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| 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
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| 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.
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| Overall design |
Identification of genome-wide Fur bindings for transcription factors in multi-strains using ChIP-exo technology
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| Contributor(s) |
Gao Y, Palsson B |
| Citation(s) |
37026477 |
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| Submission date |
Jan 23, 2023 |
| Last update date |
Aug 05, 2023 |
| Contact name |
Ye Gao |
| E-mail(s) |
yeg002@ucsd.edu
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| Organization name |
UCSD
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| Street address |
9500 Gilman Dr.
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| City |
La Jolla |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (1) |
| GPL25368 |
Illumina NovaSeq 6000 (Escherichia coli) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA926523 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE223483_RAW.tar |
150.9 Mb |
(http)(custom) |
TAR (of GFF) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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