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Your search keyword '"Yuan, Bi-Feng"' showing total 622 results
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622 results on '"Yuan, Bi-Feng"'

1. Single-Nucleotide Resolution Mapping of N6-Methyladenine in Genomic DNA.

Author

Ma, Cheng-Jie, Li, Gaojie, Shao, Wen-Xuan, Min, Yi-Hao, Wang, Ping, Ding, Jiang-Hui, Xie, Neng-Bin, Wang, Min, Tang, Feng, Feng, Yu-Qi, Ci, Weimin, Yuan, Bi-Feng, and Wang, Yinsheng

Abstract

N6-Methyladenine (6mA) is a naturally occurring DNA modification in both prokaryotes and eukaryotes. Herein, we developed a deaminase-mediated sequencing (DM-seq) method for genome-wide mapping of 6mA at single-nucleotide resolution. The method capitalizes on the selective deamination of adenine, but not 6mA, in DNA mediated by an evolved adenine deaminase, ABE8e. By employing this method, we achieved genome-wide mapping of 6mA in Escherichia coli and in mammalian mitochondrial DNA (mtDNA) at single-nucleotide resolution. We found that the 6mA sites are mainly located in the GATC motif in the E. coli genome. We also identified 17 6mA sites in mtDNA of HepG2 cells, where all of the 6mA sites are distributed in the heavy strand of mtDNA. We envision that DM-seq will be a valuable tool for uncovering new functions of 6mA in DNA and for exploring its potential roles in mitochondria-related human diseases.

Published
2023

5. DNA-Protein Cross-Linking Sequencing for Genome-Wide Mapping of Thymidine Glycol.

Author

Tang, Feng, Yuan, Jun, Yuan, Bi-Feng, and Wang, Yinsheng

Subjects
Thymidine
Abstract

Thymidine glycol (Tg) is the most prevalent form of oxidatively induced pyrimidine lesions in DNA. Tg can arise from direct oxidation of thymidine in DNA. In addition, 5-methyl-2-deoxycytidine (5-mdC) can be oxidized to 5-mdC glycol, and its subsequent deamination also yields Tg. However, Tgs distribution in the human genome remains unknown. Here, we presented a DNA-protein cross-linking sequencing (DPC-Seq) method for genome-wide mapping of Tg in human cells. Our approach capitalizes on the specificity of a bifunctional DNA glycosylase, i.e., NTHL1, for the covalent labeling, as well as DPC pulldown, SDS-PAGE fractionation, and membrane transfer for highly efficient and selective enrichment of Tg-bearing DNA. By employing DPC-Seq, we detected thousands of Tg sites in the human genome, where dual ablation of NTHL1 and NEIL1, the major DNA glycosylases responsible for Tg repair, led to pronounced increases in the number of Tg peaks. In addition, Tg is depleted in genomic regions associated with active transcription but enriched at nucleosome-binding sites, especially at heterochromatin sites marked with H3K9me2. Collectively, we developed a DPC-Seq method for highly efficient enrichment of Tg-containing DNA and for genome-wide mapping of Tg in human cells. Our work offers a robust tool for future functional studies of Tg in DNA, and we envision that the method can also be adapted for mapping other modified nucleosides in genomic DNA in the future.

Published
2022

10. Downregulation of the FTO m6A RNA demethylase promotes EMT-mediated progression of epithelial tumors and sensitivity to Wnt inhibitors

Author

Jeschke, Jana, Collignon, Evelyne, Al Wardi, Clémence, Krayem, Mohammad, Bizet, Martin, Jia, Yan, Garaud, Soizic, Wimana, Zéna, Calonne, Emilie, Hassabi, Bouchra, Morandini, Renato, Deplus, Rachel, Putmans, Pascale, Dube, Gaurav, Singh, Nitesh Kumar, Koch, Alexander, Shostak, Kateryna, Rizzotto, Lara, Ross, Robert L., Desmedt, Christine, Bareche, Yacine, Rothé, Françoise, Lehmann-Che, Jacqueline, Duterque-Coquillaud, Martine, Leroy, Xavier, Menschaert, Gerben, Teixeira, Luis, Guo, Mingzhou, Limbach, Patrick A., Close, Pierre, Chariot, Alain, Leucci, Eleonora, Ghanem, Ghanem, Yuan, Bi-Feng, Willard-Gallo, Karen, Sotiriou, Christos, Marine, Jean-Christophe, and Fuks, François

Published
2021
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14. Nucleic Acids Analysis

Author

Zhao, Yongxi, Zuo, Xiaolei, Li, Qian, Chen, Feng, Chen, Yan-Ru, Deng, Jinqi, Han, Da, Hao, Changlong, Huang, Fujian, Huang, Yanyi, Ke, Guoliang, Kuang, Hua, Li, Fan, Li, Jiang, Li, Min, Li, Na, Lin, Zhenyu, Liu, Dingbin, Liu, Juewen, Liu, Libing, Liu, Xiaoguo, Lu, Chunhua, Luo, Fang, Mao, Xiuhai, Sun, Jiashu, Tang, Bo, Wang, Fei, Wang, Jianbin, Wang, Lihua, Wang, Shu, Wu, Lingling, Wu, Zai-Sheng, Xia, Fan, Xu, Chuanlai, Yang, Yang, Yuan, Bi-Feng, Yuan, Quan, Zhang, Chao, Zhu, Zhi, Yang, Chaoyong, Zhang, Xiao-Bing, Yang, Huanghao, Tan, Weihong, and Fan, Chunhai

Published
2021
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25. Dynamic changes in RNA m6A and 5 hmC influence gene expression programs during macrophage differentiation and polarisation.

Author

Pinello, Natalia, Song, Renhua, Lee, Quintin, Calonne, Emilie, Duan, Kun-Long, Wong, Emilie, Tieng, Jessica, Mehravar, Majid, Rong, Bowen, Lan, Fei, Roediger, Ben, Ma, Cheng-Jie, Yuan, Bi-Feng, Rasko, John E. J., Larance, Mark, Ye, Dan, Fuks, François, and Wong, Justin J.-L.

Subjects
RNA modification & restriction, GENE expression, GENETIC regulation, MACROPHAGES, NATURAL immunity
Abstract

RNA modifications are essential for the establishment of cellular identity. Although increasing evidence indicates that RNA modifications regulate the innate immune response, their role in monocyte-to-macrophage differentiation and polarisation is unclear. While m6A has been widely studied, other RNA modifications, including 5 hmC, remain poorly characterised. We profiled m6A and 5 hmC epitranscriptomes, transcriptomes, translatomes and proteomes of monocytes and macrophages at rest and pro- and anti-inflammatory states. Transcriptome-wide mapping of m6A and 5 hmC reveals enrichment of m6A and/or 5 hmC on specific categories of transcripts essential for macrophage differentiation. Our analyses indicate that m6A and 5 hmC modifications are present in transcripts with critical functions in pro- and anti-inflammatory macrophages. Notably, we also discover the co-occurrence of m6A and 5 hmC on alternatively-spliced isoforms and/or opposing ends of the untranslated regions (UTR) of mRNAs with key roles in macrophage biology. In specific examples, RNA 5 hmC controls the decay of transcripts independently of m6A. This study provides (i) a comprehensive dataset to interrogate the role of RNA modifications in a plastic system (ii) a resource for exploring different layers of gene expression regulation in the context of human monocyte-to-macrophage differentiation and polarisation, (iii) new insights into RNA modifications as central regulators of effector cells in innate immunity. [ABSTRACT FROM AUTHOR]

Published
2024
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27. Recent Advances in Deciphering the Mechanisms and Biological Functions of DNA Demethylation.

Author

Feng, Yang, Chen, Sheng‐Jun, and Yuan, Bi‐Feng

Subjects
DNA demethylation, EXCISION repair, DEMETHYLATION, METHYLCYTOSINE, EPIGENETICS, THYMINE
Abstract

Comprehensive Summary: 5‐Methylcytosine (5mC) is a dynamic and reversible epigenetic modification in genomic DNA of higher eukaryotes. It has been well‐established that the demethylation of 5mC occurs through the ten‐eleven translocation (TET)‐mediated oxidation of 5mC followed by thymine DNA glycosylase (TDG)‐initiated base excision repair (BER). Recent findings also have identified an alternative pathway of DNA demethylation. In this pathway, TET enzymes directly oxidize 5mC to form 5‐formylcytosine (5fC) or 5‐carboxylcytosine (5caC). These modified bases can undergo direct deformylation or decarboxylation, respectively. Additionally, DNA demethylation can also occur through the deamination of 5mC and 5hmC, resulting in the production of thymine and 5‐hydroxymethyluracil (5hmU), respectively. Various DNA demethylation pathways possess critical functional implications and roles in biological processes. This Recent Advances article will focus on the studies of mechanisms and biological functions of DNA demethylation, shedding light on the reversible nature of the epigenetic modification of 5mC. [ABSTRACT FROM AUTHOR]

Published
2024
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