Research Projects

Rationale of the research: Genomic imprinting in plants is a unique and intricate process that governs gene expression based on parental origin. In this process, genes inherited from one parent are selectively silenced while those from the other parent remain active. In flowering plants, it is mainly confined to the endosperm and significantly impacts endosperm development and seed size. Previously, using tissue-specific chromatin interactome analysis in Arabidopsis, we identified several imprinted genes that were exclusively interacting in the endosperm (Nucleic Acids Res. 2021). This project focuses on elucidating the regulation of imprinted genes in the context of parental-specific chromatin interactome to better understand seed development. Hypothesis: It has been shown that RNA-directed DNA methylation negatively correlates with chromatin interaction and asymmetries in DNA methylation between parental genomes influence parentally biased gene expression (imprinting). This suggest that chromatin interaction directly or indirectly influences the expression of imprinted genes. Based on this, I hypothesize that asymmetries in DNA methylation of the parental genomes in endosperm lead to different chromatin interactomes of the maternal and paternal genomes. Scientific approach: I have developed the INT-Hi-C protocol, which allows the use of lower input material than conventional Hi-C, providing a framework for understanding cell type-specific nuclear organization, which remains poorly understood in plants. I propose to apply INT-Hi-C on endosperm isolated from inter-accession (Ler x INT-Col-0) crosses to generate the parental-specific chromatin interactome. RNA-seq will also be performed from the endosperm of the inter-accession cross at the same developmental stage. Comparative analysis of allele-specific interactome and transcriptome will establish a relationship between chromatin interaction and imprinted gene regulation. The allele-specific interactome will also be compared with allele-specific epigenetic marks to determine how parental-specific epigenetic marks are associated with chromatin interactome. T-DNA insertion lines will potentially disrupt the interaction of imprinted genes, which will be determined using locus-specific primers. After establishing disrupted interactions, the expression of imprinted genes will be measured for functional validation. Significance: The presence of parental-specific chromatin organization and their functional roles are largely unknown. Considering the importance of endosperm to human nutrition and its unique genetic and epigenetic constitution leading to parental conflict, the endosperm is rendered a unique and relevant system for understanding the impact of maternal and paternal-specific chromatin organization for gene regulation. This study will establish the basis of parental-specific genome regulation in the endosperm, potentially relevant for seed production and, thus a boon to agricultural yield.