Novel RNA regulatory mechanisms revealed in the epitranscriptome

References

• Desrosiers RC, Friderici KH, Rottman FM. Characterization of Novikoff hepatoma mRNA methylation and heterogeneity in the methylated 5′ terminus. Biochemistry 1975; 14:4367 - 74; http://dx.doi.org/10.1021/bi00691a004; PMID: 169893
   PubMed Web of Science ®Google Scholar
• 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; http://dx.doi.org/10.1016/j.cell.2012.05.003; PMID: 22608085
   PubMed Web of Science ®Google Scholar
• Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S, et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 2012; 485:201 - 6; http://dx.doi.org/10.1038/nature11112; PMID: 22575960
   PubMed Web of Science ®Google Scholar
• Cantara WA, Crain PF, Rozenski J, McCloskey JA, Harris KA, Zhang X, et al. The RNA modification database, RNAMDB: 2011 update. Nucleic Acids Res 2011; 39:Database issue D195 - 201; http://dx.doi.org/10.1093/nar/gkq1028; PMID: 21071406
   PubMed Web of Science ®Google Scholar
• Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I, et al. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet 2012; 8:e1002781; http://dx.doi.org/10.1371/journal.pgen.1002781; PMID: 22737091
   PubMed Web of Science ®Google Scholar
• Carey BW, Markoulaki S, Hanna JH, Faddah DA, Buganim Y, Kim J, et al. Reprogramming factor stoichiometry influences the epigenetic state and biological properties of induced pluripotent stem cells. Cell Stem Cell 2011; 9:588 - 98; http://dx.doi.org/10.1016/j.stem.2011.11.003; PMID: 22136932
   PubMed Web of Science ®Google Scholar
• Lister R, Ecker JR. Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res 2009; 19:959 - 66; http://dx.doi.org/10.1101/gr.083451.108; PMID: 19273618
   PubMed Web of Science ®Google Scholar
• Münzel M, Globisch D, Carell T. 5-Hydroxymethylcytosine, the sixth base of the genome. Angew Chem Int Ed Engl 2011; 50:6460 - 8; http://dx.doi.org/10.1002/anie.201101547; PMID: 21688365
   PubMed Web of Science ®Google Scholar
• Dubin DT, Taylor RH. The methylation state of poly A-containing messenger RNA from cultured hamster cells. Nucleic Acids Res 1975; 2:1653 - 68; http://dx.doi.org/10.1093/nar/2.10.1653; PMID: 1187339
   PubMed Web of Science ®Google Scholar
• Perry RP, Scherrer K. The methylated constituents of globin mRNA. FEBS Lett 1975; 57:73 - 8; http://dx.doi.org/10.1016/0014-5793(75)80155-4; PMID: 1182024
   PubMed Web of Science ®Google Scholar
• Wei CM, Gershowitz A, Moss B. Methylated nucleotides block 5′ terminus of HeLa cell messenger RNA. Cell 1975; 4:379 - 86; http://dx.doi.org/10.1016/0092-8674(75)90158-0; PMID: 164293
   PubMed Web of Science ®Google Scholar
• 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 - 52; http://dx.doi.org/10.1016/0022-2836(79)90174-8; PMID: 537090
   PubMed Web of Science ®Google Scholar
• Saneyoshi M, Harada F, Nishimura S. Isolation and characterization of N6-methyladenosine from Escherichia coli valine transfer RNA. Biochim Biophys Acta 1969; 190:264 - 73; http://dx.doi.org/10.1016/0005-2787(69)90078-1; PMID: 4900574
   PubMed Web of Science ®Google Scholar
• Iwanami Y, Brown GM. Methylated bases of ribosomal ribonucleic acid from HeLa cells. Arch Biochem Biophys 1968; 126:8 - 15; http://dx.doi.org/10.1016/0003-9861(68)90553-5; PMID: 5671075
   PubMed Web of Science ®Google Scholar
• Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol 2011; 7:885 - 7; http://dx.doi.org/10.1038/nchembio.687; PMID: 22002720
   PubMed Web of Science ®Google Scholar
• Falnes PØ, Klungland A, Alseth I. Repair of methyl lesions in DNA and RNA by oxidative demethylation. Neuroscience 2007; 145:1222 - 32; http://dx.doi.org/10.1016/j.neuroscience.2006.11.018; PMID: 17175108
   PubMed Web of Science ®Google Scholar
• Gerken T, Girard CA, Tung Y-CL, Webby CJ, Saudek V, Hewitson KS, et al. The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase. Science 2007; 318:1469 - 72; http://dx.doi.org/10.1126/science.1151710; PMID: 17991826
   PubMed Web of Science ®Google Scholar
• 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 - 47; PMID: 9409616
   PubMed Web of Science ®Google Scholar
• Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang CM, Li CJ, et al. ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility. Mol Cell 2013; 49:18 - 29; PMID: 23177736
   PubMed Web of Science ®Google Scholar
• Saletore Y, Meyer K, Korlach J, Vilfan ID, Jaffrey S, Mason CE. The birth of the Epitranscriptome: deciphering the function of RNA modifications. Genome Biol 2012; 13:175; http://dx.doi.org/10.1186/gb-2012-13-10-175; PMID: 23113984
   PubMed Web of Science ®Google Scholar
• Bayley H. Individual RNA Base Recognition in Immobilized Oligonucleotides using a Protein Nanopore. Nano Lett 2012; 2013 In press
   Google Scholar
• Brown JW, Echeverria M, Qu L-H. Plant snoRNAs: functional evolution and new modes of gene expression. Trends Plant Sci 2003; 8:42 - 9; http://dx.doi.org/10.1016/S1360-1385(02)00007-9; PMID: 12523999
   PubMed Web of Science ®Google Scholar
• Zhong S, Li H, Bodi Z, Button J, Vespa L, Herzog M, 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 - 88; http://dx.doi.org/10.1105/tpc.108.058883; PMID: 18505803
   PubMed Web of Science ®Google Scholar
• Bodi Z, Zhong S, Mehra S, Song J, Graham N, Li H, et al. Adenosine Methylation in Arabidopsis mRNA is Associated with the 3′ End and Reduced Levels Cause Developmental Defects. Front Plant Sci 2012; 3:48; http://dx.doi.org/10.3389/fpls.2012.00048; PMID: 22639649
   PubMed Web of Science ®Google Scholar
• Modrek B, Lee CJ. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat Genet 2003; 34:177 - 80; http://dx.doi.org/10.1038/ng1159; PMID: 12730695
   PubMed Web of Science ®Google Scholar
• Xhemalce B, Robson SC, Kouzarides T. Human RNA methyltransferase BCDIN3D regulates microRNA processing. Cell 2012; 151:278 - 88; http://dx.doi.org/10.1016/j.cell.2012.08.041; PMID: 23063121
   PubMed Web of Science ®Google Scholar
• Véliz EA, Easterwood LM, Beal PA. Substrate analogues for an RNA-editing adenosine deaminase: mechanistic investigation and inhibitor design. J Am Chem Soc 2003; 125:10867 - 76; http://dx.doi.org/10.1021/ja029742d; PMID: 12952466
   PubMed Web of Science ®Google Scholar
• Garrett S, Rosenthal JJC. RNA editing underlies temperature adaptation in K+ channels from polar octopuses. Science 2012; 335:848 - 51; http://dx.doi.org/10.1126/science.1212795; PMID: 22223739
   PubMed Web of Science ®Google Scholar
• Yeo GSH. FTO and obesity: a problem for a billion people. J Neuroendocrinol 2012; 24:393 - 4; http://dx.doi.org/10.1111/j.1365-2826.2011.02254.x; PMID: 22248259
   PubMed Web of Science ®Google Scholar
• Frayling TM, Timpson NJ, Weedon MN, Zeggini E, Freathy RM, Lindgren CM, et al. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 2007; 316:889 - 94; http://dx.doi.org/10.1126/science.1141634; PMID: 17434869
   PubMed Web of Science ®Google Scholar
• Ho AJ, Stein JL, Hua X, Lee S, Hibar DP, Leow AD, et al, Alzheimer’s Disease Neuroimaging Initiative. A commonly carried allele of the obesity-related FTO gene is associated with reduced brain volume in the healthy elderly. Proc Natl Acad Sci USA 2010; 107:8404 - 9; http://dx.doi.org/10.1073/pnas.0910878107; PMID: 20404173
   PubMed Web of Science ®Google Scholar
• Benedict C, Jacobsson JA, Rönnemaa E, Sällman-Almén M, Brooks S, Schultes B, et al. The fat mass and obesity gene is linked to reduced verbal fluency in overweight and obese elderly men. Neurobiol Aging 2011; 32:1159 - , e1-5; http://dx.doi.org/10.1016/j.neurobiolaging.2011.02.006; PMID: 21458110
   PubMed Web of Science ®Google Scholar
• Keller L, Xu W, Wang H-X, Winblad B, Fratiglioni L, Graff C. The obesity related gene, FTO, interacts with APOE, and is associated with Alzheimer’s disease risk: a prospective cohort study. J Alzheimers Dis 2011; 23:461 - 9; PMID: 21098976
   PubMed Web of Science ®Google Scholar
• Chen B, Ye F, Yu L, Jia G, Huang X, Zhang X, et al. Development of cell-active N6-methyladenosine RNA demethylase FTO inhibitor. J Am Chem Soc 2012; 134:17963 - 71; http://dx.doi.org/10.1021/ja3064149; PMID: 23045983
   PubMed Web of Science ®Google Scholar