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Series GSE138845 Query DataSets for GSE138845
Status Public on Feb 01, 2020
Title Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria
Organism Brevundimonas subvibrioides
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Transcriptional rewiring is the regulation of different targets genes by orthologous regulators in different organisms. While this phenomenon has been observed, it has not been extensively studied, particularly in core regulatory systems. Several global cell cycle regulators are conserved in the Alphaproteobacteria, providing an excellent model to study this phenomenon. First characterized in Caulobacter crescentus, GcrA and CcrM compose a DNA methylation-based regulatory system that helps coordinate the complex life cycle of this organism. These regulators are well-conserved across Alphaproteobacteria, but the extent to which their regulatory targets are conserved is not known. In this study, the regulatory targets of GcrA and CcrM were analyzed by SMRT-seq, RNA-seq, and ChIP-seq technologies in the Alphaproteobacterium Brevundimonas subvibrioides, and then compared to those of its close relative C. crescentus that inhabits the same environment. Although the regulators themselves are highly conserved, the genes they regulate are vastly different. GcrA directly regulates 204 genes in C. crescentus, and though B. subvibrioides has orthologs to 147 of those genes, only 48 genes retained GcrA binding in their promoter regions. Additionally, only 12 of those 48 genes demonstrated significant transcriptional change in a gcrA mutant, suggesting extensive transcriptional rewiring between these organisms. Similarly, out of hundreds of genes CcrM regulates in each of these organisms, only 2 genes were found in common. When multiple Alphaproteobacterial genomes were analyzed bioinformatically for potential GcrA regulatory targets, the regulation of genes involved in DNA replication and cell division was well conserved across the Caulobacterales but not outside this order. This work suggests that significant transcriptional rewiring can occur in cell cycle regulatory systems even over short evolutionary distances.
 
Overall design ChIp-seq was performed in 3 biological replicates of gDNA of WT before (input DNA/control) and after immunoprecipitation.
 
Contributor(s) Adhikari S, Curtis PD
Citation(s) 33705385
Submission date Oct 15, 2019
Last update date Apr 07, 2021
Contact name Satish Adhikari
E-mail(s) [email protected]
Organization name University of Mississippi
Street address 415 Shoemaker Hall
City Oxford
State/province MS
ZIP/Postal code 38677
Country USA
 
Platforms (1)
GPL27606 Illumina NextSeq 500 (Brevundimonas subvibrioides)
Samples (6)
GSM4120364 IP/WT1
GSM4120365 IP/WT2
GSM4120366 IP/WT3
This SubSeries is part of SuperSeries:
GSE138847 Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria
Relations
BioProject PRJNA577593
SRA SRP225671

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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
GSE138845_RAW.tar 1.6 Mb (http)(custom) TAR (of BW)
GSE138845_sampe_combine_MACS2_output_peaks.txt.gz 31.8 Kb (ftp)(http) TXT
GSE138845_sampe_combine_MACS2_output_summits.bed.gz 13.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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