
@article {33715,
	title = {Regulation of Global Transcription in  by Rsd and 6S RNA.},
	journal = {G3 (Bethesda)},
	year = {2018},
	month = {2018 Apr 23},
	abstract = {<p>In , the sigma factor σ directs RNA polymerase to transcribe growth-related genes, while σ directs transcription of stress response genes during stationary phase. Two molecules hypothesized to regulate RNA polymerase are the protein Rsd, which binds to σ, and the non-coding 6S RNA which binds to the RNA polymerase-σ holoenzyme. Despite multiple studies, the functions of Rsd and 6S RNA remain controversial. Here we use RNA-Seq in five phases of growth to elucidate their function on a genome-wide scale. We show for the first time that Rsd and 6S RNA facilitate σ activity throughout bacterial growth, while 6S RNA also regulates widely different genes depending upon growth phase. We discover novel interactions between 6S RNA and Rsd and show widespread expression changes in a strain lacking both regulators. Finally, we present a mathematical model of transcription which highlights the crosstalk between Rsd and 6S RNA as a crucial factor in controlling sigma factor competition and global gene expression.</p>
},
	issn = {2160-1836},
	doi = {10.1534/g3.118.200265},
	author = {Lal, Avantika and Krishna, Sandeep and Seshasayee, Aswin Sai Narain}
}
@article {3566,
	title = {Genome scale patterns of supercoiling in a bacterial chromosome.},
	journal = {Nat Commun},
	volume = {7},
	year = {2016},
	month = {2016},
	pages = {11055},
	abstract = {<p>DNA in bacterial cells primarily exists in a negatively supercoiled state. The extent of supercoiling differs between regions of the chromosome, changes in response to external conditions and regulates gene expression. Here we report the use of trimethylpsoralen intercalation to map the extent of supercoiling across the Escherichia coli chromosome during exponential and stationary growth phases. We find that stationary phase E. coli cells display a gradient of negative supercoiling, with the terminus being more negatively supercoiled than the origin of replication, and that such a gradient is absent in exponentially growing cells. This stationary phase pattern is correlated with the binding of the nucleoid-associated protein HU, and we show that it is lost in an HU deletion strain. We suggest that HU establishes higher supercoiling near the terminus of the chromosome during stationary phase, whereas during exponential growth DNA gyrase and/or transcription equalizes supercoiling across the chromosome.</p>
},
	issn = {2041-1723},
	doi = {10.1038/ncomms11055},
	author = {Lal, Avantika and Dhar, Amlanjyoti and Trostel, Andrei and Kouzine, Fedor and Seshasayee, Aswin S N and Adhya, Sankar}
}
