Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm

Area of Science:

• Plant genetics
• Epigenetics
• Genomics

Background:

• Genetic imprinting, discovered 40 years ago in maize, regulates gene expression based on parental origin.
• The full extent of genetic imprinting in the triploid maize endosperm remains largely uncharacterized.

Purpose of the Study:

• To globally analyze allelic gene expression patterns in developing maize endosperm.
• To define and quantify imprinted genes and long noncoding RNAs in maize endosperm.
• To investigate allele-specific methylation patterns associated with imprinted loci.

Main Methods:

• Reciprocal crosses between maize inbreds B73 and Mo17.
• Analysis of global patterns of allelic gene expression in developing endosperms.
• Definition of imprinted genes based on a fivefold difference in maternal/paternal allele expression.
• Identification of allele-specific methylation patterns in imprinted loci.

Main Results:

• At least 179 protein-coding genes (1.6%) and 38 long noncoding RNAs exhibit imprinted expression.
• 68 imprinted genes show maternal preferential expression, while 111 show paternal preferential expression.
• Imprinted genes and ncRNAs display genomic clustering, and 21 differentially methylated regions (DMRs) were identified, uniformly hypomethylated in maternal alleles and hypermethylated in paternal alleles.

Conclusions:

• Maize endosperm exhibits extensive and complex genetic imprinting regulation.
• Imprinted genes and ncRNAs are associated with distinct, parent-of-origin-specific methylation patterns.
• Genetic imprinting likely plays a role in balancing gene dosage in the triploid maize endosperm.