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DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome

Author(s): Beh, Leslie Y.; Müller, Manuel M.; Muir, Thomas W.; Kaplan, Noam; Landweber, Laura F.

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Abstract: A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream from 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. Given that the AT-rich Tetrahymena genome is intrinsically unfavorable for nucleosome formation, we propose that these “seed” nucleosomes—together with trans-acting factors—may facilitate the establishment of nucleosome arrays within genes in vivo, while minimizing changes to the underlying coding sequences.
Publication Date: Nov-2015
Electronic Publication Date: 1-Sep-2015
Citation: Beh, Leslie Y., Müller, Manuel M., Muir, Thomas W., Kaplan, Noam, Landweber, Laura F. (2015). DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome. Genome Research, 25 (11), 1727 - 1738. doi:10.1101/gr.188516.114
DOI: doi:10.1101/gr.188516.114
ISSN: 1088-9051
EISSN: 1549-5469
Pages: 25:1727 - 1738
Type of Material: Journal Article
Journal/Proceeding Title: Genome Research
Version: Final published version. Article is made available in OAR by the publisher's permission or policy.

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