TY - JOUR
T1 - Topological characterization of human and mouse M5C epitranscriptome revealed by bisulfite sequencing
AU - Wei, Zhen
AU - Panneerdoss, Subbarayalu
AU - Timilsina, Santosh
AU - Zhu, Jingting
AU - Mohammad, Tabrez A.
AU - Lu, Zhi Liang
AU - De Magalhães, João Pedro
AU - Chen, Yidong
AU - Rong, Rong
AU - Huang, Yufei
AU - Rao, Manjeet K.
AU - Meng, Jia
N1 - Funding Information:
This work was supported by the National Natural Science Foundation of China (61401370 and 31671373 to Jia Meng, 81373469 to Zhi-Liang Lu), the Jiangsu Natural Science Foundation (BK20140403 to Jia Meng), the Jiangsu University Natural Science Program (16KJB180027 to Jia Meng), the US National Institutes of Health (R01GM113245 to Yufei Huang), the IIMS Translational Technology Resource (TTR) Award to Manjeet K. Rao and Yidong Chen, and NCI Cancer Center Shared Resources NCI P30CA54174 to Yidong Chen. Part of the BS-Seq experiment was performed by the Genome Sequencing Facility of the Greehey Children’s Cancer Research Institute, UTHSCSA. The authors thank the computational support from the UTSA Computational Systems Biology Core, funded by the National Institute on Minority Health and Health Disparities (G12MD007591) from the National Institutes of Health.
Publisher Copyright:
Copyright © 2018 Zhen Wei et al.
PY - 2018
Y1 - 2018
N2 - 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 (5′UTRs) 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.
AB - 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 (5′UTRs) 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.
UR - http://www.scopus.com/inward/record.url?scp=85050022403&partnerID=8YFLogxK
U2 - 10.1155/2018/1351964
DO - 10.1155/2018/1351964
M3 - Article
AN - SCOPUS:85050022403
SN - 2314-436X
VL - 2018
JO - International Journal of Genomics
JF - International Journal of Genomics
M1 - 1351964
ER -