RT Journal Article
SR Electronic
T1 DNA-guided establishment of canonical nucleosome patterns in a eukaryotic genome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 013250
DO 10.1101/013250
A1 Leslie Y. Beh
A1 Noam Kaplan
A1 Manuel M. Müller
A1 Tom W. Muir
A1 Laura F. Landweber
YR 2014
UL http://biorxiv.org/content/early/2014/12/26/013250.abstract
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.