메뉴 건너뛰기




Volumn 2, Issue 1, 2015, Pages e995524-1-e995524-9

Identification and expression patterns of novel long non-coding RNAs in neural progenitors of the developing mammalian cortex

Author keywords

Cortical development; lncRNAs; Neurogenesis

Indexed keywords

LONG UNTRANSLATED RNA;

EID: 84926144723     PISSN: None     EISSN: 23262133     Source Type: Journal    
DOI: 10.1080/23262133.2014.995524     Document Type: Article
Times cited : (12)

References (37)
  • 1
    • 60149099385 scopus 로고    scopus 로고
    • Evolution and functions of long noncoding RNAs
    • PMID:19239885
    • Ponting, CP, Oliver, PL, Reik, W. Evolution and functions of long noncoding RNAs. Cell 136, 629-41, (2009); PMID:19239885; http://dx.doi.org/10.1016/j.cell.2009.02.006
    • (2009) Cell , vol.136 , pp. 629-641
    • Ponting, C.P.1    Oliver, P.L.2    Reik, W.3
  • 2
    • 84879987789 scopus 로고    scopus 로고
    • LincRNAs: Genomics, evolution, and mechanisms
    • PMID:23827673
    • Ulitsky, I, Bartel, DP. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26-46, (2013); PMID:23827673; http://dx.doi.org/10.1016/j.cell.2013.06.020
    • (2013) Cell , vol.154 , pp. 26-46
    • Ulitsky, I.1    Bartel, D.P.2
  • 3
    • 79953858658 scopus 로고    scopus 로고
    • No-nonsense functions for long noncoding RNAs
    • PMID:21496640
    • Nagano, T, Fraser, P. No-nonsense functions for long noncoding RNAs. Cell 145, 178-81, (2011); PMID:21496640; http://dx.doi.org/10.1016/j.cell.2011.03.014
    • (2011) Cell , vol.145 , pp. 178-181
    • Nagano, T.1    Fraser, P.2
  • 4
    • 84875183056 scopus 로고    scopus 로고
    • Structure and function of long noncoding RNAs in epigenetic regulation
    • PMID:23463315
    • Mercer, TR, Mattick, JS. Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol 20, 300-7, (2013); PMID:23463315; http://dx.doi.org/10.1038/nsmb.2480
    • (2013) Nat Struct Mol Biol , vol.20 , pp. 300-307
    • Mercer, T.R.1    Mattick, J.S.2
  • 5
    • 60349120914 scopus 로고    scopus 로고
    • Long non-coding RNAs: Insights into functions
    • PMID:19188922
    • Mercer, TR, Dinger, ME, Mattick, JS. Long non-coding RNAs: insights into functions. Nat Rev Genet 10, 155-9, (2009); PMID:19188922; http://dx.doi.org/10.1038/nrg2521
    • (2009) Nat Rev Genet , vol.10 , pp. 155-159
    • Mercer, T.R.1    Dinger, M.E.2    Mattick, J.S.3
  • 10
    • 84902141800 scopus 로고    scopus 로고
    • Long Noncoding RNAs in Cell-Fate programming and reprogramming
    • PMID:24905165
    • Flynn, RA, Chang, HY, Long Noncoding RNAs in Cell-Fate programming and reprogramming. Cell Stem Cell 14, 752-61, (2014); PMID:24905165; http://dx.doi.org/10.1016/j.stem.2014.05.014
    • (2014) Cell Stem Cell , vol.14 , pp. 752-761
    • Flynn, R.A.1    Chang, H.Y.2
  • 11
    • 81055155799 scopus 로고    scopus 로고
    • Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    • PMID:22056041
    • Ingolia, NT, Lareau, LF, Weissman, JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147, 789-802, (2011); PMID:22056041; http://dx.doi.org/10.1016/j.cell.2011.10.002
    • (2011) Cell , vol.147 , pp. 789-802
    • Ingolia, N.T.1    Lareau, L.F.2    Weissman, J.S.3
  • 12
    • 84879969127 scopus 로고    scopus 로고
    • Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins
    • PMID:23810193
    • Guttman, M, Russell, P, Ingolia, NT, Weissman, JS, Lander, ES. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell 154, 240-51, (2013); PMID:23810193; http://dx.doi.org/10.1016/j.cell.2013.06.009
    • (2013) Cell , vol.154 , pp. 240-251
    • Guttman, M.1    Russell, P.2    Ingolia, N.T.3    Weissman, J.S.4    Lander, E.S.5
  • 14
    • 84881511705 scopus 로고    scopus 로고
    • Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data
    • PMID:23967161
    • Lv, J, Cui W, Liu H, He H, Xiu Y, Guo J, Liu H, Liu Q, Zeng T, Chen Y, et al. Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data. PLoS One 8, e71152, (2013); PMID:23967161; http://dx.doi.org/10.1371/journal.pone.0071152
    • (2013) Plos One , vol.8
    • Lv, J.1    Cui, W.2    Liu, H.3    He, H.4    Xiu, Y.5    Guo, J.6    Liu, H.7    Liu, Q.8    Zeng, T.9    Chen, Y.10
  • 15
    • 38649114329 scopus 로고    scopus 로고
    • Specific expression of long noncoding RNAs in the mouse brain
    • PMID:18184812
    • Mercer, TR, Dinger, ME, Sunkin, SM, Mehler, MF, Mattick, JS. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 105, 716-21, (2008); PMID:18184812; http://dx.doi.org/10.1073/pnas.0706729105
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 716-721
    • Mercer, T.R.1    Dinger, M.E.2    Sunkin, S.M.3    Mehler, M.F.4    Mattick, J.S.5
  • 16
    • 84880569773 scopus 로고    scopus 로고
    • Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome
    • PMID:22555619
    • Wood, SH, Craig, T, Li, Y, Merry, B, de Magalhaes, JP. Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome. Age 35, 763-76, (2013); PMID:22555619; http://dx.doi.org/10.1007/s11357-012-9410-1
    • (2013) Age , vol.35 , pp. 763-776
    • Wood, S.H.1    Craig, T.2    Li, Y.3    Merry, B.4    de Magalhaes, J.P.5
  • 17
    • 84877575447 scopus 로고    scopus 로고
    • Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo
    • PMID:23583100
    • Ramos, AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA. et al. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell 12, 616-28, (2013); PMID:23583100; http://dx.doi.org/10.1016/j.stem.2013.03.003
    • (2013) Cell Stem Cell , vol.12 , pp. 616-628
    • Ramos, A.D.1    Diaz, A.2    Nellore, A.3    Delgado, R.N.4    Park, K.Y.5    Gonzales-Roybal, G.6    Oldham, M.C.7    Song, J.S.8    Lim, D.A.9
  • 18
    • 84890567188 scopus 로고    scopus 로고
    • Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment
    • PMID:24240175
    • Aprea, J, Prenninger S, Dori M, Ghosh T, Monasor LS, Wessendorf E, Zocher S, Massalini S, Alexopoulou D, Lesche M., et al. Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment. EMBO J 32, 3145-60, (2013); PMID:24240175; http://dx.doi.org/10.1038/emboj.2013.245
    • (2013) EMBO J , vol.32 , pp. 3145-3160
    • Aprea, J.1    Prenninger, S.2    Dori, M.3    Ghosh, T.4    Monasor, L.S.5    Wessendorf, E.6    Zocher, S.7    Massalini, S.8    Alexopoulou, D.9    Lesche, M.10
  • 19
    • 1542297728 scopus 로고    scopus 로고
    • Neurons arise in the basal neuroepithelium of the early mammalian telencephalon: A major site of neurogenesis
    • PMID:14963232
    • Haubensak, W, Attardo, A, Denk, W, Huttner, WB. Neurons arise in the basal neuroepithelium of the early mammalian telencephalon: a major site of neurogenesis. Proc. Natl. Acad. Sci. USA 101, 3196-201 (2004); PMID:14963232
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 3196-3201
    • Haubensak, W.1    Attardo, A.2    Denk, W.3    Huttner, W.B.4
  • 20
    • 48649083476 scopus 로고    scopus 로고
    • Live imaging at the onset of cortical neurogenesis reveals differential appearance of the neuronal phenotype in apical vs. Basal progenitor progeny
    • PMID:18545663
    • Attardo, A, Calegari, F, Haubensak, W, Wilsch-Brauninger, M, Huttner, WB. Live imaging at the onset of cortical neurogenesis reveals differential appearance of the neuronal phenotype in apical vs. basal progenitor progeny. PLoS ONE 3, e2388, (2008); PMID:18545663; http://dx.doi.org/10.1371/journal. pone.0002388
    • (2008) Plos ONE , vol.3
    • Attardo, A.1    Calegari, F.2    Haubensak, W.3    Wilsch-Brauninger, M.4    Huttner, W.B.5
  • 21
    • 80052584757 scopus 로고    scopus 로고
    • Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing
    • PMID:21873192
    • Ayoub, AE, Oh S, Xie Y, Leng J, Cotney J, Dominguez MH, Noonan JP, Rakic P. et al. Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing. Proc Natl Acad Sci U S A 108, 14950-5, (2011); PMID:21873192; http://dx.doi.org/10.1073/pnas.1112213108
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 14950-14955
    • Ayoub, A.E.1    Oh, S.2    Xie, Y.3    Leng, J.4    Cotney, J.5    Dominguez, M.H.6    Noonan, J.P.7    Rakic, P.8
  • 22
    • 69149097967 scopus 로고    scopus 로고
    • Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing
    • PMID:19617558
    • Han, X, Wu X, Chung WY, Li T, Nekrutenko A, Altman NS, Chen G, Ma H. Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing. Proc Natl Acad Sci U S A 106, 12741-6, (2009); PMID:19617558; http://dx.doi.org/10.1073/pnas.0902417106
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 12741-12746
    • Han, X.1    Wu, X.2    Chung, W.Y.3    Li, T.4    Nekrutenko, A.5    Altman, N.S.6    Chen, G.7    Ma, H.8
  • 23
    • 84861994366 scopus 로고    scopus 로고
    • Transcriptome analysis of microRNAs in developing cerebral cortex of rat
    • PMID:22691069
    • Yao, MJ, Chen G, Zhao PP, Lu MH, Jian J, Liu MF, Yuan XB. Transcriptome analysis of microRNAs in developing cerebral cortex of rat. BMC genomics 13, 232, (2012); PMID:22691069; http://dx.doi.org/10.1186/1471-2164-13-232
    • (2012) BMC Genomics , vol.13 , pp. 232
    • Yao, M.J.1    Chen, G.2    Zhao, P.P.3    Lu, M.H.4    Jian, J.5    Liu, M.F.6    Yuan, X.B.7
  • 24
    • 84863946985 scopus 로고    scopus 로고
    • Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal
    • PMID:22753484
    • Fietz, SA, Lachmann R, Brandl H, Kircher M, Samusik N, Schröder R, Lakshmanaperumal N, Henry I, Vogt J, Riehn A, et al. Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. Proc Natl Acad Sci U S A 109, 11836-41, (2012); PMID:22753484; http://dx.doi.org/10.1073/pnas. 1209647109
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 11836-11841
    • Fietz, S.A.1    Lachmann, R.2    Brandl, H.3    Kircher, M.4    Samusik, N.5    Schröder, R.6    Lakshmanaperumal, N.7    Henry, I.8    Vogt, J.9    Riehn, A.10
  • 25
  • 26
    • 70449704529 scopus 로고    scopus 로고
    • Computational methods for discovering structural variation with nextgeneration sequencing
    • PMID:19844226
    • Medvedev, P, Stanciu, M, Brudno, M. Computational methods for discovering structural variation with nextgeneration sequencing. Nat Methods 6, S13-20, (2009); PMID:19844226; http://dx.doi.org/10.1038/nmeth.1374
    • (2009) Nat Methods , vol.6 , pp. S13-S20
    • Medvedev, P.1    Stanciu, M.2    Brudno, M.3
  • 27
    • 84883496216 scopus 로고    scopus 로고
    • Predicting long non-coding RNAs using RNA sequencing
    • PMID:23541739
    • Ilott, NE, Ponting, CP. Predicting long non-coding RNAs using RNA sequencing. Methods 63, 50-9, (2013); PMID:23541739; http://dx.doi.org/10.1016/j.ymeth.2013.03.019
    • (2013) Methods , vol.63 , pp. 50-59
    • Ilott, N.E.1    Ponting, C.P.2
  • 29
    • 70149123708 scopus 로고    scopus 로고
    • Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain
    • PMID:19696892
    • Ponjavic, J, Oliver, PL, Lunter, G, Ponting, CP, Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet 5, e1000617, (2009); PMID:19696892; http://dx.doi.org/10.1371/journal.pgen.1000617
    • (2009) Plos Genet , vol.5
    • Ponjavic, J.1    Oliver, P.L.2    Lunter, G.3    Ponting, C.P.4
  • 31
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with bowtie 2
    • PMID:22388286
    • Langmead, B, Salzberg, SL. Fast gapped-read alignment with bowtie 2. Nat Methods 9, 357-9, (2012); PMID:22388286; http://dx.doi.org/10.1038/nmeth.1923
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 32
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • PMID:23618408
    • Kim, D. Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14, R36, (2013); PMID:23618408; http://dx.doi.org/10.1186/gb-2013-14-4-r36
    • (2013) Genome Biol , vol.14
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 33
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • PMID:20436464
    • Trapnell, C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28, 511-5, (2010); PMID:20436464; http://dx.doi.org/10.1038/nbt.1621
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    Van Baren, M.J.6    Salzberg, S.L.7    Wold, B.J.8    Pachter, L.9
  • 34
    • 84897397058 scopus 로고    scopus 로고
    • Featurecounts: An efficient general purpose program for assigning sequence reads to genomic features
    • PMID:24227677
    • Liao, Y, Smyth, GK, Shi, W. Featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-30, (2014); PMID:24227677; http://dx.doi.org/10.1093/bioinformatics/btt656
    • (2014) Bioinformatics , vol.30 , pp. 923-930
    • Liao, Y.1    Smyth, G.K.2    Shi, W.3
  • 35
    • 79953009230 scopus 로고    scopus 로고
    • RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data
    • PMID:21357752
    • Washietl, S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N. et al. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA 17, 578-94, (2011); PMID:21357752; http://dx.doi.org/10.1261/rna.2536111
    • (2011) RNA , vol.17 , pp. 578-594
    • Washietl, S.1    Findeiss, S.2    Müller, S.A.3    Kalkhof, S.4    von Bergen, M.5    Hofacker, I.L.6    Stadler, P.F.7    Goldman, N.8
  • 36
    • 84868097156 scopus 로고    scopus 로고
    • A “forward genomics” approach links genotype to phenotype using independent phenotypic losses among related species
    • PMID:23022484
    • Hiller, M, Schaar BT, Indjeian VB, Kingsley DM, Hagey LR, Bejerano G. A “forward genomics” approach links genotype to phenotype using independent phenotypic losses among related species. Cell Rep 2, 817-23, (2012); PMID:23022484; http://dx.doi.org/10.1016/j.celrep.2012.08.032
    • (2012) Cell Rep , vol.2 , pp. 817-823
    • Hiller, M.1    Schaar, B.T.2    Indjeian, V.B.3    Kingsley, D.M.4    Hagey, L.R.5    Bejerano, G.6
  • 37
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • PMID:19033363
    • Huang da, W, Sherman, BT, Lempicki, RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37, 1-13, (2009); PMID:19033363; http://dx.doi.org/10.1093/nar/gkn923
    • (2009) Nucleic Acids Res , vol.37 , pp. 1-13
    • Huang da, W.1    Sherman, B.T.2    Lempicki, R.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.