N6 -methyladenosine modification destabilizes developmental regulators in embryonic stem cells

Nature Cell Biology

Volumn 16, Issue 2, 2014, Pages 191-198

  Wang, Yang ^a   Li, Yue ^b   Toth, Julia I ^a   Petroski, Matthew D ^a   Zhang, Zhaolei ^b   Zhao, Jing Crystal ^a  

^a BURNHAM INSTITUTE   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE; DRUG DERIVATIVE; MESSENGER RNA; METHYLTRANSFERASE; METTL14 PROTEIN, HUMAN; METTL3 PROTEIN, HUMAN; N(6) METHYLADENOSINE; N(6)-METHYLADENOSINE;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CELL LINE; CHEMISTRY; CYTOLOGY; EMBRYONIC STEM CELL; GENE EXPRESSION REGULATION; GENE SILENCING; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; MOUSE; SEQUENCE HOMOLOGY;

ADENOSINE; AMINO ACID SEQUENCE; ANIMALS; CELL LINE; EMBRYONIC STEM CELLS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE KNOCKDOWN TECHNIQUES; HUMANS; METHYLTRANSFERASES; MICE; MOLECULAR SEQUENCE DATA; RNA, MESSENGER; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84893310526     PISSN: 14657392     EISSN: 14764679     Source Type: Journal    
DOI: 10.1038/ncb2902     Document Type: Article

References (37)

1. Jia, G., Fu, Y. & He, C. Reversible RNA adenosine methylation in biological regulation. Trends Genet. 29, 108-115 (2013).
2. Clancy, M. J., Shambaugh, M. E., Timpte, C. S. & Bokar, J. A. 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, 4509-4518 (2002).
3. Agarwala, S. D., Blitzblau, H. G., Hochwagen, A. & Fink, G. R. RNA methylation by the MIS complex regulates a cell fate decision in yeast. PLoS Genet. 8, e1002732 (2012).
4. Zhong, S. et al. MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor. Plant Cell 20, 1278-1288 (2008).
5. Bodi, Z. et al. Adenosine methylation in Arabidopsis mRNA is associated with the 3' end and reduced levels cause developmental defects. Front. Plant Sci. 3, 1-10 (2012).
6. Meyer, K. D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell 149, 1635-1646 (2012).
7. Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201-206 (2012).
8. Zheng, G. et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49, 18-29 (2013).
9. Jia, G. et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7, 885-887 (2011).
10. Bokar, J. A., Shambaugh, M. E., Polayes, D., Matera, A. G. & Rottman, F. M. Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase. RNA 3, 1233-1247 (1997).
11. Bujnicki, J. M., Feder, M., Radlinska, M. & Blumenthal, R. M. 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. 55, 431-444 (2002).
12. Petrossian, T. C. & Clarke, S. G. Uncovering the human methyltransferasome. Mol. Cell. Proteom. 10, M110.000976-1-12 (2011).
13. Ku, M. et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 4, e1000242 (2008).
14. van den Berg, D. L. et al. An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell 6, 369-381 (2010).
15. Srikantan, S., Tominaga, K. & Gorospe, M. Functional interplay between RNA-binding protein HuR and microRNAs. Curr. Protein Peptide Sci. 13, 372-379 (2012).
16. Kundu, P., Fabian, M. R., Sonenberg, N., Bhattacharyya, S. N. & Filipowicz, W. HuR protein attenuates miRNA-mediated repression by promoting miRISC dissociation from the target RNA. Nucleic Acids Res. 40, 5088-5100 (2012).
17. Kishore, S. et al. A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nat. Methods 8, 559-564 (2011).
18. Lebedeva, S. et al. Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR. Mol. Cell 43, 340-352 (2011).
19. Le, M. T. et al. Conserved regulation of p53 network dosage by microRNA- 125b occurs through evolving miRNA-target gene pairs. PLoS Genet. 7, e1002242 (2011).
20. Lu, L., Katsaros, D., de la Longrais, I. A., Sochirca, O. & Yu, H. Hypermethylation of let-7a-3 in epithelial ovarian cancer is associated with low insulin-like growth factor- II expression and favorable prognosis. Cancer Res. 67, 10117-10122 (2007).
21. Leung, A. K. et al. Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. Nat. Struct. Mol. Biol. 18, 237-244 (2011).
22. Zhao, J., Sun, B. K., Erwin, J. A., Song, J. J. & Lee, J. T. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322, 750-756 (2008).
23. Harper, J. E., Miceli, S. M., Roberts, R. J. & Manley, J. L. Sequence specificity of the human mRNA N6-adenosine methylase in vitro. Nucleic Acids Res. 18, 5735-5741 (1990).
24. Zhao, J. et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 40, 939-953 (2010).
25. Wang, Y. et al. Reprogramming of mouse and human somatic cells by high- performance engineered factors. EMBO Rep. 12, 373-378 (2011).
26. Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545-15550 (2005).
27. Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10-12 (2011).
28. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
29. Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
30. Li, H. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
31. Quinlan, A. R. & Hall, I. M. BEDTools: a fiexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
32. Robinson, J. T. et al. Integrative genomics viewer. Nature Publishing Group 29, 24-26 (2011).
33. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Gen. Biol. 9, R137 (2008).
34. Durinck, S., Spellman, P. & Birney, E. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat. Protocol. 4, 1184-1191 (2009).
35. Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protocol. 4, 44-57 (2009).
36. Smyth, G. in Bioinformatics and Computational Biology Solutions Using R and Bioconductor (eds Gentle- man, R., Carey, V., Dudoit, S., Irizarry, R. & Huber, W.) 397-420 (Springer, 2005).
37. Mukherjee, N. et al. Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol. Cell 43, 327-339 (2011).