Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli.
Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli.
复制标题
DOI：
10.1093/nar/gkq934
复制
发表时间：
2011-03
影响因子：
14.9
通讯作者：
Luscombe NM
中科院分区：
文献类型：
--
作者：
Kahramanoglou C;Seshasayee AS;Prieto AI;Ibberson D;Schmidt S;Zimmermann J;Benes V;Fraser GM;Luscombe NM
类核相关蛋白(NAPs)是大肠杆菌中基因表达的全球调节因子，通过弯曲、包裹和桥接DNA来影响DNA的构象。其中两个-H-NS和fis-与特定的DNA序列和结构结合。由于它们对全球基因表达的重要性，以前使用芯片在全基因组范围内研究了这些NAP与DNA的结合。然而，它们在整个生长阶段结合谱的变化以及它们对基因表达的影响的基因组规模的性质仍然知之甚少。在这里，我们提出了一个基因组规模的H-NS和FIS与大肠杆菌染色体结合的研究，使用染色质免疫沉淀结合高通量测序(CHIP-SEQ)。通过在富介质中生长的多个时间点进行实验，我们发现在我们的实验条件下，这两种蛋白质的结合区是相互排斥的。H-NS与DNA的结合比FIS长得多，这与H-NS结合从高亲和力位点到周围低亲和力位点的线性扩散一致；结合区的长度与H-NS施加的转录抑制程度有关。对于FIS，大多数结合事件不会导致近端基因的差异表达，但它对基因表达有显著的间接影响，部分是通过影响其他转录因子的表达。我们认为，FIS的直接转录调控与FIS分子串联阵列与DNA的相互作用和可能的DNA弯曲有关，特别是在操纵子上游区域。我们的研究为在细菌中使用芯片序列来处理全球DNA结合蛋白提供了原理证明，随着多重技术的发展，这种方法应该会变得更加经济和可行。
Nucleoid-associated proteins (NAPs) are global regulators of gene expression in Escherichia coli, which affect DNA conformation by bending, wrapping and bridging the DNA. Two of these—H-NS and Fis—bind to specific DNA sequences and structures. Because of their importance to global gene expression, the binding of these NAPs to the DNA was previously investigated on a genome-wide scale using ChIP-chip. However, variation in their binding profiles across the growth phase and the genome-scale nature of their impact on gene expression remain poorly understood. Here, we present a genome-scale investigation of H-NS and Fis binding to the E. coli chromosome using chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-seq). By performing our experiments under multiple time-points during growth in rich media, we show that the binding regions of the two proteins are mutually exclusive under our experimental conditions. H-NS binds to significantly longer tracts of DNA than Fis, consistent with the linear spread of H-NS binding from high- to surrounding lower-affinity sites; the length of binding regions is associated with the degree of transcriptional repression imposed by H-NS. For Fis, a majority of binding events do not lead to differential expression of the proximal gene; however, it has a significant indirect effect on gene expression partly through its effects on the expression of other transcription factors. We propose that direct transcriptional regulation by Fis is associated with the interaction of tandem arrays of Fis molecules to the DNA and possible DNA bending, particularly at operon-upstream regions. Our study serves as a proof-of-principle for the use of ChIP-seq for global DNA-binding proteins in bacteria, which should become significantly more economical and feasible with the development of multiplexing techniques.
登录
查看更多内容
影响因子：
3.6
作者：
Browning, DF;Grainger, DC;Busby, SJW
通讯作者：
Busby, SJW
影响因子：
2.8
作者：
Bradley, Meranda D.;Beach, Michael B.;Osuna, Robert
通讯作者：
Osuna, Robert
模因套件：用于发现和搜索的工具。
影响因子：
14.9
作者：
Bailey TL;Boden M;Buske FA;Frith M;Grant CE;Clementi L;Ren J;Li WW;Noble WS
通讯作者：
Noble WS
DOI：
10.1073/pnas.120163297
发表时间：
2000-06-06
影响因子：
11.1
作者：
Datsenko, KA;Wanner, BL
通讯作者：
Wanner, BL
影响因子：
3.2
作者：
Grainger, DC;Overton, TW;Busby, SJW
通讯作者：
Busby, SJW