Unknown

Dataset Information

0

Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize.


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.

SUBMITTER: Dong X 

PROVIDER: S-EPMC6028132 | BioStudies | 2018-01-01

REPOSITORIES: biostudies

Similar Datasets

2014-01-01 | S-EPMC3875858 | BioStudies
2011-01-01 | S-EPMC3174879 | BioStudies
2013-01-01 | S-EPMC3854695 | BioStudies
2020-01-01 | S-EPMC7002495 | BioStudies
2018-01-01 | S-EPMC6196528 | BioStudies
2014-01-01 | S-EPMC4066788 | BioStudies
2013-01-01 | S-EPMC3651473 | BioStudies
2019-01-01 | S-EPMC6692421 | BioStudies
2015-01-01 | S-EPMC4331533 | BioStudies
2011-12-16 | E-GEOD-33730 | ArrayExpress