Diane Jofuku Okamuro
IOS Division of Integrative Organismal Systems
BIO Directorate for Biological Sciences
Start Date:
October 1, 2004
Expires:
September 30, 2010 (Estimated)
Awarded Amount to Date:
$5245054
Investigator(s):
William Thompson William_Thompson@ncsu.edu (Principal Investigator)
George Allen (Co-Principal Investigator) Robert Martienssen (Co-Principal Investigator) Linda Hanley-Bowdoin (Co-Principal Investigator) Bryon Sosinski (Co-Principal Investigator)
Sponsor:
North Carolina State University
CAMPUS BOX 7514
RALEIGH, NC 27695 919/515-2444
NSF Program(s):
PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):
BIOT, 9109, 7218, 1228
Program Element Code(s):
1329
ABSTRACT
It is well known that higher organisms, including plants, begin the process of replicating their DNA at many different places in their genomes. However, as yet we know very little about how these starting points ("replication origins") are defined, or how they relate to other chromosomal features. An interdisciplinary team from three leading research institutions will pool their efforts and expertise to investigate this question and attain a deeper understanding of spatial and biochemical parameters affecting genome function.
Specific objectives:
(1) A primary goal of their research project is to construct maps of replication origins in large regions of representative plant chromosomes, as well as to construct and overlay maps of key chromosomal features such as matrix attachment regions, regions enriched in modified histones or methylated DNA.
(2) A parallel effort will map DNA replication activity and gene activity (transcription) in the same chromosomal regions under several different developmental conditions, which will lead to a better understanding of the interrelationship of chromosome structure and function.
Outcomes:
When completed, the project will help scientists understand how chromosome functions are spatially organized and coordinated in structural and functional domains, and help define chromosomal features that play key roles in these functions. The proposed experiments will combine powerful genomic technologies with molecular, cellular and biochemical tools. The team will focus on the short arm of rice chromosome 1 and the full length of Arabidopsis chromosome 4, thus providing extensive data for model organisms representing each of the two major groups of crop plants. Comparing chromosomal features for these plant species with data for animals and other organisms will help identify chromosomal features important enough to be broadly conserved in evolution, as well as highlight features that may be unique to the plant kingdom. New genomic information and tools that are generated (including the carefully designed set of sequences to be used as mapping landmarks on genomic microarrays) will be made available to other members of the scientific community via the web as well as through conventional publications. Data will be submitted to the Gene Expression Omnibus homepage (http://www.ncbi.nlm.nih.gov/geo/) and ArrayExpress, a public repository (http://www.ebi.ac.uk/arrayexpress/) . All sequence annotation for the chromosomal elements will be submitted to GenBank.
The basic information on chromosome structure generated by this project will help support a new generation of genetic engineering technologies, which may include new methods for directing gene expression, targeted gene insertion, and construction of artificial chromosomes. In addition, the project will provide training in state-of-the-art functional genomic and bioinformatics techniques. Trainees at the undergraduate, graduate and postdoctoral levels will participate in the research, and workshops will be organized for scientists in the southeastern US, including faculty and students at historically black and minority institutions. The team will also work with local educators to develop teaching tools useful for presenting genomics concepts to high school students.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
Allen, G. C. , M.A. Flores-Vergara, S. Krasynanski, S. Kumar, and W. F. Thompson. "A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide (CTAB)," Nature Protocols, v.1, 2006, p. 2320.
Boccara M, Sarazin A, Billoud B, Jolly V, Martienssen R, Baulcombe D, Colot V.. "New approaches for the analysis of Arabidopsis thaliana small RNAs," Biochimie, v.89, 2007, p. 1252.
Garcia D, Collier SA, Byrne ME, Martienssen RA. "Specification of leaf polarity in Arabidopsis via the trans-acting siRNA pathway," Current Biology, v.16, 2006, p. 933.
Gendrel AV, Lippman Z, Martienssen R, Colot V. (2005). "Profiling histone modification patterns in plants using genomic tiling microarrays.," Nat .Methods 2:213-218., v.22, 2005, p. 213.
Halweg, C., W. F. Thompson and S. Spiker (2005).. "The rb7 matrix attachment region increases the likelihood and magnitude of transgene
expression in tobacco cells: a flow cytometric study.," Plant Cell 17: 418-429., v.17, 2005, p. 418.
Kloc A, Zaratiegui M, Nora E, Martienssen R.. "RNA Interference Guides Histone Modification during the S Phase of Chromosomal Replication," Current Biology, v.18, 2008, p. 490.
Kumar, S., G. C. Allen and W. F. Thompson. "Gene targeting in plants: fingers on the move," Trends Plant Sci, v.11, 2006, p. 159.
Lee, T.-J., Shultz, R.W., Hanley-Bowdoin, L., Thompson, W.F. (2004). "Establishment of rapidly proliferating rice cell suspension culture and its characterization
by fluorescence-activated cell sorting analysis.," Plant Mol. Biol. Rep. 22:259?267., v.22, 2004, p. 259.
Lippman Z, Gendrel AV, Colot V, Martienssen R. (2005). "Profiling DNA methylation patterns using genomic tiling microarrays.," Nat. Methods 2:219-224., v.22, 2005, p. 219.
Martienssen R.A., Doerge R.W. and Colot V. (2005). "Epigenomic mapping in Arabidopsis using tiling microarrays.," Chromosome Research 13:299-308., v.13, 2005, p. 299.
Rabinowicz, P.D., Citek, R., Budiman, M.A., Nunberg, A., Bedell, J.A., Lakey, N., O'Shaughnessy, A.L., Nascimento, L.U., McCombie, W.R., and Martienssen, R.A.. "Differential methylation of genes and repeats in land plants," Genome Res., v.15, 2005, p. 1431.
Ronemus M, Vaughn MW, Martienssen RA. "MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis," Plant Cell, v.18, 2007, p. 1559.
Santos, A.P., E. Wegal, G. C. Allen, W.F. Thompson, E. Stoger, P.J. Shaw, and R. Abranches. "In situ methods to localize transgenes and transcripts in interphase nuclei: A tool for transgenic plant research," Plant Methods. 2: 18.1-18.13, v.2, 2006, p. 18.
Shultz, R., S. Settlage, L. Hanley-Bowdoin and W. Thompson. "A trichloroacetic acid-acetone method greatly reduces infrared autofluorescence of protein extracts from plant tissue," Plant Molecular Biology Reporter 23: 405-409., v.23, 2006, p. 405.
Shultz, R., S. Settlage, L. Hanley-Bowdoin and W.F. Thompson. "A trichloroacetic acid-acetone method greatly reduces infrared autofluorescence of protein extracts from plant tissue," Plant Molecular Biology Reporter, v.23, 2006, p. 405.
Shultz, RW; Tatineni, VM; Hanley-Bowdoin, L; Thompson, WF. "Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice(1[W][OA])," PLANT PHYSIOLOGY, v.144, 2007, p. 1697-1714.
Slotkin RK, Martienssen R. (2007). "Transposable elements and the epigenetic regulation of the genome," Nat Rev Genet., v.8, 2007, p. 272.
Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland G, Colot V. (2007). "Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27," PLoS Genetics, v.3, 2007, p. e86.
Vaughn MW, Tanurd Ić M, Lippman Z, Jiang H, Carrasquillo R, Rabinowicz PD, Dedhia N, McCombie WR, Agier N, Bulski A, Colot V, Doerge RW, Martienssen RA. (2007). "Epigenetic Natural Variation in Arabidopsis thaliana," PLoS Biology, v.5, 2007, p. e174.
Vaughn, M.W. and Martienssen, R.. "It's a Small RNA World, After All," Science, v.309, 2005, p. 1525.
Vaughn, M.W., Tanurdzic, M., and Martienssen, R.. "Replication, Repair, and Reactivation," Dev. Cell, v.9, 2005, p. 724.
Weil C, Martienssen R.. "Epigenetic interactions between transposons and genes: lessons from plants," Curr Opin Genet Dev. 2008 Mar 12. [Epub ahead of print], 2008.
