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Biochemical Analysis of Dimethyl Suberimidate-crosslinked Yeast Nucleosomes

dc.contributor.authorIchikawa, Yuichi
dc.contributor.authorKaufman, Paul D.
dc.date2022-08-11T08:09:49.000
dc.date.accessioned2022-08-23T16:44:57Z
dc.date.available2022-08-23T16:44:57Z
dc.date.issued2018-03-20
dc.date.submitted2018-05-30
dc.identifier.citation<p>Bio Protoc. 2018 Mar 20;8(6). doi: 10.21769/BioProtoc.2770. <a href="https://doi.org/10.21769/BioProtoc.2770">Link to article on publisher's site</a></p>
dc.identifier.issn2331-8325 (Linking)
dc.identifier.doi10.21769/BioProtoc.2770
dc.identifier.pmid29644260
dc.identifier.urihttp://hdl.handle.net/20.500.14038/40599
dc.description.abstractNucleosomes are the fundamental unit of eukaryotic chromosome packaging, comprised of 147 bp of DNA wrapped around two molecules of each of the core histone proteins H2A, H2B, H3, and H4. Nucleosomes are symmetrical, with one axis of symmetry centered on the homodimeric interaction between the C-termini of the H3 molecules. To explore the functional consequences of nucleosome symmetry, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, allowing us to compare cells with single or double H3 alterations. Our biochemical validation of the heterodimeric X-Y interaction included intra-nucleosomal H3 crosslinking using dimethyl suberimidate (DMS). Here, we provide a detailed protocol for the use of DMS to analyze yeast nucleosomes.
dc.language.isoen_US
dc.relation<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=29644260&dopt=Abstract">Link to Article in PubMed</a></p>
dc.relation.urlhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5891137/
dc.rightsCopyright Ichikawa and Kaufman. This article is distributed under the terms of the Creative Commons Attribution License (CC BY 4.0).
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectChromatin
dc.subjectCrosslink
dc.subjectHistone
dc.subjectNucleosome
dc.subjectProtein-protein interaction
dc.subjectStreptavidin affinity chromatography
dc.subjectAmino Acids, Peptides, and Proteins
dc.subjectBiochemistry
dc.subjectCell Biology
dc.subjectCells
dc.subjectFungi
dc.subjectGenetic Phenomena
dc.subjectInvestigative Techniques
dc.subjectLaboratory and Basic Science Research
dc.subjectMicrobiology
dc.subjectMolecular Biology
dc.titleBiochemical Analysis of Dimethyl Suberimidate-crosslinked Yeast Nucleosomes
dc.typeJournal Article
dc.source.journaltitleBio-protocol
dc.source.volume8
dc.source.issue6
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=4414&amp;context=oapubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/oapubs/3403
dc.identifier.contextkey12222284
refterms.dateFOA2022-08-23T16:44:57Z
html.description.abstract<p>Nucleosomes are the fundamental unit of eukaryotic chromosome packaging, comprised of 147 bp of DNA wrapped around two molecules of each of the core histone proteins H2A, H2B, H3, and H4. Nucleosomes are symmetrical, with one axis of symmetry centered on the homodimeric interaction between the C-termini of the H3 molecules. To explore the functional consequences of nucleosome symmetry, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, allowing us to compare cells with single or double H3 alterations. Our biochemical validation of the heterodimeric X-Y interaction included intra-nucleosomal H3 crosslinking using dimethyl suberimidate (DMS). Here, we provide a detailed protocol for the use of DMS to analyze yeast nucleosomes.</p>
dc.identifier.submissionpathoapubs/3403
dc.contributor.departmentDepartment of Molecular, Cell, and Cancer Biology


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Copyright Ichikawa and Kaufman. This article is distributed under the terms of the Creative Commons Attribution License (CC BY 4.0).
Except where otherwise noted, this item's license is described as Copyright Ichikawa and Kaufman. This article is distributed under the terms of the Creative Commons Attribution License (CC BY 4.0).