Acetylation of Cytidine in mRNA Promotes Translation Efficiency

Agris, 2007, tRNA’s wobble decoding of the genome: 40 years of modification, J. Mol. Biol., 366, 1, 10.1016/j.jmb.2006.11.046 Anders, 2015, HTSeq--a Python framework to work with high-throughput sequencing data, Bioinformatics, 31, 166, 10.1093/bioinformatics/btu638 Bailey, 1994, Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28 Basanta-Sanchez, 2016, Attomole quantification and global profile of RNA modifications: Epitranscriptome of human neural stem cells, Nucleic Acids Res., 44, e26, 10.1093/nar/gkv971 Boccaletto, 2018, MODOMICS: A database of RNA modification pathways. 2017 update, Nucleic Acids Res., 46, D303, 10.1093/nar/gkx1030 Castello, 2012, Insights into RNA biology from an atlas of mammalian mRNA-binding proteins, Cell, 149, 1393, 10.1016/j.cell.2012.04.031 Chimnaronk, 2009, RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon, EMBO J., 28, 1362, 10.1038/emboj.2009.69 Delatte, 2016, RNA biochemistry. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine, Science, 351, 282, 10.1126/science.aac5253 Dong, 2016, tRNA modification profiles of the fast-proliferating cancer cells, Biochem. Biophys. Res. Commun., 476, 340, 10.1016/j.bbrc.2016.05.124 Hanson, 2018, Codon optimality, bias and usage in translation and mRNA decay, Nat. Rev. Mol. Cell Biol., 19, 20, 10.1038/nrm.2017.91 Hauenschild, 2015, The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent, Nucleic Acids Res., 43, 9950 Ingolia, 2010, Genome-wide translational profiling by ribosome footprinting, Methods Enzymol., 470, 119, 10.1016/S0076-6879(10)70006-9 Ito, 2014, Human NAT10 is an ATP-dependent RNA acetyltransferase responsible for N4-acetylcytidine formation in 18 S ribosomal RNA (rRNA), J. Biol. Chem., 289, 35724, 10.1074/jbc.C114.602698 Khatter, 2015, Structure of the human 80S ribosome, Nature, 520, 640, 10.1038/nature14427 Kim, 2015, HISAT: A fast spliced aligner with low memory requirements, Nat. Methods, 12, 357, 10.1038/nmeth.3317 Kumbhar, 2013, Conformational preferences of modified nucleoside N(4)-acetylcytidine, ac4C occur at “wobble” 34th position in the anticodon loop of tRNA, Cell Biochem. Biophys., 66, 797, 10.1007/s12013-013-9525-8 Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 Larrieu, 2014, Chemical inhibition of NAT10 corrects defects of laminopathic cells, Science, 344, 527, 10.1126/science.1252651 Liu, 2016, NAT10 regulates p53 activation through acetylating p53 at K120 and ubiquitinating Mdm2, EMBO Rep., 17, 349, 10.15252/embr.201540505 Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, 10.1186/s13059-014-0550-8 Lv, 2003, Molecular cloning of a novel human gene encoding histone acetyltransferase-like protein involved in transcriptional activation of hTERT, Biochem. Biophys. Res. Commun., 311, 506, 10.1016/j.bbrc.2003.09.235 Parthasarathy, 1978, Conformation of N4-acetylcytidine, a modified nucleoside of tRNA, and stereochemistry of codon-anticodon interaction, Biochem. Biophys. Res. Commun., 83, 657, 10.1016/0006-291X(78)91040-9 Quinlan, 2014, BEDTools: The Swiss-Army tool for genome feature analysis, Curr. Protoc. Bioinformatics, 47, 1, 10.1002/0471250953.bi1112s47 Ramírez, 2014, deepTools: A flexible platform for exploring deep-sequencing data, Nucleic Acids Res., 42, W187, 10.1093/nar/gku365 Ran, 2013, Genome engineering using the CRISPR-Cas9 system, Nat. Protoc., 8, 2281, 10.1038/nprot.2013.143 Roundtree, 2017, Dynamic RNA modifications in gene expression regulation, Cell, 169, 1187, 10.1016/j.cell.2017.05.045 Sharma, 2015, Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1, Nucleic Acids Res., 43, 2242, 10.1093/nar/gkv075 Shen, 2009, NAT10, a nucleolar protein, localizes to the midbody and regulates cytokinesis and acetylation of microtubules, Exp. Cell Res., 315, 1653, 10.1016/j.yexcr.2009.03.007 Shen, 2014, rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data, Proc. Natl. Acad. Sci. USA, 111, E5593, 10.1073/pnas.1419161111 Sinclair, 2017, Profiling cytidine acetylation with specific affinity and reactivity, ACS Chem. Biol., 12, 2922, 10.1021/acschembio.7b00734 Squires, 2012, Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA, Nucleic Acids Res., 40, 5023, 10.1093/nar/gks144 Stern, 1978, The role of the minor base N4-acetylcytidine in the function of the Escherichia coli noninitiator methionine transfer RNA, J. Biol. Chem., 253, 6132, 10.1016/S0021-9258(17)34590-8 Sturgill, 2013, Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki), BMC Bioinformatics, 14, 320, 10.1186/1471-2105-14-320 Tafforeau, 2013, The complexity of human ribosome biogenesis revealed by systematic nucleolar screening of Pre-rRNA processing factors, Mol. Cell, 51, 539, 10.1016/j.molcel.2013.08.011 Tani, 2012, Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals, Genome Res., 22, 947, 10.1101/gr.130559.111 Taniguchi, 2018, Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis, Nat. Chem. Biol., 14, 1010, 10.1038/s41589-018-0119-z Taoka, 2018, Landscape of the complete RNA chemical modifications in the human 80S ribosome, Nucleic Acids Res., 46, 9289, 10.1093/nar/gky811 Trapnell, 2009, TopHat: Discovering splice junctions with RNA-Seq, Bioinformatics, 25, 1105, 10.1093/bioinformatics/btp120 Yang, 2017, 5-methylcytosine promotes mRNA export - NSUN2 as the methyltransferase and ALYREF as an m5C reader, Cell Res., 27, 606, 10.1038/cr.2017.55 Zhang, 2008, Model-based analysis of ChIP-Seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137