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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
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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.
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Overall design |
ChIP-seq method described in Cockram et al. 2015 doi: 10.1073/pnas.142426911
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Contributor(s) |
Bignaud A, Cockram C, Allemand E, Mozziconnacci J, Espeli O, Koszul R |
Citation missing |
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BioProject |
PRJNA844206 |
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Submission date |
Sep 09, 2022 |
Last update date |
Dec 01, 2023 |
Contact name |
Amaury Bignaud |
E-mail(s) |
amaury.bignaud@pasteur.fr
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Organization name |
Institut Pasteur
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Street address |
28 Rue du Docteur Roux
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City |
Paris |
ZIP/Postal code |
75015 |
Country |
France |
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Platforms (1) |
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Samples (15)
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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 |
GSM6569547 |
ChIP-seq T7 RNAP of Escherichia coli: RSG_B837 - 2h arabinose + 10 min rifampicin |
GSM6569548 |
ChIP-seq T7 RNAP of Escherichia coli: RSG_B838 - 2h arabinose + 10 min rifampicin |
GSM6569549 |
ChIP-seq T7 RNAP of Escherichia coli: RSG_B229 - 2h arabinose + 10 min rifampicin |
GSM6569550 |
ChIP-seq GapR of Escherichia coli: RSG_B791 - 2h arabinose + 10 min rifampicin |
GSM6569551 |
ChIP-seq GapR of Escherichia coli: RSG_B792 - 2h arabinose + 10 min rifampicin |
GSM6569552 |
ChIP-seq GapR of Escherichia coli: RSG_B793 - 2h arabinose + 10 min rifampicin |
GSM6569553 |
ChIP-seq GapR of Escherichia coli: RSG_B794 - 2h arabinose + 10 min rifampicin |
GSM6569554 |
ChIP-seq GapR of Escherichia coli: RSG_B795 - 2h arabinose + 10 min rifampicin |
GSM6569555 |
ChIP-seq GapR of Escherichia coli: RSG_B789 - 2h arabinose + 10 min rifampicin |
GSM6569556 |
ChIP-seq T7 RNAP of E coli: RSG_B012 - 2h glucoseHi-C (HpaII) of E coli: RSG_B834 - 2h arabinose + 10 min novobiocin |
GSM6569557 |
ChIP-seq T7 RNAP of E coli: RSG_B012 - 2h arabinoseHi-C (HpaII) of E coli: RSG_B834 - 2h arab. + 10 min rifam/novob |
GSM6569558 |
ChIP-seq T7 RNAP of E coli: RSG_B012 - 2h arabinose + 10 min rifampicinHi-C (HpaII) of E coli: RSG_B212 - 2h arabinose |
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