| Autor: |
Sarah, Diermeier, Petros, Kolovos, Leonhard, Heizinger, Uwe, Schwartz, Theodore, Georgomanolis, Anne, Zirkel, Gero, Wedemann, Frank, Grosveld, Tobias A, Knoch, Rainer, Merkl, Peter R, Cook, Gernot, Längst, Argyris, Papantonis |
| Rok vydání: |
2014 |
| Předmět: |
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| Zdroj: |
Genome Biology |
| ISSN: |
1474-760X |
| Popis: |
Background The rearrangement of nucleosomes along the DNA fiber profoundly affects gene expression, but little is known about how signalling reshapes the chromatin landscape, in three-dimensional space and over time, to allow establishment of new transcriptional programs. Results Using micrococcal nuclease treatment and high-throughput sequencing, we map genome-wide changes in nucleosome positioning in primary human endothelial cells stimulated with tumour necrosis factor alpha (TNFα) - a proinflammatory cytokine that signals through nuclear factor kappa-B (NF-κB). Within 10 min, nucleosomes reposition at regions both proximal and distal to NF-κB binding sites, before the transcription factor quantitatively binds thereon. Similarly, in long TNFα-responsive genes, repositioning precedes transcription by pioneering elongating polymerases and appears to nucleate from intragenic enhancer clusters resembling super-enhancers. By 30 min, widespread repositioning throughout megabase pair-long chromosomal segments, with consequential effects on three-dimensional structure (detected using chromosome conformation capture), is seen. Conclusions Whilst nucleosome repositioning is viewed as a local phenomenon, our results point to effects occurring over multiple scales. Here, we present data in support of a TNFα-induced priming mechanism, mostly independent of NF-κB binding and/or elongating RNA polymerases, leading to a plastic network of interactions that affects DNA accessibility over large domains. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0536-6) contains supplementary material, which is available to authorized users. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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