Profiling DNA supercoiling domains in vivo.

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DNA supercoiling is the over- or under-winding of the DNA double helix, which occurs as a consequence of polymerase activity and is modulated by topoisomerase activity [5]. To map the distribution of DNA supercoiling in nuclei, we developed biotinylated 4,5,8-trimethylpsoralen (bTMP) pull-down to preferentially enrich for under-wound DNA. Here we describe in detail the experimental design, quality controls and analyses associated with the study by Naughton et al. [13] that characterised for the first time the large-scale distribution of DNA supercoiling in human cells (GEO: GSE43488 and GSE43450GSE43488GSE43450).", "claims": [{"id": "claim-method", "statement": "To further characterise supercoiling domains observed in the smoothed data a custom edge filter was designed based on Guelen et al. [6]. Smoothed data from bTMP pull-down experiments on untreated cells (‘Con’) and cells treated with the transcription inhibitor α-amanitin (‘Am) identify consistent domain boundaries, with substantial changes to the distribution of DNA supercoiling within these boundaries (Fig. 2b). Therefore, edges were defined based on the difference between ‘Con’ and ‘Am’ DNA supercoil distribution.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484106", "locator": "sections[8] \"Data analysis\" paragraph 4", "quote": "To further characterise supercoiling domains observed in the smoothed data a custom edge filter was designed based on Guelen et al. [6]. Smoothed data from bTMP pull-down experiments on untreated cells (‘Con’) and cells treated with the transcription inhibitor α-amanitin (‘Am) identify consistent domain boundaries, with substantial changes to the distribution of DNA supercoiling within these boundaries (Fig. 2b). Therefore, edges were defined based on the difference between ‘Con’ and ‘Am’ DNA supercoil distribution."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Microarray samples from Naughton et al. [13] are deposited in GEO under accession numbers GSE43448 and GSE43450GSE43448GSE43450.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484106", "locator": "sections[6] \"bTMP pull down data\" paragraph 3", "quote": "Microarray samples from Naughton et al. 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