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核小体影响局部转化效率。

Nucleosomes affect local transformation efficiency.

机构信息

Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, B-3001 Leuven, Belgium.

出版信息

Nucleic Acids Res. 2012 Oct;40(19):9506-12. doi: 10.1093/nar/gks777. Epub 2012 Aug 16.

DOI:10.1093/nar/gks777
PMID:22904077
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3479212/
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.

摘要

遗传转化是一种自然过程，在此过程中外源 DNA 进入细胞并整合到基因组中。除了在自然界中对水平基因转移具有重要意义外，转化也是当今重组基因技术的基石。尽管其重要性不言而喻，但人们对决定转化效率的因素知之甚少。我们假设与核小体定位相关的 DNA 可及性差异可能会影响局部转化效率。我们研究了酿酒酵母基因组中不同位置的转化效率图谱，并将这些测量结果与核小体定位相关联。我们发现，转化效率与相对核小体密度呈高度显著的负相关。当改变核小体模式而不是潜在序列时，这种相关性就会丢失。总之，我们的研究结果证明了核小体的新作用，也使研究人员能够预测目标区域的转化效率，并选择基因组中可能产生更高转化效率的区域。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b940/3479212/199fbccf9a56/gks777f4p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b940/3479212/76d57c1b6944/gks777f1p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b940/3479212/554b39aee1cf/gks777f2p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b940/3479212/e1cd1abcd6f9/gks777f3p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b940/3479212/199fbccf9a56/gks777f4p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b940/3479212/76d57c1b6944/gks777f1p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b940/3479212/554b39aee1cf/gks777f2p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b940/3479212/e1cd1abcd6f9/gks777f3p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b940/3479212/199fbccf9a56/gks777f4p.jpg

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2
A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon.核小体表面定义了酿酒酵母 Ty1 反转录转座子的整合热点。
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3
Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots.
Biotechnol Biofuels. 2017 Jul 18;10:189. doi: 10.1186/s13068-017-0872-3. eCollection 2017.
4
Enhanced targeted integration mediated by translocated I-SceI during the Agrobacterium mediated transformation of yeast.农杆菌介导的酵母转化过程中，易位的I-SceI介导的增强靶向整合。
Sci Rep. 2015 Feb 9;5:8345. doi: 10.1038/srep08345.
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amdSYM, a new dominant recyclable marker cassette for Saccharomyces cerevisiae.amdSYM，一种新型的酿酒酵母优势可回收标记盒。
FEMS Yeast Res. 2013 Feb;13(1):126-39. doi: 10.1111/1567-1364.12024. Epub 2012 Dec 17.
逆转座子 Ty1 的整合目标是 tRNA 热点中特定定位的不对称核小体 DNA 片段。
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Nucleosome positioning in Saccharomyces cerevisiae.酵母中核小体的定位。
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