Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase
Tóm tắt
Từ khóa
Tài liệu tham khảo
Jia G, Fu Y, He C . Reversible RNA adenosine methylation in biological regulation. Trends Genet 2013; 29:108–115.
Niu Y, Zhao X, Wu YS, Li MM, Wang XJ, Yang YG . N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. Genomics Proteomics Bioinformatics 2013; 11:8–17.
Zheng G, Dahl JA, Niu Y, et al. Sprouts of RNA epigenetics: The discovery of mammalian RNA demethylases. RNA Biol 2013; 10:915–918.
Chen-Kiang S, Nevins JR, Darnell JE Jr . N-6-methyl-adenosine in adenovirus type 2 nuclear RNA is conserved in the formation of messenger RNA. J Mol Biol 1979; 135:733–752.
Desrosiers RC, Friderici KH, Rottman FM . Characterization of Novikoff hepatoma mRNA methylation and heterogeneity in the methylated 5′ terminus. Biochemistry 1975; 14:4367–4374.
Levis R, Penman S . 5′-terminal structures of poly(A)+ cytoplasmic messenger RNA and of poly(A)+ and poly(A)- heterogeneous nuclear RNA of cells of the dipteran Drosophila melanogaster. J Mol Biol 1978; 120:487–515.
Narayan P, Ayers DF, Rottman FM, Maroney PA, Nilsen TW . Unequal distribution of N6-methyladenosine in influenza virus mRNAs. Mol Cell Biol 1987; 7:1572–1575.
Pan T . N6-methyl-adenosine modification in messenger and long non-coding RNA. Trends Biochem Sci 2013; 38:204–209.
Dominissini D, Moshitch-Moshkovitz S, Schwartz S, et al. Topology of the human and mouse m(6)A RNA methylomes revealed by m(6)A-seq. Nature 2012; 485:201–206.
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; 149:1635–1646.
Dimock K, Stoltzfus CM . Sequence specificity of internal methylation in B77 avian sarcoma virus RNA subunits. Biochemistry 1977; 16:471–478.
Schibler U, Kelley DE, Perry RP . Comparison of methylated sequences in messenger RNA and heterogeneous nuclear RNA from mouse L cells. J Mol Biol 1977; 115:695–714.
Wei CM, Moss B . Nucleotide sequences at the N6-methyladenosine sites of HeLa cell messenger ribonucleic acid. Biochemistry 1977; 16:1672–1676.
Jia G, Fu Y, Zhao X, et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol 2011; 7:885–887.
Zheng G, Dahl JA, Niu Y, et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell 2013; 49:18–29.
Schwartz S, Agarwala SD, Mumbach MR, et al. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell 2013; 155:1409–1421.
Sibbritt T, Patel HR, Preiss T . Mapping and significance of the mRNA methylome. Wiley Interdiscip Rev RNA 2013; 4:397–422.
Wang X, Lu Z, Gomez A, et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 2013 Nov 27. doi:10.1038/nature12730
Bokar JA, Rath-Shambaugh ME, Ludwiczak R, Narayan P, Rottman F . Characterization and partial purification of mRNA N6-adenosine methyltransferase from HeLa cell nuclei. Internal mRNA methylation requires a multisubunit complex. J Biol Chem 1994; 269:17697–17704.
Tuck MT . Partial purification of a 6-methyladenine mRNA methyltransferase which modifies internal adenine residues. Biochem J 1992; 288:233–240.
Bokar JA, Shambaugh ME, Polayes D, Matera AG, Rottman FM . Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase. RNA 1997; 3:1233–1247.
Bujnicki JM, Feder M, Radlinska M, Blumenthal RM . Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA: m(6)A methyltransferase. J Mol Evol 2002; 55:431–444.
Hongay CF, Orr-Weaver TL . Drosophila Inducer of MEiosis 4 (IME4) is required for Notch signaling during oogenesis. Proc Natl Acad Sci USA 2011; 108:14855–14860.
Shah JC, Clancy MJ . IME4, a gene that mediates MAT and nutritional control of meiosis in Saccharomyces cerevisiae. Mol Cell Biol 1992; 12:1078–1086.
Zhong S, Li H, Bodi Z, et al. MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor. Plant Cell 2008; 20:1278–1288.
Kane SE, Beemon K . Precise localization of m6A in Rous sarcoma virus RNA reveals clustering of methylation sites: implications for RNA processing. Mol Cell Biol 1985; 5:2298–2306.
Agarwala SD, Blitzblau HG, Hochwagen A, Fink GR . RNA methylation by the MIS complex regulates a cell fate decision in yeast. PLoS Genet 2012; 8:e1002732.
Rottman FM, Bokar JA, Narayan P, Shambaugh ME, Ludwiczak R . N6-adenosine methylation in mRNA: substrate specificity and enzyme complexity. Biochimie 1994; 76:1109–1114.
Liu J, Yue Y, Han D, et al. A hMETTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol 2013 Dec 6. doi:10.1038/nchembio.1432
Little NA, Hastie, ND, Davies RC . Identification of WTAP, a novel Wilms' tumour 1-associating protein. Hum Mol Genet 2000; 9:2231–2239.
Carroll SM, Narayan P, Rottman FM . N6-methyladenosine residues in an intron-specific region of prolactin pre-mRNA. Mol Cell Biol 1990; 10:4456–4465.
Finkel D, Groner Y . Methylations of adenosine residues (m6A) in pre-mRNA are important for formation of late simian virus 40 mRNAs. Virology 1983; 131:409–425.
Shimba S, Bokar JA, Rottman F, Reddy R . Accurate and efficient N-6-adenosine methylation in spliceosomal U6 small nuclear RNA by HeLa cell extract in vitro. Nucleic Acids Res 1995; 23:2421–2426.
Stoltzfus CM, Dane RW . Accumulation of spliced avian retrovirus mRNA is inhibited in S-adenosylmethionine-depleted chicken embryo fibroblasts. J Virol 1982; 42:918–931.
Corcoran DL, Georgiev S, Mukherjee N, et al. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol 2011; 12:R79.
Mukherjee N, Corcoran DL, Nusbaum JD, et al. Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol Cell 2011; 43:327–339.
Heinz S, Benner C, Spann N, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 2010; 38:576–589.
Quinlan AR, Hall IM . BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010; 26:841–842.
Trapnell C, Pachter L, Salzberg SL . TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25:1105–1111.
Zhang Y, Liu T, Meyer CA, Eeckhoute J, et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol 2008; 9:R137
Clancy MJ, Shambaugh ME, Timpte CS, Bokar JA . Induction of sporulation in Saccharomyces cerevisiae leads to the formation of N6-methyladenosine in mRNA: a potential mechanism for the activity of the IME4 gene. Nucleic Acids Res 2002; 30:4509–4518.
Bodi Z, Button JD, Grierson D, Fray RG . Yeast targets for mRNA methylation. Nucleic Acids Res 2010; 38:5327–5335.
Vespa L, Vachon G, Berger F, Perazza D, Faure JD, Herzog M . The immunophilin-interacting protein AtFIP37 from Arabidopsis is essential for plant development and is involved in trichome endoreduplication. Plant Physiol 2004; 134:1283–1292.
McGraw S, Vigneault, C, Sirard MA . Temporal expression of factors involved in chromatin remodeling and in gene regulation during early bovine in vitro embryo development. Reproduction 2007; 133:597–608.
Ortega A, Niksic M, Bachi A, et al. Biochemical function of female-lethal (2)D/Wilms' tumor suppressor-1-associated proteins in alternative pre-mRNA splicing. J Biol Chem 2003; 278:3040–3047.
Penn JK, Graham P, Deshpande G, et al. Functioning of the Drosophila Wilms'-tumor-1-associated protein homolog, Fl(2)d, in sex-lethal-dependent alternative splicing. Genetics 2008; 178:737–748.
Maddika S, Sy SM, Chen J . Functional interaction between Chfr and Kif22 controls genomic stability. J Biol Chem 2009; 284:12998–13003.
Mayer C, Schmitz KM, Li J, Grummt I, Santoro R . Intergenic transcripts regulate the epigenetic state of rRNA genes. Mol Cell 2006; 22:351–361.
Sytnikova YA, Kubarenko AV, Schäfer A, Weber AN, Niehrs C . Gadd45a is an RNA binding protein and is localized in nuclear speckles. PLoS One 2011; 6:e14500.
Hafner M, Landthaler M, Burger L, et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010; 141:129–141.
Langmead B, Trapnell C, Pop M, Salzberg SL . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10:R25.
Mortimer SA, Trapnell C, Aviran S, Pachter L, Lucks JB . SHAPE-Seq: High-Throughput RNA Structure Analysis. Curr Protoc Chem Biol 2012; 4:275–297.
Anders S . HTSeq: analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html . 2010
Wang L, Feng Z, Wang X, Wang X, Zhang X . DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 2010; 26:136–138.
Huang da W, Sherman BT, Lempicki RA . Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009; 4:44–57.
Huang da, 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.
Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010; 28:511–515.