Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm

Imprinting describes the differential expression of alleles based upon their parent of origin. Deep sequencing of RNAs isolated from 14 days after pollination maize endosperm and embryo tissue was used to identify imprinted genes in a set of ~12,000 genes that were expressed and contained sequence polymorphisms in the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm including 54 maternally expressed genes (MEGs) and 46 paternally expressed genes (PEGs). Three of these genes have been previously identified as imprinted while the remaining 97 genes represent novel imprinted maize genes. The 100 imprinted genes are distributed throughout the maize genome with little evidence for any clustering. A genome-wide analysis of DNA methylation identified regions with reduced endosperm DNA methylation in, or near, 19 of the 100 imprinted genes. The reduced levels of DNA methylation in endosperm are caused by specific hypomethylation of the maternal allele for both MEGs and PEGs in all cases tested. Many of the imprinted genes with reduced DNA methylation levels also show endosperm-specific expression patterns. The imprinted maize genes were compared with imprinted genes identified in genome-wide screens of rice and Arabidopsis and at least 10 examples of conserved imprinting between maize and each of the other species were identified. The genes that are imprinted in multiple species may provide insights into the conserved functions of imprinting.

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Waters AJ, Makarevitch I, Eichten SR, Swanson-Wagner RA, Yeh CT, Xu W, Schnable PS, Vaughn MW, Gehring M, Springer NM