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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.

Original publication

DOI

10.1186/s13059-014-0536-6

Type

Journal article

Journal

Genome Biol

Publication Date

03/12/2014

Volume

15

Keywords

Binding Sites, Chromosomes, Human, DNA, DNA-Directed RNA Polymerases, High-Throughput Nucleotide Sequencing, Human Umbilical Vein Endothelial Cells, Humans, Molecular Sequence Data, NF-kappa B p50 Subunit, Nucleosomes, Sequence Analysis, RNA, Signal Transduction, Tumor Necrosis Factor-alpha