Computational protocol: Generation of a synthetic GlcNAcylated nucleosome reveals regulation of stability by H2A-Thr101 GlcNAcylation

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[…] OGT ChIP data published by Vella et al. was used for the analysis. DNase I sensitivity data were obtained from data deposited by the ENCODE project (Digital DNaseI from ENCODE/ University of Washington; ES-E14; 129/Ola; E0; hotspot-broadPeak: wgEncodeUwDnaseEse14129olaME0HotspotsRep1). Previously called peaks reported in Vella et al. and the DNaseI hotspot-broadPeak were used to analyse overlap between OGT and DNaseI sensitive sites. Data was analysed using Galaxy and visualized using the UCSC genome browser.Overlapping regions were found using the ‘Operate on Genomic Intervals/intersect' tool in Galaxy. For 11552 OGT peaks 11233 overlap with DNase-sensitive sites (97%). For DNase-sensitive sites 12257 of 270487 peaks overlap with OGT peaks (4.5%). Further statistical analysis was performed using The Genomic HyperBrowser (https://hyperbrowser.uio.no/). Using the Statistical analysis tool, we tested for significance of the overlap using following settings: Alternative hypothesis: more, Null model: Preserve segments (T2) and segment length (T1); Randomize Positions (T1) (MC), MCFDR sampling depth: Moderate resolution of global and local P-values, Random seed: Random. With these setting we obtained a P-value of 0.000999 for the overlap of OGT (T1) and DNase (T2) sensitive sites.To analyse peaks that are close at TSS, we included all OGT (4,000) and DNase (12,677) peaks that are within +− 500 bp of an annotated TSS. Of these 3,894 OGT peaks (97%) overlap with DNase-sensitive sites and 3,983 DNase-sensitive regions overlap with OGT peaks (31%). Using the same parameters as described above a P-value of 0.000999 was obtained for the overlap of OGT (T1) and DNase (T2) sensitive sites. […]

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