Literature DB >> 31844291

Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor.

Haiqi Chen1, Sophia Liu1,2,3, Samuel Padula1, Daniel Lesman1, Kettner Griswold4,5,6,7, Allen Lin8,9, Tongtong Zhao1,10, Jamie L Marshall1, Fei Chen11.   

Abstract

Here we describe TRACE (T7 polymerase-driven continuous editing), a method that enables continuous, targeted mutagenesis in human cells using a cytidine deaminase fused to T7 RNA polymerase. TRACE induces high rates of mutagenesis over multiple cell generations in genes under the control of a T7 promoter integrated in the genome. We used TRACE in a MEK1 inhibitor-resistance screen, and identified functionally correlated mutations.

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Year:  2019        PMID： 31844291      PMCID： PMC7775643          DOI： 10.1038/s41587-019-0331-8

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


  27 in total

1.  High level gene expression in mammalian cells by a nuclear T7-phase RNA polymerase.

Authors:  A Lieber; U Kiessling; M Strauss
Journal:  Nucleic Acids Res       Date:  1989-11-11       Impact factor: 16.971

2.  CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window.

Authors:  Shakked O Halperin; Connor J Tou; Eric B Wong; Cyrus Modavi; David V Schaffer; John E Dueber
Journal:  Nature       Date:  2018-08-01       Impact factor: 49.962

3.  Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds.

Authors:  Arjun Ravikumar; Garri A Arzumanyan; Muaeen K A Obadi; Alex A Javanpour; Chang C Liu
Journal:  Cell       Date:  2018-11-08       Impact factor: 41.582

4.  Characterization of a set of T7 RNA polymerase active site mutants.

Authors:  G Bonner; E M Lafer; R Sousa
Journal:  J Biol Chem       Date:  1994-10-07       Impact factor: 5.157

5.  Random mutagenesis by error-prone pol plasmid replication in Escherichia coli.

Authors:  David L Alexander; Joshua Lilly; Jaime Hernandez; Jillian Romsdahl; Christopher J Troll; Manel Camps
Journal:  Methods Mol Biol       Date:  2014

6.  A Processive Protein Chimera Introduces Mutations across Defined DNA Regions In Vivo.

Authors:  Christopher L Moore; Louis J Papa; Matthew D Shoulders
Journal:  J Am Chem Soc       Date:  2018-07-18       Impact factor: 15.419

7.  Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.

Authors:  Melanie Schirmer; Umer Z Ijaz; Rosalinda D'Amore; Neil Hall; William T Sloan; Christopher Quince
Journal:  Nucleic Acids Res       Date:  2015-01-13       Impact factor: 16.971

8.  A system for the continuous directed evolution of biomolecules.

Authors:  Kevin M Esvelt; Jacob C Carlson; David R Liu
Journal:  Nature       Date:  2011-04-10       Impact factor: 49.962

9.  A CRISPR-Cas9 Assisted Non-Homologous End-Joining Strategy for One-step Engineering of Bacterial Genome.

Authors:  Tianyuan Su; Fapeng Liu; Pengfei Gu; Haiying Jin; Yizhao Chang; Qian Wang; Quanfeng Liang; Qingsheng Qi
Journal:  Sci Rep       Date:  2016-11-24       Impact factor: 4.379

10.  Automatic thresholding from the gradients of region boundaries.

Authors:  G Landini; D A Randell; S Fouad; A Galton
Journal:  J Microsc       Date:  2016-09-20       Impact factor: 1.758
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  18 in total

Review 1.  Proteomic and interactomic insights into the molecular basis of cell functional diversity.

Authors:  Isabell Bludau; Ruedi Aebersold
Journal:  Nat Rev Mol Cell Biol       Date:  2020-03-31       Impact factor: 94.444

2.  Mapping single-cell-resolution cell phylogeny reveals cell population dynamics during organ development.

Authors:  Kehui Liu; Shanjun Deng; Chang Ye; Zeqi Yao; Jianguo Wang; Han Gong; Li Liu; Xionglei He
Journal:  Nat Methods       Date:  2021-12-02       Impact factor: 28.547

Review 3.  Improvement of base editors and prime editors advances precision genome engineering in plants.

Authors:  Kai Hua; Peijin Han; Jian-Kang Zhu
Journal:  Plant Physiol       Date:  2022-03-28       Impact factor: 8.340

Review 4.  Discovering new biology with drug-resistance alleles.

Authors:  Allyson M Freedy; Brian B Liau
Journal:  Nat Chem Biol       Date:  2021-11-19       Impact factor: 16.174

Review 5.  Chemical Biology Framework to Illuminate Proteostasis.

Authors:  Rebecca M Sebastian; Matthew D Shoulders
Journal:  Annu Rev Biochem       Date:  2020-02-25       Impact factor: 23.643

Review 6.  Directed evolution in mammalian cells.

Authors:  Samuel J Hendel; Matthew D Shoulders
Journal:  Nat Methods       Date:  2021-04-07       Impact factor: 28.547

Review 7.  Systems for in vivo hypermutation: a quest for scale and depth in directed evolution.

Authors:  Gordon Rix; Chang C Liu
Journal:  Curr Opin Chem Biol       Date:  2021-03-27       Impact factor: 8.972

8.  Improved yellow-green split fluorescent proteins for protein labeling and signal amplification.

Authors:  Shuqin Zhou; Siyu Feng; David Brown; Bo Huang
Journal:  PLoS One       Date:  2020-11-23       Impact factor: 3.240

Review 9.  Full-Spectrum Targeted Mutagenesis in Plant and Animal Cells.

Authors:  Brian Iaffaldano; Jakob Reiser
Journal:  Int J Mol Sci       Date:  2021-01-16       Impact factor: 5.923

Review 10.  Genome editor-directed in vivo library diversification.

Authors:  Cristina Cheng; Mi Zhou; Qiwen Su; Alexandra Steigmeyer; Jia Niu
Journal:  Cell Chem Biol       Date:  2021-06-08       Impact factor: 9.039
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