Literature DB >> 33742653

De novo assembly and delivery to mouse cells of a 101 kb functional human gene.

Leslie A Mitchell1,2, Laura H McCulloch1,2, Sudarshan Pinglay1,2, Henri Berger1,2, Nazario Bosco1,2, Ran Brosh1,3, Milica Bulajić4, Emily Huang1,3, Megan S Hogan1,3, James A Martin1,2, Esteban O Mazzoni4, Teresa Davoli1,2, Matthew T Maurano1,3, Jef D Boeke1,2,5.   

Abstract

Design and large-scale synthesis of DNA has been applied to the functional study of viral and microbial genomes. New and expanded technology development is required to unlock the transformative potential of such bottom-up approaches to the study of larger mammalian genomes. Two major challenges include assembling and delivering long DNA sequences. Here, we describe a workflow for de novo DNA assembly and delivery that enables functional evaluation of mammalian genes on the length scale of 100 kilobase pairs (kb). The DNA assembly step is supported by an integrated robotic workcell. We demonstrate assembly of the 101 kb human HPRT1 gene in yeast from 3 kb building blocks, precision delivery of the resulting construct to mouse embryonic stem cells, and subsequent expression of the human protein from its full-length human gene in mouse cells. This workflow provides a framework for mammalian genome writing. We envision utility in producing designer variants of human genes linked to disease and their delivery and functional analysis in cell culture or animal models.
© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Entities:  

Keywords:  genome writing; mammalian genome engineering; recombinase-mediated cassette exchange; synthetic genomics

Mesh:

Substances:

Year:  2021        PMID: 33742653      PMCID: PMC8128383          DOI: 10.1093/genetics/iyab038

Source DB:  PubMed          Journal:  Genetics        ISSN: 0016-6731            Impact factor:   4.562


  51 in total

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2.  Assembly of large, high G+C bacterial DNA fragments in yeast.

Authors:  Vladimir N Noskov; Bogumil J Karas; Lei Young; Ray-Yuan Chuang; Daniel G Gibson; Ying-Chi Lin; Jason Stam; Isaac T Yonemoto; Yo Suzuki; Cynthia Andrews-Pfannkoch; John I Glass; Hamilton O Smith; Clyde A Hutchison; J Craig Venter; Philip D Weyman
Journal:  ACS Synth Biol       Date:  2012-05-21       Impact factor: 5.110

3.  Creation of a bacterial cell controlled by a chemically synthesized genome.

Authors:  Daniel G Gibson; John I Glass; Carole Lartigue; Vladimir N Noskov; Ray-Yuan Chuang; Mikkel A Algire; Gwynedd A Benders; Michael G Montague; Li Ma; Monzia M Moodie; Chuck Merryman; Sanjay Vashee; Radha Krishnakumar; Nacyra Assad-Garcia; Cynthia Andrews-Pfannkoch; Evgeniya A Denisova; Lei Young; Zhi-Qing Qi; Thomas H Segall-Shapiro; Christopher H Calvey; Prashanth P Parmar; Clyde A Hutchison; Hamilton O Smith; J Craig Venter
Journal:  Science       Date:  2010-05-20       Impact factor: 47.728

4.  Gene and genome construction in yeast.

Authors:  Daniel G Gibson
Journal:  Curr Protoc Mol Biol       Date:  2011-04

5.  Generation of transgenic mice with megabase-sized human yeast artificial chromosomes by yeast spheroplast-embryonic stem cell fusion.

Authors:  Liangping Li; Thomas Blankenstein
Journal:  Nat Protoc       Date:  2013-07-18       Impact factor: 13.491

6.  New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae.

Authors:  A Wach; A Brachat; R Pöhlmann; P Philippsen
Journal:  Yeast       Date:  1994-12       Impact factor: 3.239

7.  Design of a synthetic yeast genome.

Authors:  Sarah M Richardson; Leslie A Mitchell; Giovanni Stracquadanio; Kun Yang; Jessica S Dymond; James E DiCarlo; Dongwon Lee; Cheng Lai Victor Huang; Srinivasan Chandrasegaran; Yizhi Cai; Jef D Boeke; Joel S Bader
Journal:  Science       Date:  2017-03-10       Impact factor: 47.728

8.  A dual molecular analogue tuner for dissecting protein function in mammalian cells.

Authors:  Ran Brosh; Iryna Hrynyk; Jessalyn Shen; Avinash Waghray; Ning Zheng; Ihor R Lemischka
Journal:  Nat Commun       Date:  2016-05-27       Impact factor: 14.919

9.  In vitro DNA SCRaMbLE.

Authors:  Yi Wu; Rui-Ying Zhu; Leslie A Mitchell; Lu Ma; Rui Liu; Meng Zhao; Bin Jia; Hui Xu; Yun-Xiang Li; Zu-Ming Yang; Yuan Ma; Xia Li; Hong Liu; Duo Liu; Wen-Hai Xiao; Xiao Zhou; Bing-Zhi Li; Ying-Jin Yuan; Jef D Boeke
Journal:  Nat Commun       Date:  2018-05-22       Impact factor: 14.919

10.  DICE, an efficient system for iterative genomic editing in human pluripotent stem cells.

Authors:  Fangfang Zhu; Matthew Gamboa; Alfonso P Farruggio; Simon Hippenmeyer; Bosiljka Tasic; Birgitt Schüle; Yanru Chen-Tsai; Michele P Calos
Journal:  Nucleic Acids Res       Date:  2013-12-04       Impact factor: 16.971

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  4 in total

Review 1.  Programmable RNA-Guided Large DNA Transgenesis by CRISPR/Cas9 and Site-Specific Integrase Bxb1.

Authors:  Vishnu Hosur; Benjamin E Low; Michael V Wiles
Journal:  Front Bioeng Biotechnol       Date:  2022-07-05

2.  A conditional counterselectable Piga knockout in mouse embryonic stem cells for advanced genome writing applications.

Authors:  Weimin Zhang; Ran Brosh; Laura H McCulloch; Yinan Zhu; Hannah Ashe; Gwen Ellis; Brendan R Camellato; Sang Yong Kim; Matthew T Maurano; Jef D Boeke
Journal:  iScience       Date:  2022-05-23

3.  Big DNA as a tool to dissect an age-related macular degeneration-associated haplotype.

Authors:  Jon M Laurent; Xin Fu; Sergei German; Matthew T Maurano; Kang Zhang; Jef D Boeke
Journal:  Precis Clin Med       Date:  2019-01-22

Review 4.  Synthetic Genomics From a Yeast Perspective.

Authors:  Charlotte C Koster; Eline D Postma; Ewout Knibbe; Céline Cleij; Pascale Daran-Lapujade
Journal:  Front Bioeng Biotechnol       Date:  2022-03-21
  4 in total

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