Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology
Genetic Phenomena | Genomics | Molecular Biology | Structural Biology
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.
genomics, Tetrahymena thermophila, chromatin, transcription start sites, nucleosome, eukaryotes, DNA
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The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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.
DOI of Published Version
bioRxiv 013250; doi: https://doi.org/10.1101/013250. Link to preprint on bioRxiv service.
Beh LY, Kaplan N, Muller MM, Muir TW, Landweber LF. (2014). DNA-guided establishment of canonical nucleosome patterns in a eukaryotic genome [preprint]. UMass Chan Medical School Faculty Publications. https://doi.org/10.1101/013250. Retrieved from https://escholarship.umassmed.edu/faculty_pubs/1567
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