@article{Dong01072018,
author = {Dong, Xiaomei and Chen, Jian and Li, Tong and Li, En and Zhang, Xiangbo and Zhang, Mei and Song, Weibin and Zhao, Haiming and Lai, Jinsheng}, 
title = {Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize},
volume = {28}, 
number = {7}, 
pages = {1020-1028}, 
year = {2018}, 
doi = {10.1101/gr.230201.117}, 
abstract ={Genomic imprinting refers to allele-specific expression of genes depending on their parental origin. Nucleosomes, the fundamental units of chromatin, play a critical role in gene transcriptional regulation. However, it remains unknown whether differential nucleosome organization is related to the allele-specific expression of imprinted genes. Here, we generated a genome-wide map of allele-specific nucleosome occupancy in maize endosperm and presented an integrated analysis of its relationship with parent-of-origin-dependent gene expression and DNA methylation. We found that ∼2.3% of nucleosomes showed significant parental bias in maize endosperm. The parent-of-origin-dependent nucleosomes mostly exist as single isolated nucleosomes. Parent-of-origin-dependent nucleosomes were significantly associated with the allele-specific expression of imprinted genes, with nucleosomes positioned preferentially in the promoter of nonexpressed alleles of imprinted genes. Furthermore, we found that most of the paternal specifically positioned nucleosomes (pat-nucleosomes) were associated with parent-of-origin-dependent differential methylated regions, suggesting a functional link between the maternal demethylation and the occurrence of pat-nucleosome. Maternal specifically positioned nucleosomes (mat-nucleosomes) were independent of allele-specific DNA methylation but seem to be associated with allele-specific histone modification. Our study provides the first genome-wide map of allele-specific nucleosome occupancy in plants and suggests a mechanistic connection between chromatin organization and genomic imprinting.}, 
URL = {http://genome.cshlp.org/content/28/7/1020.abstract}, 
eprint = {http://genome.cshlp.org/content/28/7/1020.full.pdf+html}, 
journal = {Genome Research} 
}