Award Abstract #0421619
Functional Genomics of Maize Chromatin

NSF Org:	IOS Division of Integrative Organismal Systems
Initial Amendment Date:	September 7, 2004
Latest Amendment Date:	December 19, 2008
Award Number:	0421619
Award Instrument:	Cooperative Agreement
Program Manager:	Diane Jofuku Okamuro IOS Division of Integrative Organismal Systems BIO Directorate for Biological Sciences
Start Date:	September 1, 2004
Expires:	August 31, 2009 (Estimated)
Awarded Amount to Date:	$6740749
Investigator(s):	Candace Galen galenc@missouri.edu (Principal Investigator) Karen Cone (Former Principal Investigator) Vicki Chandler (Co-Principal Investigator) Craig Pikaard (Co-Principal Investigator) R. Kelly Dawe (Co-Principal Investigator) Shawn Kaeppler (Co-Principal Investigator)
Sponsor:	University of Missouri-Columbia 310 JESSE HALL COLUMBIA, MO 65211 573/882-7560
NSF Program(s):	PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):	BIOT, 9232, 9109
Program Element Code(s):	1329

ABSTRACT

Chromatin plays a central role in gene expression during eukaryotic development and mediates epigenetic phenomena. Our goal is to determine the mechanisms that contribute to chromatin-based control of gene expression using maize, a premier model for these studies. It is becoming increasingly clear that understanding chromatin-level control of gene expression in plants cannot be extrapolated from other eukaryotes. Rather, direct experimentation in plants is needed. Understanding how chromatin controls gene expression in maize will provide new knowledge and molecular tools for precisely and effectively manipulating gene expression and phenotypes in this and other important crop plants.



We will identify additional maize chromatin genes, including RNA-based silencing genes; complete a new set of chromatin mutants for maize (both RNA interference lines and recessive mutations); test function by assaying lines for 1) paramutation and epigenetic variegation; 2) transgene silencing; 3) loss of imprinting; 4) DNA methylation; 5) histone modification of repetitive elements; 6) changes in gene and transposon expression profiles; and 6) chromosome cytology. New vectors will enable high-throughput screens of cellular localization and protein-protein interactions. The combination of different types of functional data will provide an integrated picture of chromatin-level regulation of gene expression.

This project will contribute to the education and training of students and postdoctoral students who will work in the participating research groups. In addition, plant genomics will be the focus of programs for science teachers and for undergraduate student interns. At the University of Arizona, high school teachers will join plant genomics labs for an 8-week summer program featuring individual lab work and development of genomics modules to use in their high school science classes. At the University of Missouri, science teachers will take part in a one-day workshop called "Chromatin: All Wrapped Up" as part of a year-long workshop series focusing on different aspects of plant genetics and genomics. The University of Missouri will also host undergraduate students from around the country to participate in 8-week summer internships as part of the Plant Genomics Internships @ MU program. All of these educational programs actively seek participants from underrepresented groups.

Access to project outcomes

All resources will be available through the Maize Genetics Stock Cooperation (http://w3.aces.uiuc.edu/maize-coop/) and data will be available through The Plant Chromatin Database (ChromDB: http://www.chromdb.org/).

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

Earley, KW, MS Shook, B Brower-Toland, L Hicks and CS Pikaard. "In vitro specificities of Arabidopsis co-activator histone acetyltransferases: implications for histone hyperacetylation in gene activation," Plant J, v.52, 2007, p. 615.

Haun WJ, S Laoueille-Duprat, MJ O'Connell, C Spillane, U Grossniklaus, AR Phillips, SM Kaeppler and NM Springer. "Genomic imprinting, methylation and molecular evolution of maize Enhancer of zeste (Mez) homologs," The Plant Journal, v.49, 2007, p. 325.

Haun, WJ, S Laoueille-Duprat, MJ O'Connell, C Spillane, U Grossiniklaus, AR Phillips, SM Kaeppler and NM Springer. "Genomic imprinting, methylation and molecular evolution of maize Enhancer of zeste (Mez) homologs," Plant J, v.49, 2007, p. 325.

Keith Earley, Richard J. Lawrence, Olga Pontes, Rachel Reuther, Angel J. Enciso, Manuela Silva, Nuno Neves, Michael Gross, Wanda Viegas, and Craig S. Pikaard. "Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance.," Genes & Developmen, v.20, 2006, p. 1283.

Keith W. Earley, Jeremy R. Haag, Olga Pontes, Kristen Opper, Tom Juehne, Keming Song, and Craig S. Pikaard. "Gateway-compatible vectors for plant functional genomics and proteomics.," The Plant Journal, v.45, 2005, p. 616.

McGinnis, K, N Murphy, AR Carlson, A Akula, C Akula, H Basinger, M Carlson, P Hermanson, N Kovacevic, MA McGill, V Seshadri, J Yoyoki, K Cone, HF Kaeppler, SM Kaeppler, NM Springer. "Assessing the efficiency of RNA interference for maize functional genomics," Plant Physiol, v.143, 2007, p. 1441.

Nathan M. Springer and Shawn M. Kaeppler. "Evolutionary divergence of moncot and dicot methyl-CpG-binding domain proteins," Plant Physiology, v.138, 2005, p. 92.

Shi, Jinghua and R. Kelly Dawe. "Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27," Genetics, v.173, 2006, p. 1571.

Stupar RM, JM Gardiner, AG Oldre, WJ Haun, VL Chander and NM Springer. "Gene expression analyses in maize inbreds and hybrids with varying levels of heterosi," BMC Plant Biology, v.8, 2008, p. 33.

Stupar RM, PJ Hermanson and NM Springer. "Non-additive and imprinted gene expression in hybrid maize endosperm," Plant Physiology, v.145, 2007, p. 411.

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