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Genomic Science Program

2013 Awardee

Global analysis of epigenetic regulation of gene expression in response to drought stress in Sorghum

INVESTIGATORS: A.S.N. Reddy, Professor, Dept. of Biology; Asa Ben-Hur, Associate Professor, Dept. of Computer Sciences

INSTITUTIONS: Colorado State University

NON-TECHNICAL SUMMARY: Abiotic stresses such as drought and heat are major limiting factors of crop yields.  Acquisition of tolerance to stress requires coordinated changes in gene expression. Little is known about stress-induced global epigenetic changes and alterations in alternative splicing of pre-mRNAs in C4 grasses.  Sorghum, a C4 grass, is an excellent model to investigate drought-induced epigenetic changes and alterations in levels and types of splice variants as it is one of the best drought-adapted cereals.  In addition, its genome is fully sequenced and drought-tolerant and -susceptible cultivars exist.  The overall goal of this research is to investigate the impact of drought stress on epigenetic modifications and alternative splicing in drought resistant and susceptible cultivars.  We propose to investigate genome-wide changes in the chromatin landscape and patterns of alternative splicing in two drought-sensitive and two drought-tolerant cultivars under normal conditions and in response to drought stress using recently developed high-throughput tools.  Understanding how plants respond and adapt to drought stress at the molecular level will help in developing plants that can grow under water- limiting conditions.

OBJECTIVES: 1) Perform genome-wide analysis of accessible chromatin landscape changes in drought-sensitive and drought-tolerant cultivars in the presence and absence of drought stress. 2) Analyze genome-wide epigenetic changes in drought-sensitive and drought-tolerant cultivars in the presence and absence of drought stress. 3) Perform global analysis of the differential regulation of expression and alternative splicing and correlate the observed patterns with the observed patterns of epigenetic changes.

APPROACH: Global analysis of DNAaseI hypersensitive sites will be used as a proxy to monitor changes in the chromatin (objective 1).  Objective 2 will be accomplished by performing genome-wide analysis of stress-induced activating and repressive histone marks using ChIP-seq.  Global transcriptome analysis using RNA-seq will be used to analyze gene expression and alternative splicing in drought-sensitive and drought-tolerant cultivars.  Computational tools will then be used to correlate changes in chromatin, gene expression and splicing to identify genes (coding and non-coding) and regulated splicing events that play a role in drought tolerance. This project exploits natural variation to investigate the roles of chromatin modifications and alternative splicing in drought tolerance in Sorghum.

PROJECT CONTACT:
Name:Reddy, A.S.N.
Phone:970-491-5773
Fax: 970-491-0649
Email: reddy@colostate.edu

 

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