Arabidopsis thaliana Transcriptome or Gene expression

We investigated the relationship between transposable elements (TEs), small RNA and gene expression in hybrids by sequencing small RNA and mRNA in parents and hybrid offspring. Both the presence of TEs in a gene, and the expression of small RNA with sequence matching a gene, were associated with higher probability of non-additive mRNA inheritance patterns in hybrids. Genes with TEs present within the gene boundaries were mainly associated with low-parent inheritance, and many of these genes also expressed both sense and antisense strand small RNA. In addition to the expected patterns of repression of mRNA expression by small RNA, we also found that highly expressed and high-parent inherited mRNAs are also associated with small RNA. In these cases, the small RNA was expressed predominantly or exclusively from the sense strand. Highly expressed genes showing high-parent inheritance in hybrids were also less likely to harbor TEs, especially retrotransposons. Furthermore, the two distinct classes of small RNA were correlated with different chromatin marks. While small RNA consisting of a mixed population of sense and antisense, consistent with siRNA, was associated with repressive C methylation, small RNA expressed exclusively or predominantly from the sense strand was associated with regions of CG methylation, known to be an activating mark. Thus, activation as well as repression of gene expression in hybrids can be associated with gene-derived small RNA, with strandedness of the small RNA, presence of TEs and C versus CG methylation distinguishing the two patterns.