Comment[ArrayExpressAccession] E-GEOD-41975 MAGE-TAB Version 1.1 Public Release Date 2013-07-22 Investigation Title Avoiding chromosome pathology when replication forks collide Comment[Submitted Name] Avoiding chromosome pathology when replication forks collide Experiment Description Chromosome duplication normally initiates via the assembly of replication fork complexes at defined origins. DNA synthesis by any one fork is thought to cease when it meets another travelling in the opposite direction, at which stage the replication machinery may simply dissociate before the nascent strands are finally ligated. But what actually happens is not clear. Here we present evidence consistent with the idea that every fork collision has the potential to trigger re-replication of the already replicated DNA, thus posing a threat to genomic integrity. In Escherichia coli this threat is kept at bay by the RecG DNA translocase. Without RecG, replication initiates where forks meet, establishing new forks with the potential to sustain cell growth and division in the absence of an active origin. The studies reported raise the question of how eukaryotic and archaeal cells are able to exploit multiple origins for the duplication of each chromosome without any apparent ill effect from the consequent multiple fork collisions. Measurement of replication dynamics (marker frequency analysis; MFA) for E. coli strains, including wild-type and various mutants. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Nieduszynski Nieduszynski Rudolph Upton Stockum Lloyd Person First Name Conrad Conrad Christian Amy Anna Robert Person Mid Initials A A J L G Person Email conrad.nieduszynski@nottingham.ac.uk Person Affiliation University of Nottingham Person Address University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom Person Roles submitter Protocol Name P-GSE41975-3 P-GSE41975-1 P-GSE41975-2 Protocol Description None Samples from cultures of a strain grown to an A650 of ~1.2 in LB broth were diluted 400-fold in fresh broth and incubated with vigorous aeration until the A650 reached 0.4 at the temperature indicated. Samples from these exponential phase cultures were frozen in liquid nitrogen at this point for subsequent DNA extraction. Incubation of the remaining culture was continued until several hours after the culture had saturated and showed no further increase in the A650. A further sample (stationary phase) was frozen at this point. DNA was extracted using the GenElute Bacterial Genomic DNA Kit (Sigma-Aldrich). Library preparation and sequencing was carried out according to SOLiD instructions. Protocol Type sample treatment protocol growth protocol nucleic acid extraction protocol Experimental Factor Name RELEVANT GENOTYPE STRAIN OR LINE GROWTH PHASE Experimental Factor Type relevant genotype strain or line growth phase Publication Title Avoiding chromosome pathology when replication forks collide. Publication Author List Rudolph CJ, Upton AL, Stockum A, Nieduszynski CA, Lloyd RG PubMed ID 23892781 Publication DOI 10.1038/nature12312 Comment[SecondaryAccession] GSE41975 Comment[GEOReleaseDate] 2013-07-22 Comment[ArrayExpressSubmissionDate] 2012-11-01 Comment[GEOLastUpdateDate] 2013-08-11 Comment[AEExperimentType] other Comment[AdditionalFile:Data1] GSE41975.txt Comment[AdditionalFile:Data2] GSE41975_AB1157_MFA.wig Comment[AdditionalFile:Data3] GSE41975_AM1581_MFA.wig Comment[AdditionalFile:Data4] GSE41975_AM2018_MFA.wig Comment[AdditionalFile:Data5] GSE41975_AM2123_MFA.wig Comment[AdditionalFile:Data6] GSE41975_JJ1268_MFA.wig Comment[AdditionalFile:Data7] GSE41975_JJ1378_MFA.wig Comment[AdditionalFile:Data8] GSE41975_MG1655_MFA.wig Comment[AdditionalFile:Data9] GSE41975_N4702_MFA.wig Comment[AdditionalFile:Data10] GSE41975_N5740_MFA.wig Comment[AdditionalFile:Data11] GSE41975_N6576_MFA.wig Comment[AdditionalFile:Data12] GSE41975_N6576_stat_MFA.wig Comment[AdditionalFile:Data13] GSE41975_N6859_MFA.wig Comment[AdditionalFile:Data14] GSE41975_N6953_MFA.wig Comment[AdditionalFile:Data15] GSE41975_N7957_MFA.wig Comment[AdditionalFile:Data16] GSE41975_N7957_stat_MFA.wig Comment[AdditionalFile:Data17] GSE41975_N8226_MFA.wig Comment[AdditionalFile:Data18] GSE41975_N8227_MFA.wig Comment[AdditionalFile:Data19] GSE41975_N8227_stat_MFA.wig Comment[AdditionalFile:Data20] GSE41975_RCe260_MFA.wig Comment[AdditionalFile:Data21] GSE41975_RCe261_MFA.wig Comment[AdditionalFile:Data22] GSE41975_RCe268_MFA.wig Comment[AdditionalFile:Data23] GSE41975_RCe391_MFA.wig Comment[AdditionalFile:Data24] GSE41975_RCe399_MFA.wig Comment[AdditionalFile:Data25] GSE41975_RCe455_MFA.wig Comment[AdditionalFile:Data26] GSE41975_RCe475_MFA.wig Comment[AdditionalFile:Data27] GSE41975_WX296_MFA.wig Comment[SecondaryAccession] SRP016947 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR610427-SRR610451,SRR857925-SRR857932 SDRF File E-GEOD-41975.sdrf.txt