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Genomic Science Program

2010 Awardee

Genome-Wide Analysis of miRNA Targets in Brachypodium and Biomass Energy Crops

INVESTIGATORS: Pamela J. Green

INSTITUTION: University of Delaware

NON-TECHNICAL SUMMARY: MicroRNAs (miRNAs) are important regulatory molecules that repress selected “target” genes to enable normal development, stress responses, and other processes.  In plants, they act by causing cleavage and degradation of a subset of the messenger RNAs (mRNAs) that genes must produce to function. This project will identify the targets of miRNAs by sifting through the population of partially degraded mRNAs produced in different organs and under adverse environmental conditions.  In addition to identifying the targets of miRNAs in Brachypodium, a functional genomic model for energy crops and temperate grasses, this project will include analyses of the energy crops themselves. The research should provide missing links in our understanding of regulatory networks, useful information for crop breeding, and may suggest new strategies for the improvement of biomass energy crops.

OBJECTIVES: 1) Construct libraries for Parallel Analysis of RNA Ends (PARE) from different tissues and environmental stress treatments of Brachypodium, Switchgrass, Miscanthus, and Sorghum. 2) Sequence these libraries to a depth of > 10 million reads and match to available genomic and cDNA sequence of the source species. 3) Identify and comparatively analyze miRNA targets and new small RNAs that cause target cleavage and evaluate their functional associations. 4) Identify tissue- and stress-regulated changes in target cleavage and other mRNA decay events. 5) Release the data to the public on a user-friendly website that provides comparative analysis tools.

APPROACH: 1) The PARE libraries will be made using a strategy that results in the cloning of the 3’ products of miRNA-guided target RNA cleavage. 2) Deep sequencing will be done with Illumina’s sequencing by synthesis technology. PARE sequences will be matched to cDNA and genomic sequence using pipelines and tools developed by our computational collaborator Blake Meyers. 3) Bioinformatics approaches will identify high-abundance PARE sequences that match to known miRNAs or other small RNAs not yet known to guide target RNA cleavage. Targets that correspond to known genes and/or particular GO categories will be evaluated to characterize functional associations. 4) Differential target cleavage will be evaluated by comparing the abundances of PARE sequences in different samples. 5) A PARE database will be constructed and a user-friendly web interface will be developed to make the data publicly available.

PROJECT CONTACT:
Name: Pamela J. Green
Email: green@dbi.udel.edu

 

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