Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

Abstract

The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here, we report highly integrated maps of the epigenome, mRNA, and small RNA transcriptomes of two rice (Oryza sativa) subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic modifications in reciprocal hybrids were observed. Through analyses of single nucleotide polymorphisms from our sequence data, we observed a high correlation of allelic bias of epigenetic modifications or gene expression in reciprocal hybrids with their differences in the parental lines. The abundance of distinct small RNA size classes differed between the parents, and more small RNAs were downregulated than upregulated in the reciprocal hybrids. Together, our data reveal a comprehensive overview of transcriptional and epigenetic trends in heterotic rice crosses and provide a useful resource for the rice community.

Genomic DNA methylation analyses reveal the distinct profiles in castor bean seeds with persistent endosperms

“…Generally, the low methylation level in the upstream genes could promote gene expression and the presence of DNA methylation inhibits transcriptional initiation. In this study, we noted that the relationship between DNA methylation and global gene expression is not strong in castor bean seed tissues, consistent with previous reports in Arabidopsis (Hsieh et al, 2009) and rice (He et al, 2010). Our investigations appeared to demonstrate that DNA methylation, in a way, mainly repressed gene expression in castor bean seeds, although the associations were variable, depending on the methylated regions (such as upstream, downstream, and gene body) and different methylation sequence contexts.…”

Imprinting meets genomics: new insights and new challenges

“…This fits with the idea that imprinting is restricted to the endosperm, thus obviating the need for epigenetic resetting between generations [28]. Indeed, assays of allele-specific expression in Arabidopsis, maize, and rice seedlings have found no evidence for parent-of-origin dependent expression [29][30][31].…”

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns inArabidopsisand rice

“…activity, we classified a total of~40,000 rice genes into 5 groups based on their expression levels in rice seedlings. 54 While 87.2% of H4K16ac and 88.2% of H3K23ac peaks are enriched at the TSS in Arabidopsis, only 56.5% of H4K16ac and 52.6% of H3K23ac peaks are at the TSS in rice (Fig. 5B).…”