Literature DB >> 21212778

Isolation of circular yeast artificial chromosomes for synthetic biology and functional genomics studies.

Vladimir N Noskov1, Ray-Yuan Chuang, Daniel G Gibson, Sun-Hee Leem, Vladimir Larionov, Natalay Kouprina.   

Abstract

Circular yeast artificial chromosomes (YACs) provide significant advantages for cloning and manipulating large segments of genomic DNA in Saccharomyces cerevisiae. However, it has been difficult to exploit these advantages, because circular YACs are difficult to isolate and purify. Here we describe a method for purification of large circular YACs that is more reliable compared with previously described protocols. This method has been used to purify YACs up to 600 kb in size. The purified YAC DNA is suitable for restriction enzyme digestion, DNA sequencing and functional studies. For example, YACs carrying full-size genes can be purified from yeast and used for transfection into mammalian cells or for the construction of a synthetic genome that can be used to produce a synthetic cell. This method for isolating high-quality YAC DNA in microgram quantities should be valuable for functional and synthetic genomic studies. The entire protocol takes ∼3 d to complete.

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Year:  2010        PMID： 21212778      PMCID： PMC7380547          DOI： 10.1038/nprot.2010.174

Source DB:  PubMed          Journal:  Nat Protoc        ISSN： 1750-2799            Impact factor:   13.491


  24 in total

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Journal:  Proc Natl Acad Sci U S A       Date:  1992-09-15       Impact factor: 11.205

2.  Amplification of large artificial chromosomes.

Authors:  D R Smith; A P Smyth; D T Moir
Journal:  Proc Natl Acad Sci U S A       Date:  1990-11       Impact factor: 11.205

3.  Direct isolation of human BRCA2 gene by transformation-associated recombination in yeast.

Authors:  V Larionov; N Kouprina; G Solomon; J C Barrett; M A Resnick
Journal:  Proc Natl Acad Sci U S A       Date:  1997-07-08       Impact factor: 11.205

4.  Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors.

Authors:  D T Burke; G F Carle; M V Olson
Journal:  Science       Date:  1987-05-15       Impact factor: 47.728

5.  A novel expression system for genomic DNA loci using a human artificial chromosome vector with transformation-associated recombination cloning.

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6.  Cloning whole bacterial genomes in yeast.

Authors:  Gwynedd A Benders; Vladimir N Noskov; Evgeniya A Denisova; Carole Lartigue; Daniel G Gibson; Nacyra Assad-Garcia; Ray-Yuan Chuang; William Carrera; Monzia Moodie; Mikkel A Algire; Quang Phan; Nina Alperovich; Sanjay Vashee; Chuck Merryman; J Craig Venter; Hamilton O Smith; John I Glass; Clyde A Hutchison
Journal:  Nucleic Acids Res       Date:  2010-03-07       Impact factor: 16.971

7.  Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.

Authors:  Daniel G Gibson; Gwynedd A Benders; Cynthia Andrews-Pfannkoch; Evgeniya A Denisova; Holly Baden-Tillson; Jayshree Zaveri; Timothy B Stockwell; Anushka Brownley; David W Thomas; Mikkel A Algire; Chuck Merryman; Lei Young; Vladimir N Noskov; John I Glass; J Craig Venter; Clyde A Hutchison; Hamilton O Smith
Journal:  Science       Date:  2008-01-24       Impact factor: 47.728

Review 8.  Exploiting the yeast Saccharomyces cerevisiae for the study of the organization and evolution of complex genomes.

Authors:  Natalay Kouprina; Vladimir Larionov
Journal:  FEMS Microbiol Rev       Date:  2003-12       Impact factor: 16.408

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Journal:  Nucleic Acids Res       Date:  2005-09-01       Impact factor: 16.971
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  16 in total

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Authors:  Natalay Kouprina; Vladimir N Noskov; Vladimir Larionov
Journal:  Nat Protoc       Date:  2020-01-31       Impact factor: 13.491

2.  Direct cloning and heterologous expression of natural product biosynthetic gene clusters by transformation-associated recombination.

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Journal:  Methods Enzymol       Date:  2019-03-21       Impact factor: 1.600

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Journal:  J Biotechnol       Date:  2016-04-12       Impact factor: 3.307

4.  A Stable, Autonomously Replicating Plasmid Vector Containing Pichia pastoris Centromeric DNA.

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Journal:  Appl Environ Microbiol       Date:  2018-07-17       Impact factor: 4.792

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

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Journal:  Nat Protoc       Date:  2013-07-18       Impact factor: 13.491

6.  Assembly of long DNA sequences using a new synthetic Escherichia coli-yeast shuttle vector.

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Review 8.  Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life.

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9.  Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast.

Authors:  Christian Tagwerker; Christopher L Dupont; Bogumil J Karas; Li Ma; Ray-Yuan Chuang; Gwynedd A Benders; Adi Ramon; Mark Novotny; Michael G Montague; Pratap Venepally; Daniel Brami; Ariel Schwartz; Cynthia Andrews-Pfannkoch; Daniel G Gibson; John I Glass; Hamilton O Smith; J Craig Venter; Clyde A Hutchison
Journal:  Nucleic Acids Res       Date:  2012-08-31       Impact factor: 16.971

10.  Simultaneous non-contiguous deletions using large synthetic DNA and site-specific recombinases.

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Journal:  Nucleic Acids Res       Date:  2014-06-09       Impact factor: 16.971
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