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 sequence of miRNAs is often conserved across considerable evolutionary distances, and several identical miRNAs have been found in both Arabidopsis thaliana and rice. Similarly, many miRNAs are conserved across all bilaterally symmetric animals.

In animals, the primary effects of most miRNAs are translational repression or destabilization of mRNAs by deadenylation. In contrast, plant miRNAs appear to act mainly by guiding cleavage of specific target mRNAs, with the mechanism of cleavage being similar to cleavage guided by short interfering RNAs (siRNAs). 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).

To deduce common mechanisms of miRNA action in plants, we are studying several groups of miRNAs. As a first step, we have empirically deduced the sequence parameters that allow plant miRNAs to recognize their targets (Schwab et al., 2005; Palatnik et al., 2007). This knowledge has already 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 the context of development, we are focusing on the specific role of the miR156 and miR172 miRNAs in regulating flowering. In addition, we are collaborating with the Carrington and Dangl groups to correlate genome-wide patterns of small RNA and mRNA expression. Finally, we are investigating the role of small RNAs in natural variation. These projects intersect with other studies in the department.

Key publications

• 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.
• Palatnik, J. F., Wollmann, H., Schommer, C., Schwab, R., Boisbouvier, J., Rodriguez, R., Allen, E., Dezulian, T., Huson, D., Carrington, J. C., and Weigel, D. (2007) Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Dev. Cell 13, 115-125.
• 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.

Personnel

Felipe Felippes

PhD Student

Dr. Stefan Henz

Staff scientist in bioinformatics

Stephan Ossowski

PhD Student (also Natural Variation group)

Dr. Ignacio Rubio

Postdoctoral fellow

Dr. Sascha Laubinger

Postdoctoral fellow

Dr. Lisa Smith

Postdoctoral fellow (also Natural Variation group)

Marco Todesco

PhD Student (also Natural Variation group)

Dr. Jiawei Wang

Postdoctoral fellow

Schallum Werner

PhD Student

Heike Wollmann

PhD Student

Dr. Detlef Weigel

Director

Collaborators

Dr. James Carrington

Oregon State University, USA

Dr. Jeffery Dangl

University of North Carolina, USA

Dr. Daniel Huson

University of Tübingen