Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing
5-Methylcytosine (m5C) is one of the posttranscriptional modifications in mRNA and is involved in the pathogenesis of various diseases. However, the capacity of existing assays for accurately and comprehensively transcriptome-wide m5C mapping still needs improvement. Here, we develop a detection met...
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eLife Sciences Publications Ltd
2025-04-01
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| Online Access: | https://elifesciences.org/articles/98166 |
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| author | Jiale Zhou Ding Zhao Jinze Li Deqiang Kong Xiangrui Li Renquan Zhang Yuru Liang Xun Gao Yuqiang Qian Di Wang Jiahui Chen Liangxue Lai Yang Han Zhanjun Li |
| author_facet | Jiale Zhou Ding Zhao Jinze Li Deqiang Kong Xiangrui Li Renquan Zhang Yuru Liang Xun Gao Yuqiang Qian Di Wang Jiahui Chen Liangxue Lai Yang Han Zhanjun Li |
| author_sort | Jiale Zhou |
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| description | 5-Methylcytosine (m5C) is one of the posttranscriptional modifications in mRNA and is involved in the pathogenesis of various diseases. However, the capacity of existing assays for accurately and comprehensively transcriptome-wide m5C mapping still needs improvement. Here, we develop a detection method named DRAM (deaminase and reader protein assisted RNA methylation analysis), in which deaminases (APOBEC1 and TadA-8e) are fused with m5C reader proteins (ALYREF and YBX1) to identify the m5C sites through deamination events neighboring the methylation sites. This antibody-free and bisulfite-free approach provides transcriptome-wide editing regions which are highly overlapped with the publicly available bisulfite-sequencing (BS-seq) datasets and allows for a more stable and comprehensive identification of the m5C loci. In addition, DRAM system even supports ultralow input RNA (10 ng). We anticipate that the DRAM system could pave the way for uncovering further biological functions of m5C modifications. |
| format | Article |
| id | doaj-art-926f4106ebbd4cf09a960d398b91df3f |
| institution | OA Journals |
| issn | 2050-084X |
| language | English |
| publishDate | 2025-04-01 |
| publisher | eLife Sciences Publications Ltd |
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| spelling | doaj-art-926f4106ebbd4cf09a960d398b91df3f2025-08-20T02:08:46ZengeLife Sciences Publications LtdeLife2050-084X2025-04-011310.7554/eLife.98166Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencingJiale Zhou0https://orcid.org/0009-0006-9199-8647Ding Zhao1Jinze Li2Deqiang Kong3Xiangrui Li4Renquan Zhang5Yuru Liang6Xun Gao7Yuqiang Qian8Di Wang9Jiahui Chen10Liangxue Lai11https://orcid.org/0000-0002-5256-6802Yang Han12https://orcid.org/0000-0001-6249-370XZhanjun Li13https://orcid.org/0000-0001-6914-8589Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, ChinaJilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, China; Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, First Hospital of Jilin University, Changchun, ChinaJilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, China; Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, First Hospital of Jilin University, Changchun, ChinaJilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, ChinaJilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, ChinaJilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, ChinaJilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, ChinaJilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, ChinaJilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, ChinaJilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, ChinaJilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, ChinaJilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, ChinaJilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, ChinaJilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun, China; Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, First Hospital of Jilin University, Changchun, China; Sanya Institute of Swine Resource, Hainan Provincial Research Center of Laboratory Animals, Sanya, China5-Methylcytosine (m5C) is one of the posttranscriptional modifications in mRNA and is involved in the pathogenesis of various diseases. However, the capacity of existing assays for accurately and comprehensively transcriptome-wide m5C mapping still needs improvement. Here, we develop a detection method named DRAM (deaminase and reader protein assisted RNA methylation analysis), in which deaminases (APOBEC1 and TadA-8e) are fused with m5C reader proteins (ALYREF and YBX1) to identify the m5C sites through deamination events neighboring the methylation sites. This antibody-free and bisulfite-free approach provides transcriptome-wide editing regions which are highly overlapped with the publicly available bisulfite-sequencing (BS-seq) datasets and allows for a more stable and comprehensive identification of the m5C loci. In addition, DRAM system even supports ultralow input RNA (10 ng). We anticipate that the DRAM system could pave the way for uncovering further biological functions of m5C modifications.https://elifesciences.org/articles/98166RNA5-methylcytosinedeaminasem5C reader |
| spellingShingle | Jiale Zhou Ding Zhao Jinze Li Deqiang Kong Xiangrui Li Renquan Zhang Yuru Liang Xun Gao Yuqiang Qian Di Wang Jiahui Chen Liangxue Lai Yang Han Zhanjun Li Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing eLife RNA 5-methylcytosine deaminase m5C reader |
| title | Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing |
| title_full | Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing |
| title_fullStr | Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing |
| title_full_unstemmed | Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing |
| title_short | Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing |
| title_sort | transcriptome wide identification of 5 methylcytosine by deaminase and reader protein assisted sequencing |
| topic | RNA 5-methylcytosine deaminase m5C reader |
| url | https://elifesciences.org/articles/98166 |
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