PT  - JOURNAL ARTICLE
AU  - Leslie Y. Beh
AU  - Noam Kaplan
AU  - Manuel M. Müller
AU  - Tom W. Muir
AU  - Laura F. Landweber
TI  - DNA-guided establishment of canonical nucleosome patterns in a eukaryotic genome
AID  - 10.1101/013250
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 013250
4099  - http://biorxiv.org/content/early/2014/12/26/013250.short
4100  - http://biorxiv.org/content/early/2014/12/26/013250.full
AB  - 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.