title: Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm.
abstract: Imprinting describes the differential expression of alleles based on their parent of origin. Deep sequencing of RNAs from maize (Zea mays) endosperm and embryo tissue 14 d after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between 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. 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 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 (Oryza sativa) and Arabidopsis thaliana, and at least 10 examples of conserved imprinting between maize and each of the other species were identified.
authors.affiliation: Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minesota, Saint Paul, Minesota 55108, USA.
authors.forename: Amanda J
authors.initials: AJ
authors.lastname: Waters
authors.forename: Irina
authors.initials: I
authors.lastname: Makarevitch
authors.forename: Steve R
authors.initials: SR
authors.lastname: Eichten
authors.forename: Ruth A
authors.initials: RA
authors.lastname: Swanson-Wagner
authors.forename: Cheng-Ting
authors.initials: CT
authors.lastname: Yeh
authors.forename: Wayne
authors.initials: W
authors.lastname: Xu
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Schnable
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Vaughn
authors.forename: Mary
authors.initials: M
authors.lastname: Gehring
authors.forename: Nathan M
authors.initials: NM
authors.lastname: Springer
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000737:chemistry / Q000235:genetics; D032461:Chromosomes, Plant / Q000737:chemistry / Q000235:genetics; D017124:Conserved Sequence; D019175:DNA Methylation; D056625:Endosperm / Q000737:chemistry / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D056426:Genetic Loci; D018392:Genomic Imprinting; D040582:Inheritance Patterns; D012275:Oryza / Q000737:chemistry / Q000235:genetics; D054817:Pollination; D011110:Polymorphism, Genetic; D017423:Sequence Analysis, RNA; D003313:Zea mays / Q000737:chemistry / Q000235:genetics*