2010 Annual Report 4.Accomplishments 1. Identification of Function for ULT1 as Chromatin Regulatory Protein: This work addresses the question of how the critical meristem cell fate specification gene ULTRAPETALA1 (ULT1) functions in Arabidopsis for future application to crop plants. ARS scientists in the Plant Gene Expression Center in Albany, CA determined that ULT1 acts as a part of an epigenetic regulatory complex that counteracts the repressive activity of a well-known chromatin-associated repression complex. We also showed that ULT1 induces the expression of the master floral regulatory gene AG by directly associating with DNA sequences, leading to changes in its methylation status. This accomplishment identifies a novel mechanism that mediates epigenetic switches controlling a key developmental trait, providing a foundation for improving this trait in crop plants. 2. Functional Analysis of BOP-Mediated Organ Formation: This work addresses the characterization of genes controlling Arabidopsis organ identity that can be translated to crop species. ARS scientists in the Plant Gene Expression Center in Albany, CA demonstrated that the BOP1 and BOP2 regulatory proteins control leaf formation by suppressing KNOX1 and YABBY protein activity at the base of leaves. We showed that reducing the expression of multiple KNOX and YABBY genes progressively attenuated the phenotype, uncovering a genetic pathway consisting of several protein families that control leaf patterning. This accomplishment may lead to the manipulation of a similar pathway in crop plants for increasing biomass, benefiting domestic farmers as well as biotechnological efforts to achieve energy independence. 3. Characterization of Small Regulatory RNA in Fertilization: This work addresses the function of small regulatory RNA molecules during Arabidopsis development for future application to crop plants. ARS scientists in the Plant Gene Expression Center in Albany, CA reported in the peer-reviewed journal Genes & Development that the small regulatory RNA KOKOPELLI (KPL) is essential for the process of double fertilization in Arabidopsis. In collaboration with other ARS scientists from the same location, we reported that KPL is specifically expressed in sperm and controls sperm function during fertilization by affecting the expression of a gene that codes for a putative component of the protein degradation pathway. This accomplishment identifies a key controlling factor of double fertilization in plants, a process of enormous agricultural value to domestic farmers. Review Publications Carles, C.C., Fletcher, J.C. 2009. The SAND domain protein ULTRAPETALA1 acts as a trithorax group factor to regulate cell fate in plants. Genes and Development. 23(23)2723-2728. Carles, C.C., Fletcher, J.C. 2010. Missing links between histones and RNA Pol II arising from SAND?. Epigenetics. 5(5):381-385. Jun, J., Ha, C., Fletcher, J.C. 2010. BLADE-ON-PETIOLE1 coordinates organ determinacy and axial polarity in Arabidopsis by directly activating ASYMMETRIC LEAVES2. The Plant Cell. 22:62-76. Meng, L., Ruth, K.C., Fletcher, J.C., Feldman, L. 2010. The Roles of Different CLE Domains in Arabidopsis CLE Polypeptide Activity and Functional Specificity. Molecular Plant. Published online doi:10.1093/mp/ssq021.