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International Journal of Genomics
Volume 2018, Article ID 1351964, 19 pages
https://doi.org/10.1155/2018/1351964
Research Article

Topological Characterization of Human and Mouse m5C Epitranscriptome Revealed by Bisulfite Sequencing

1Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
2Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, L7 8TX Liverpool, UK
3Greehey Children’s Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
4Department of Cellular Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
5Institute of Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
6Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
7Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA

Correspondence should be addressed to Rong Rong; nc.ude.ultjx@gnor.gnor, Yufei Huang; ude.astu@gnauhy, Manjeet K. Rao; ude.ascshtu@moar, and Jia Meng; nc.ude.ultjx@gnem.aij

Received 17 January 2018; Revised 14 April 2018; Accepted 17 April 2018; Published 13 June 2018

Academic Editor: Yujing Li

Copyright © 2018 Zhen Wei et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background. Compared with the well-studied 5-methylcytosine (m5C) in DNA, the role and topology of epitranscriptome m5C remain insufficiently characterized. Results. Through analyzing transcriptome-wide m5C distribution in human and mouse, we show that the m5C modification is significantly enriched at 5 untranslated regions (5UTRs) of mRNA in human and mouse. With a comparative analysis of the mRNA and DNA methylome, we demonstrate that, like DNA methylation, transcriptome m5C methylation exhibits a strong clustering effect. Surprisingly, an inverse correlation between mRNA and DNA m5C methylation is observed at CpG sites. Further analysis reveals that RNA m5C methylation level is positively correlated with both RNA expression and RNA half-life. We also observed that the methylation level of mitochondrial RNAs is significantly higher than RNAs transcribed from the nuclear genome. Conclusions. This study provides an in-depth topological characterization of transcriptome-wide m5C modification by associating RNA m5C methylation patterns with transcriptional expression, DNA methylations, RNA stabilities, and mitochondrial genome.