BACKGROUND: Epigenetic regulation is well recognized for its importance in gene expression in organisms. DNA methylation, an important epigenetic mark, has received enormous attention in recent years as it's a key player in many biological processes. It remains unclear how DNA methylation contributes to gene transcription regulation in @entity2829 seeds. Here, we take advantage of recent technologies to examine the genome-wide association of DNA methylation with transcription of four types of DNA sequences, including protein-coding genes, pseudogenes, transposable elements, and repeats in @entity2829 embryo and endosperm, respectively. RESULTS: The methylation in CG, CHG and @entity5557 contexts plays different roles in the control of gene expression. Methylation around the transcription start sites and transcription stop regions of protein-coding genes is negatively correlated, but in gene bodies positively correlated, to gene expression level. The upstream regions of protein-coding genes are enriched with 24-nt siRNAs and contain high levels of @entity5557 methylation, which is correlated to gene expression level. The analysis of sequence content within CG, CHG, or @entity5557 contexts reveals that only @entity5557 methylation is affected by its local sequences, which is different from @entity958 . CONCLUSIONS: In summary, we conclude that methylation-regulated transcription varies with the types of DNA sequences, sequence contexts or parts of a specific gene in @entity2829 seeds and differs from that in other plant species. Our study helps @entity1 better understand from a genome-wide viewpoint that how transcriptional expression is controlled by DNA methylation, one of the important factors influencing transcription, and how the methylation is associated with small RNAs.

Genome-Wide Epigenetic Regulation of Gene Transcription in XXXX Seeds.

@entity5557 :: ('MESH:C535916', 'Disease') :: ['CHH'] @entity958 :: ('3702', 'Species') :: ['Arabidopsis'] @entity1 :: ('9606', 'Species') :: ['people'] @entity2829 :: ('4577', 'Species') :: ['maize']
@entity2829 :: (4577,Species) :: ['Maize']
