Histone Modification And DNA Methylation Function In Epigenetic Control Of Rice Development

Epigenetic modification plays important roles in plant genome stability and gene regulation required for normal plant development and responses to environmental conditions.To date,the mechanism of epigenetic regulation involved in rice plant development remains largely unexplored,albeit rice is one of the major cereal crops in the world.In addition,the relationship between different epigenetic processes in regulating rice plant development remains unclear.My thesis work was focused on the study of histone modification and DNA methylation mechanism and their function in gene regulation and plant developmental control from three different aspects: 1.Histone methylation regulation and its functions in reprogramming of gene expression in rice inflorescence meristem;2.Cooperation between the H3K27me3 chromatin mark and non-CG DNA methylation in epigenetic repression of developmental genes;3.Histone acetylaton function in establishing programs of crown root meristem development.Main results are summarized as below:a.Rice inflorescence meristem(IM)activity and development are essential for rice yield.The chromatin and epigenetic mechanism regulating IM development remains unclear.Analysis of high throughput data revealed that in addition to transcription factor and kinase genes,those involved in metabolism and protein synthesis were massively activated during SAM-to-IM transition,and that a change in the H3K27me3/H3K4me3 ratio was an important factor for the differential expression of many genes.Down-regulation of the H3K27 methyltransferase gene SET DOMAIN GROUP 711(SDG711)or mutation of the H3K4 demethylase gene JMJ703 eliminates the increase of H3K27me3 in many genes during the process.SDG711-mediated H3K27me3 repressed several functional genes involved in SAM activity and genes that were silent in IM but activated during floral organogenesis or other developmental stages.These data indicated that SDG711 and JMJ703 together participated in reprogramming genome-wide H3K27me3/H3K4me3 to modulate gene expression during IM development.b.H3K27me3 is a repressive chromatin mark of gene expression and is catalyzed by Polycomb-repressive complex 2(PRC2),while DNA methylation that occurs in CG and non-CG(CHG and CHH,where H is A,C,or T)contexts is a hallmark of transposon silencing.However,the relationship between H3K27me3 and DNA methylation in gene repression remains unclear.In addition,how PRC2 is recruited to specific genes is unknown in plants.In this thesis work,we found that SDG711 was required to maintain H3K27me3 of many developmental genes during leaf organogenesis and that many H3K27me3-marked developmental genes were also methylated at non-CG(CHG and CHH)sites in the body regions.SDG711-binding and SDG711-mediated ectopic H3K27me3 were preferentially target to genes methylated at non-CG sites.Furthermore,we found that SDG711 physically interacted with Os DRM2(CHH methyltransferase)and a SRA domain(capable of binding methylated CHG site)containing protein SDG703.Mutation of Os DRM2 resulted in loss of H3K27me3 from many genes.These results together suggest that the repression of many developmental genes may involve both DRM2-mediated non-CG methylation and PRC2-mediated H3K27me3 and that the two marks are not generally mutually exclusive but may cooperate in repression of developmentally regulated genes in rice.c.Shoot-born crown roots are the major root systems in rice.Previous work indicates that Wuschel-related homeobox gene WOX11 was necessary and sufficient to promote rice crown root emergence and elongation.In this thesis,we found that WOX11 could recruit ADA2-GCN5 acetyltransferase(HAT)module to activate downstream gene to control crown root development.ADA2 and GCN5 were expressed in all cell layers of crown meristem zone.Down-regulation of ADA2 and GCN5 decreases crown root number and length.Crown root meristem cell division rate was decreased in wox11 mutant and GCN5 RNAi plants.WOX11 and ADA2-GCN5 commonly regulated a set of genes involved in auxin transport or response,cellulose metabolism,and energy metabolism.These data indicate the recruitment of ADA2-GCN5 acetyltransferase module by WOX11 is a strategy for WOX11 to establish gene expression program and promote root meristem cell proliferation and crown root development.