The signi cant increase in interaction frequency was lost when com parisons were made with random sets that have conserved linear spacing.Note that the differences observed in signicance when the test data set was compared with randomly generated data sets conrm that the linear spacing of E. coli loci is important. Whether this is an effect or cause of spatial organization remains to be determined. Intra or inter NAP binding site clustering does not contribute to the global organization of the E. coli nucleoid We investigated the clustering and interaction properties of H NS,IHF and Fis binding sites, which are not enriched in any particular macrodomain. There is no de tectable clustering for the 200 bp regions surrounding the Fis,H NS and IHF binding sites in either the exponen tial or SHX treated nucleoids.Moreover, the classical NAP binding sites have depleted levels of inter actions in exponentially growing E.
coli cells. These results can be explained by restrictions PTC124 clinical trial in the exi bility of the DNA because of the binding of the NAP. However, increasing the length of the region surrounding the binding site has no effect on the clustering.Additionally, we do not observe intra NAP,binding site clustering,consistent with the temporal isolation of the expression of these NAPs.Genes up or downregulated after SHX treatment exist in different spatial environments, conrming functional compartmentalization of the nucleoid Eukaryotic inhibitor price studies have identied a non random distribu tion of gene expression associated with the presence of spatially distinct environments that promote or inhibit nuclear functions.Similarly, we observe that E. coli genes whose transcript levels increased or decreased in response to SHX treatment are overrepre sented in some gene ontology terms and are non randomly distributed across the linear genome in a manner that does not correlate with GC content.
There is no correlation between transcript level and interaction frequency at the level of specic restriction fragments.However, the SHX downregulated genes have high average tran script,clustering and interaction levels in exponential phase cells. These results suggest that genes that are highly ex pressed in exponential phase and downregulated after SHX treatment are not only linearly but also highly spa tially clustered. In conjunction with microscopic observations of large RNA polymerase clusters within exponentially growing E. coli cells,our results support the hypothesis that the highly expressed exponential phase genes are associated with transcription foci. Despite this, genes downregulated in response to SHX treatment remained highly clustered.Similarly, upregulated genes within lowly clustered regions do not increase their clustering on activation.