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Figure 1 | Genome Biology

Figure 1

From: TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning

Figure 1

Nucleosome repositioning in TNFα-responsive genes. (A) Strategy: HUVECs were serum-starved and stimulated with ΤΝFα (0, 10, 30 min), treated with MNase, and DNA associated with mononucleosomes (highlighted yellow) deep-sequenced. Nucleosomes reposition within 10 min to unmask NF-κB binding sites (magenta), before NF-κB enters the nucleus. (B) Browser tracks (vertical axes - reads/million; magnifications of transcription start sites shown below) for typical up- or down-regulated genes obtained by MNase-seq (green; reflects nucleosomal profiles; 0-min levels in grey underlie 10- and 30-min ones to facilitate comparison), p65 ChIP-seq (black; reflects NF-κB binding), and total RNA-seq (magenta; reflects RNAPII activity). (C) Nucleosome occupancy (reads/million; MNase-seq) at 0 (grey) or 30 min post-stimulation (green) along metagenes derived from 109 up-regulated (>0.6 log2 fold-change at 30 compared to 0 min, plus >100 reads mapping to each), 69 down-regulated (<−0.6 log2 fold-change, plus >100 reads mapping to each), and 509 constitutively expressed genes (±0.01 log2 fold-change, plus >100 reads mapping to each). Genes were aligned at transcription start/termination sites (dotted lines), gene bodies divided into 50-bp windows, lengths scaled proportionately, and MNase-seq reads in each window summed; profiles from 5 kbp up- and downstream are also displayed. ChIP-seq, chromatin immunoprecipitation coupled to high-throughput sequencing; kbp, kilobase pair; MNase-seq, micrococcal nuclease digestion followed by sequencing; NF-κB, nuclear factor kappa-B; RNA-seq, sequencing of total RNA; TNFα, tumour necrosis factor alpha; TSS, transcription start site; TTS, transcription termination site.

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