A High-Throughput Quantitative Approach Reveals More Small RNA Modifications in Mouse Liver and Their Correlation with Diabetes

被引：52
作者：
Yan, Menghong [1 ]
Wang, Yuangao [1 ]
Hu, Yanan [1 ]
Feng, Yan [1 ]
Dai, Changgui [1 ]
Wu, Jingxia [1 ]
Wu, Dongmei [1 ]
Zhang, Fang [1 ]
Zhai, Qiwei [1 ]
机构：
[1] Chinese Acad Sci, Shanghai Inst Biol Sci, Key Lab Nutr & Metab, Inst Nutr Sci, Shanghai 200031, Peoples R China
来源：
ANALYTICAL CHEMISTRY | 2013年 / 85卷 / 24期
基金：
中国国家自然科学基金; 中国博士后科学基金;
关键词：
PIWI-INTERACTING RNAS; RIBOSOMAL-RNA; MASS-SPECTROMETRY; 5S RNA; CANCER; METHYLATION; STABILIZATION; PSEUDOURIDINE; MICRORNAS; SEQUENCE;
D O I：
10.1021/ac4036026
中图分类号：
O65 [分析化学];
学科分类号：
070302 ; 081704 ;
摘要：
Studies of RNA modification are usually focused on tRNA. However the modification of other small RNAs, including 5.8S rRNA, SS rRNA, and small RNA sized at 10-60 nt, is still largely unknown. In this study, we established an efficient method based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) to simultaneously identify and quantify more than 40 different types of nucleosides in small RNAs. With this method, we revealed 23 modified nucleosides of tRNA from mouse liver, and 6 of them were observed for the first time in eukaryotic tRNA. Moreover, 5 and 4 modified nucleosides were detected for the first time in eukaryotic 5.8S and SS rRNA, respectively, and 22 modified nucleosides were identified in the small RNAs sized at 30-60 or 10-30 nt. Interestingly, two groups of 5S rRNA peaks were observed when analyzed by HPLC, and the abundance of modified nucleosides is significantly different between the two groups of peaks. Further studies show that multiple modifications in small RNA from diabetic mouse liver are significantly increased or decreased. Taken together, our data revealed more modified nucleosides in various small RNAs and showed the correlation of small RNA modifications with diabetes. These results provide new insights to the role of modifications of small RNAs in their stability, biological functions, and correlation with diseases.
引用
收藏
页码：12173 / 12181
页数：9
相关论文
共 55 条
[1]   A conserved modified wobble nucleoside (mcm5s2U) in lysyl-tRNA is required for viability in yeast [J].
Bjork, Glenn R. ;
Huang, Bo ;
Persson, Olof P. ;
Bystrom, Anders S. .
RNA, 2007, 13 (08) :1245-1255
[2]   Parallel Isotope-Based Quantification of Modified tRNA Nucleosides [J].
Brueckl, Tobias ;
Globisch, Daniel ;
Wagner, Mirko ;
Mueller, Markus ;
Carell, Thomas .
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2009, 48 (42) :7932-7934
[3]   Discovery and characterization of Acanthamoeba castellanii mitochondrial 5S rRNA [J].
Bullerwell, CE ;
Schnare, MN ;
Gray, MW .
RNA, 2003, 9 (03) :287-292
[4]   Structural and biochemical insights into 2′-O-methylation at the 3′-terminal nucleotide of RNA by Hen1 [J].
Chan, Chio Mui ;
Zhou, Chun ;
Brunzelle, Joseph S. ;
Huang, Raven H. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (42) :17699-17704
[5]   A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress [J].
Chan, Clement T. Y. ;
Dyavaiah, Madhu ;
DeMott, Michael S. ;
Taghizadeh, Koli ;
Dedon, Peter C. ;
Begley, Thomas J. .
PLOS GENETICS, 2010, 6 (12) :1-9
[6]   Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases [J].
Chen, Xi ;
Ba, Yi ;
Ma, Lijia ;
Cai, Xing ;
Yin, Yuan ;
Wang, Kehui ;
Guo, Jigang ;
Zhang, Yujing ;
Chen, Jiangning ;
Guo, Xing ;
Li, Qibin ;
Li, Xiaoying ;
Wang, Wenjing ;
Zhang, Yan ;
Wang, Jin ;
Jiang, Xueyuan ;
Xiang, Yang ;
Xu, Chen ;
Zheng, Pingping ;
Zhang, Juanbin ;
Li, Ruiqiang ;
Zhang, Hongjie ;
Shang, Xiaobin ;
Gong, Ting ;
Ning, Guang ;
Wang, Jun ;
Zen, Ke ;
Zhang, Junfeng ;
Zhang, Chen-Yu .
CELL RESEARCH, 2008, 18 (10) :997-1006
[7]   TRANSFER-RNA IS AN ESSENTIAL COMPONENT OF THE UBIQUITIN-DEPENDENT AND ATP-DEPENDENT PROTEOLYTIC SYSTEM [J].
CIECHANOVER, A ;
WOLIN, SL ;
STEITZ, JA ;
LODISH, HF .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1985, 82 (05) :1341-1345
[8]   Chemical modification: the key to clinical application of RNA interference? [J].
Corey, David R. .
JOURNAL OF CLINICAL INVESTIGATION, 2007, 117 (12) :3615-3622
[9]   PREPARATION AND ENZYMATIC-HYDROLYSIS OF DNA AND RNA FOR MASS-SPECTROMETRY [J].
CRAIN, PF .
METHODS IN ENZYMOLOGY, 1990, 193 :782-790
[10]   Study of the mass spectrometric fragmentation of pseudouridine:: comparison of fragmentation data obtained by matrix-assisted laser desorption/ionisation post-source decay, electrospray ion trap multistage mass spectrometry, and by a method utilising electrospray quadrupole time-of-flight tandem mass spectrometry and in-source fragmentation [J].
Dudley, E ;
Tuytten, R ;
Bond, A ;
Lemière, F ;
Brenton, AG ;
Esmans, EL ;
Newton, RP .
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 2005, 19 (21) :3075-3085
123456