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Series GSE102091 Query DataSets for GSE102091
Status Public on Aug 10, 2017
Title The Nucleoid Protein Dps Binds Genomic DNA of Escherichia coli in a Non-random Manner
Organism Escherichia coli str. K-12 substr. MG1655
Experiment type Expression profiling by high throughput sequencing
Summary Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. Ferroxidase activity of Dps is rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. Using the ChIP-seq data presented here, we found a non-random distribution of Dps binding sites in the bacterial chromosome of exponentially growing cells and showed their enrichment with inverted repeats prone to form secondary structures. We found that the Dps-bound regions overlap with sites occupied by other nucleoid proteins, and contain overrepresented motifs typical for their consensus sequences. Of the two types of genomic domains with extensive protein occupancy, which can be highly expressed or transcriptionally silent only those that are enriched with RNA polymerase molecules were preferentially occupied by Dps. The transcription activity of several Dps-targeted genes evaluated by qRT-PCR, showed dependence on the presence of Dps. Thus, protecting bacterial cells from different stresses during exponential growth, Dps can modulate transcriptional integrity of the bacterial chromosome hampering RNA biosynthesis from some genes via competition with RNA or, vice versa, competing with inhibitors to activate transcription.
 
Overall design ChIP-Seq for Dps from Escherichia coli K12 MG1655
 
Contributor(s) Antipov SS, Tutukina MN, Preobrazhenskaya EV, Kondrashov FA, Patrushev MV, Toshchakov SV, Dominova I, Shvyreva US, Vrublevskaya VV, Morenkov OS, Sukharicheva NA, Panyukov VV, Ozoline ON
Citation(s) 28800583
Submission date Jul 31, 2017
Last update date May 15, 2019
Contact name Olga N Ozoline
E-mail(s) [email protected]
Organization name Institute of Cell Biophysics of Russian Academy of Sciences
Department Functional Genomics and Cellular Stress
Lab Functional Genomics and Cellular Stress
Street address Institutskaya
City Pushchino
State/province Moscow Region
ZIP/Postal code 142290
Country Russia
 
Platforms (2)
GPL15010 Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)
GPL17439 Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)
Samples (4)
GSM2723763 Exp 1_control
GSM2723764 Exp 1_IP sample
GSM2723765 Exp 2_control
Relations
BioProject PRJNA396582
SRA SRP114473

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE102091_Dps-bound_regions.txt.gz 7.7 Kb (ftp)(http) TXT
GSE102091_Dps-unbound_regions.txt.gz 13.3 Kb (ftp)(http) TXT
GSE102091_Experiment_1_CLC_GW_peaks.txt.gz 231.0 Kb (ftp)(http) TXT
GSE102091_Experiment_1_Matcher_peaks.txt.gz 3.5 Kb (ftp)(http) TXT
GSE102091_Experiment_2_CLC_GW_peaks.txt.gz 84.5 Kb (ftp)(http) TXT
GSE102091_Experiment_2_Matcher_peaks.txt.gz 27.1 Kb (ftp)(http) TXT
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