Dynamics of imprinted genes and their epigenetic mechanisms in castor bean seed with persistent endosperm

Genomic imprinting refers to parent-of-origin-dependent gene expression and primarily occurs in the endosperm of flowering plants, but its functions and epigenetic mechanisms remain to be elucidated in eudicots. Castor bean, a eudicot with large and persistent endosperm, provides an excellent system...

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Bibliographic Details
Published in:The New phytologist 2023-12, Vol.240 (5), p.1868-1882
Main Authors: Han, Bing, Li, Yelan, Wu, Di, Li, De-Zhu, Liu, Aizhong, Xu, Wei
Format: Article
Language:English
Subjects:
Alleles
Arabidopsis - genetics
Arabidopsis Proteins - metabolism
Beans
Demethylation
Deoxyribonucleic acid
DNA
DNA (Cytosine-5-)-Methyltransferases - genetics
DNA methylation
DNA Methylation - genetics
DNA methyltransferase
Endosperm
Endosperm - genetics
Endosperm - metabolism
Epigenesis, Genetic
Epigenetics
Flowering
Gene expression
Gene Expression Regulation, Plant
Gene silencing
Genes
Genomes
Genomic Imprinting
Germination
Histones
Imprinting
Plants (botany)
Ricinus communis
Ricinus communis - genetics
Ricinus communis - metabolism
Seed germination
Seeds
Seeds - metabolism
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Summary:Genomic imprinting refers to parent-of-origin-dependent gene expression and primarily occurs in the endosperm of flowering plants, but its functions and epigenetic mechanisms remain to be elucidated in eudicots. Castor bean, a eudicot with large and persistent endosperm, provides an excellent system for studying the imprinting. Here, we identified 131 imprinted genes in developing endosperms and endosperm at seed germination phase of castor bean, involving into the endosperm development, accumulation of storage compounds and specially seed germination. Our results showed that the transcriptional repression of maternal allele of DNA METHYLTRANSFERASE 1 (MET1) may be required for maternal genome demethylation in the endosperm. DNA methylation analysis showed that only a small fraction of imprinted genes was associated with allele-specific DNA methylation, and most of them were closely associated with constitutively unmethylated regions (UMRs), suggesting a limited role for DNA methylation in controlling genomic imprinting. Instead, histone modifications can be asymmetrically deposited in maternal and paternal genomes in a DNA methylation-independent manner to control expression of most imprinted genes. These results expanded our understanding of the occurrence and biological functions of imprinted genes and showed the evolutionary flexibility of the imprinting machinery and mechanisms in plants.
ISSN:0028-646X
1469-8137
DOI:10.1111/nph.19265