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| Status |
Public on Dec 25, 2017 |
| Title |
The Escherichia coli nucleoid is shaped around replication and transcription [GCC] |
| Organism |
Escherichia coli |
| Experiment type |
Other
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| Summary |
The Escherichia coli nucleoid is confined within a rod shaped cell many times smaller than the outstretched chromosome. While extensive compaction is necessary for this process, the chromosome must at the same time remain accessible to essential cellular processes such as replication and transcription. Currently, the individual contributions of cellular confinement, chromosome topology, replication and transcription on nucleoid organization are not well understood. Here we synchronize E. coli cells in stationary phase, where replication has ceased, each cell contains only one copy of the chromosome, and transcription is minimal. We then release the cells and capture chromosome contacts and transcription immediately following release and through-out one cell cycle. Polymer models of confined and topologically constrained circular polymers revealed that cellular confinement and topology do not contribute extensively to the organization of the E. coli nucleoid. Rather, local nucleoid structure is established concurrent with replication, and higher order organization is formed by the replication dependant clustering of linearly distant SeqA bound sites and cell cycle specific gene transcription.
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| Overall design |
There are six proximity ligation (GCC) samples, two biological replicates at t=0, at t=1 and t=2 hours following release of E. coli cells from the stationary phase.
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| Contributor(s) |
Bowden R, O'Sullivan JM |
| Citation missing |
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| Submission date |
Sep 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Justin M. O'Sullivan |
| E-mail(s) |
justin.osullivan@auckland.ac.nz
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| Organization name |
University of Auckland
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| Department |
Liggins Institute
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| Street address |
85 Park Road, Grafton
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| City |
Auckland |
| ZIP/Postal code |
1023 |
| Country |
New Zealand |
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| Platforms (1) |
| GPL14548 |
Illumina HiSeq 2000 (Escherichia coli) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE87118 |
The Escherichia coli nucleoid is shaped around replication and transcription |
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| Relations |
| BioProject |
PRJNA343606 |
| SRA |
SRP090168 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE87117_RAW.tar |
2.1 Gb |
(http)(custom) |
TAR (of FASTA, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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