基因环在酵母中的生理作用。
A physiological role for gene loops in yeast.
作者信息
Lainé Jean-Philippe, Singh Badri Nath, Krishnamurthy Shankarling, Hampsey Michael
机构信息
Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA.
出版信息
Genes Dev. 2009 Nov 15;23(22):2604-9. doi: 10.1101/gad.1823609.
Abstract
DNA loops that juxtapose the promoter and terminator regions of RNA polymerase II-transcribed genes have been identified in yeast and mammalian cells. Loop formation is transcription-dependent and requires components of the pre-mRNA 3'-end processing machinery. Here we report that looping at the yeast GAL10 gene persists following a cycle of transcriptional activation and repression. Moreover, GAL10 and a GAL1p-SEN1 reporter undergo rapid reactivation kinetics following a cycle of activation and repression-a phenomenon defined as "transcriptional memory"-and this effect correlates with the persistence of looping. We propose that gene loops facilitate transcriptional memory in yeast.
摘要
在酵母和哺乳动物细胞中已鉴定出使RNA聚合酶II转录基因的启动子和终止子区域并列的DNA环。环的形成依赖于转录，并且需要前体mRNA 3'末端加工机制的组分。在此，我们报道酵母GAL10基因处的环化在转录激活和抑制循环后持续存在。此外，GAL10和GAL1p-SEN1报告基因在激活和抑制循环后经历快速的再激活动力学——一种被定义为“转录记忆”的现象——并且这种效应与环化的持续性相关。我们提出基因环促进酵母中的转录记忆。
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1
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2
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J Biol Chem. 2009 Sep 11;284(37):25015-25. doi: 10.1074/jbc.M109.007948. Epub 2009 Jul 14.
3
Detection of gene loops by 3C in yeast.通过3C技术在酵母中检测基因环。
Methods. 2009 Aug;48(4):361-7. doi: 10.1016/j.ymeth.2009.02.018. Epub 2009 Mar 6.
4
Transcriptional memory at the nuclear periphery.核周的转录记忆
Curr Opin Cell Biol. 2009 Feb;21(1):127-33. doi: 10.1016/j.ceb.2009.01.007. Epub 2009 Jan 30.
5
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Mol Cell. 2008 Jul 11;31(1):104-13. doi: 10.1016/j.molcel.2008.05.015.
6
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7
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