The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA loops, and form oligomeric structures connected to repression of gene expression. Motivated by the link between chromosome organization, protein binding and gene expression, we analyzed publicly available genomic data sets of various origins, from genome-wide protein binding profiles to evolutionary information, exploring the connections between chromosomal organization, genesilencing, pseudo-gene localization and horizontal gene transfer. We report the existence of transcriptionally silent contiguous areas corresponding to large regions of H-NS protein binding along the genome, their position indicates a possible relationship with the known large-scale features of chromosome organization.
Deciphering the regulatory genome of $\textit{Escherichia coli}$, one hundred promoters at a time
DNA测序的进步彻底改变了我们阅读基因组的能力。然而，即使在研究最充分的生物体，细菌${\it Escherichia coli}$中，对于启动子的$\approx$ 65 $\%$，我们仍然完全不知道它们的调节。除非我们破解了这个监管的罗塞塔石碑，否则读写基因组的努力将仍然是偶然的。我们介绍了一种新的方法（Reg-Seq）连接一个平行的报告分析和质谱法产生一个碱基对分辨率解剖超过100个启动子在${\it E. coli}$在12个不同的生长条件。首先，我们表明，我们的方法概括了已知序列的监管信息。然后，我们研究了${\it E. coli}$基因组中80多个启动子的调控结构，这些启动子以前没有已知的调控。在许多情况下，我们还确定哪些转录因子介导其调节。本文介绍的方法为充分表征模式生物的调控基因组扫清了道路，并有可能转移到一系列具有生态和医学相关性的其他微生物上。
NSF-Simons National Institute for Theory and Mathematics in Biology（NSF-Simons生物理论与数学国家研究所）；James Franck Institute, The University of Chicago（芝加哥大学詹姆斯·弗兰克研究所）；Division of Biology and Biological Engineering, California Institute of Technology（加州理工学院生物学与生物工程系）；Department of Bioengineering, Stanford University（斯坦福大学生物工程系）；Department of Applied Physics, Stanford University（斯坦福大学应用物理系）；Departments of Molecular & Cell Biology and of Physics, Biophysics Graduate Group, Institute for Quantitative Biosciences-QB3, University of California, Berkeley（加州大学伯克利分校分子与细胞生物学系、物理学系、生物物理学研究生组、定量生物科学研究所-QB3）；Chan Zuckerberg Biohub–San Francisco（陈·扎克伯格生物枢纽旧金山中心）；Department of Physics, California Institute of Technology（加州理工学院物理学系）；Leinweber Institute for Theoretical Physics, The University of Chicago（芝加哥大学莱因韦伯理论物理研究所）；Chan Zuckerberg Biohub–Chicago（陈·扎克伯格生物枢纽芝加哥中心）
