Reading Time and DNA Sequence Preference of TET3 CXXC Domain Revealed by Single-Molecule Profiling  

作　　者：Zeyu Wang Zhiqiang Cao Kangkang Ma Man Lu Meije Wang Han Gao Deshun Gong Lin Liang Zhongbo Yu 

机构地区：[1]Frontiers Science Center for Cell Responses,State Key Laboratory of Medicinal Chemical Biology,and College of Pharmacy,Nankai University,38 Tongyan Road,Tianjin 300350,China [2]State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences,Nankai University,Tianjin 300350,China [3]College of Animal Science,Shanxi Agricultural University,Taigu,Shanxi 030801,China

出　　处：《Chinese Journal of Chemistry》2023年第10期1177-1184,共8页中国化学（英文版）

基　　金：Professor Chao Xu of the University of Science and Technology of China(UsTC)for constructive discussions.We acknowledge support from the National Natural Science Foundation of China[Grant 32071227 to Z.Y.];State Key Laboratory of Precision Measuring Technology and Instruments(Tianjin University)[Grant pilab2210 to Z.Y.];the Natural Science Foundation of Tianjin[Grant 22JCYBJC01070 to Z.Y.];the Science and Technology Innovation Program of Shanxi Agricultural University[Grant 2022BQ23 to L.L.].

摘　　要：Recognition of CpG dinucleotide DNA in epigenetic information flow plays a pivotal role for cellular differentiation and development.The TET3 CXXC domain binds to CpG DNA,serving a basic epigenetic information reading mechanism.During the selective recognition of a CpG motif by a CXXC domain from crowded binding sites in a gene sequence,the protein-DNA interactions are beyond CpG dinu-cleotide.However,the selective binding dynamics of CpG within a long DNA context by epigenetic enzymes have been rarely exploit-ed,which is hard for ensemble methods to probe.Here,we used single-molecule magnetic tweezers to quantitatively examine the dynamics of TET3's CXXC domain on a Hoxa9 promoter DNA.Our single-molecule binding profile revealed that CXXC-DNA interactions involve both CpG motifs and their flanking sequences.The residence time of TET3 CXXC differs by about 1000 times in five distin-guished CpG clusters in the context of a CpG island.Moreover,we performed multi-state hidden Markov modeling analysis on the zip-ping/unzipping dynamics of a CpG hairpin,discovering TET3 CXXC's preference on CpG motifs regarding the-2 to+2 flanking bases.Our results shed light on the selective binding dynamics of a CXXC on a gene sequence,facilitating studies on epigenetic information reading mechanisms.

关 键 词：ENZYMES DNA recognition CpG flanking sequence Single-molecule studies Magnetic tweezers 

分 类 号：O6[理学—化学]