Nucleosomal signatures impose nucleosome positioning in coding and non-coding sequences in the genome
- Sara González1,
- Alicia García1,
- Enrique Vázquez1,
- Rebeca Serrano1,
- Mar Sánchez1,
- Luis Quintales2 and
- Francisco Antequera1,3
- 1 Instituto de Biología Funcional y Genómica;
- 2 Departamento de Informática y Automática, Universidad de Salamanca
- ↵* Corresponding author; email: cpg{at}usal.es
Abstract
In the yeast genome, a large proportion of nucleosomes occupy well-defined and stable positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genome remains controversial. Through quantitative analysis of nucleosome positioning, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes in three species of Schizosaccharomyces and in Saccharomyces cerevisiae. This effect is equally detected in transcribed and non-transcribed regions, suggesting the existence of sequence elements contributing to positioning. To identify such elements, we incorporated information from nucleosomal signatures into artificial synthetic DNA molecules, and found they generated regular nucleosomal arrays indistinguishable from those of endogenous sequences. Strikingly, this information is species-specific and can be combined with coding information through the use of synonymous codons such that genes from one species can be engineered to adopt the nucleosomal organization of another. These findings open the possibility of designing coding and non-coding DNA molecules capable of directing their own nucleosomal organization.
- Received March 18, 2016.
- Accepted September 19, 2016.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International license), as described at http://creativecommons.org/licenses/by-nc/4.0/.
