NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE74364 Query DataSets for GSE74364
Status Public on Jun 05, 2016
Title Transcription rate and transcript length drive the formation of chromosomal interaction domain
Organism Caulobacter vibrioides CB15
Experiment type Other
Expression profiling by high throughput sequencing
Summary Chromosomes in all organisms are highly organized and divided into multiple chromosomal interaction domains, or topological domains. Regions of active, high transcription help establish and maintain domain boundaries, but precisely how this occurs remains unclear. Here, using fluorescence microscopy and chromosome conformation capture in conjunction with deep sequencing (Hi-C), we show that in Caulobacter crescentus both transcription rate and transcript length, independent of concurrent translation, drive the formation of domain boundaries. We find that long, highly expressed genes do not form topological boundaries simply through the inhibition of supercoil diffusion. Instead, our results support a model in which long, active regions of transcription drive local decompaction of the chromosome, with these more open regions of the chromosome forming spatial gaps in vivo that diminish contacts between DNA in neighboring domains. These insights into the molecular forces responsible for domain formation in Caulobacter likely generalize to other bacteria and possibly eukaryotes.
 
Overall design Hi-C experiments were performed on (i) untreated wild type swarmer cells and drug-treated swarmer cells (Chloramphenicol) of Caulobacter crescentus CB15N; (ii) on swarmer cells that are starved in M2 salts for 90 minutes; (iii) on swarmer cells harboring van::PrsaA_rsaA as well as derivatives of rsaA with a cassette of 2xTAA 2x transcription terminator inserted at 60bp, 560bp, 1060 and 2060 bp from the transcription start site of the ectopic rsaA; (iv) on CB15N strain ML2000 (Plac::dnaA) at time points 90 min, 150 min, 210 min and 270 min after IPTG withdrawal; and (v) on CB15N strain overexpressing CtrAD51E_delta_omega at time point 0 min, 120 min and 180 min after addition of the inducer (xylose). RNA-seq experiment were performed on RNA extracted from (i) wild-type CB15N cells growing at exponential phase in PYE; and (ii) wild-type CB15N cells starved in M2 salts for 90 min.
 
Contributor(s) Le TB, Laub MT
Citation(s) 27288403
Submission date Oct 26, 2015
Last update date May 15, 2019
Contact name Tung Ba Khanh Le
E-mail(s) tung.le@jic.ac.uk
Phone 01603450776
Organization name John Innes Centre
Department Department of Molecular Microbiology
Lab www.tunglelab.org
Street address Colney Lane
City Norwich
State/province Norfolk
ZIP/Postal code NR4 7UH
Country United Kingdom
 
Platforms (1)
GPL17001 Illumina HiSeq 2000 (Caulobacter crescentus CB15)
Samples (23)
GSM1918945 Laublab_BglII_NA1000_Chloramphenicol50_30min
GSM1918946 Laublab_BglII_NA1000_ML2000_150min_after_IPTG_withdrawal
GSM1918947 Laublab_BglII_NA1000_ML2000_210min_after_IPTG_withdrawal
Relations
BioProject PRJNA299824
SRA SRP065280

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
GSE74364_RAW.tar 32.9 Mb (http)(custom) TAR (of TXT)
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