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dc.contributor.authorBeh, Leslie Y.
dc.contributor.authorKaplan, Noam
dc.contributor.authorMuller, Manuel M.
dc.contributor.authorMuir, Tom W.
dc.contributor.authorLandweber, Laura F.
dc.date2022-08-11T08:08:23.000
dc.date.accessioned2022-08-23T15:53:22Z
dc.date.available2022-08-23T15:53:22Z
dc.date.issued2014-12-26
dc.date.submitted2018-06-21
dc.identifier.citation<p>bioRxiv 013250; doi: https://doi.org/10.1101/013250. <a href="https://doi.org/10.1101/013250" target="_blank">Link to preprint on bioRxiv service. </a></p>
dc.identifier.doi10.1101/013250
dc.identifier.urihttp://hdl.handle.net/20.500.14038/29341
dc.description.abstractA conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream of transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from the presence of subsets of nucleosomes, rather than the whole array, in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes, and affects codon usage and amino acid composition in genes. We propose that these ‘seed’ nucleosomes may aid the AT-rich Tetrahymena genome – which is intrinsically unfavorable for nucleosome formation – in establishing nucleosome arrays in vivo in concert with trans-acting factors, while minimizing changes to the coding sequences they are embedded within.
dc.language.isoen_US
dc.relationNow published in Genome Research doi: 10.1101/gr.188516.114
dc.rightsThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectgenomics
dc.subjectTetrahymena thermophila
dc.subjectchromatin
dc.subjecttranscription start sites
dc.subjectnucleosome
dc.subjecteukaryotes
dc.subjectDNA
dc.subjectGenetic Phenomena
dc.subjectGenomics
dc.subjectMolecular Biology
dc.subjectStructural Biology
dc.titleDNA-guided establishment of canonical nucleosome patterns in a eukaryotic genome [preprint]
dc.typePreprint
dc.source.journaltitlebioRxiv
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=2577&amp;context=faculty_pubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/faculty_pubs/1567
dc.identifier.contextkey12352693
refterms.dateFOA2022-08-23T15:53:23Z
html.description.abstract<p>A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream of transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from the presence of subsets of nucleosomes, rather than the whole array, in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes, and affects codon usage and amino acid composition in genes. We propose that these ‘seed’ nucleosomes may aid the AT-rich Tetrahymena genome – which is intrinsically unfavorable for nucleosome formation – in establishing nucleosome arrays in vivo in concert with trans-acting factors, while minimizing changes to the coding sequences they are embedded within.</p>
dc.identifier.submissionpathfaculty_pubs/1567
dc.contributor.departmentDepartment of Biochemistry and Molecular Pharmacology
dc.contributor.departmentProgram in Systems Biology


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The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
Except where otherwise noted, this item's license is described as The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.