Plant small RNAs (Weigel)

Time- and position-dependent mRNA expression plays a critical role in both plant and animal development. Only recently has it been recognized that small RNAs including microRNAs (miRNAs) are widely used to regulate mRNA accumulation. The sequences of plant miRNAs are often conserved over considerable evolutionary distances, similar to the many miRNAs that are conserved across all bilaterally symmetric animals.

In collaboration with Jim Carrington, the Weigel group identified the first specific developmental process regulated by miRNA-guided degradation of target mRNAs (Palatnik et al., 2003; Schommer et al., 2008). To deduce common mechanisms of miRNA action in plants, we empirically deduced the sequence parameters that allow plant miRNAs to recognize their targets (Schwab et al., 2005). This knowledge has been applied to engineer artifical miRNAs with which endogenous genes can be knocked down in a very efficient and specific manner (Schwab et al., 2006). A convenient online tool for the automated design of artificial miRNAs is available here. In addition, we recently introduced a new gene silencing method, MiRNA Induced Gene Silencing (MIGS) (de Felippes et al., 2012). We have also produced a comprehensive collection of artificial target mimics for the functional analysis of miRNAs (Todesco et al., 2010).

In the context of development, we are focusing on the specific role of the miR156 and miR172 miRNAs in regulating flowering (Wang et al., 2009; Wollmann et al., 2010). Other areas of current research include the use of innovative genetic screens and chemical genetics to identify new factors required for small RNA function and biogenesis. In addition, we are investigating the role of small RNAs in natural variation (Todesco et al., 2012), and we are studying spontaneous variation in the methylome (Becker et al., 2011). These projects intersect with other studies in the department.

Key publications

• Becker, C., Hagmann, J., Müller, J., Koenig, D., Stegle, O., Borgwardt, K., and Weigel, D. (2011) Spontaneous epigenetic variatino in the Arabidopsis thaliana methylome. Nature 470, 245-249.
• de Felippes, F. F., Wang, J.-W., and Weigel, D. (2012) MIGS: MiRNA Induced Gene Silencing. Plant J., published online December 28, 2012.
• Palatnik, J. F., Allen, E., Wu, X., Schommer, C., Schwab, R., Carrington, J. C., and Weigel, D. (2003) Control of leaf morphogenesis by microRNAs. Nature, 425, 257-263.
• Schommer, C., Palatnik, J. F., Aggarwal, P., Chételat, A., Cubas, P., Farmer, E. E., Nath, U., and Weigel, D. (2008) Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol. 9, e230.
• Schwab, R., Palatnik, J. F., Riester, M., Schommer, C., Schmid, M. and Weigel, D. (2005) Specific effects of microRNAs on the plant transcriptome. Dev. Cell 8, 517-527.
• Schwab, R., Ossowski, S., Riester, M., and Weigel, D. (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18, 1121-1133.
• Todesco, M., Rubio-Somoza, I., Paz-Ares, J., and Weigel, D. (2010) A collection of target mimics for comprehensive analysis of miRNA function in Arabidopsis thaliana. PLoS Genet 6, e1001031.
• Todesco, M., Balasubramanian, S., Cao, J., Ott, F., Sureshkumar, S., Schneeberger, K., Meyer, R. C., Altmann, T., and Weigel, D. (2012) Natural variation in biogenesis efficiency of individual Arabidopsis thaliana microRNAs. Current Biology, published online December 28, 2011.
• Wang, J. W. , Czech, B., and Weigel, D. (2009) MiR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell 138, 738-749.
• Wollmann, H. Mica, E., Todesco, M., Long, J. A., and Weigel, D. (2010) On reconciling the interactions of APETALA2, miR172 and AGAMOUS with the ABC model of flower development. Development 137, 3633-3642.

Personnel

Dr. Detlef Weigel weigel@weigelworld.org

Director

Dr. Stefan Henz

Staff scientist in bioinformatics

Johannes Kaut

PhD Student

Dr. Pablo Manavella

Postdoctoral fellow

Felix Ott

PhD Student

Dr. Ignacio Rubio

Postdoctoral fellow

Dr. Lisa Smith

Postdoctoral fellow (also Natural Variation group)

Dr. Marco Todesco

Postdoctoral fellow (also Natural Variation group)

Recent Collaborators

Dr. Brandon Gaut

UC Irvine, USA

Dr. James Carrington

Donald Danforth Center, USA

Dr. Scott Poethig

University of Pennsylvania, USA