Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.
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DOI：
10.1186/1471-2105-9-484
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发表时间：
2008-11-17
影响因子：
3
通讯作者：
Komorowski J
中科院分区：
文献类型：
--
作者：
Westholm JO;Xu F;Ronne H;Komorowski J
mRNA 转录速率由转录因子控制，转录因子与蛋白质编码基因上游启动子区域的特定 DNA 基序结合。最近的结果表明，不仅基序的存在，基序背景（例如基序的方向或其相对于编码序列的位置）对于基因调控也很重要。在这项研究中，我们提出了 ContextFinder，这是一种专门用于识别主题背景可能影响基因调控的情况的工具。我们使用 ContextFinder 来检查基序上下文在酿酒酵母中对转录因子 DNA 结合和对基因表达的影响的作用。对于 DNA 结合，我们发现了显着的基序位置偏差模式，而基序方向似乎并不重要。基序背景似乎对基因表达的影响甚至超过对 DNA 结合的影响，因为基序位置和方向的偏差在共表达基因的启动子中更为常见。我们根据核小体定位数据验证了我们的结果，发现首选基序位置和核小体占用之间存在负相关。我们得出的结论是，转录因子与 DNA 稳定结合的要求及其随后在基因调控中的功能可能会对基序背景施加限制。
The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence) is important for gene regulation. In this study we present ContextFinder, a tool that is specifically aimed at identifying cases where motif context is likely to affect gene regulation. We used ContextFinder to examine the role of motif context in S. cerevisiae both for DNA binding by transcription factors and for effects on gene expression. For DNA binding we found significant patterns of motif location bias, whereas motif orientations did not seem to matter. Motif context appears to affect gene expression even more than it affects DNA binding, as biases in both motif location and orientation were more frequent in promoters of co-expressed genes. We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy. We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.
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影响因子：
--
作者：
Andersson CR;Hvidsten TR;Isaksson A;Gustafsson MG;Komorowski J
通讯作者：
Komorowski J
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
11.4
作者：
BOORSTEIN, WR;CRAIG, EA
通讯作者：
CRAIG, EA
DOI：
10.1073/pnas.0605645103
发表时间：
2006-11-21
影响因子：
11.1
作者：
Miura, Fumihito;Kawaguchi, Noriko;Ito, Takashi
通讯作者：
Ito, Takashi
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y