Coordinated regulation of floral transition by protein and long noncoding RNA components Project Summary Epigenetic mechanisms enable the genome 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. We use the floral transition as a model system to study epigenetic regulation of gene expression in eukaryotes. Recent recognition of long noncoding RNAs (lncRNAs) in eukaryotes and growing examples of their function in various developmental programs indicate that lncRNAs play roles in developmental programs, carcinogenesis and other human diseases. Despite some well-characterized examples, mechanistic details of lncRNAs and their underlying roles in development are not well understood. Our recent study identified the first functional lncRNA in plants, which is necessary for the proper epigenetic silencing of a developmentally regulated gene, FLC. Here we seek to understand mechanistic details on the role of lncRNAs in development. Our proposal is to elucidate structural and regulatory components governing protein-lncRNA mediated epigenetic regulation of developmental genes. Our overriding goals are built around three specific aims: 1) Identify and characterize lncRNAs, 2) Study mechanisms in which protein and RNA components are coordinated to regulate developmental genes, 3) Employ genetic approaches to address the mechanisms to sense and measure the duration of environmental changes (i.e. cold), which are upstream events of protein-lncRNAs mediated regulation of developmental gene expression. Our approach to dissect the mechanistic details of lncRNA- mediated epigenetic regulation will be useful not only for understanding a key mechanism of plant development (i.e. flowering) but also for elucidating the mechanism of epigenetic regulation of gene expression which has a deep evolutionary root among eukaryotes.
Long noncoding RNA-mediated regulation of gene expression is increasingly recognized as one of uncharted areas to fully understand epigenetic mechanisms to control developmental fates of cells. Floral transition regulatory pathways provide a model system to study the environmentally-induced epigenetic switch of a developmental program. Rich knowledge on protein components as well as recently recognized long noncoding RNA components makes the floral transition a suitable model to understand epigenetic mechanism of gene regulation. Epigenetic regulation of gene expression is a major regulatory theme in eukaryotic gene regulation, including Yeast, Drosophila and Human. Thus our study is of broader scientific interest. Furthermore, the environmentally induced nature of floral transition will provide a unique opportunity to study the effect of environment on the epigenetic regulation of gene expression in developmental programs.
|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|
|Kim, Dong-Hwan; Xi, Yanpeng; Sung, Sibum (2017) Modular function of long noncoding RNA, COLDAIR, in the vernalization response. PLoS Genet 13:e1006939|
|Kim, Eun-Deok; Xiong, Yuqing; Pyo, Youngjae et al. (2017) Spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development. Sci Rep 7:3838|
|Kim, Dong-Hwan; Sung, Sibum (2017) Accelerated vernalization response by an altered PHD-finger protein in Arabidopsis. Plant Signal Behav 12:e1308619|
|Kim, Dong-Hwan; Sung, Sibum (2017) The Binding Specificity of the PHD-Finger Domain of VIN3 Moderates Vernalization Response. Plant Physiol 173:1258-1268|
|Kim, Dong-Hwan; Sung, Sibum (2017) Vernalization-Triggered Intragenic Chromatin Loop Formation by Long Noncoding RNAs. Dev Cell 40:302-312.e4|
|Zhang, Fan; Wang, Likai; Lim, Jae Yun et al. (2016) Phosphorylation of CBP20 Links MicroRNA to Root Growth in the Ethylene Response. PLoS Genet 12:e1006437|
|Kim, Dong-Hwan; Sung, Sibum (2014) Polycomb-mediated gene silencing in Arabidopsis thaliana. Mol Cells 37:841-50|
|Kim, Dong-Hwan; Sung, Sibum (2014) Genetic and epigenetic mechanisms underlying vernalization. Arabidopsis Book 12:e0171|
|Jones, Ashley L; Sung, Sibum (2014) Mechanisms underlying epigenetic regulation in Arabidopsis thaliana. Integr Comp Biol 54:61-7|
Showing the most recent 10 out of 12 publications