NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE213028 Query DataSets for GSE213028
Status Public on Dec 01, 2023
Title Transcriptional units form the elementary constraining building blocks of the bacterial chromosome
Organism Escherichia coli
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Transcription generates local topological and mechanical constraints along the DNA fiber, driving for instance the generation of supercoiled chromosomal domains in bacteria. However, the global impact of transcription-based regulation of chromosome organization remains elusive. Notably, the scale of genes and operons in bacteria remains well below the resolution of chromosomal contact maps generated using Hi-C (~ 5 - 10 kb), preventing to resolve the impact of transcription on genomic organization at the fine-scale. Here, we combined sub-kb Hi-C contact maps and chromosome engineering to visualize individual transcriptional units (TUs) while turning off transcription across the rest of the genome. We show that each TU forms a discrete, transcription-induced 3D domain (TIDs). These local structures impose mechanical and topological constraints on their neighboring sequences at larger scales, bringing them closer together and restricting their dynamics. These results show that the primary building blocks of bacteria chromosome folding consists of transcriptional domains that together shape the global genome structure.
 
Overall design ChIP-seq method described in Cockram et al. 2015 doi: 10.1073/pnas.142426911
 
Contributor(s) Bignaud A, Cockram C, Allemand E, Mozziconnacci J, Espeli O, Koszul R
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA844206
Submission date Sep 09, 2022
Last update date Dec 01, 2023
Contact name Amaury Bignaud
E-mail(s) amaury.bignaud@pasteur.fr
Organization name Institut Pasteur
Street address 28 Rue du Docteur Roux
City Paris
ZIP/Postal code 75015
Country France
 
Platforms (1)
GPL28126 NextSeq 550 (Escherichia coli)
Samples (15)
GSM6569544 ChIP-seq T7 RNAP of Escherichia coli: RSG_B834 - 2h arabinose + 10 min rifampicin
GSM6569545 ChIP-seq T7 RNAP of Escherichia coli: RSG_B835 - 2h arabinose + 10 min rifampicin
GSM6569546 ChIP-seq T7 RNAP of Escherichia coli: RSG_B836 - 2h arabinose + 10 min rifampicin

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
GSE213028_RAW.tar 171.3 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.