RESEARCH
The research in XU lab focus on epigenetic regulation of plant reproductive development and transgenerational inheritance in Arabidopsis, rice or orchid. Our research will combine epigenome, transcriptome, forward (mutant screening) and reverse genetics to understand how floral organ identity genes coordinate epigenetic regulators to control cell identity or function in Arabidopsis and orchid. Thus, NGS, genetics, biochemistry, molecular and cellular biology assays would be conducted.
>The regulatory network of the chromatin proteins in plant reproductive developmentplant
The epigenome in plants is regulated by “writers”, "erasers" and “readers” proteins. We have shown that MRG1 and MRG2 are the "reader" proteins for H3K36me3, which recruits histone acetyltransferase HAM1/2to modify the chromatin accessibility (Xu et al., 2014). To understand the biological function of MRG1/2 proteins during flower development, we introducedmrg1 mrg2 mutations into the floral inducible system 35S::AP1-GRap1 cal.We will study the MRG functions in plant inflorescence meristem (stem cells) and flower buds (differentiated cells) with RNA-seq and ChIP-seq for epigenetic modifications. Hi-C and ATAC-analysis will be carried out to check the effect of mrg1 mrg2 mutations on chromosome architectures. With the inducible linepMRG2::MRG2-GR, the sequential changes of the multiple epigenetic modifications at the target loci, and the dynamical changes of 3D chromosome structure will be determined to gain insight how the epigenetic regulators, coordinates with the floral homeotic genes, to control the flower development.
> The dynamic binding profiles and organ- and/or stage-specific partners of floral homeotic genes during plant reproductive development
The homeotic floral organ identity genes, namely the five classes of MADS-box genes in the ABCDE model, control the cell fate of the organs in the Arabidopsis flower. While studies demonstrated that MADS-domain transcription factors bind to the CArG box, it is a longstanding mystery and intriguing question how different combination of MADS box domain transcription factors forms protein complexes to control specific sets of downstream genes. We will utilize the floral inducible system coupled with floral homeotic mutants to enrich each kind of floral organ. Using such tissue samples, we will perform a high-resolution ChIP-seq to analyze the binding pattern of the floral organ identity proteins APETALA3 (AP3, Class B gene), AGAMOUS (AG, Class C gene) and SEPALLATA3 (SEP3, Class E gene). Through bioinformatics, the complex-specific co-factors and co-motifs for AP3/PI-AG-SEP3 or AP3/PI-SEP3 on the target loci will be identified.Together with the epigenetic profiles, these studies will enhance our knowledge on the network of transcription regulation and epigenetic coordination during plant reproductive development.
> Biological response to cold treatment (vernalization) and hot treatment (devernalization)
During vernalization (induction of flowering after long exposure to cold), FLC is gradually repressed by the PRC2 mediated repressive H3K27me3 histone modification in Arabidopsis. While PRC2 deposits the repressive mark on the FLC locus, JMJ30/32 actively removes it. The preliminary data showed that, indeed, phenotypically jmj30 jmj32 are more sensitized for vernalization. It has been known that the effect of vernalization can be reversed by exposing the seeds or plantlets to a short period of high temperature, a process termed devernalization. The similar phenomenon can be observed in the model organism of Brassicaceae, Arabidopsis (Napp-Zinn, 1957, Planta 210), and FLC is involved in this pathway (Périlleux, 2013, Plant Journal 75). Reversal of the floral induction is important for certain crop plants that are harvests for their leaves (e.g. cabbage) or roots (root chicory). Thus, the vernalization and devernalization will be utilized to study the cross-talk between the repressive mark H3K27me3 and the active marks H3K4/36me3. We will characterize the dynamic binding profiles and the dynamic epigenetic profiles to understand the interplay of different epigenetic regulators.
> Epigenetic mechanisms of transgenerational inheritance in plant adaptation to short-day and low temperature
With global warming, the extreme weather is more frequent. As sessile organisms, plants are constantly challenged by environmental perturbations. When they adapt to environmental stress, they can transmit the stress memories to accelerate the response when the events recur in the same generation. Very rarely, this stress memory can also be transmitted to the next generation through DNA CpG methylation (5-Methylcytosine, 5mC). In animals, transgenerational inheritance of histone modifications including H3K27me3 and H3K4me2/3, together with N6-Methyladenine (6mA) DNA methylation, have been documented recently. However, this is still not well studied in plants. We have observed the transgenerational inheritance of acquired traits in histone modification mutants. Our preliminary data have shownthat the heritable traits are not associated with 5mC. In this study, we will combine epigenome, transcriptome, genetics, biochemistry and molecular biology assays to figure out the factor(s) involved in the transgenerational inheritance. We will also investigate whether the molecular mechanism is conserved in rice. Our research will promise for the application in future breeding system.