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

TitleDNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome.
Publication TypeJournal Article
Year of Publication2015
AuthorsBeh, LY, Müller, MM, Muir, TW, Kaplan, N, Landweber, LF
JournalGenome Res
Volume25
Issue11
Pagination1727-38
Date Published2015 Nov
ISSN1549-5469
KeywordsChromosome Mapping, DNA, Protozoan, Genetic Association Studies, Genome, Protozoan, Nucleosomes, Open Reading Frames, Sequence Analysis, DNA, Tetrahymena thermophila, Transcription, Genetic
Abstract

<p>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.</p>

DOI10.1101/gr.188516.114
Alternate JournalGenome Res.
PubMed ID26330564
PubMed Central IDPMC4617968
Grant ListR01 GM059708 / GM / NIGMS NIH HHS / United States
R01 GM107047 / GM / NIGMS NIH HHS / United States
GM59708 / GM / NIGMS NIH HHS / United States