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Volumn 19, Issue 1, 2018, Pages

RNA m6A methylation participates in regulation of postnatal development of the mouse cerebellum

Author keywords

ALKBH5; Cerebellar development; METTL3; N6 methyladenosine; RNA methylation

Indexed keywords

6 N METHYLADENOSINE; ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 5; FTO PROTEIN; MESSENGER RNA; METHYLTRANSFERASE; METTL14 PROTEIN; METTL3 PROTEIN; OXYGENASE; UNCLASSIFIED DRUG; WTAP PROTEIN; ADENOSINE; ALKBH5 PROTEIN, MOUSE; METTL3 PROTEIN, MOUSE; N(6)-METHYLADENOSINE; RNA;

EID: 85047912076     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-018-1435-z     Document Type: Article
Times cited : (176)

References (81)
  • 3
    • 84862649489 scopus 로고    scopus 로고
    • Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons
    • Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell. 2012;149:1635-46.
    • (2012) Cell , vol.149 , pp. 1635-1646
    • Meyer, K.D.1    Saletore, Y.2    Zumbo, P.3    Elemento, O.4    Mason, C.E.5    Jaffrey, S.R.6
  • 5
    • 84994108096 scopus 로고    scopus 로고
    • Post-transcriptional gene regulation by mRNA modifications
    • Zhao BS, Roundtree IA, He C. Post-transcriptional gene regulation by mRNA modifications. Nat Rev Mol Cell Biol. 2017;18:31-42.
    • (2017) Nat Rev Mol Cell Biol , vol.18 , pp. 31-42
    • Zhao, B.S.1    Roundtree, I.A.2    He, C.3
  • 6
    • 84964727206 scopus 로고    scopus 로고
    • Recent advances in dynamic m6A RNA modification
    • Cao G, Li HB, Yin Z, Flavell RA. Recent advances in dynamic m6A RNA modification. Open Biol. 2016;6:160003
    • (2016) Open Biol. , vol.6 , pp. 160003
    • Cao, G.1    Li, H.B.2    Yin, Z.3    Flavell, R.A.4
  • 7
    • 84920273757 scopus 로고    scopus 로고
    • FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis
    • Zhao X, Yang Y, Sun BF, Shi Y, Yang X, Xiao W, Hao YJ, Ping XL, Chen YS, Wang WJ, et al. FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res. 2014;24:1403-19.
    • (2014) Cell Res , vol.24 , pp. 1403-1419
    • Zhao, X.1    Yang, Y.2    Sun, B.F.3    Shi, Y.4    Yang, X.5    Xiao, W.6    Hao, Y.J.7    Ping, X.L.8    Chen, Y.S.9    Wang, W.J.10
  • 13
    • 84945288814 scopus 로고    scopus 로고
    • Dynamic m(6)A mRNA methylation directs translational control of heat shock response
    • Zhou J, Wan J, Gao X, Zhang X, Jaffrey SR, Qian SB. Dynamic m(6)A mRNA methylation directs translational control of heat shock response. Nature. 2015;526:591-4.
    • (2015) Nature , vol.526 , pp. 591-594
    • Zhou, J.1    Wan, J.2    Gao, X.3    Zhang, X.4    Jaffrey, S.R.5    Qian, S.B.6
  • 20
    • 85030610496 scopus 로고    scopus 로고
    • The RNA helicase DDX46 inhibits innate immunity by entrapping m6A-demethylated antiviral transcripts in the nucleus
    • Zheng Q, Hou J, Zhou Y, Li Z, Cao X. The RNA helicase DDX46 inhibits innate immunity by entrapping m6A-demethylated antiviral transcripts in the nucleus. Nat Immunol. 2017;18:1094-103.
    • (2017) Nat Immunol , vol.18 , pp. 1094-1103
    • Zheng, Q.1    Hou, J.2    Zhou, Y.3    Li, Z.4    Cao, X.5
  • 21
    • 85028692045 scopus 로고    scopus 로고
    • Ythdc2 is an N6-methyladenosine binding protein that regulates mammalian spermatogenesis
    • Hsu PJ, Zhu Y, Ma H, Guo Y, Shi X, Liu Y, Qi M, Lu Z, Shi H, Wang J, et al. Ythdc2 is an N6-methyladenosine binding protein that regulates mammalian spermatogenesis. Cell Res. 2017;27:1115-27.
    • (2017) Cell Res , vol.27 , pp. 1115-1127
    • Hsu, P.J.1    Zhu, Y.2    Ma, H.3    Guo, Y.4    Shi, X.5    Liu, Y.6    Qi, M.7    Lu, Z.8    Shi, H.9    Wang, J.10
  • 24
    • 85016160834 scopus 로고    scopus 로고
    • m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition
    • Zhao BS, Wang X, Beadell AV, Lu Z, Shi H, Kuuspalu A, Ho RK, He C. m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition. Nature. 2017;542:475-8.
    • (2017) Nature , vol.542 , pp. 475-478
    • Zhao, B.S.1    Wang, X.2    Beadell, A.V.3    Lu, Z.4    Shi, H.5    Kuuspalu, A.6    Ho, R.K.7    He, C.8
  • 33
    • 0031928291 scopus 로고    scopus 로고
    • The cells and molecules that make a cerebellum
    • Goldowitz D, Hamre K. The cells and molecules that make a cerebellum. Trends Neurosci. 1998;21:375-82.
    • (1998) Trends Neurosci , vol.21 , pp. 375-382
    • Goldowitz, D.1    Hamre, K.2
  • 38
    • 0029842459 scopus 로고    scopus 로고
    • Oxygen sensing and molecular adaptation to hypoxia
    • Bunn HF, Poyton RO. Oxygen sensing and molecular adaptation to hypoxia. Physiol Rev. 1996;76:839-85.
    • (1996) Physiol Rev , vol.76 , pp. 839-885
    • Bunn, H.F.1    Poyton, R.O.2
  • 39
    • 84962632914 scopus 로고    scopus 로고
    • Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m6A-demethylation of NANOG mRNA
    • Zhang C, Samanta D, Lu H, Bullen JW, Zhang H, Chen I, He X, Semenza GL. Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m6A-demethylation of NANOG mRNA. Proc Natl Acad Sci U S A. 2016;113:E2047-56.
    • (2016) Proc Natl Acad Sci U S A , vol.113 , pp. E2047-E2056
    • Zhang, C.1    Samanta, D.2    Lu, H.3    Bullen, J.W.4    Zhang, H.5    Chen, I.6    He, X.7    Semenza, G.L.8
  • 42
    • 84889039535 scopus 로고    scopus 로고
    • Wdpcp, a PCP protein required for ciliogenesis, regulates directional cell migration and cell polarity by direct modulation of the actin cytoskeleton
    • Cui C, Chatterjee B, Lozito TP, Zhang Z, Francis RJ, Yagi H, Swanhart LM, Sanker S, Francis D, Yu Q, et al. Wdpcp, a PCP protein required for ciliogenesis, regulates directional cell migration and cell polarity by direct modulation of the actin cytoskeleton. PLoS Biol. 2013;11:e1001720.
    • (2013) PLoS Biol , vol.11
    • Cui, C.1    Chatterjee, B.2    Lozito, T.P.3    Zhang, Z.4    Francis, R.J.5    Yagi, H.6    Swanhart, L.M.7    Sanker, S.8    Francis, D.9    Yu, Q.10
  • 43
    • 84878961842 scopus 로고    scopus 로고
    • Letm1, the mitochondrial Ca2+/H+ antiporter, is essential for normal glucose metabolism and alters brain function in Wolf-Hirschhorn syndrome
    • Jiang D, Zhao L, Clish CB, Clapham DE. Letm1, the mitochondrial Ca2+/H+ antiporter, is essential for normal glucose metabolism and alters brain function in Wolf-Hirschhorn syndrome. Proc Natl Acad Sci U S A. 2013;110:E2249-54.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. E2249-E2254
    • Jiang, D.1    Zhao, L.2    Clish, C.B.3    Clapham, D.E.4
  • 44
    • 53249098510 scopus 로고    scopus 로고
    • Cerebellar development transcriptome database (CDT-DB): profiling of spatio-temporal gene expression during the postnatal development of mouse cerebellum
    • Sato A, Sekine Y, Saruta C, Nishibe H, Morita N, Sato Y, Sadakata T, Shinoda Y, Kojima T, Furuichi T. Cerebellar development transcriptome database (CDT-DB): profiling of spatio-temporal gene expression during the postnatal development of mouse cerebellum. Neural Netw. 2008;21:1056-69.
    • (2008) Neural Netw , vol.21 , pp. 1056-1069
    • Sato, A.1    Sekine, Y.2    Saruta, C.3    Nishibe, H.4    Morita, N.5    Sato, Y.6    Sadakata, T.7    Shinoda, Y.8    Kojima, T.9    Furuichi, T.10
  • 47
    • 85016037231 scopus 로고    scopus 로고
    • m(6)A Demethylase ALKBH5 maintains tumorigenicity of glioblastoma stem-like cells by sustaining FOXM1 expression and cell proliferation program
    • Zhang S, Zhao BS, Zhou A, Lin K, Zheng S, Lu Z, Chen Y, Sulman EP, Xie K, Bogler O, et al. m(6)A Demethylase ALKBH5 maintains tumorigenicity of glioblastoma stem-like cells by sustaining FOXM1 expression and cell proliferation program. Cancer Cell. 2017;31:591-606. e596
    • (2017) Cancer Cell , vol.31 , pp. 591-606
    • Zhang, S.1    Zhao, B.S.2    Zhou, A.3    Lin, K.4    Zheng, S.5    Lu, Z.6    Chen, Y.7    Sulman, E.P.8    Xie, K.9    Bogler, O.10
  • 50
    • 84921714625 scopus 로고    scopus 로고
    • Transcriptome-wide N(6)-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification
    • Li Y, Wang X, Li C, Hu S, Yu J, Song S. Transcriptome-wide N(6)-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification. RNA Biol. 2014;11:1180-8.
    • (2014) RNA Biol , vol.11 , pp. 1180-1188
    • Li, Y.1    Wang, X.2    Li, C.3    Hu, S.4    Yu, J.5    Song, S.6
  • 51
    • 85018458234 scopus 로고    scopus 로고
    • Transcriptome-wide N 6 -methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern
    • Tao X, Chen J, Jiang Y, Wei Y, Chen Y, Xu H, Zhu L, Tang G, Li M, Jiang A, et al. Transcriptome-wide N 6 -methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern. BMC Genomics. 2017;18:336.
    • (2017) BMC Genomics , vol.18 , pp. 336
    • Tao, X.1    Chen, J.2    Jiang, Y.3    Wei, Y.4    Chen, Y.5    Xu, H.6    Zhu, L.7    Tang, G.8    Li, M.9    Jiang, A.10
  • 53
    • 85016092289 scopus 로고    scopus 로고
    • Cell type-specific transcriptome profiling in mammalian brains
    • LoVerso PR, Cui F. Cell type-specific transcriptome profiling in mammalian brains. Front Biosci (Landmark Ed). 2016;21:973-85.
    • (2016) Front Biosci (Landmark Ed) , vol.21 , pp. 973-985
    • LoVerso, P.R.1    Cui, F.2
  • 54
    • 84872032385 scopus 로고    scopus 로고
    • Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing
    • Dominissini D, Moshitch-Moshkovitz S, Salmon-Divon M, Amariglio N, Rechavi G. Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing. Nat Protoc. 2013;8:176-89.
    • (2013) Nat Protoc , vol.8 , pp. 176-189
    • Dominissini, D.1    Moshitch-Moshkovitz, S.2    Salmon-Divon, M.3    Amariglio, N.4    Rechavi, G.5
  • 55
    • 84908432902 scopus 로고    scopus 로고
    • NF1 regulation of RAS/ERK signaling is required for appropriate granule neuron progenitor expansion and migration in cerebellar development
    • Sanchez-Ortiz E, Cho W, Nazarenko I, Mo W, Chen J, Parada LF. NF1 regulation of RAS/ERK signaling is required for appropriate granule neuron progenitor expansion and migration in cerebellar development. Genes Dev. 2014;28:2407-20.
    • (2014) Genes Dev , vol.28 , pp. 2407-2420
    • Sanchez-Ortiz, E.1    Cho, W.2    Nazarenko, I.3    Mo, W.4    Chen, J.5    Parada, L.F.6
  • 57
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • 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. 2013;14: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
  • 58
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105-11.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 62
    • 84985018933 scopus 로고    scopus 로고
    • Optimizing RNA-Seq mapping with STAR
    • Dobin A, Gingeras TR. Optimizing RNA-Seq mapping with STAR. Methods Mol Biol. 2016;1415:245-62.
    • (2016) Methods Mol Biol , vol.1415 , pp. 245-262
    • Dobin, A.1    Gingeras, T.R.2
  • 64
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq-a Python framework to work with high-throughput sequencing data
    • Anders S, Pyl PT, Huber W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166-9.
    • (2015) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 65
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139-40.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 66
    • 84878874512 scopus 로고    scopus 로고
    • Exome-based analysis for RNA epigenome sequencing data
    • Meng J, Cui X, Rao MK, Chen Y, Huang Y. Exome-based analysis for RNA epigenome sequencing data. Bioinformatics. 2013;29:1565-7.
    • (2013) Bioinformatics , vol.29 , pp. 1565-1567
    • Meng, J.1    Cui, X.2    Rao, M.K.3    Chen, Y.4    Huang, Y.5
  • 67
    • 84919387619 scopus 로고    scopus 로고
    • Decomposition of RNA methylome reveals co-methylation patterns induced by latent enzymatic regulators of the epitranscriptome
    • Liu L, Zhang SW, Zhang YC, Liu H, Zhang L, Chen R, Huang Y, Meng J. Decomposition of RNA methylome reveals co-methylation patterns induced by latent enzymatic regulators of the epitranscriptome. Mol BioSyst. 2015;11:262-74.
    • (2015) Mol BioSyst , vol.11 , pp. 262-274
    • Liu, L.1    Zhang, S.W.2    Zhang, Y.C.3    Liu, H.4    Zhang, L.5    Chen, R.6    Huang, Y.7    Meng, J.8
  • 68
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    • Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38:576-89.
    • (2010) Mol Cell , vol.38 , pp. 576-589
    • Heinz, S.1    Benner, C.2    Spann, N.3    Bertolino, E.4    Lin, Y.C.5    Laslo, P.6    Cheng, J.X.7    Murre, C.8    Singh, H.9    Glass, C.K.10
  • 69
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841-2.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 72
    • 84875634162 scopus 로고    scopus 로고
    • Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
    • Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14:178-92.
    • (2013) Brief Bioinform , vol.14 , pp. 178-192
    • Thorvaldsdottir, H.1    Robinson, J.T.2    Mesirov, J.P.3
  • 73
    • 85047952393 scopus 로고    scopus 로고
    • Published 11 Dec 2015.
    • Kolde R: pheatmap. 2015. https://CRAN.R-project.org/package=pheatmap. Published 11 Dec 2015.
    • (2015) pheatmap
    • Kolde, R.1
  • 74
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang d W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44-57.
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 77
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    • Huang d W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37:1-13.
    • (2009) Nucleic Acids Res , vol.37 , pp. 1-13
    • Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 78
    • 85047930306 scopus 로고    scopus 로고
    • RNA m6A methylation participates in regulation of postnatal development of the mouse cerebellum
    • Accessed 25 Apr 2018.
    • Chunhui Ma, Mengqi Chang, Hongyi Lv, Yamei Niu, Shuhui Song, Wei-Min Tong, et al: RNA m6A methylation participates in regulation of postnatal development of the mouse cerebellum. SRA PRJNA400297. 2017. https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA400297. Accessed 25 Apr 2018.
    • (2017) SRA PRJNA400297
    • Ma, C.1    Chang, M.2    Lv, H.3    Niu, Y.4    Song, S.5    Tong, W.-M.6
  • 80
    • 85016104570 scopus 로고    scopus 로고
    • The BIG Data Center: from deposition to integration to translation
    • Members BIGDC. The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res. 2017;45:D18-24.
    • (2017) Nucleic Acids Res , vol.45 , pp. D18-D24
    • Members, B.I.G.D.C.1
  • 81
    • 85047955060 scopus 로고    scopus 로고
    • RNA m6A methylation participates in regulation of postnatal development of the mouse cerebellum
    • Accessed 25 Apr 2018
    • Chunhui Ma, Mengqi Chang, Hongyi Lv, Yamei Niu, Shuhui Song, Wei-Min Tong, et al: RNA m6A methylation participates in regulation of postnatal development of the mouse cerebellum. GSA CRA000472. 2017. http://bigd.big.ac.cn/search?dbId=gsa&q=CRA000472. Accessed 25 Apr 2018.
    • (2017) GSA CRA000472
    • Ma, C.1    Chang, M.2    Lv, H.3    Niu, Y.4    Song, S.5    Tong, W.-M.6


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