Searching for transcriptomic and epigenomic basis of hybrid vigor (heterosis)
Xing Wang Deng and He Hang

Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China;
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA;
*Correspond author: Xing Wang Deng: deng@pku.edu.cn

Abstract
Chromatin state and genome activity of the hybrid and their differences from that of parental lines are pivotal to understanding the molecular mechanisms of heterosis in plant. In recent studies, we generated genome-wide integrated maps of mRNA and small RNA transcripts, DNA methylation, and representative histone modifications (H3K4me3, H3K9ac and H3K27me3) of Arabidopsis, rice and maize hybrid crosses using high-throughput Illumina sequencing approaches. 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. As compared to gene expression and active histone modifications, repressive epigenetic marks of DNA methylation and H3K27me3 tend to diverge more strongly among hybrid crosses and between organs. Hybrids show highly organ-specific variation in gene expression and epigenetic modifications and exhibit distinct functional enrichments between shoots and roots for differential expressed genes. We observed a high correlation of allelic bias of epigenetic modifications or gene expression in reciprocal hybrids with their differences in the parental lines. Among genes exhibiting allelic expression bias in hybrids, nucleosome assembly pathway is highly enriched in shoots, while no functional enrichment was observed in roots. We observed simultaneous increase in the number and decrease in the expression levels of smRNA clusters in both organs of hybrids, and found that the increased smRNA expression was accompanied by the enhanced DNA methylation within the same genomic locus in hybrids relative to parents. Together, our data reveal a comprehensive overview of transcriptional and epigenetic trends in hybrid crosses and suggested that hybrid probably evolved divergent genetic and epigenetic regulatory mechanisms for the  growth vigor of different organs.