High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Arabidopsis Endosperm

Abstract

Genomic imprinting is an epigenetic phenomenon leading to parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, genomic imprinting has mainly been observed in the endosperm, an ephemeral triploid tissue derived after fertilization of the diploid central cell with a haploid sperm cell. In an effort to identify novel imprinted genes in Arabidopsis thaliana, we generated deep sequencing RNA profiles of F1 hybrid seeds derived after reciprocal crosses of Arabidopsis Col-0 and Bur-0 accessions. Using polymorphic sites to quantify allele-specific expression levels, we could identify more than 60 genes with potential parent-of-origin specific expression. By analyzing the distribution of DNA methylation and epigenetic marks established by Polycomb group (PcG) proteins using publicly available datasets, we suggest that for maternally expressed genes (MEGs) repression of the paternally inherited alleles largely depends on DNA methylation or PcG-mediated repression, whereas repression of the maternal alleles of paternally expressed genes (PEGs) predominantly depends on PcG proteins. While maternal alleles of MEGs are also targeted by PcG proteins, such targeting does not cause complete repression. Candidate MEGs and PEGs are enriched for cis-proximal transposons, suggesting that transposons might be a driving force for the evolution of imprinted genes in Arabidopsis. In addition, we find that MEGs and PEGs are significantly faster evolving when compared to other genes in the genome. In contrast to the predominant location of mammalian imprinted genes in clusters, cluster formation was only detected for few MEGs and PEGs, suggesting that clustering is not a major requirement for imprinted gene regulation in Arabidopsis.

Imprinting meets genomics: new insights and new challenges

“…Deep sequencing of mRNA libraries derived from reciprocal intraspecific crosses of Arabidopsis thaliana, rice, and maize has proven to be an effective strategy to identify genes that are preferentially expressed from one parental allele during seed development [4][5][6][7][8][9]. These studies have confirmed that imprinting is mostly endosperm-specific and have significantly expanded the number of imprinted genes to between about 50-200 in each species.…”

“…While the cause is still unknown, partial imprinting might be a reflection of past conflict between alleles (kinship theory) [12] or of a dosage balance, as in the case of transcriptional regulators functioning as part of macromolecular complexes [13]. Imprinting can also be specific to particular strain [6], further highlighting the need to assess imprinting in multiple genetic backgrounds within a species.…”

“…Among paternally expressed imprinted genes (PEGs), transcription factors and chromatin-related proteins are enriched [4]. Examples of imprinted genes include 5-methylcytosine binding proteins, histone lysine methyltransferases, a Class IV homeodomain transcription factor, and several members of the MADS-box transcription factor family [4][5][6]. Interestingly, different members of the HDG and MADS families are maternally expressed imprinted genes (MEGs).…”

“…MEDEA and FWA, two MEGs, and PHERES1, a PEG, are the most extensively studied endosperm imprinted genes in terms of mechanism of monoallelic expression. By performing expression analysis on seeds with mutations in known regulators of imprinting, many more imprinted genes regulated like MEA, FWA, or PHE1 were discovered [5,6].…”

“…About a third of imprinted genes, particularly those that encode regulatory proteins, are associated with differentially methylated regions. These are enriched in Helitron TE sequences [6,22]. For some genes, like FWA, methylation likely controls expression by occluding the promoter (Figure 2A).…”