TY  - JOUR
A1  - Routhier, Etienne
A1  - Pierre, Edgard
A1  - Khodabandelou, Ghazaleh
A1  - Mozziconacci, Julien
T1  - Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics
Y1  - 2021/02/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 317 
EP  - 326 
DO  - 10.1101/gr.264416.120 
VL  - 31 
IS  - 2 
UR  - http://genome.cshlp.org/content/31/2/317.abstract 
N2  - Genetically modified genomes are often used today in many areas of fundamental and applied research. In many studies, coding or noncoding regions are modified in order to change protein sequences or gene expression levels. Modifying one or several nucleotides in a genome can also lead to unexpected changes in the epigenetic regulation of genes. When designing a synthetic genome with many mutations, it would thus be very informative to be able to predict the effect of these mutations on chromatin. We develop here a deep learning approach that quantifies the effect of every possible single mutation on nucleosome positions on the full Saccharomyces cerevisiae genome. This type of annotation track can be used when designing a modified S. cerevisiae genome. We further highlight how this track can provide new insights on the sequence-dependent mechanisms that drive nucleosomes’ positions in vivo. 
ER  -