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DddA homolog search and engineering expand sequence compatibility of mitochondrial base editing. Nat Commun 2023; 14:874. [PMID: 36797253 PMCID: PMC9935910 DOI: 10.1038/s41467-023-36600-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
Expanding mitochondrial base editing tools with broad sequence compatibility is of high need for both research and therapeutic purposes. In this study, we identify a DddA homolog from Simiaoa sunii (Ddd_Ss) which can efficiently deaminate cytosine in DC context in double-stranded DNA (dsDNA). We successfully develop Ddd_Ss-derived cytosine base editors (DdCBE_Ss) and introduce mutations at multiple mitochondrial DNA (mtDNA) loci including disease-associated mtDNA mutations in previously inaccessible GC context. Finally, by introducing a single amino acid substitution from Ddd_Ss, we successfully improve the activity and sequence compatibility of DdCBE derived from DddA of Burkholderia cenocepacia (DdCBE_Bc). Our study expands mtDNA editing tool boxes and provides resources for further screening and engineering dsDNA base editors for biological and therapeutic applications.
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Hu H, Yang X, Tang C. Visualization of Genomic Loci in Living Cells with BiFC-TALE. ACTA ACUST UNITED AC 2018; 82:e78. [PMID: 30375749 DOI: 10.1002/cpcb.78] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Tracking the dynamics of genomic loci is essential for understanding a variety of cellular processes. However, earlier methods have all suffered from a low signal-to-background ratio (SBR), mainly caused by the background fluorescence from diffuse full-length fluorescent proteins in the nucleus. We have developed a novel method (BiFC-TALE) for labeling and tracking genomic loci in live mammalian cells, combining bimolecular fluorescence complementation (BiFC) and transcription activator-like effector (TALE) technologies. Since only the sequences-targeted BiFC fragments can be pulled together by TALE modules to recombine intact fluorescent proteins, the background fluorescence in the living nucleus can be largely reduced, which significantly improves SBR. Using telomere and centromere labeling as examples, this unit describes in detail the design and implementation of BiFC-TALE system. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Huan Hu
- School of Life Sciences, Peking University, Beijing, China.,Center for Quantitative Biology, Peking University, Beijing, China
| | - Xiaojing Yang
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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Deciphering TAL effectors for 5-methylcytosine and 5-hydroxymethylcytosine recognition. Nat Commun 2017; 8:901. [PMID: 29026078 PMCID: PMC5638953 DOI: 10.1038/s41467-017-00860-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/01/2017] [Indexed: 12/29/2022] Open
Abstract
DNA recognition by transcription activator-like effector (TALE) proteins is mediated by tandem repeats that specify nucleotides through repeat-variable diresidues. These repeat-variable diresidues form direct and sequence-specific contacts to DNA bases; hence, TALE-DNA interaction is sensitive to DNA chemical modifications. Here we conduct a thorough investigation, covering all theoretical repeat-variable diresidue combinations, for their recognition capabilities for 5-methylcytosine and 5-hydroxymethylcytosine, two important epigenetic markers in higher eukaryotes. We identify both specific and degenerate repeat-variable diresidues for 5-methylcytosine and 5-hydroxymethylcytosine. Utilizing these novel repeat-variable diresidues, we achieve methylation-dependent gene activation and genome editing in vivo; we also report base-resolution detection of 5hmC in an in vitro assay. Our work deciphers repeat-variable diresidues for 5-methylcytosine and 5-hydroxymethylcytosine, and provides tools for TALE-dependent epigenome recognition.Transcription activator-like effector proteins recognise specific DNA sequences via tandem repeats. Here the authors demonstrate TALEs can recognise the methylated bases 5mC and 5hmC, enabling them to detect epigenetic modifications.
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Hu H, Zhang H, Wang S, Ding M, An H, Hou Y, Yang X, Wei W, Sun Y, Tang C. Live visualization of genomic loci with BiFC-TALE. Sci Rep 2017; 7:40192. [PMID: 28074901 PMCID: PMC5225478 DOI: 10.1038/srep40192] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 12/02/2016] [Indexed: 11/08/2022] Open
Abstract
Tracking the dynamics of genomic loci is important for understanding the mechanisms of fundamental intracellular processes. However, fluorescent labeling and imaging of such loci in live cells have been challenging. One of the major reasons is the low signal-to-background ratio (SBR) of images mainly caused by the background fluorescence from diffuse full-length fluorescent proteins (FPs) in the living nucleus, hampering the application of live cell genomic labeling methods. Here, combining bimolecular fluorescence complementation (BiFC) and transcription activator-like effector (TALE) technologies, we developed a novel method for labeling genomic loci (BiFC-TALE), which largely reduces the background fluorescence level. Using BiFC-TALE, we demonstrated a significantly improved SBR by imaging telomeres and centromeres in living cells in comparison with the methods using full-length FP.
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Affiliation(s)
- Huan Hu
- School of Life Sciences, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Hongmin Zhang
- School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, People’s Republic of China
| | - Sheng Wang
- School of Life Sciences, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
| | - Miao Ding
- School of Life Sciences, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
| | - Hui An
- School of Life Sciences, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Yingping Hou
- School of Life Sciences, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
| | - Xiaojing Yang
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Wensheng Wei
- School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, People’s Republic of China
| | - Yujie Sun
- School of Life Sciences, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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