Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.
Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.
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DOI：
10.1093/nar/gkr1236
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发表时间：
2012-04
影响因子：
14.9
通讯作者：
Luscombe NM
中科院分区：
文献类型：
--
作者：
Prieto AI;Kahramanoglou C;Ali RM;Fraser GM;Seshasayee AS;Luscombe NM
IHF和HU是两种异源二聚体的核苷酸相关蛋白（NAP），属于同一个蛋白质家族，但与DNA的相互作用不同。IHF是一种序列特异性DNA结合蛋白，可使DNA弯曲超过160°。HU是最保守的NAP，其非特异性地结合双链体DNA，特别偏好靶向有切口和弯曲的DNA。尽管它们的重要性，在体内的两种蛋白质的相互作用的DNA仍然是在一个高分辨率和全基因组规模的描述。此外，这些蛋白质在全球范围内对基因表达的影响仍然存在争议。最后，同源和异源二聚体形式的蛋白质的功能之间的对比值得进一步研究的注意。在这里，我们提出了一个基因组规模的研究HU和IHF结合大肠杆菌K12染色体使用ChIP-seq。我们还进行了基因表达的微阵列分析，在每个蛋白质的单和双缺失突变体，以确定其调节子。IHF的序列特异性结合谱涵盖了所有操纵子的约30%，尽管这些操纵子中<10%的表达受到其缺失的影响，表明了组合控制或分子备份。HU的结合谱反映了与染色体的相对非特异性结合，然而，优选富含A/T的DNA。HU调节子包含高度保守的基因，包括那些必需的和可能超螺旋敏感的基因。最后，在可能的情况下，通过对IHF和HU的每个亚基在不存在其他亚基的情况下进行ChIP-seq实验，我们定义了异源和同源二聚体形式的蛋白质的DNA结合的全基因组图谱。
IHF and HU are two heterodimeric nucleoid-associated proteins (NAP) that belong to the same protein family but interact differently with the DNA. IHF is a sequence-specific DNA-binding protein that bends the DNA by over 160°. HU is the most conserved NAP, which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. Despite their importance, the in vivo interactions of the two proteins to the DNA remain to be described at a high resolution and on a genome-wide scale. Further, the effects of these proteins on gene expression on a global scale remain contentious. Finally, the contrast between the functions of the homo- and heterodimeric forms of proteins deserves the attention of further study. Here we present a genome-scale study of HU- and IHF binding to the Escherichia coli K12 chromosome using ChIP-seq. We also perform microarray analysis of gene expression in single- and double-deletion mutants of each protein to identify their regulons. The sequence-specific binding profile of IHF encompasses ∼30% of all operons, though the expression of <10% of these is affected by its deletion suggesting combinatorial control or a molecular backup. The binding profile for HU is reflective of relatively non-specific binding to the chromosome, however, with a preference for A/T-rich DNA. The HU regulon comprises highly conserved genes including those that are essential and possibly supercoiling sensitive. Finally, by performing ChIP-seq experiments, where possible, of each subunit of IHF and HU in the absence of the other subunit, we define genome-wide maps of DNA binding of the proteins in their hetero- and homodimeric forms.
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影响因子：
3.6
作者：
Corcoran, Colin P.;Dorman, Charles J.
通讯作者：
Dorman, Charles J.
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
影响因子：
3.6
作者：
Jovanovic, G;Model, P
通讯作者：
Model, P
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：
4.8
作者：
Balandina, A;Kamashev, D;Rouviere-Yaniv, J
通讯作者：
Rouviere-Yaniv, J