Chemical tagging for sensitive determination of uridine modifications in RNA
The discovery of dynamic and reversible modifications in messenger RNA (mRNA) is opening new directions in RNA modification-mediated regulation of biological processes. Methylation is the most prevalent modification occurring in mRNA and the methyl group is mainly decorated in the adenine, cytosine,...
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| Veröffentlicht in: | Chemical science (Cambridge) 2020-02, Vol.11 (7), p.1878-1891 |
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| creator | Cheng, Qing-Yun Xiong, Jun Ma, Cheng-Jie Dai, Yi Ding, Jiang-Hui Liu, Fei-Long Yuan, Bi-Feng Feng, Yu-Qi |
| description | The discovery of dynamic and reversible modifications in messenger RNA (mRNA) is opening new directions in RNA modification-mediated regulation of biological processes. Methylation is the most prevalent modification occurring in mRNA and the methyl group is mainly decorated in the adenine, cytosine, and guanine base or in the 2′-hydroxyl group of ribose. However, methylation of the uracil base (5-methyluridine, m
5
U) has not been discovered in mRNA of eukaryotes. In the current study, we established a method of
N
-cyclohexyl-
N
′-
β
-(4-methylmorpholinium) ethylcarbodiimide
p
-toluenesulfonate (CMCT) labelling coupled with liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) analysis for the sensitive determination of uridine modifications in RNA. Our results demonstrated that the detection sensitivities of uridine modifications in RNA increased up to 1408 fold upon CMCT labelling. Using the developed method, we identified the distinct existence of m
5
U in mRNA of various mammalian cells and tissues. In addition, the stable isotope tracing monitored by mass spectrometry revealed that the methyl group of m
5
U originated from
S
-adenosyl-
l
-methionine (SAM). Our study expanded the list of modifications occurring in mRNA of mammals. Future work on transcriptome-wide mapping of m
5
U will further uncover the functional roles of m
5
U in mRNA of mammals.
The discovery of dynamic and reversible modifications in messenger RNA is opening new directions in RNA modification-mediated regulation of biological processes. |
| doi_str_mv | 10.1039/c9sc05094a |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_proquest_miscellaneous_2540722993</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2540722993</sourcerecordid><originalsourceid>FETCH-LOGICAL-c405t-aec91d3eade5856b4a8ca8440ef8708331c995d3ec2a13bd7fb94ebbc362b8f63</originalsourceid><addsrcrecordid>eNpdkc1r3DAQxUVp6IYkl94DglxKYBN92tKlsJh8wZJA2p6FLI93tdjSVrID-e_jzYYtjS4jZn7zeMND6DslV5Rwfe10dkQSLewXdMyIoPNCcv318Gdkhs5y3pDpcU4lK7-hGReUcaboMVpWa-i9sx0e7Grlwwq3MeEMIfvBvwBuYIDU-2AHHwOOLR6Tb3wA3MfGt9Pirp-xD_j5cXGKjlrbZTj7qCfoz-3N7-p-vny6e6gWy7kTRA5zC07ThoNtQCpZ1MIqZ5UQBFpVEjW5dFrLCXDMUl43ZVtrAXXteMFq1Rb8BP3c627HuofGQRiS7cw2-d6mVxOtN_9Pgl-bVXwxigrFNZkEfnwIpPh3hDyY3mcHXWcDxDEbJgUpGdOaT-jFJ3QTxxSm8wzjshSFVHrn6HJPuRRzTtAezFBidjmZSv-q3nNaTPD5Hk7ZHbh_OfI3Yv2OqQ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2357465896</pqid></control><display><type>article</type><title>Chemical tagging for sensitive determination of uridine modifications in RNA</title><source>DOAJ Directory of Open Access Journals</source><source>PubMed Central Open Access</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><creator>Cheng, Qing-Yun ; Xiong, Jun ; Ma, Cheng-Jie ; Dai, Yi ; Ding, Jiang-Hui ; Liu, Fei-Long ; Yuan, Bi-Feng ; Feng, Yu-Qi</creator><creatorcontrib>Cheng, Qing-Yun ; Xiong, Jun ; Ma, Cheng-Jie ; Dai, Yi ; Ding, Jiang-Hui ; Liu, Fei-Long ; Yuan, Bi-Feng ; Feng, Yu-Qi</creatorcontrib><description>The discovery of dynamic and reversible modifications in messenger RNA (mRNA) is opening new directions in RNA modification-mediated regulation of biological processes. Methylation is the most prevalent modification occurring in mRNA and the methyl group is mainly decorated in the adenine, cytosine, and guanine base or in the 2′-hydroxyl group of ribose. However, methylation of the uracil base (5-methyluridine, m
5
U) has not been discovered in mRNA of eukaryotes. In the current study, we established a method of
N
-cyclohexyl-
N
′-
β
-(4-methylmorpholinium) ethylcarbodiimide
p
-toluenesulfonate (CMCT) labelling coupled with liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) analysis for the sensitive determination of uridine modifications in RNA. Our results demonstrated that the detection sensitivities of uridine modifications in RNA increased up to 1408 fold upon CMCT labelling. Using the developed method, we identified the distinct existence of m
5
U in mRNA of various mammalian cells and tissues. In addition, the stable isotope tracing monitored by mass spectrometry revealed that the methyl group of m
5
U originated from
S
-adenosyl-
l
-methionine (SAM). Our study expanded the list of modifications occurring in mRNA of mammals. Future work on transcriptome-wide mapping of m
5
U will further uncover the functional roles of m
5
U in mRNA of mammals.
The discovery of dynamic and reversible modifications in messenger RNA is opening new directions in RNA modification-mediated regulation of biological processes.</description><identifier>ISSN: 2041-6520</identifier><identifier>EISSN: 2041-6539</identifier><identifier>DOI: 10.1039/c9sc05094a</identifier><identifier>PMID: 34123281</identifier><language>eng</language><publisher>Cambridge: Royal Society of Chemistry</publisher><subject>Adenine ; Biological activity ; Cerium oxides ; Chemistry ; Eukaryotes ; Gene sequencing ; Hydroxyl groups ; Labelling ; Liquid chromatography ; Mammals ; Mapping ; Mass spectrometry ; Methionine ; Methylation ; Organic chemistry ; Ribose ; Scientific imaging ; Spectroscopy ; Uracil</subject><ispartof>Chemical science (Cambridge), 2020-02, Vol.11 (7), p.1878-1891</ispartof><rights>Copyright Royal Society of Chemistry 2020</rights><rights>This journal is © The Royal Society of Chemistry 2020 The Royal Society of Chemistry</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c405t-aec91d3eade5856b4a8ca8440ef8708331c995d3ec2a13bd7fb94ebbc362b8f63</citedby><cites>FETCH-LOGICAL-c405t-aec91d3eade5856b4a8ca8440ef8708331c995d3ec2a13bd7fb94ebbc362b8f63</cites><orcidid>0000-0001-5223-4659 ; 0000-0003-1107-5385</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8148390/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8148390/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27915,27916,53782,53784</link.rule.ids></links><search><creatorcontrib>Cheng, Qing-Yun</creatorcontrib><creatorcontrib>Xiong, Jun</creatorcontrib><creatorcontrib>Ma, Cheng-Jie</creatorcontrib><creatorcontrib>Dai, Yi</creatorcontrib><creatorcontrib>Ding, Jiang-Hui</creatorcontrib><creatorcontrib>Liu, Fei-Long</creatorcontrib><creatorcontrib>Yuan, Bi-Feng</creatorcontrib><creatorcontrib>Feng, Yu-Qi</creatorcontrib><title>Chemical tagging for sensitive determination of uridine modifications in RNA</title><title>Chemical science (Cambridge)</title><description>The discovery of dynamic and reversible modifications in messenger RNA (mRNA) is opening new directions in RNA modification-mediated regulation of biological processes. Methylation is the most prevalent modification occurring in mRNA and the methyl group is mainly decorated in the adenine, cytosine, and guanine base or in the 2′-hydroxyl group of ribose. However, methylation of the uracil base (5-methyluridine, m
5
U) has not been discovered in mRNA of eukaryotes. In the current study, we established a method of
N
-cyclohexyl-
N
′-
β
-(4-methylmorpholinium) ethylcarbodiimide
p
-toluenesulfonate (CMCT) labelling coupled with liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) analysis for the sensitive determination of uridine modifications in RNA. Our results demonstrated that the detection sensitivities of uridine modifications in RNA increased up to 1408 fold upon CMCT labelling. Using the developed method, we identified the distinct existence of m
5
U in mRNA of various mammalian cells and tissues. In addition, the stable isotope tracing monitored by mass spectrometry revealed that the methyl group of m
5
U originated from
S
-adenosyl-
l
-methionine (SAM). Our study expanded the list of modifications occurring in mRNA of mammals. Future work on transcriptome-wide mapping of m
5
U will further uncover the functional roles of m
5
U in mRNA of mammals.
The discovery of dynamic and reversible modifications in messenger RNA is opening new directions in RNA modification-mediated regulation of biological processes.</description><subject>Adenine</subject><subject>Biological activity</subject><subject>Cerium oxides</subject><subject>Chemistry</subject><subject>Eukaryotes</subject><subject>Gene sequencing</subject><subject>Hydroxyl groups</subject><subject>Labelling</subject><subject>Liquid chromatography</subject><subject>Mammals</subject><subject>Mapping</subject><subject>Mass spectrometry</subject><subject>Methionine</subject><subject>Methylation</subject><subject>Organic chemistry</subject><subject>Ribose</subject><subject>Scientific imaging</subject><subject>Spectroscopy</subject><subject>Uracil</subject><issn>2041-6520</issn><issn>2041-6539</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><recordid>eNpdkc1r3DAQxUVp6IYkl94DglxKYBN92tKlsJh8wZJA2p6FLI93tdjSVrID-e_jzYYtjS4jZn7zeMND6DslV5Rwfe10dkQSLewXdMyIoPNCcv318Gdkhs5y3pDpcU4lK7-hGReUcaboMVpWa-i9sx0e7Grlwwq3MeEMIfvBvwBuYIDU-2AHHwOOLR6Tb3wA3MfGt9Pirp-xD_j5cXGKjlrbZTj7qCfoz-3N7-p-vny6e6gWy7kTRA5zC07ThoNtQCpZ1MIqZ5UQBFpVEjW5dFrLCXDMUl43ZVtrAXXteMFq1Rb8BP3c627HuofGQRiS7cw2-d6mVxOtN_9Pgl-bVXwxigrFNZkEfnwIpPh3hDyY3mcHXWcDxDEbJgUpGdOaT-jFJ3QTxxSm8wzjshSFVHrn6HJPuRRzTtAezFBidjmZSv-q3nNaTPD5Hk7ZHbh_OfI3Yv2OqQ</recordid><startdate>20200221</startdate><enddate>20200221</enddate><creator>Cheng, Qing-Yun</creator><creator>Xiong, Jun</creator><creator>Ma, Cheng-Jie</creator><creator>Dai, Yi</creator><creator>Ding, Jiang-Hui</creator><creator>Liu, Fei-Long</creator><creator>Yuan, Bi-Feng</creator><creator>Feng, Yu-Qi</creator><general>Royal Society of Chemistry</general><general>The Royal Society of Chemistry</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7SR</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-5223-4659</orcidid><orcidid>https://orcid.org/0000-0003-1107-5385</orcidid></search><sort><creationdate>20200221</creationdate><title>Chemical tagging for sensitive determination of uridine modifications in RNA</title><author>Cheng, Qing-Yun ; Xiong, Jun ; Ma, Cheng-Jie ; Dai, Yi ; Ding, Jiang-Hui ; Liu, Fei-Long ; Yuan, Bi-Feng ; Feng, Yu-Qi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c405t-aec91d3eade5856b4a8ca8440ef8708331c995d3ec2a13bd7fb94ebbc362b8f63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Adenine</topic><topic>Biological activity</topic><topic>Cerium oxides</topic><topic>Chemistry</topic><topic>Eukaryotes</topic><topic>Gene sequencing</topic><topic>Hydroxyl groups</topic><topic>Labelling</topic><topic>Liquid chromatography</topic><topic>Mammals</topic><topic>Mapping</topic><topic>Mass spectrometry</topic><topic>Methionine</topic><topic>Methylation</topic><topic>Organic chemistry</topic><topic>Ribose</topic><topic>Scientific imaging</topic><topic>Spectroscopy</topic><topic>Uracil</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Cheng, Qing-Yun</creatorcontrib><creatorcontrib>Xiong, Jun</creatorcontrib><creatorcontrib>Ma, Cheng-Jie</creatorcontrib><creatorcontrib>Dai, Yi</creatorcontrib><creatorcontrib>Ding, Jiang-Hui</creatorcontrib><creatorcontrib>Liu, Fei-Long</creatorcontrib><creatorcontrib>Yuan, Bi-Feng</creatorcontrib><creatorcontrib>Feng, Yu-Qi</creatorcontrib><collection>CrossRef</collection><collection>Engineered Materials Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Materials Research Database</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Chemical science (Cambridge)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Cheng, Qing-Yun</au><au>Xiong, Jun</au><au>Ma, Cheng-Jie</au><au>Dai, Yi</au><au>Ding, Jiang-Hui</au><au>Liu, Fei-Long</au><au>Yuan, Bi-Feng</au><au>Feng, Yu-Qi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Chemical tagging for sensitive determination of uridine modifications in RNA</atitle><jtitle>Chemical science (Cambridge)</jtitle><date>2020-02-21</date><risdate>2020</risdate><volume>11</volume><issue>7</issue><spage>1878</spage><epage>1891</epage><pages>1878-1891</pages><issn>2041-6520</issn><eissn>2041-6539</eissn><abstract>The discovery of dynamic and reversible modifications in messenger RNA (mRNA) is opening new directions in RNA modification-mediated regulation of biological processes. Methylation is the most prevalent modification occurring in mRNA and the methyl group is mainly decorated in the adenine, cytosine, and guanine base or in the 2′-hydroxyl group of ribose. However, methylation of the uracil base (5-methyluridine, m
5
U) has not been discovered in mRNA of eukaryotes. In the current study, we established a method of
N
-cyclohexyl-
N
′-
β
-(4-methylmorpholinium) ethylcarbodiimide
p
-toluenesulfonate (CMCT) labelling coupled with liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) analysis for the sensitive determination of uridine modifications in RNA. Our results demonstrated that the detection sensitivities of uridine modifications in RNA increased up to 1408 fold upon CMCT labelling. Using the developed method, we identified the distinct existence of m
5
U in mRNA of various mammalian cells and tissues. In addition, the stable isotope tracing monitored by mass spectrometry revealed that the methyl group of m
5
U originated from
S
-adenosyl-
l
-methionine (SAM). Our study expanded the list of modifications occurring in mRNA of mammals. Future work on transcriptome-wide mapping of m
5
U will further uncover the functional roles of m
5
U in mRNA of mammals.
The discovery of dynamic and reversible modifications in messenger RNA is opening new directions in RNA modification-mediated regulation of biological processes.</abstract><cop>Cambridge</cop><pub>Royal Society of Chemistry</pub><pmid>34123281</pmid><doi>10.1039/c9sc05094a</doi><tpages>14</tpages><orcidid>https://orcid.org/0000-0001-5223-4659</orcidid><orcidid>https://orcid.org/0000-0003-1107-5385</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
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| language | eng |
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| source | DOAJ Directory of Open Access Journals; PubMed Central Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central |
| subjects | Adenine Biological activity Cerium oxides Chemistry Eukaryotes Gene sequencing Hydroxyl groups Labelling Liquid chromatography Mammals Mapping Mass spectrometry Methionine Methylation Organic chemistry Ribose Scientific imaging Spectroscopy Uracil |
| title | Chemical tagging for sensitive determination of uridine modifications in RNA |
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