Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise.
Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise.
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DOI：
10.1101/gr.149096.112
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发表时间：
2013-06
期刊：
影响因子：
7
通讯作者：
Segal E
中科院分区：
文献类型：
--
作者：
Dadiani M;van Dijk D;Segal B;Field Y;Ben-Artzi G;Raveh-Sadka T;Levo M;Kaplow I;Weinberger A;Segal E
来自基因相同群体的单个细胞在基因表达上表现出很大的差异。这种变异的很大一部分是由于转录过程中的噪音，这是每个基因固有的，并由一些因素决定，如启动子在转录活跃和非活跃状态之间的转换速度，以及在活跃状态期间产生的转录本的数量。然而，我们对DNA序列如何影响这种启动子动力学的了解有限。在这里，我们使用单细胞时间推移显微镜来比较两种不同类型的启动子序列变化对转录动力学的影响，这两种类型的序列变化都可以增加细胞群体的平均表达量，但通过不同的机制。我们发现，与通过添加不利于核小体的序列增加表达相比，通过加强转录因子结合位点来增加表达会导致较慢的启动子动力学和更高的噪音。我们的结果表明，当获得相同的平均表达时，使用更强的结合位点的策略会导致从活性状态产生更多的转录本，而添加核小体不利序列的策略会导致启动子在活性状态和非活性状态之间转换的频率更高。在后一种策略中，这种增加的活性状态采样可能会降低细胞群体的表达变异性。因此，我们的研究证明了顺式调控元件对表达可变性的影响，并指出了可能允许表达水平和噪声部分解耦的具体类型的序列变化。
Individual cells from a genetically identical population exhibit substantial variation in gene expression. A significant part of this variation is due to noise in the process of transcription that is intrinsic to each gene, and is determined by factors such as the rate with which the promoter transitions between transcriptionally active and inactive states, and the number of transcripts produced during the active state. However, we have a limited understanding of how the DNA sequence affects such promoter dynamics. Here, we used single-cell time-lapse microscopy to compare the effect on transcriptional dynamics of two distinct types of sequence changes in the promoter that can each increase the mean expression of a cell population by similar amounts but through different mechanisms. We show that increasing expression by strengthening a transcription factor binding site results in slower promoter dynamics and higher noise as compared with increasing expression by adding nucleosome-disfavoring sequences. Our results suggest that when achieving the same mean expression, the strategy of using stronger binding sites results in a larger number of transcripts produced from the active state, whereas the strategy of adding nucleosome-disfavoring sequences results in a higher frequency of promoter transitions between active and inactive states. In the latter strategy, this increased sampling of the active state likely reduces the expression variability of the cell population. Our study thus demonstrates the effect of cis-regulatory elements on expression variability and points to concrete types of sequence changes that may allow partial decoupling of expression level and noise.
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DOI：
10.1126/science.1202142
发表时间：
2011-04-22
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Larson DR;Zenklusen D;Wu B;Chao JA;Singer RH
通讯作者：
Singer RH
影响因子：
12.3
作者：
Carpenter AE;Jones TR;Lamprecht MR;Clarke C;Kang IH;Friman O;Guertin DA;Chang JH;Lindquist RA;Moffat J;Golland P;Sabatini DM
通讯作者：
Sabatini DM
影响因子：
56.9
作者：
Suter, David M.;Molina, Nacho;Naef, Felix
通讯作者：
Naef, Felix
影响因子：
16
作者：
Blake, William J.;Balazsi, Gbor;Collins, James J.
通讯作者：
Collins, James J.
影响因子：
30.8
作者：
Choi, Jung Kyoon;Kim, Young-Joon
通讯作者：
Kim, Young-Joon