m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells

Bodi, 2012, Adenosine Methylation in Arabidopsis mRNA is Associated with the 3′ End and Reduced Levels Cause Developmental Defects, Front Plant Sci., 3, 48, 10.3389/fpls.2012.00048 Clancy, 2002, 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., 30, 4509, 10.1093/nar/gkf573 Dawlaty, 2011, Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development, Cell Stem Cell, 9, 166, 10.1016/j.stem.2011.07.010 Dawlaty, 2013, Combined deficiency of Tet1 and Tet2 causes epigenetic abnormalities but is compatible with postnatal development, Dev. Cell, 24, 310, 10.1016/j.devcel.2012.12.015 Dominissini, 2012, Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq, Nature, 485, 201, 10.1038/nature11112 Dunn, 2014, Defining an essential transcription factor program for naïve pluripotency, Science, 344, 1156, 10.1126/science.1248882 Fu, 2012, Nucleic acid modifications with epigenetic significance, Curr. Opin. Chem. Biol., 16, 516, 10.1016/j.cbpa.2012.10.002 Fukusumi, 2008, Wtap is required for differentiation of endoderm and mesoderm in the mouse embryo, Dev. Dyn., 237, 618, 10.1002/dvdy.21444 Fustin, 2013, RNA-methylation-dependent RNA processing controls the speed of the circadian clock, Cell, 155, 793, 10.1016/j.cell.2013.10.026 Guttman, 2011, lincRNAs act in the circuitry controlling pluripotency and differentiation, Nature, 477, 295, 10.1038/nature10398 Harcourt, 2013, Identification of a selective polymerase enables detection of N(6)-methyladenosine in RNA, J. Am. Chem. Soc., 135, 19079, 10.1021/ja4105792 Heinz, 2010, Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities, Mol. Cell, 38, 576, 10.1016/j.molcel.2010.05.004 Horiuchi, 2013, Identification of Wilms’ tumor 1-associating protein complex and its role in alternative splicing and the cell cycle, J Biol. Chem., 288, 33292, 10.1074/jbc.M113.500397 Hsu, 2013, DNA targeting specificity of RNA-guided Cas9 nucleases, Nat. Biotechnol., 31, 827, 10.1038/nbt.2647 Ingolia, 2011, Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes, Cell, 147, 789, 10.1016/j.cell.2011.10.002 Jia, 2011, N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO, Nat. Chem. Biol., 7, 885, 10.1038/nchembio.687 Kang, 2014, A novel protein, Pho92, has a conserved YTH domain and regulates phosphate metabolism by decreasing the mRNA stability of PHO4 in Saccharomyces cerevisiae, Biochem. J., 457, 391, 10.1042/BJ20130862 Lin, 2014, An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment, Mol. Cell, 53, 1005, 10.1016/j.molcel.2014.01.021 Liu, 2013, Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA, RNA, 19, 1848, 10.1261/rna.041178.113 Liu, 2014, A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation, Nat. Chem. Biol., 10, 93, 10.1038/nchembio.1432 Loewer, 2010, Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells, Nat. Genet., 42, 1113, 10.1038/ng.710 Loh, 2011, A precarious balance: pluripotency factors as lineage specifiers, Cell Stem Cell, 8, 363, 10.1016/j.stem.2011.03.013 Loos, 2014, The bigger picture of FTO-the first GWAS-identified obesity gene, Nat. Rev. Endocrinol., 10, 51, 10.1038/nrendo.2013.227 Meyer, 2014, The dynamic epitranscriptome: N6-methyladenosine and gene expression control, Nat. Rev. Mol. Cell Biol., 15, 313, 10.1038/nrm3785 Meyer, 2012, Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons, Cell, 149, 1635, 10.1016/j.cell.2012.05.003 Montserrat, 2013, Reprogramming of human fibroblasts to pluripotency with lineage specifiers, Cell Stem Cell, 13, 341, 10.1016/j.stem.2013.06.019 Neff, 2012, Global analysis reveals multiple pathways for unique regulation of mRNA decay in induced pluripotent stem cells, Genome Res., 22, 1457, 10.1101/gr.134312.111 Niu, 2013, N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function, Genomics Proteomics Bioinformatics, 11, 8, 10.1016/j.gpb.2012.12.002 Rahl, 2010, c-Myc regulates transcriptional pause release, Cell, 141, 432, 10.1016/j.cell.2010.03.030 Schnerch, 2010, Distinguishing between mouse and human pluripotent stem cell regulation: the best laid plans of mice and men, Stem Cells, 28, 419, 10.1002/stem.298 Schwartz, 2013, High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis, Cell, 155, 1409, 10.1016/j.cell.2013.10.047 Schwartz, 2014, Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5′ sites, Cell Rep., 8, 284, 10.1016/j.celrep.2014.05.048 Segal, 2003, Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data, Nat. Genet., 34, 166, 10.1038/ng1165 Sharova, 2009, Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells, DNA Res., 16, 45, 10.1093/dnares/dsn030 Shu, 2013, Induction of pluripotency in mouse somatic cells with lineage specifiers, Cell, 153, 963, 10.1016/j.cell.2013.05.001 Sibbritt, 2013, Mapping and significance of the mRNA methylome, Wiley Interdiscip. Rev. RNA, 4, 397, 10.1002/wrna.1166 Sigova, 2013, Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells, Proc. Natl. Acad. Sci. USA, 110, 2876, 10.1073/pnas.1221904110 Trapnell, 2009, TopHat: discovering splice junctions with RNA-Seq, Bioinformatics, 25, 1105, 10.1093/bioinformatics/btp120 Ulitsky, 2011, Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution, Cell, 147, 1537, 10.1016/j.cell.2011.11.055 Wang, 2014, N6-methyladenosine-dependent regulation of messenger RNA stability, Nature, 505, 117, 10.1038/nature12730 Wang, 2014, N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells, Nat. Cell Biol., 16, 191, 10.1038/ncb2902 Wong, 2008, Module map of stem cell genes guides creation of epithelial cancer stem cells, Cell Stem Cell, 2, 333, 10.1016/j.stem.2008.02.009 Young, 2011, Control of the embryonic stem cell state, Cell, 144, 940, 10.1016/j.cell.2011.01.032 Zheng, 2013, ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility, Mol. Cell, 49, 18, 10.1016/j.molcel.2012.10.015