| pubmed-article:18340041 | rdf:type | pubmed:Citation | lld:pubmed |
| pubmed-article:18340041 | lifeskim:mentions | umls-concept:C0035820 | lld:lifeskim |
| pubmed-article:18340041 | lifeskim:mentions | umls-concept:C0014834 | lld:lifeskim |
| pubmed-article:18340041 | lifeskim:mentions | umls-concept:C1167622 | lld:lifeskim |
| pubmed-article:18340041 | lifeskim:mentions | umls-concept:C0936012 | lld:lifeskim |
| pubmed-article:18340041 | pubmed:issue | 6 | lld:pubmed |
| pubmed-article:18340041 | pubmed:dateCreated | 2008-6-3 | lld:pubmed |
| pubmed-article:18340041 | pubmed:abstractText | We determined the genome-wide distribution of the nucleoid-associated protein Fis in Escherichia coli using chromatin immunoprecipitation coupled with high-resolution whole genome-tiling microarrays. We identified 894 Fis-associated regions across the E. coli genome. A significant number of these binding sites were found within open reading frames (33%) and between divergently transcribed transcripts (5%). Analysis indicates that A-tracts and AT-tracts are an important signal for preferred Fis-binding sites, and that A(6)-tracts in particular constitute a high-affinity signal that dictates Fis phasing in stretches of DNA containing multiple and variably spaced A-tracts and AT-tracts. Furthermore, we find evidence for an average of two Fis-binding regions per supercoiling domain in the chromosome of exponentially growing cells. Transcriptome analysis shows that approximately 21% of genes are affected by the deletion of fis; however, the changes in magnitude are small. To address the differential Fis bindings under growth environment perturbation, ChIP-chip analysis was performed using cells grown under aerobic and anaerobic growth conditions. Interestingly, the Fis-binding regions are almost identical in aerobic and anaerobic growth conditions-indicating that the E. coli genome topology mediated by Fis is superficially identical in the two conditions. These novel results provide new insight into how Fis modulates DNA topology at a genome scale and thus advance our understanding of the architectural bases of the E. coli nucleoid. | lld:pubmed |
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| pubmed-article:18340041 | pubmed:language | eng | lld:pubmed |
| pubmed-article:18340041 | pubmed:journal | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:18340041 | pubmed:citationSubset | IM | lld:pubmed |
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| pubmed-article:18340041 | pubmed:status | MEDLINE | lld:pubmed |
| pubmed-article:18340041 | pubmed:month | Jun | lld:pubmed |
| pubmed-article:18340041 | pubmed:issn | 1088-9051 | lld:pubmed |
| pubmed-article:18340041 | pubmed:author | pubmed-author:PalssonBernha... | lld:pubmed |
| pubmed-article:18340041 | pubmed:author | pubmed-author:ChoByung-Kwan... | lld:pubmed |
| pubmed-article:18340041 | pubmed:author | pubmed-author:KnightEric... | lld:pubmed |
| pubmed-article:18340041 | pubmed:author | pubmed-author:BarrettChrist... | lld:pubmed |
