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Series GSE223483 Query DataSets for GSE223483
Status Public on Aug 04, 2023
Title The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets
Organism Escherichia coli
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary While global transcription factors (TFs) have been studied extensively in Escherichia coli model strains, conservation and diversity in TF regulation between strains is still unknown. Here we use a combination of ChIP-exo--to define ferric uptake regulator (Fur) binding sites--and differential gene expression--to define the Fur regulon in nine E. coli strains. We then define a pan-regulon consisting of 469 target genes that includes all Fur target genes in all nine strains. The pan-regulon is then divided into the core regulon (target genes found in all the strains, n=36), the accessory regulon (target found in two to eight strains, n=158) and the unique regulon (target genes found in one strain, n=275). Thus, there is a small set of Fur regulated genes common to all nine strains, but a large number of regulatory targets unique to a particular strain. Many of the unique regulatory targets are genes unique to that strain. This first-established pan-regulon reveals a common core of conserved regulatory targets and significant diversity in transcriptional regulation amongst E. coli strains, reflecting diverse niche specification and strain history.
Overall design Identification of genome-wide Fur bindings for transcription factors in multi-strains using ChIP-exo technology
Contributor(s) Gao Y, Palsson B
Citation(s) 37026477
Submission date Jan 23, 2023
Last update date Aug 05, 2023
Contact name Ye Gao
Organization name UCSD
Street address 9500 Gilman Dr.
City La Jolla
ZIP/Postal code 92093
Country USA
Platforms (1)
GPL25368 Illumina NovaSeq 6000 (Escherichia coli)
Samples (4)
GSM6957441 MG1655_fe_1
GSM6957442 MG1655_fe_2
GSM6957443 MG1655_fe_dpd_1
BioProject PRJNA926523

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE223483_RAW.tar 150.9 Mb (http)(custom) TAR (of GFF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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