Genome organisation and chromatin structure in Escherichia coli
Genome organisation and chromatin structure in Escherichia coli
复制标题
DOI：
10.1016/s0300-9084(00)01225-6
复制
发表时间：
2001-02-01
期刊：
影响因子：
3.9
通讯作者：
Brunak, S
中科院分区：
文献类型：
--
作者：
Ussery, D;Larsen, TS;Brunak, S
我们分析了大肠杆菌K12分离株MG1655基因组染色质相关蛋白结合位点的完整序列，并将预测位点的位置与“DNA芯片”实验的实验表达数据进行了比较。在大肠杆菌中与染色质相关的12种蛋白中，只有3种显示出明显的结合偏好：整合宿主因子（IHF）具有最强的结合位点偏好，FIS位点表现出弱共识，H-NS蛋白的结合位点没有明确的共识。利用隐马尔可夫模型（hmm），我们预测了608个IHF位点的位置，它们分散在整个基因组中。与重复有关的IHF位点的一个子集倾向于聚集在复制起点周围。我们估计大肠杆菌中可能有大约6000个FIS位点，这些位点往往位于复制末端两侧的两个区域。我们还发现，受H-NS调控的基因的上游区域比其他基因的上游区域更弯曲，AT含量更高。这些区域通常也会定位在复制末端附近。(C) 2001法国生物化学和生物分子学会/ Elsevier SAS科学和医学版。
We have analysed the complete sequence of the Escherichia coli K12 isolate MG1655 genome for chromatin-associated protein binding sites, and compared the predicted location of predicted sites with experimental expression data from 'DNA chip' experiments. Of the dozen proteins associated with chromatin in E. coli, only three have been shown to have significant binding preferences: integration host factor (IHF) has the strongest binding site preference, and FIS sites show a weak consensus, and there is no clear consensus site for binding of the H-NS protein. Using hidden Markov models (HMMs), we predict the location of 608 IHF sites, scattered throughout the genome. A subset of the IHF sites associated with repeats tends to be clustered around the origin of replication. We estimate there could be roughly 6000 FIS sites in E. coli, and the sites tend to be localised in two regions flanking the replication termini. We also show that the regions upstream of genes regulated by H-NS are more curved and have a higher AT content than regions upstream of other genes. These regions in general would also be localised near the replication terminus. (C) 2001 Societe francaise de biochimie et biologie moleculaire / Editions scientifiques et medicales Elsevier SAS.