Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm

Original manuscript: http://www.plantcell.org/content/early/2011/12/22/tpc.111.092668.short

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.

Data files

Browseable data files formatted for the Broad Institute's Integrated Genomics Viewer are presented here:

IGV-formatted Coverage maps of hybrid RNA-seq reads (tdf):

To use these files:

  1. Navigate to the IGV start page (http://www.broadinstitute.org/software/igv/StartIGV)
  2. Launch the IGV with 2 GB RAM
  3. Set the genome to Maize (ZmB73 5a) which will use the AGPv2 coordinate set
  4. Select File...Load from URL and paste in the URL for any of the data tracks you wish to browse. You can determine the URL by right-clicking on the link on this page and choosing Copy Link Location/Copy URL/etc in your browser.
  5. Alternatively, you can download the files to disk and interact with them locally. However, these files can be quite large!
  6. When you have set up the view in the IGV Browser to your liking, you can save the session by choosing File...Save Session. When you launch the browser next time, you will be able to use the resulting XML file to restore your view.

Original data

The original data files for this experiment can be found at NCBI GEO under accession GSE33730.