TY  - JOUR
A1  - Dong, Xiaomei
A1  - Chen, Jian
A1  - Li, Tong
A1  - Li, En
A1  - Zhang, Xiangbo
A1  - Zhang, Mei
A1  - Song, Weibin
A1  - Zhao, Haiming
A1  - Lai, Jinsheng
T1  - Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize
Y1  - 2018/07/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1020 
EP  - 1028 
DO  - 10.1101/gr.230201.117 
VL  - 28 
IS  - 7 
UR  - http://genome.cshlp.org/content/28/7/1020.abstract 
N2  - 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. 
ER  -