The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA
Open accessAbstract
The modified base 5-methylcytosine (m(5)C) is well studied in DNA, but investigations of its prevalence in cellular RNA have been largely confined to tRNA and rRNA. In animals, the two m(5)C methyltransferases NSUN2 and TRDMT1 are known to modify specific tRNAs and have roles in the control of cell growth and differentiation. To map modified cytosine sites across a human transcriptome, we coupled bisulfite conversion of cellular RNA with next-generation sequencing. We confirmed 21 of the 28 previously known m(5)C sites in human tRNAs and identified 234 novel tRNA candidate sites, mostly in anticipated structural positions. Surprisingly, we discovered 10,275 sites in mRNAs and other non-coding RNAs. We observed that distribution of modified cytosines between RNA types was not random; within mRNAs they were enriched in the untranslated regions and near Argonaute binding regions. We also identified five new sites modified by NSUN2, broadening its known substrate range to another tRNA, the RPPH1 subunit of RNase P and two mRNAs. Our data demonstrates the widespread presence of modified cytosines throughout coding and non-coding sequences in a transcriptome, suggesting a broader role of this modification in the post-transcriptional control of cellular RNA function.
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Cites
Human DNA methylomes at base resolution show widespread epigenomic differences
Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature · doi:10.1038/nature08514 · Cited by 4,673
miRBase: integrating microRNA annotation and deep-sequencing data
Kozomara, A., & Griffiths-Jones, S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1027 · Cited by 3,634
DNA methylation landscapes: Provocative insights from epigenomics
Suzuki, M. M., & Bird, A. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2341 · Cited by 3,039
Warren, L., Manos, P. D., Ahfeldt, T., Loh, Y.-H., Li, H., Lau, F., Ebina, W., Mandal, P. K., Smith, Z. D., Meissner, A., et al. (2010) · Cell Stem Cell · doi:10.1016/j.stem.2010.08.012 · Cited by 2,662
Young, J. I., Hong, E. P., Castle, J. C., Crespo-Barreto, J., Bowman, A. B., Rose, M. F., Kang, D., Richman, R., Johnson, J. M., Berget, S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507856102 · Cited by 484
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Wang, X., Zhao, B. S., Roundtree, I. A., Lu, Z., Han, D., Ma, H., Weng, X., Chen, K., Shi, H., & He, C. (2015) · Cell · doi:10.1016/j.cell.2015.05.014 · Cited by 3,483
Efficient genome editing in zebrafish using a CRISPR-Cas system
Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J.-R. J., & Joung, J. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2501 · Cited by 2,937
Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome
Linder, B., Grozhik, A. V., Olarerin-George, A. O., Meydan, C., Mason, C. E., & Jaffrey, S. R. (2015) · Nature Methods · doi:10.1038/nmeth.3453 · Cited by 1,569
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Barbieri, I., & Kouzarides, T. (2020) · Nature Reviews Cancer · doi:10.1038/s41568-020-0253-2 · Cited by 1,312
5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader
Yang, X., Yang, Y., Sun, B.-F., Chen, Y.-S., Xu, J.-W., Lai, W.-Y., Li, A., Wang, X., Bhattarai, D. P., Xiao, W., et al. (2017) · Cell Research · doi:10.1038/cr.2017.55 · Cited by 1,062
Metadata
- Authors
- Squires, J. E., Patel, H. R., Nousch, M., Sibbritt, T., Humphreys, D. T., Parker, B. J., Suter, C. M., & Preiss, T.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-02-16
- Volume
- 40
- Issue
- 11
- Pages
- 5023-5033
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2060902122
- Cited by
- 1,007
- References
- 5
- FWCI
- 13.48
- Type
- journal article
- Language
- en
- Open access
- gold
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- Squires, J. E., Patel, H. R., Nousch, M., Sibbritt, T., Humphreys, D. T., Parker, B. J., Suter, C. M., & Preiss, T. (2012). Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Research. https://doi.org/10.1093/nar/gks144
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