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Subtracting the sequence bias from partially digested MNase‑seq data reveals a general contribution of TFIIS to nucleosome positioning

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Subtracting the sequence bias from partially digested MNase‑seq data reveals a general contribution of TFIIS to nucleosome positioning

dc.contributor.author	Gutiérrez, Gabriel
dc.contributor.author	Millán-Zambrano, G.
dc.contributor.author	Medina Salas, Daniel Alejandro
dc.contributor.author	Jordán Plá, Antonio
dc.contributor.author	Pérez Ortín, José Enrique
dc.contributor.author	Peñate, Xenia
dc.contributor.author	Chávez, Sebastián
dc.date.accessioned	2017-12-11T15:24:21Z
dc.date.available	2017-12-11T15:24:21Z
dc.date.issued	2017
dc.identifier.citation	Gutiérrez, Gabriel Millán-Zambrano, G. Medina Salas, Daniel Alejandro Jordán Plá, Antonio Pérez Ortín, José Enrique Peñate, Xenia Chávez, Sebastián 2017 Subtracting the sequence bias from partially digested MNase‑seq data reveals a general contribution of TFIIS to nucleosome positioning Epigenetics & Chromatin 10 58 1 22
dc.identifier.uri	http://hdl.handle.net/10550/63528
dc.description.abstract	Background TFIIS stimulates RNA cleavage by RNA polymerase II and promotes the resolution of backtracking events. TFIIS acts in the chromatin context, but its contribution to the chromatin landscape has not yet been investigated. Co-transcriptional chromatin alterations include subtle changes in nucleosome positioning, like those expected to be elicited by TFIIS, which are elusive to detect. The most popular method to map nucleosomes involves intensive chromatin digestion by micrococcal nuclease (MNase). Maps based on these exhaustively digested samples miss any MNase-sensitive nucleosomes caused by transcription. In contrast, partial digestion approaches preserve such nucleosomes, but introduce noise due to MNase sequence preferences. A systematic way of correcting this bias for massively parallel sequencing experiments is still missing. Results To investigate the contribution of TFIIS to the chromatin landscape, we developed a refined nucleosome-mapping method in Saccharomyces cerevisiae. Based on partial MNase digestion and a sequence-bias correction derived from naked DNA cleavage, the refined method efficiently mapped nucleosomes in promoter regions rich in MNase-sensitive structures. The naked DNA correction was also important for mapping gene body nucleosomes, particularly in those genes whose core promoters contain a canonical TATA element. With this improved method, we analyzed the global nucleosomal changes caused by lack of TFIIS. We detected a general increase in nucleosomal fuzziness and more restricted changes in nucleosome occupancy, which concentrated in some gene categories. The TATA-containing genes were preferentially associated with decreased occupancy in gene bodies, whereas the TATA-like genes did so with increased fuzziness. The detected chromatin alterations correlated with functional defects in nascent transcription, as revealed by genomic run-on experiments. Conclusions The combination of partial MNase digestion and naked DNA correction of the sequence bias is a precise nucleosomal mapping method that does not exclude MNase-sensitive nucleosomes. This method is useful for detecting subtle alterations in nucleosome positioning produced by lack of TFIIS. Their analysis revealed that TFIIS generally contributed to nucleosome positioning in both gene promoters and bodies. The independent effect of lack of TFIIS on nucleosome occupancy and fuzziness supports the existence of alternative chromatin dynamics during transcription elongation.
dc.language.iso	eng
dc.relation.ispartof	Epigenetics & Chromatin, 2017, vol. 10, num. 58, p. 1-22
dc.subject	Biotecnologia
dc.subject	Genètica
dc.title	Subtracting the sequence bias from partially digested MNase‑seq data reveals a general contribution of TFIIS to nucleosome positioning
dc.type	journal article	es_ES
dc.date.updated	2017-12-11T15:24:21Z
dc.identifier.doi	10.1186/s13072-017-0165-x
dc.identifier.idgrec	121516
dc.rights.accessRights	open access	es_ES