Coordinated regulation of floral transition by protein and long noncoding RNA components Project Summary Epigenetic mechanisms enable organisms to adapt to developmental and environmental cues. Flowering is one of the major developmental commitments in the plant life cycle. Plants have evolved intricate regulatory networks to control flowering time in response to both endogenous and environmental conditions. For example, prolonged cold triggers vernalization, a process that accelerates flowering through epigenetic changes in genes involved in development. Therefore, the vernalization response in Arabidopsis is an excellent model system for study of complex epigenetic regulation of gene expression triggered by environmental cues in eukaryotes. Vernalization-mediated epigenetic changes include the formation of chromatin loops and alterations in chromatin modifications and in expression of long noncoding RNAs (lncRNAs). Changes in three-dimensional structure of genome, such as formation of local chromatin loops, are increasingly recognized as important gene regulatory events in eukaryotes; however, how chromatin modifications and lncRNAs coordinate to influence gene expression through changes in three-dimensional structure of genome is not well understood. Here we seek to understand the mechanistic details of how chromatin modifications and lncRNAs mediate gene regulation. Our overriding goal is to elucidate structural and regulatory components governing protein-lncRNA mediated epigenetic gene regulation during vernalization in Arabidopsis through three specific aims designed to: 1) elucidate the detailed mechanisms of lncRNA-mediated gene regulation focusing on two lncRNAs that we showed coordinate the repression of gene involved flowing through the formation of intragenic chromatin loop, 2) evaluate coordination between protein and lncRNA components that mediate chromatin modification, 3) perform functional characterization of additional loci that undergo epigenetic changes upon developmental transition. Our approach will reveal the mechanistic details of lncRNA-mediated epigenetic regulation as it occurs during a key process of plant development (i.e., flowering). These findings will further our understanding of the mechanism of epigenetic regulation of gene expression, which has a deep evolutionary root among eukaryotes.

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Vernalization is the environmentally induced epigenetic switch that triggers the flowering of plants, a developmental program that involves chromatin modifications and long noncoding RNAs (lncRNAs). Rich knowledge on protein components as well as lncRNA components makes the vernalization process in Arabidopsis a useful model for study of the epigenetic mechanism of gene regulation with relevance to gene regulation in all eukaryotes including yeast, Drosophila, and human. Furthermore, the environmentally induced nature of vernalization response provides a unique opportunity to study the effect of environment on the epigenetic regulation of gene expression in developmental programs.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Development - 1 Study Section (DEV1)
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Hoodbhoy, Tanya
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University of Texas Austin
Schools of Arts and Sciences
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Wang, Likai; Xi, Yanpeng; Sung, Sibum et al. (2018) RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes. BMC Genomics 19:546
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