title: Genomic analysis of parent-of-origin allelic expression in Arabidopsis thaliana seeds.
abstract: Differential expression of maternally and paternally inherited alleles of a gene is referred to as gene imprinting, a form of epigenetic gene regulation common to flowering plants and mammals. In plants, imprinting primarily occurs in the endosperm, a seed tissue that supports the embryo during its growth and development. Previously, we demonstrated that widespread DNA demethylation at remnants of transposable elements accompanies endosperm development and that a subset of these methylation changes are associated with gene imprinting. Here we assay imprinted gene expression genome-wide by performing high-throughput sequencing of RNA derived from seeds of reciprocal intraspecific crosses. We identify more than 200 loci that exhibit parent-of-origin effects on gene expression in the endosperm, including a large number of transcription factors, hormone biosynthesis and response genes, and genes that encode regulators of epigenetic information, such as methylcytosine binding proteins, histone methyltransferases, and chromatin remodelers. The majority of these genes are partially, rather than completely, imprinted, suggesting that gene dosage regulation is an important aspect of imprinted gene expression.
authors.affiliation: Howard Hughes Medical Institute, Seattle, Washington, United States of America. mgehring@wi.mit.edu
authors.forename: Mary
authors.initials: M
authors.lastname: Gehring
authors.forename: Victor
authors.initials: V
authors.lastname: Missirian
authors.forename: Steven
authors.initials: S
authors.lastname: Henikoff
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000196:embryology / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D056625:Endosperm / Q000196:embryology / Q000235:genetics; D057890:Epigenomics / Q000379:methods; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D018392:Genomic Imprinting; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012639:Seeds / Q000196:embryology / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D004251:DNA Transposable Elements