Literature DB >> 28852223

Beyond editing to writing large genomes.

Raj Chari1, George M Church2.   

Abstract

Recent exponential advances in genome sequencing and engineering technologies have enabled an unprecedented level of interrogation into the impact of DNA variation (genotype) on cellular function (phenotype). Furthermore, these advances have also prompted realistic discussion of writing and radically re-writing complex genomes. In this Perspective, we detail the motivation for large-scale engineering, discuss the progress made from such projects in bacteria and yeast and describe how various genome-engineering technologies will contribute to this effort. Finally, we describe the features of an ideal platform and provide a roadmap to facilitate the efficient writing of large genomes.

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Year:  2017        PMID: 28852223      PMCID: PMC5793211          DOI: 10.1038/nrg.2017.59

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  167 in total

1.  Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.

Authors:  Gang Sheng; Hongtu Zhao; Jiuyu Wang; Yu Rao; Wenwen Tian; Daan C Swarts; John van der Oost; Dinshaw J Patel; Yanli Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2013-12-27       Impact factor: 11.205

2.  Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.

Authors:  Zhucheng Chen; Haijuan Yang; Nikola P Pavletich
Journal:  Nature       Date:  2008-05-22       Impact factor: 49.962

3.  Engineering the mouse genome with bacterial artificial chromosomes to create multipurpose alleles.

Authors:  Giuseppe Testa; Youming Zhang; Kristina Vintersten; Vladimir Benes; W W M Pim Pijnappel; Ian Chambers; Andrew J H Smith; Austin G Smith; A Francis Stewart
Journal:  Nat Biotechnol       Date:  2003-03-10       Impact factor: 54.908

Review 4.  Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases.

Authors:  Shengdar Q Tsai; J Keith Joung
Journal:  Nat Rev Genet       Date:  2016-05       Impact factor: 53.242

Review 5.  A Comprehensive TALEN-Based Knockout Library for Generating Human-Induced Pluripotent Stem Cell-Based Models for Cardiovascular Diseases.

Authors:  Ioannis Karakikes; Vittavat Termglinchan; Diana A Cepeda; Jaecheol Lee; Sebastian Diecke; Ayal Hendel; Ilanit Itzhaki; Mohamed Ameen; Rajani Shrestha; Haodi Wu; Ning Ma; Ning-Yi Shao; Timon Seeger; Nicole Woo; Kitchener D Wilson; Elena Matsa; Matthew H Porteus; Vittorio Sebastiano; Joseph C Wu
Journal:  Circ Res       Date:  2017-02-28       Impact factor: 17.367

6.  Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9.

Authors:  Shota Nakade; Takuya Tsubota; Yuto Sakane; Satoshi Kume; Naoaki Sakamoto; Masanobu Obara; Takaaki Daimon; Hideki Sezutsu; Takashi Yamamoto; Tetsushi Sakuma; Ken-ichi T Suzuki
Journal:  Nat Commun       Date:  2014-11-20       Impact factor: 14.919

7.  Inclusion of homologous DNA in nuclease-mediated gene targeting facilitates a higher incidence of bi-allelically modified cells.

Authors:  Benjamin P Beaton; Deug-Nam Kwon; Yun-Jung Choi; Jae-Hwan Kim; Melissa S Samuel; Joshua A Benne; Kevin D Wells; Kiho Lee; Jin-Hoi Kim; Randall S Prather
Journal:  Xenotransplantation       Date:  2015 Sep-Oct       Impact factor: 3.907

8.  megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering.

Authors:  Sandrine Boissel; Jordan Jarjour; Alexander Astrakhan; Andrew Adey; Agnès Gouble; Philippe Duchateau; Jay Shendure; Barry L Stoddard; Michael T Certo; David Baker; Andrew M Scharenberg
Journal:  Nucleic Acids Res       Date:  2013-11-26       Impact factor: 16.971

9.  Homology-driven genome editing in hematopoietic stem and progenitor cells using ZFN mRNA and AAV6 donors.

Authors:  Jianbin Wang; Colin M Exline; Joshua J DeClercq; G Nicholas Llewellyn; Samuel B Hayward; Patrick Wai-Lun Li; David A Shivak; Richard T Surosky; Philip D Gregory; Michael C Holmes; Paula M Cannon
Journal:  Nat Biotechnol       Date:  2015-11-09       Impact factor: 54.908

10.  DSBCapture: in situ capture and sequencing of DNA breaks.

Authors:  Stefanie V Lensing; Giovanni Marsico; Robert Hänsel-Hertsch; Enid Y Lam; David Tannahill; Shankar Balasubramanian
Journal:  Nat Methods       Date:  2016-08-15       Impact factor: 28.547

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  10 in total

Review 1.  Controlling the Implementation of Transgenic Microbes: Are We Ready for What Synthetic Biology Has to Offer?

Authors:  Finn Stirling; Pamela A Silver
Journal:  Mol Cell       Date:  2020-05-21       Impact factor: 17.970

2.  Harnessing stepping-stone hosts to engineer, select, and reboot synthetic bacteriophages in one pot.

Authors:  Li Cheng; Ziqing Deng; Haoran Tao; Wenchen Song; Bo Xing; Wenfeng Liu; Lingxin Kong; Shengjian Yuan; Yingfei Ma; Yayun Wu; Xun Huang; Yun Peng; Nai-Kei Wong; Yingxia Liu; Yun Wang; Yue Shen; Junhua Li; Minfeng Xiao
Journal:  Cell Rep Methods       Date:  2022-05-23

3.  CRISPR-C: circularization of genes and chromosome by CRISPR in human cells.

Authors:  Henrik Devitt Møller; Lin Lin; Xi Xiang; Trine Skov Petersen; Jinrong Huang; Luhan Yang; Eigil Kjeldsen; Uffe Birk Jensen; Xiuqing Zhang; Xin Liu; Xun Xu; Jian Wang; Huanming Yang; George M Church; Lars Bolund; Birgitte Regenberg; Yonglun Luo
Journal:  Nucleic Acids Res       Date:  2018-12-14       Impact factor: 16.971

4.  An EU Perspective on Biosafety Considerations for Plants Developed by Genome Editing and Other New Genetic Modification Techniques (nGMs).

Authors:  Michael F Eckerstorfer; Marion Dolezel; Andreas Heissenberger; Marianne Miklau; Wolfram Reichenbecher; Ricarda A Steinbrecher; Friedrich Waßmann
Journal:  Front Bioeng Biotechnol       Date:  2019-03-05

Review 5.  Organizing genome engineering for the gigabase scale.

Authors:  Bryan A Bartley; Jacob Beal; Jonathan R Karr; Elizabeth A Strychalski
Journal:  Nat Commun       Date:  2020-02-04       Impact factor: 14.919

6.  Chromosome Transplantation: A Possible Approach to Treat Human X-linked Disorders.

Authors:  Marianna Paulis; Lucia Susani; Alessandra Castelli; Teruhiko Suzuki; Takahiko Hara; Letizia Straniero; Stefano Duga; Dario Strina; Stefano Mantero; Elena Caldana; Lucia Sergi Sergi; Anna Villa; Paolo Vezzoni
Journal:  Mol Ther Methods Clin Dev       Date:  2020-01-21       Impact factor: 6.698

7.  Meaning of Ambiguity: A Japanese Survey on Synthetic Biology and Genome Editing.

Authors:  Aiko Hibino; Go Yoshizawa; Jusaku Minari
Journal:  Front Sociol       Date:  2019-12-17

8.  Modulating DNA Repair Pathways to Diversify Genomic Alterations in Saccharomyces cerevisiae.

Authors:  Zhen Wang; Yuping Lin; Zongjie Dai; Qinhong Wang
Journal:  Microbiol Spectr       Date:  2022-03-30

Review 9.  Genome Writing: Current Progress and Related Applications.

Authors:  Yueqiang Wang; Yue Shen; Ying Gu; Shida Zhu; Ye Yin
Journal:  Genomics Proteomics Bioinformatics       Date:  2018-02-21       Impact factor: 7.691

10.  Designing and running an advanced Bioinformatics and genome analyses course in Tunisia.

Authors:  Fatma Z Guerfali; Dhafer Laouini; Abdellatif Boudabous; Fredj Tekaia
Journal:  PLoS Comput Biol       Date:  2019-01-28       Impact factor: 4.475

  10 in total

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