Genome-Wide Maps of m6A circRNAs Identify Widespread and Cell-Type-Specific Methylation Patterns that Are Distinct from mRNAs

Capel, 1993, Circular transcripts of the testis-determining gene Sry in adult mouse testis, Cell, 73, 1019, 10.1016/0092-8674(93)90279-Y

Caudron-Herger, 2016, Regulation of nucleolus assembly by non-coding RNA polymerase II transcripts, Nucleus, 7, 308, 10.1080/19491034.2016.1190890

Chen, 1995, Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs, Science, 268, 415, 10.1126/science.7536344

Chen, 2015, High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing, Angew. Chem. Int. Ed. Engl., 54, 1587, 10.1002/anie.201410647

Dominissini, 2012, Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq, Nature, 485, 201, 10.1038/nature11112

Du, 2016, Foxo3 circular RNA retards cell cycle progression via forming ternary complexes with p21 and CDK2, Nucleic Acids Res., 44, 2846, 10.1093/nar/gkw027

Gilbert, 2016, Messenger RNA modifications: Form, distribution, and function, Science, 352, 1408, 10.1126/science.aad8711

Hansen, 2013, Natural RNA circles function as efficient microRNA sponges, Nature, 495, 384, 10.1038/nature11993

Hansen, 2016, Comparison of circular RNA prediction tools, Nucleic Acids Res., 44, e58, 10.1093/nar/gkv1458

Holley, 1965, Structure of a Ribonucleic Acid, Science, 147, 1462, 10.1126/science.147.3664.1462

Jia, 2013, Reversible RNA adenosine methylation in biological regulation, Trends Genet., 29, 108, 10.1016/j.tig.2012.11.003

Ke, 2015, A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation, Genes Dev., 29, 2037, 10.1101/gad.269415.115

Ke, 2017, m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover, Genes Dev., 31, 990, 10.1101/gad.301036.117

Kelley, 2014, Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions, Genome Biol., 15, 537, 10.1186/s13059-014-0537-5

Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923

Lasda, 2016, Circular RNAs Co-Precipitate with Extracellular Vesicles: A Possible Mechanism for circRNA Clearance, PLoS ONE, 11, e0148407, 10.1371/journal.pone.0148407

Legnini, 2017, Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis, Mol. Cell, 66, 22, 10.1016/j.molcel.2017.02.017

Liang, 2014, Short intronic repeat sequences facilitate circular RNA production, Genes Dev., 28, 2233, 10.1101/gad.251926.114

Lin, 2015, Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins, Mol. Cell, 60, 208, 10.1016/j.molcel.2015.08.018

Linder, 2015, Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome, Nat. Methods, 12, 767, 10.1038/nmeth.3453

Liu, 2014, A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation, Nat. Chem. Biol., 10, 93, 10.1038/nchembio.1432

Liu, 2015, N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions, Nature, 518, 560, 10.1038/nature14234

Marzahn, 2016, Higher-order oligomerization promotes localization of SPOP to liquid nuclear speckles, EMBO J., 35, 1254, 10.15252/embj.201593169

Memczak, 2013, Circular RNAs are a large class of animal RNAs with regulatory potency, Nature, 495, 333, 10.1038/nature11928

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

Mishima, 2015, Immuno-northern blotting: Detection of RNA modifications by using antibodies against modified nucleosides, PLoS ONE, 10, e0143756, 10.1371/journal.pone.0143756

Molinie, 2016, m(6)A-LAIC-seq reveals the census and complexity of the m(6)A epitranscriptome, Nat. Methods, 13, 692, 10.1038/nmeth.3898

Nigro, 1991, Scrambled exons, Cell, 64, 607, 10.1016/0092-8674(91)90244-S

Ozanick, 2005, The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans, RNA, 11, 1281, 10.1261/rna.5040605

Pamudurti, 2017, Translation of CircRNAs, Mol. Cell, 66, 9, 10.1016/j.molcel.2017.02.021

Ping, 2014, Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase, Cell Res., 24, 177, 10.1038/cr.2014.3

Salzman, 2012, Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types, PLoS ONE, 7, e30733, 10.1371/journal.pone.0030733

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

Shang, 2016, Comprehensive Circular RNA Profiling Reveals That hsa_circ_0005075, a New Circular RNA Biomarker, Is Involved in Hepatocellular Carcinoma Development, Medicine (Baltimore), 95, e3811, 10.1097/MD.0000000000003811

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

Spitale, 2015, Structural imprints in vivo decode RNA regulatory mechanisms, Nature, 519, 486, 10.1038/nature14263

Squires, 2012, Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA, Nucleic Acids Res., 40, 5023, 10.1093/nar/gks144

Staehelin, 1971, The primary structure of transfer ribonucleic acid, Experientia, 27, 1, 10.1007/BF02137708

Suzuki, 2006, Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing, Nucleic Acids Res., 34, e63, 10.1093/nar/gkl151

Wang, 2015, Efficient backsplicing produces translatable circular mRNAs, RNA, 21, 172, 10.1261/rna.048272.114

Wang, 2014, N6-methyladenosine-dependent regulation of messenger RNA stability, Nature, 505, 117, 10.1038/nature12730

Wang, 2015, N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency, Cell, 161, 1388, 10.1016/j.cell.2015.05.014

Wang, 2017, Structural basis of N6-adenosine methylation by the METTL3–METTL14 complex, Nature, 542, 260, 10.1038/nature21073

Yang, 2017, Extensive translation of circular RNAs driven by N(6)-methyladenosine, Cell Res., 27, 626, 10.1038/cr.2017.31

Zhang, 2014, Complementary sequence-mediated exon circularization, Cell, 159, 134, 10.1016/j.cell.2014.09.001

Zhang, 2015, RNA Controls PolyQ Protein Phase Transitions, Mol. Cell, 60, 220, 10.1016/j.molcel.2015.09.017