LEAVE OF ABSENCE
Bioinformatics, Functional Genomics, Promoter Architecture, Gene Expression, RNA processing, Alternative Splicing, RNA Binding Proteins, Arabidopsis thaliana, Brachypodium distachyon, Flowering Time, Circadian Clock
Description of Research
Plant RNA-binding Proteins and RNA Processing. The members of the RNA-binding protein (RBP) superfamily play important roles in all aspects of RNA metabolism including alternative splicing, yet the functions of most plant RBPs remain unknown. Multiple RBPs function in regulating some aspect of the metabolism of every transcript at some point in its life, and collectively this "RBPome" serves as an additional layer of regulatory control on top of transcriptional regulation of gene expression. Molecular, genetic and biochemical approaches will be used to connect individual RBPs to specific physiological, developmental, or signaling pathways, and identify their transcript targets. We will use DNA microarrays to monitor transcript processing on a whole-genome scale, and develop new approaches for alternative splicing detection using emerging ultra high-throughput sequencing technologies.
Promoter Architecture and Genomic Control of Gene Expression. The genome interacts with the environment in the regulation of transcription, and changes in promoter architecture play a role in phenotypic variation observed between and within species. Computational methods will be employed to identify DNA motifs (ie. transcription-factor binding sites) in the regulatory sequences upstream of co-expressed/co-regulated genes in Arabidopsis and other plant species with completed genome sequences, including rice and poplar. Molecular, genetic and biochemical approaches will be used to validate the computational predictions, identify interacting transcription factors, and further dissect the transcriptional networks.
Brachypodium distachyon , an experimental model for cereal genomics. Brachypodium distachyon ( Brachypodium.org ) is a grass species related to the major cereal grain species wheat, barley, oats, maize, rice, rye, sorghum, and millet. It has many qualities that make it an excellent model organism for functional genomics research in temperate grasses and cereals, and dedicated biofuel crops such as Switchgrass. These attributes include small genome (~300-320Mbp) diploid accessions, a series of polyploid accessions, a small physical stature, self-fertility, a short lifecycle, simple growth requirements, and an efficient transformation system. We will work towards developing genomic, genetic, and bioinformatics resources for Brachypodium and use these tools to facilitate study of flowering time control in grasses.
Research Group Members
Faculty Research Assistants/Associates
Erik Rowley (MCB)
Garvin DF, Gu Y-Q, Hasterok R, Hazen SP, Jenkins G, Mockler TC, Mur LAJ, and Vogel JP. Development of Genetic and Genomic Research Resources for Brachypodium distachyon, a New Model System for Grass Crop Research. 2008. The Plant Genome [A Supplement to Crop Science] 48(S1) S69-S84.