • 84887412533 scopus 로고    scopus 로고
    • A single-molecule long-read survey of the human transcriptome
    • Sharon D., et al. A single-molecule long-read survey of the human transcriptome. Nat. Biotechnol. 2013, 31:1009-1014.
    • (2013) Nat. Biotechnol. , vol.31 , pp. 1009-1014
    • Sharon, D.1
  • 41
    • 84926651710 scopus 로고    scopus 로고
    • A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus
    • Lazorthes S., et al. A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus. Nat. Commun. 2015, 6:5971.
    • (2015) Nat. Commun. , vol.6 , pp. 5971
    • Lazorthes, S.1
  • 42
    • 84868611629 scopus 로고    scopus 로고
    • HELLP babies link a novel lincRNA to the trophoblast cell cycle
    • van Dijk M., et al. HELLP babies link a novel lincRNA to the trophoblast cell cycle. J. Clin. Invest. 2012, 122:4003-4011.
    • (2012) J. Clin. Invest. , vol.122 , pp. 4003-4011
    • van Dijk, M.1
  • 43
    • 24644519490 scopus 로고    scopus 로고
    • The transcriptional landscape of the mammalian genome
    • Carninci P., et al. The transcriptional landscape of the mammalian genome. Science 2005, 309:1559-1563.
    • (2005) Science , vol.309 , pp. 1559-1563
    • Carninci, P.1
  • 44
    • 22244442468 scopus 로고    scopus 로고
    • Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
    • Kapranov P., et al. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 2005, 15:987-997.
    • (2005) Genome Res. , vol.15 , pp. 987-997
    • Kapranov, P.1
  • 45
    • 84855539848 scopus 로고    scopus 로고
    • Targeted RNA sequencing reveals the deep complexity of the human transcriptome
    • Mercer T.R., et al. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat. Biotechnol. 2012, 30:99-104.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 99-104
    • Mercer, T.R.1
  • 46
    • 34250369629 scopus 로고    scopus 로고
    • Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions
    • Denoeud F., et al. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. 2007, 17:746-759.
    • (2007) Genome Res. , vol.17 , pp. 746-759
    • Denoeud, F.1
  • 47
    • 46249089426 scopus 로고    scopus 로고
    • Efficient targeted transcript discovery via array-based normalization of RACE libraries
    • Djebali S., et al. Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat. Methods 2008, 5:629-635.
    • (2008) Nat. Methods , vol.5 , pp. 629-635
    • Djebali, S.1
  • 48
    • 69549107705 scopus 로고    scopus 로고
    • Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls
    • Makrythanasis P., et al. Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls. Hum. Mutat. 2009, 30:E866-E879.
    • (2009) Hum. Mutat. , vol.30 , pp. E866-E879
    • Makrythanasis, P.1
  • 49
    • 34250189924 scopus 로고    scopus 로고
    • Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription
    • Nakaya H.I., et al. Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription. Genome Biol. 2007, 8:R43.
    • (2007) Genome Biol. , vol.8 , pp. R43
    • Nakaya, H.I.1
  • 50
    • 84866508252 scopus 로고    scopus 로고
    • Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells
    • St Laurent G., et al. Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. BMC Genomics 2012, 13:504.
    • (2012) BMC Genomics , vol.13 , pp. 504
    • St Laurent, G.1
  • 51
    • 84887512740 scopus 로고    scopus 로고
    • Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations
    • Fachel A.A., et al. Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations. Mol. Cancer 2013, 12:140.
    • (2013) Mol. Cancer , vol.12 , pp. 140
    • Fachel, A.A.1
  • 52
    • 84860243435 scopus 로고    scopus 로고
    • Hidden treasures in unspliced EST data
    • Engelhardt J., Stadler P.F. Hidden treasures in unspliced EST data. Theory Biosci. 2012, 131:49-57.
    • (2012) Theory Biosci. , vol.131 , pp. 49-57
    • Engelhardt, J.1    Stadler, P.F.2
  • 53
    • 84881175425 scopus 로고    scopus 로고
    • Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA
    • Moss W.N., Steitz J.A. Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA. BMC Genomics 2013, 14:543.
    • (2013) BMC Genomics , vol.14 , pp. 543
    • Moss, W.N.1    Steitz, J.A.2
  • 54
    • 84869151299 scopus 로고    scopus 로고
    • Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis
    • Gardner E.J., et al. Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis. Genes Dev. 2012, 26:2550-2559.
    • (2012) Genes Dev. , vol.26 , pp. 2550-2559
    • Gardner, E.J.1
  • 55
    • 84884566546 scopus 로고    scopus 로고
    • Circular intronic long noncoding RNAs
    • Zhang Y., et al. Circular intronic long noncoding RNAs. Mol. Cell 2013, 51:792-806.
    • (2013) Mol. Cell , vol.51 , pp. 792-806
    • Zhang, Y.1
  • 56
    • 21044431735 scopus 로고    scopus 로고
    • Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
    • Cheng J., et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 2005, 308:1149-1154.
    • (2005) Science , vol.308 , pp. 1149-1154
    • Cheng, J.1
  • 57
    • 24644472515 scopus 로고    scopus 로고
    • Antisense transcription in the mammalian transcriptome
    • Katayama S., et al. Antisense transcription in the mammalian transcriptome. Science 2005, 309:1564-1566.
    • (2005) Science , vol.309 , pp. 1564-1566
    • Katayama, S.1
  • 58
    • 60549115605 scopus 로고    scopus 로고
    • Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs
    • Affymetrix ENCODE Transcriptome Project; Cold Spring Harbor Laboratory ENCODE Transcriptome Project
    • Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature 2009, 457:1028-1032. Affymetrix ENCODE Transcriptome Project; Cold Spring Harbor Laboratory ENCODE Transcriptome Project.
    • (2009) Nature , vol.457 , pp. 1028-1032
  • 59
    • 64649087770 scopus 로고    scopus 로고
    • Identification of a cytoplasmic complex that adds a cap onto 5'-monophosphate RNA
    • Otsuka Y., et al. Identification of a cytoplasmic complex that adds a cap onto 5'-monophosphate RNA. Mol. Cell. Biol. 2009, 29:2155-2167.
    • (2009) Mol. Cell. Biol. , vol.29 , pp. 2155-2167
    • Otsuka, Y.1
  • 60
    • 79953673245 scopus 로고    scopus 로고
    • Expression of distinct RNAs from 3' untranslated regions
    • Mercer T.R., et al. Expression of distinct RNAs from 3' untranslated regions. Nucleic Acids Res. 2011, 39:2393-2403.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 2393-2403
    • Mercer, T.R.1
  • 61
    • 84905394878 scopus 로고    scopus 로고
    • Multiplicity of 5' cap structures present on short RNAs
    • Abdelhamid R.F., et al. Multiplicity of 5' cap structures present on short RNAs. PLoS ONE 2014, 9:e102895.
    • (2014) PLoS ONE , vol.9 , pp. e102895
    • Abdelhamid, R.F.1
  • 62
    • 84872531655 scopus 로고    scopus 로고
    • Circular RNAs are abundant, conserved, and associated with ALU repeats
    • Jeck W.R., et al. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 2013, 19:141-157.
    • (2013) RNA , vol.19 , pp. 141-157
    • Jeck, W.R.1
  • 63
    • 84855396196 scopus 로고    scopus 로고
    • Evidence for transcript networks composed of chimeric RNAs in human cells
    • Djebali S., et al. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS ONE 2012, 7:e28213.
    • (2012) PLoS ONE , vol.7 , pp. e28213
    • Djebali, S.1
  • 64
    • 0037155267 scopus 로고    scopus 로고
    • Intergenic mRNA molecules resulting from trans-splicing
    • Finta C., Zaphiropoulos P.G. Intergenic mRNA molecules resulting from trans-splicing. J. Biol. Chem. 2002, 277:5882-5890.
    • (2002) J. Biol. Chem. , vol.277 , pp. 5882-5890
    • Finta, C.1    Zaphiropoulos, P.G.2
  • 65
    • 0033168090 scopus 로고    scopus 로고
    • RNA molecules containing exons originating from different members of the cytochrome P450 2C gene subfamily (CYP2C) in human epidermis and liver
    • Zaphiropoulos P.G. RNA molecules containing exons originating from different members of the cytochrome P450 2C gene subfamily (CYP2C) in human epidermis and liver. Nucleic Acids Res. 1999, 27:2585-2590.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 2585-2590
    • Zaphiropoulos, P.G.1
  • 66
    • 77955140071 scopus 로고    scopus 로고
    • New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism
    • Kapranov P., et al. New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism. Nature 2010, 466:642-646.
    • (2010) Nature , vol.466 , pp. 642-646
    • Kapranov, P.1
  • 67
    • 0029978049 scopus 로고    scopus 로고
    • Antisense globin RNA in mouse erythroid tissues: structure, origin, and possible function
    • Volloch V., et al. Antisense globin RNA in mouse erythroid tissues: structure, origin, and possible function. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:2476-2481.
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 2476-2481
    • Volloch, V.1
  • 68
    • 80054688742 scopus 로고    scopus 로고
    • Coding RNAs with a non-coding function: maintenance of open chromatin structure
    • Caudron-Herger M., et al. Coding RNAs with a non-coding function: maintenance of open chromatin structure. Nucleus 2011, 2:410-424.
    • (2011) Nucleus , vol.2 , pp. 410-424
    • Caudron-Herger, M.1
  • 69
    • 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. 2012, 81:145-166.
    • (2012) Annu. Rev. Biochem. , vol.81 , pp. 145-166
    • Rinn, J.L.1    Chang, H.Y.2
  • 70
    • 84897459814 scopus 로고    scopus 로고
    • An atlas of active enhancers across human cell types and tissues
    • Andersson R., et al. An atlas of active enhancers across human cell types and tissues. Nature 2014, 507:455-461.
    • (2014) Nature , vol.507 , pp. 455-461
    • Andersson, R.1
  • 71
    • 84895908120 scopus 로고    scopus 로고
    • The evolution of lncRNA repertoires and expression patterns in tetrapods
    • Necsulea A., et al. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 2014, 505:635-640.
    • (2014) Nature , vol.505 , pp. 635-640
    • Necsulea, A.1
  • 72
    • 77951118936 scopus 로고    scopus 로고
    • Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
    • Gupta R.A., et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010, 464:1071-1076.
    • (2010) Nature , vol.464 , pp. 1071-1076
    • Gupta, R.A.1
  • 73
    • 84880154515 scopus 로고    scopus 로고
    • Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer
    • Du Z., et al. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat. Struct. Mol. Biol. 2013, 20:908-913.
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 908-913
    • Du, Z.1
  • 74
    • 84864395101 scopus 로고    scopus 로고
    • Long non-coding RNAs and human disease
    • Harries L.W. Long non-coding RNAs and human disease. Biochem. Soc. Trans. 2012, 40:902-906.
    • (2012) Biochem. Soc. Trans. , vol.40 , pp. 902-906
    • Harries, L.W.1
  • 75
    • 67349173665 scopus 로고    scopus 로고
    • The regulated retrotransposon transcriptome of mammalian cells
    • Faulkner G.J., et al. The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 2009, 41:563-571.
    • (2009) Nat. Genet. , vol.41 , pp. 563-571
    • Faulkner, G.J.1
  • 76
    • 84901651635 scopus 로고    scopus 로고
    • Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance
    • Fort A., et al. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nat. Genet. 2014, 46:558-566.
    • (2014) Nat. Genet. , vol.46 , pp. 558-566
    • Fort, A.1
  • 77
    • 84869881863 scopus 로고    scopus 로고
    • Transposable elements reveal a stem cell specific class of long noncoding RNAs
    • Kelley D.R., Rinn J.L. Transposable elements reveal a stem cell specific class of long noncoding RNAs. Genome Biol. 2012, 13:R107.
    • (2012) Genome Biol. , vol.13 , pp. R107
    • Kelley, D.R.1    Rinn, J.L.2
  • 78
    • 77953210095 scopus 로고    scopus 로고
    • On the stem cell origin of cancer
    • Sell S. On the stem cell origin of cancer. Am. J. Pathol. 2010, 176:2584-2594.
    • (2010) Am. J. Pathol. , vol.176 , pp. 2584-2594
    • Sell, S.1
  • 79
    • 39549103642 scopus 로고    scopus 로고
    • Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock
    • Mariner P.D., et al. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol. Cell 2008, 29:499-509.
    • (2008) Mol. Cell , vol.29 , pp. 499-509
    • Mariner, P.D.1
  • 80
    • 77953234794 scopus 로고    scopus 로고
    • LINE dancing in the human genome: transposable elements and disease
    • Belancio V.P., et al. LINE dancing in the human genome: transposable elements and disease. Genome Med. 2009, 1:97.
    • (2009) Genome Med. , vol.1 , pp. 97
    • Belancio, V.P.1
  • 81
    • 50549099314 scopus 로고    scopus 로고
    • Expression patterns of transcribed human endogenous retrovirus HERV-K(HML-2) loci in human tissues and the need for a HERV Transcriptome Project
    • Flockerzi A., et al. Expression patterns of transcribed human endogenous retrovirus HERV-K(HML-2) loci in human tissues and the need for a HERV Transcriptome Project. BMC Genomics 2008, 9:354.
    • (2008) BMC Genomics , vol.9 , pp. 354
    • Flockerzi, A.1
  • 82
    • 84876240496 scopus 로고    scopus 로고
    • Control of myogenesis by rodent SINE-containing lncRNAs
    • Wang J., et al. Control of myogenesis by rodent SINE-containing lncRNAs. Genes Dev. 2013, 27:793-804.
    • (2013) Genes Dev. , vol.27 , pp. 793-804
    • Wang, J.1
  • 83
    • 34250377325 scopus 로고    scopus 로고
    • Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution
    • Zheng D., et al. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res. 2007, 17:839-851.
    • (2007) Genome Res. , vol.17 , pp. 839-851
    • Zheng, D.1
  • 84
    • 79955035120 scopus 로고    scopus 로고
    • Pseudogenes: pseudo-functional or key regulators in health and disease?
    • Pink R.C., et al. Pseudogenes: pseudo-functional or key regulators in health and disease?. RNA 2011, 17:792-798.
    • (2011) RNA , vol.17 , pp. 792-798
    • Pink, R.C.1
  • 85
    • 84876177255 scopus 로고    scopus 로고
    • A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells
    • Johnsson P., et al. A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells. Nat. Struct. Mol. Biol. 2013, 20:440-446.
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 440-446
    • Johnsson, P.1
  • 86
    • 77953957633 scopus 로고    scopus 로고
    • A coding-independent function of gene and pseudogene mRNAs regulates tumour biology
    • Poliseno L., et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 2010, 465:1033-1038.
    • (2010) Nature , vol.465 , pp. 1033-1038
    • Poliseno, L.1
  • 87
    • 84859513087 scopus 로고    scopus 로고
    • A noncoding RNA antisense to moesin at 5p14.1 in autism
    • Kerin T., et al. A noncoding RNA antisense to moesin at 5p14.1 in autism. Sci. Transl. Med. 2012, 4:128ra140.
    • (2012) Sci. Transl. Med. , vol.4 , pp. 128ra140
    • Kerin, T.1
  • 88
    • 33748424364 scopus 로고    scopus 로고
    • Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3
    • Arigo J.T., et al. Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. Mol. Cell 2006, 23:841-851.
    • (2006) Mol. Cell , vol.23 , pp. 841-851
    • Arigo, J.T.1
  • 89
    • 84881474625 scopus 로고    scopus 로고
    • Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality
    • Ntini E., et al. Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality. Nat. Struct. Mol. Biol. 2013, 20:923-928.
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 923-928
    • Ntini, E.1
  • 90
    • 80052458531 scopus 로고    scopus 로고
    • Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes
    • Valen E., et al. Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. Nat. Struct. Mol. Biol. 2011, 18:1075-1082.
    • (2011) Nat. Struct. Mol. Biol. , vol.18 , pp. 1075-1082
    • Valen, E.1
  • 91
    • 79960065233 scopus 로고    scopus 로고
    • XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast
    • van Dijk E.L., et al. XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast. Nature 2011, 475:114-117.
    • (2011) Nature , vol.475 , pp. 114-117
    • van Dijk, E.L.1
  • 92
    • 60549108380 scopus 로고    scopus 로고
    • Bidirectional promoters generate pervasive transcription in yeast
    • Xu Z., et al. Bidirectional promoters generate pervasive transcription in yeast. Nature 2009, 457:1033-1037.
    • (2009) Nature , vol.457 , pp. 1033-1037
    • Xu, Z.1
  • 93
    • 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. 2012, 22:1775-1789.
    • (2012) Genome Res. , vol.22 , pp. 1775-1789
    • Derrien, T.1
  • 94
    • 2542542256 scopus 로고    scopus 로고
    • Ultraconserved elements in the human genome
    • Bejerano G., et al. Ultraconserved elements in the human genome. Science 2004, 304:1321-1325.
    • (2004) Science , vol.304 , pp. 1321-1325
    • Bejerano, G.1
  • 95
    • 84873605164 scopus 로고    scopus 로고
    • Transcription signatures encoded by ultraconserved genomic regions in human prostate cancer
    • Hudson R.S., et al. Transcription signatures encoded by ultraconserved genomic regions in human prostate cancer. Mol. Cancer 2013, 12:13.
    • (2013) Mol. Cancer , vol.12 , pp. 13
    • Hudson, R.S.1
  • 96
    • 84876049606 scopus 로고    scopus 로고
    • The genetic code as expressed through relationships between mRNA structure and protein function
    • Mauger D.M., et al. The genetic code as expressed through relationships between mRNA structure and protein function. FEBS Lett. 2013, 587:1180-1188.
    • (2013) FEBS Lett. , vol.587 , pp. 1180-1188
    • Mauger, D.M.1
  • 97
    • 14044272835 scopus 로고    scopus 로고
    • Fast and reliable prediction of noncoding RNAs
    • Washietl S., et al. Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:2454-2459.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 2454-2459
    • Washietl, S.1
  • 98
    • 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. 2006, 2:e33.
    • (2006) PLoS Comput. Biol. , vol.2 , pp. e33
    • Pedersen, J.S.1
  • 99
    • 34250331200 scopus 로고    scopus 로고
    • Structured RNAs in the ENCODE selected regions of the human genome
    • Washietl S., et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 2007, 17:852-864.
    • (2007) Genome Res. , vol.17 , pp. 852-864
    • Washietl, S.1
  • 100
    • 84887620047 scopus 로고    scopus 로고
    • HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts
    • Ferdin J., et al. HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts. Cell Death Differ. 2013, 20:1675-1687.
    • (2013) Cell Death Differ. , vol.20 , pp. 1675-1687
    • Ferdin, J.1
  • 101
    • 77952952164 scopus 로고    scopus 로고
    • Identification of long stress-induced non-coding transcripts that have altered expression in cancer
    • Silva J.M., et al. Identification of long stress-induced non-coding transcripts that have altered expression in cancer. Genomics 2010, 95:355-362.
    • (2010) Genomics , vol.95 , pp. 355-362
    • Silva, J.M.1
  • 102
    • 77954231525 scopus 로고    scopus 로고
    • Characterization of the RNA content of chromatin
    • Mondal T., et al. Characterization of the RNA content of chromatin. Genome Res. 2010, 20:899-907.
    • (2010) Genome Res. , vol.20 , pp. 899-907
    • Mondal, T.1
  • 103
    • 78650253763 scopus 로고    scopus 로고
    • Genome-wide identification of polycomb-associated RNAs by RIP-seq
    • Zhao J., et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 2010, 40:939-953.
    • (2010) Mol. Cell , vol.40 , pp. 939-953
    • Zhao, J.1
  • 104
    • 84884582059 scopus 로고    scopus 로고
    • Long non-coding RNAs: modulators of nuclear structure and function
    • Bergmann J.H., Spector D.L. Long non-coding RNAs: modulators of nuclear structure and function. Curr. Opin. Cell Biol. 2014, 26:10-18.
    • (2014) Curr. Opin. Cell Biol. , vol.26 , pp. 10-18
    • Bergmann, J.H.1    Spector, D.L.2
  • 105
    • 84891711873 scopus 로고    scopus 로고
    • Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes
    • van Heesch S., et al. Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes. Genome Biol. 2014, 15:R6.
    • (2014) Genome Biol. , vol.15 , pp. R6
    • van Heesch, S.1
  • 106
    • 81755161589 scopus 로고    scopus 로고
    • Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins
    • Rackham O., et al. 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
  • 107
    • 84875590101 scopus 로고    scopus 로고
    • Long noncoding RNAs: past, present, and future
    • Kung J.T., et al. Long noncoding RNAs: past, present, and future. Genetics 2013, 193:651-669.
    • (2013) Genetics , vol.193 , pp. 651-669
    • Kung, J.T.1
  • 108
    • 77957243921 scopus 로고    scopus 로고
    • Long noncoding RNAs with enhancer-like function in human cells
    • Orom U.A., et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 2010, 143:46-58.
    • (2010) Cell , vol.143 , pp. 46-58
    • Orom, U.A.1
  • 109
    • 84892573723 scopus 로고    scopus 로고
    • The multilayered complexity of ceRNA crosstalk and competition
    • Tay Y., et al. The multilayered complexity of ceRNA crosstalk and competition. Nature 2014, 505:344-352.
    • (2014) Nature , vol.505 , pp. 344-352
    • Tay, Y.1
  • 110
    • 84866952775 scopus 로고    scopus 로고
    • Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape
    • St Laurent G., et al. Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape. Front. Genet. 2012, 3:57.
    • (2012) Front. Genet. , vol.3 , pp. 57
    • St Laurent, G.1
  • 111
    • 56349113455 scopus 로고    scopus 로고
    • 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA
    • Wilusz J.E., et al. 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 2008, 135:919-932.
    • (2008) Cell , vol.135 , pp. 919-932
    • Wilusz, J.E.1
  • 112
    • 84898016455 scopus 로고    scopus 로고
    • An mRNA-derived noncoding RNA targets and regulates the ribosome
    • Pircher A., et al. An mRNA-derived noncoding RNA targets and regulates the ribosome. Mol. Cell 2014, 54:147-155.
    • (2014) Mol. Cell , vol.54 , pp. 147-155
    • Pircher, A.1
  • 113
    • 84923320750 scopus 로고    scopus 로고
    • Quantitative profiling of peptides from RNAs classified as noncoding
    • Prabakaran S., et al. Quantitative profiling of peptides from RNAs classified as noncoding. Nat. Commun. 2014, 5:5429.
    • (2014) Nat. Commun. , vol.5 , pp. 5429
    • Prabakaran, S.1
  • 114
    • 81055155799 scopus 로고    scopus 로고
    • Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    • Ingolia N.T., et al. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 2011, 147:789-802.
    • (2011) Cell , vol.147 , pp. 789-802
    • Ingolia, N.T.1
  • 115
    • 84865839598 scopus 로고    scopus 로고
    • Long noncoding RNAs are rarely translated in two human cell lines
    • Banfai B., et al. Long noncoding RNAs are rarely translated in two human cell lines. Genome Res. 2012, 22:1646-1657.
    • (2012) Genome Res. , vol.22 , pp. 1646-1657
    • Banfai, B.1
  • 116
    • 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 2013, 154:240-251.
    • (2013) Cell , vol.154 , pp. 240-251
    • Guttman, M.1
  • 117
    • 79551623370 scopus 로고    scopus 로고
    • ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS
    • Pasmant E., et al. ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS. FASEB J. 2011, 25:444-448.
    • (2011) FASEB J. , vol.25 , pp. 444-448
    • Pasmant, E.1
  • 118
    • 78650696753 scopus 로고    scopus 로고
    • Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk
    • Burd C.E., et al. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet. 2010, 6:e1001233.
    • (2010) PLoS Genet. , vol.6 , pp. e1001233
    • Burd, C.E.1
  • 119
    • 84880799429 scopus 로고    scopus 로고
    • Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks
    • Holdt L.M., et al. Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet. 2013, 9:e1003588.
    • (2013) PLoS Genet. , vol.9 , pp. e1003588
    • Holdt, L.M.1
  • 120
    • 34249088350 scopus 로고    scopus 로고
    • Genome-wide transcription and the implications for genomic organization
    • Kapranov P., et al. Genome-wide transcription and the implications for genomic organization. Nat. Rev. Genet. 2007, 8:413-423.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 413-423
    • Kapranov, P.1
  • 121
    • 78650972252 scopus 로고    scopus 로고
    • Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs
    • Jan C.H., et al. Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. Nature 2011, 469:97-101.
    • (2011) Nature , vol.469 , pp. 97-101
    • Jan, C.H.1
  • 122
    • 78649910014 scopus 로고    scopus 로고
    • Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation
    • Ozsolak F., et al. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 2010, 143:1018-1029.
    • (2010) Cell , vol.143 , pp. 1018-1029
    • Ozsolak, F.1
  • 123
    • 84863229628 scopus 로고    scopus 로고
    • Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome
    • Peng Z., et al. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat. Biotechnol. 2012, 30:253-260.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 253-260
    • Peng, Z.1
  • 124
    • 84887476291 scopus 로고    scopus 로고
    • Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila
    • St Laurent G., et al. Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila. Nat. Struct. Mol. Biol. 2013, 20:1333-1339.
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 1333-1339
    • St Laurent, G.1
  • 125
    • 85075274229 scopus 로고    scopus 로고
    • Nucleic acids are not boring long polymers of only four types of nucleotides:a guided tour
    • Landes Bioscience, H. Grosjean (Ed.)
    • Grosjean H. Nucleic acids are not boring long polymers of only four types of nucleotides:a guided tour. DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution 2009, 1-18. Landes Bioscience. 7th edn. H. Grosjean (Ed.).
    • (2009) DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution , pp. 1-18
    • Grosjean, H.1
  • 126
    • 84858328300 scopus 로고    scopus 로고
    • Comment on "Widespread RNA and DNA sequence differences in the human transcriptome"
    • author reply 1302
    • Kleinman C.L., Majewski J. Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science 2012, 335:1302. author reply 1302.
    • (2012) Science , vol.335 , pp. 1302
    • Kleinman, C.L.1    Majewski, J.2
  • 127
    • 77952967431 scopus 로고    scopus 로고
    • Direct detection of DNA methylation during single-molecule, real-time sequencing
    • Flusberg B.A., et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 2010, 7:461-465.
    • (2010) Nat. Methods , vol.7 , pp. 461-465
    • Flusberg, B.A.1
  • 128
    • 84867473669 scopus 로고    scopus 로고
    • Detecting chemically modified DNA bases using surface-enhanced raman spectroscopy
    • Barhoumi A., Halas N.J. Detecting chemically modified DNA bases using surface-enhanced raman spectroscopy. J. Phys. Chem. Lett. 2011, 2:3118-3123.
    • (2011) J. Phys. Chem. Lett. , vol.2 , pp. 3118-3123
    • Barhoumi, A.1    Halas, N.J.2
  • 129
    • 34250330777 scopus 로고    scopus 로고
    • What is a gene, post-ENCODE? History and updated definition
    • Gerstein M.B., et al. What is a gene, post-ENCODE? History and updated definition. Genome Res. 2007, 17:669-681.
    • (2007) Genome Res. , vol.17 , pp. 669-681
    • Gerstein, M.B.1
  • 130
    • 84890449615 scopus 로고    scopus 로고
    • Functional transcriptomics in the post-ENCODE era
    • Mudge J.M., et al. Functional transcriptomics in the post-ENCODE era. Genome Res. 2013, 23:1961-1973.
    • (2013) Genome Res. , vol.23 , pp. 1961-1973
    • Mudge, J.M.1
  • 131
    • 79960230895 scopus 로고    scopus 로고
    • Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
    • Zhang C., Darnell R.B. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat. Biotechnol. 2011, 29:607-614.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 607-614
    • Zhang, C.1    Darnell, R.B.2
  • 132
    • 85027926010 scopus 로고    scopus 로고
    • RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)
    • Siegfried N.A., et al. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat. Methods 2014, 11:959-965.
    • (2014) Nat. Methods , vol.11 , pp. 959-965
    • Siegfried, N.A.1
  • 133
    • 80054756754 scopus 로고    scopus 로고
    • Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions
    • Chu C., et al. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell 2011, 44:667-678.
    • (2011) Mol. Cell , vol.44 , pp. 667-678
    • Chu, C.1
  • 134
    • 79955836460 scopus 로고    scopus 로고
    • A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells
    • Hah N., et al. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 2011, 145:622-634.
    • (2011) Cell , vol.145 , pp. 622-634
    • Hah, N.1
  • 135
    • 34249740942 scopus 로고    scopus 로고
    • A new paradigm for developmental biology
    • Mattick J.S. A new paradigm for developmental biology. J. Exp. Biol. 2007, 210:1526-1547.
    • (2007) J. Exp. Biol. , vol.210 , pp. 1526-1547
    • Mattick, J.S.1
  • 136
    • 84885215226 scopus 로고    scopus 로고
    • Systematic classification of non-coding RNAs by epigenomic similarity
    • Dozmorov M.G., et al. Systematic classification of non-coding RNAs by epigenomic similarity. BMC Bioinform. 2013, 14(Suppl 14):S2.
    • (2013) BMC Bioinform. , vol.14 , pp. S2
    • Dozmorov, M.G.1
  • 137
    • 84900403952 scopus 로고    scopus 로고
    • On the reproducibility of TCGA ovarian cancer microRNA profiles
    • Wan Y.W., et al. On the reproducibility of TCGA ovarian cancer microRNA profiles. PLoS ONE 2014, 9:e87782.
    • (2014) PLoS ONE , vol.9 , pp. e87782
    • Wan, Y.W.1
  • 138
    • 84883527406 scopus 로고    scopus 로고
    • On the importance of small changes in RNA expression
    • St Laurent G., et al. On the importance of small changes in RNA expression. Methods 2013, 63:18-24.
    • (2013) Methods , vol.63 , pp. 18-24
    • St Laurent, G.1
  • 139
    • 79955858869 scopus 로고    scopus 로고
    • Protocol dependence of sequencing-based gene expression measurements
    • Raz T., et al. Protocol dependence of sequencing-based gene expression measurements. PLoS ONE 2011, 6:e19287.
    • (2011) PLoS ONE , vol.6 , pp. e19287
    • Raz, T.1
  • 140
    • 84893473154 scopus 로고    scopus 로고
    • Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations
    • Fu G.K., et al. Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:1891-1896.
    • (2014) Proc. Natl. Acad. Sci. U.S.A. , vol.111 , pp. 1891-1896
    • Fu, G.K.1
  • 141
    • 84906828775 scopus 로고    scopus 로고
    • Influence of RNA extraction methods and library selection schemes on RNA-seq data
    • Sultan M., et al. Influence of RNA extraction methods and library selection schemes on RNA-seq data. BMC Genomics 2014, 15:675.
    • (2014) BMC Genomics , vol.15 , pp. 675
    • Sultan, M.1
  • 142
    • 84855989774 scopus 로고    scopus 로고
    • Fast computation and applications of genome mappability
    • Derrien T., et al. Fast computation and applications of genome mappability. PLoS ONE 2012, 7:e30377.
    • (2012) PLoS ONE , vol.7 , pp. e30377
    • Derrien, T.1
  • 143
    • 70349956497 scopus 로고    scopus 로고
    • Direct RNA sequencing
    • Ozsolak F., et al. Direct RNA sequencing. Nature 2009, 461:814-818.
    • (2009) Nature , vol.461 , pp. 814-818
    • Ozsolak, F.1
  • 144
    • 84988044467 scopus 로고    scopus 로고
    • CAGE: cap analysis of gene expression
    • Kodzius R., et al. CAGE: cap analysis of gene expression. Nat. Methods 2006, 3:211-222.
    • (2006) Nat. Methods , vol.3 , pp. 211-222
    • Kodzius, R.1
  • 145
    • 84898978919 scopus 로고    scopus 로고
    • Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome
    • Philippe N., et al. Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome. Nucleic Acids Res. 2014, 42:2820-2832.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 2820-2832
    • Philippe, N.1
  • 146
    • 63849091245 scopus 로고    scopus 로고
    • Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
    • Fullwood M.J., et al. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009, 19:521-532.
    • (2009) Genome Res. , vol.19 , pp. 521-532
    • Fullwood, M.J.1
  • 147
    • 0343387151 scopus 로고
    • Locus unlinked to alpha-fetoprotein under the control of the murine raf and Rif genes
    • Pachnis V., et al. Locus unlinked to alpha-fetoprotein under the control of the murine raf and Rif genes. Proc. Natl. Acad. Sci. U.S.A. 1984, 81:5523-5527.
    • (1984) Proc. Natl. Acad. Sci. U.S.A. , vol.81 , pp. 5523-5527
    • Pachnis, V.1
  • 148
    • 79953748673 scopus 로고    scopus 로고
    • A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
    • Wang K.C., et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 2011, 472:120-124.
    • (2011) Nature , vol.472 , pp. 120-124
    • Wang, K.C.1
  • 149
    • 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 2010, 142:409-419.
    • (2010) Cell , vol.142 , pp. 409-419
    • Huarte, M.1
  • 150
    • 0026456701 scopus 로고
    • The human XIST gene: analysis of a 17kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus
    • Brown C.J., et al. The human XIST gene: analysis of a 17kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 1992, 71:527-542.
    • (1992) Cell , vol.71 , pp. 527-542
    • Brown, C.J.1
  • 151
    • 84897896279 scopus 로고    scopus 로고
    • The long non-coding RNA Paupar regulates the expression of both local and distal genes
    • Vance K.W., et al. The long non-coding RNA Paupar regulates the expression of both local and distal genes. EMBO J. 2014, 33:296-311.
    • (2014) EMBO J. , vol.33 , pp. 296-311
    • Vance, K.W.1
  • 152
    • 69549128557 scopus 로고    scopus 로고
    • The function of non-coding RNAs in genomic imprinting
    • Koerner M.V., et al. The function of non-coding RNAs in genomic imprinting. Development 2009, 136:1771-1783.
    • (2009) Development , vol.136 , pp. 1771-1783
    • Koerner, M.V.1
  • 153
    • 46749083733 scopus 로고    scopus 로고
    • Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase
    • Faghihi M.A., et al. Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat. Med. 2008, 14:723-730.
    • (2008) Nat. Med. , vol.14 , pp. 723-730
    • Faghihi, M.A.1
  • 154
    • 0033585496 scopus 로고    scopus 로고
    • AHIF: a natural antisense transcript overexpressed in human renal cancer and during hypoxia
    • Thrash-Bingham C.A., Tartof K.D. aHIF: a natural antisense transcript overexpressed in human renal cancer and during hypoxia. J. Natl. Cancer Inst. 1999, 91:143-151.
    • (1999) J. Natl. Cancer Inst. , vol.91 , pp. 143-151
    • Thrash-Bingham, C.A.1    Tartof, K.D.2
  • 155
    • 0032932528 scopus 로고    scopus 로고
    • Tsix, a gene antisense to Xist at the X-inactivation centre
    • Lee J.T., et al. Tsix, a gene antisense to Xist at the X-inactivation centre. Nat. Genet. 1999, 21:400-404.
    • (1999) Nat. Genet. , vol.21 , pp. 400-404
    • Lee, J.T.1
  • 156
    • 57849140661 scopus 로고    scopus 로고
    • Divergent transcription from active promoters
    • Seila A.C., et al. Divergent transcription from active promoters. Science 2008, 322:1849-1851.
    • (2008) Science , vol.322 , pp. 1849-1851
    • Seila, A.C.1
  • 157
    • 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 2010, 465:182-187.
    • (2010) Nature , vol.465 , pp. 182-187
    • Kim, T.K.1
  • 158
    • 79960569959 scopus 로고    scopus 로고
    • Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome
    • Flynn R.A., et al. Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:10460-10465.
    • (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 10460-10465
    • Flynn, R.A.1
  • 159
    • 69849104275 scopus 로고    scopus 로고
    • TERRA: telomeric repeat-containing RNA
    • Luke B., Lingner J. TERRA: telomeric repeat-containing RNA. EMBO J. 2009, 28:2503-2510.
    • (2009) EMBO J. , vol.28 , pp. 2503-2510
    • Luke, B.1    Lingner, J.2
  • 160
    • 84896840947 scopus 로고    scopus 로고
    • Stable C0T-1 repeat RNA is abundant and is associated with euchromatic interphase chromosomes
    • Hall L.L., et al. Stable C0T-1 repeat RNA is abundant and is associated with euchromatic interphase chromosomes. Cell 2014, 156:907-919.
    • (2014) Cell , vol.156 , pp. 907-919
    • Hall, L.L.1
  • 161
    • 76249132036 scopus 로고    scopus 로고
    • Many LINE1 elements contribute to the transcriptome of human somatic cells
    • Rangwala S.H., et al. Many LINE1 elements contribute to the transcriptome of human somatic cells. Genome Biol. 2009, 10:R100.
    • (2009) Genome Biol. , vol.10 , pp. R100
    • Rangwala, S.H.1
  • 162
    • 79551642322 scopus 로고    scopus 로고
    • Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers
    • Ting D.T., et al. Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 2011, 331:593-596.
    • (2011) Science , vol.331 , pp. 593-596
    • Ting, D.T.1
  • 163
    • 78149321674 scopus 로고    scopus 로고
    • Polypurine-repeat-containing RNAs: a novel class of long non-coding RNA in mammalian cells
    • Zheng R., et al. Polypurine-repeat-containing RNAs: a novel class of long non-coding RNA in mammalian cells. J. Cell Sci. 2010, 123:3734-3744.
    • (2010) J. Cell Sci. , vol.123 , pp. 3734-3744
    • Zheng, R.1
  • 164
    • 84889591723 scopus 로고    scopus 로고
    • Transcriptome surveillance by selective termination of noncoding RNA synthesis
    • Schulz D., et al. Transcriptome surveillance by selective termination of noncoding RNA synthesis. Cell 2013, 155:1075-1087.
    • (2013) Cell , vol.155 , pp. 1075-1087
    • Schulz, D.1
  • 165
    • 60849112259 scopus 로고    scopus 로고
    • Annotation of mammalian primary microRNAs
    • Saini H.K., et al. Annotation of mammalian primary microRNAs. BMC Genomics 2008, 9:564.
    • (2008) BMC Genomics , vol.9 , pp. 564
    • Saini, H.K.1
  • 166
    • 33847271696 scopus 로고    scopus 로고
    • The imprinted H19 noncoding RNA is a primary microRNA precursor
    • Cai X., Cullen B.R. The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA 2007, 13:313-316.
    • (2007) RNA , vol.13 , pp. 313-316
    • Cai, X.1    Cullen, B.R.2
  • 167
    • 84878600190 scopus 로고    scopus 로고
    • Defining piRNA primary transcripts
    • Li X.Z., et al. Defining piRNA primary transcripts. Cell Cycle 2013, 12:1657-1658.
    • (2013) Cell Cycle , vol.12 , pp. 1657-1658
    • Li, X.Z.1
  • 168
    • 79960622503 scopus 로고    scopus 로고
    • Biogenesis and function of nuclear bodies
    • Mao Y.S., et al. Biogenesis and function of nuclear bodies. Trends Genet. 2011, 27:295-306.
    • (2011) Trends Genet. , vol.27 , pp. 295-306
    • Mao, Y.S.1
  • 169
    • 1542748076 scopus 로고    scopus 로고
    • Aligning multiple genomic sequences with the threaded blockset aligner
    • Blanchette M., et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004, 14:708-715.
    • (2004) Genome Res. , vol.14 , pp. 708-715
    • Blanchette, M.1
  • 170
    • 67249117049 scopus 로고    scopus 로고
    • Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
    • Hindorff L.A., et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:9362-9367.
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 9362-9367
    • Hindorff, L.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.