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Nucleosomes affect local transformation efficiency

Elham Aslankoohi, Karin Voordeckers, Hong Sun, Aminael Sanchez-Rodriguez, Elisa van der Zande, Kathleen Marchal (UGent) and Kevin J Verstrepen
(2012) NUCLEIC ACIDS RESEARCH. 40(19). p.9506-9512
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Abstract
Genetic transformation is a natural process during which foreign DNA enters a cell and integrates into the genome. Apart from its relevance for horizontal gene transfer in nature, transformation is also the cornerstone of today's recombinant gene technology. Despite its importance, relatively little is known about the factors that determine transformation efficiency. We hypothesize that differences in DNA accessibility associated with nucleosome positioning may affect local transformation efficiency. We investigated the landscape of transformation efficiency at various positions in the Saccharomyces cerevisiae genome and correlated these measurements with nucleosome positioning. We find that transformation efficiency shows a highly significant inverse correlation with relative nucleosome density. This correlation was lost when the nucleosome pattern, but not the underlying sequence was changed. Together, our results demonstrate a novel role for nucleosomes and also allow researchers to predict transformation efficiency of a target region and select spots in the genome that are likely to yield higher transformation efficiency.
Keywords
SITE SELECTION, IN-VIVO, CHROMATIN-STRUCTURE, ILLEGITIMATE RECOMBINATION, RETROVIRAL INTEGRATION, GENE-EXPRESSION, T-DNA INTEGRATION, YEAST SACCHAROMYCES-CEREVISIAE, GENOME, PROMOTER

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Citation

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MLA
Aslankoohi, Elham, et al. “Nucleosomes Affect Local Transformation Efficiency.” NUCLEIC ACIDS RESEARCH, vol. 40, no. 19, 2012, pp. 9506–12, doi:10.1093/nar/gks777.
APA
Aslankoohi, E., Voordeckers, K., Sun, H., Sanchez-Rodriguez, A., van der Zande, E., Marchal, K., & Verstrepen, K. J. (2012). Nucleosomes affect local transformation efficiency. NUCLEIC ACIDS RESEARCH, 40(19), 9506–9512. https://doi.org/10.1093/nar/gks777
Chicago author-date
Aslankoohi, Elham, Karin Voordeckers, Hong Sun, Aminael Sanchez-Rodriguez, Elisa van der Zande, Kathleen Marchal, and Kevin J Verstrepen. 2012. “Nucleosomes Affect Local Transformation Efficiency.” NUCLEIC ACIDS RESEARCH 40 (19): 9506–12. https://doi.org/10.1093/nar/gks777.
Chicago author-date (all authors)
Aslankoohi, Elham, Karin Voordeckers, Hong Sun, Aminael Sanchez-Rodriguez, Elisa van der Zande, Kathleen Marchal, and Kevin J Verstrepen. 2012. “Nucleosomes Affect Local Transformation Efficiency.” NUCLEIC ACIDS RESEARCH 40 (19): 9506–9512. doi:10.1093/nar/gks777.
Vancouver
1.
Aslankoohi E, Voordeckers K, Sun H, Sanchez-Rodriguez A, van der Zande E, Marchal K, et al. Nucleosomes affect local transformation efficiency. NUCLEIC ACIDS RESEARCH. 2012;40(19):9506–12.
IEEE
[1]
E. Aslankoohi et al., “Nucleosomes affect local transformation efficiency,” NUCLEIC ACIDS RESEARCH, vol. 40, no. 19, pp. 9506–9512, 2012.
@article{3185746,
  abstract     = {{Genetic transformation is a natural process during which foreign DNA enters a cell and integrates into the genome. Apart from its relevance for horizontal gene transfer in nature, transformation is also the cornerstone of today's recombinant gene technology. Despite its importance, relatively little is known about the factors that determine transformation efficiency. We hypothesize that differences in DNA accessibility associated with nucleosome positioning may affect local transformation efficiency. We investigated the landscape of transformation efficiency at various positions in the Saccharomyces cerevisiae genome and correlated these measurements with nucleosome positioning. We find that transformation efficiency shows a highly significant inverse correlation with relative nucleosome density. This correlation was lost when the nucleosome pattern, but not the underlying sequence was changed. Together, our results demonstrate a novel role for nucleosomes and also allow researchers to predict transformation efficiency of a target region and select spots in the genome that are likely to yield higher transformation efficiency.}},
  author       = {{Aslankoohi, Elham and Voordeckers, Karin and Sun, Hong and Sanchez-Rodriguez, Aminael and van der Zande, Elisa and Marchal, Kathleen and Verstrepen, Kevin J}},
  issn         = {{0305-1048}},
  journal      = {{NUCLEIC ACIDS RESEARCH}},
  keywords     = {{SITE SELECTION,IN-VIVO,CHROMATIN-STRUCTURE,ILLEGITIMATE RECOMBINATION,RETROVIRAL INTEGRATION,GENE-EXPRESSION,T-DNA INTEGRATION,YEAST SACCHAROMYCES-CEREVISIAE,GENOME,PROMOTER}},
  language     = {{eng}},
  number       = {{19}},
  pages        = {{9506--9512}},
  title        = {{Nucleosomes affect local transformation efficiency}},
  url          = {{http://doi.org/10.1093/nar/gks777}},
  volume       = {{40}},
  year         = {{2012}},
}
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