Plants and other multicellular organisms need a precise spatio-temporal control of gene expression during their development, and to respond to changes in the environment and defend their genome. In part, this regulatory capacity resides at the RNA level through small RNA-directed gene silencing. MicroRNAs are one of the classes of small RNAs that have 21 nt and fulfill essential regulatory roles. They usually recognize target mRNAs by base complementarity and guide them to cleavage or translational arrest. Our laboratory is currently interested in the biogenesis of these small molecules and their specific functions in plants. The experimental approaches aim to address fundamental mechanistic questions using the model system Arabidopsis thaliana, but the lab also seeks to develop tools of practical relevance that can be applied to plants of agronomic importance.
Biogenesis of plant microRNAs
MicroRNAs are distinguished from other small RNAs by their unique biogenesis, which involves a precise excision from the stem of a fold-back precursor located in a long primary transcript. The type III ribonuclease DICER-LIKE1 (DCL1) with the aid of the accessory proteins cleaves the precursors to release the microRNAs. However, plant microRNA precursors come in different sizes and shapes, and we are interested in understanding how these precursors can be processed to generate the mature microRNAs. We have found that many precursors are processed in a base-to-loop direction, while others are processed by a non-canonical loop-to-base mechanism. We use a combination of approaches to study microRNA processing, including the analysis of libraries of random mutant precursors, the identification of processing intermediates with the aid of next generation sequencing techniques, as well as structural studies in collaboration with the groups of Jerome Boisbouvier and Rodolfo Rasia.
MicroRNA networks in plants
In plants, many of the evolutionary conserved miRNAs regulate transcription factors, which in turn play key biological functions. Perturbation of these miRNA regulatory networks, by mutations in microRNAs encoding genes or by interference with their activity usually causes severe developmental defects. We are interested in identifying the targets of plant microRNAs, as well as their biological functions. The lab also focuses in the control of cell proliferation and differentiation by two microRNAs, miR396 and miR319.
Beltramino M, Debernardi JM, Ferela A, Palatnik JF. ARF2 represses expression of plant GRF transcription factors in a complementary mechanism to microRNA miR396. Plant Physiol. 2021
Goldy C, Pedroza-Garcia JA, Breakfield N, Cools T, Vena R, Benfey PN, De Veylder L, Palatnik J, Rodriguez RE. The Arabidopsis GRAS-type SCL28 transcription factor controls the mitotic cell cycle and division plane orientation. PNAS 2021
Rojas AML, Drusin SI, Chorostecki U, Mateos JL, Moro B, Bologna NG, Bresso EG, Schapire A, Rasia RM, Moreno DM, Palatnik JF. Identification of key sequence features required for microRNA biogenesis in plants. Nat Commun 2020.
- Liebsch D, Palatnik JF. MicroRNA miR396, GRF transcription factors and GIF co-regulators: a conserved plant growth regulatory module with potential for breeding and biotechnology. Curr Opin Plant Biol. 2020.
- Manavella PA, Yang SW, Palatnik J. Keep calm and carry on: miRNA biogenesis under stress. Plant J. 2019.
- Moro B, Chorostecki U, Arikit S, Suarez IP, Höbartner C, Rasia RM, Meyers BC, Palatnik JF. Efficiency and precision of microRNA biogenesis modes in plants. Nucleic Acids Res. 2019.
- Beltramino M, Ercoli MF, Debernardi JM, Goldy C, Rojas AML, Nota F, Alvarez ME, Vercruyssen L, Inzé D, Palatnik JF, Rodriguez RE. Robust increase of leaf size by Arabidopsis thaliana GRF3-like transcription factors under different growth conditions. Scientific Reports. 2018.
- Bresso EG, Chorostecki U, Rodriguez RE, Palatnik JF, Schommer C. Spatial Control of Gene Expression by miR319 Regulated TCP Transcription Factors in Leaf Development. Plant Physiol. 2018.
- Ercoli MF, Ferela A, Debernardi JM, Perrone AP, Rodriguez RE, Palatnik JF. GIF Transcriptional Co-regulators Control Root Meristem Homeostasis. Plant Cell. 2018. Highlighted article: Design Stars: How GRF-INTERACTING FACTORs Help Determine the Layout of the Root Tip. The Plant Cell.
- Chorostecki U, Moro B, Rojas AML, Debernardi JM, Schapire AL, Notredame C, et al. Evolutionary Footprints Reveal Insights into Plant MicroRNA Biogenesis. Plant Cell. 2017.
- Rodriguez RE, Schommer C, Palatnik JF. Control of cell proliferation by microRNAs in plants. Current Opinion in Plant Biology. 2016.
- Rodriguez RE, Ercoli MF, Debernardi JM, Breakfield NW, Mecchia MA, Sabatini M, et al. MicroRNA miR396 Regulates the Switch between Stem Cells and Transit-Amplifying Cells in Arabidopsis Roots. Plant Cell. 2015. Highlighted: Cover of The Plant Cell issue.
- Debernardi JM, Mecchia MA, Vercruyssen L, Smaczniak C, Kaufmann K, Inze D, et al. Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity. Plant Journal. 2014.
- Chorostecki U, Palatnik JF. comTAR: a web tool for the prediction and characterization of conserved microRNA targets in plants. Bioinformatics. 2014.
- Schommer C, Debernardi JM, Bresso EG, Rodriguez RE, Palatnik JF. Repression of cell proliferation by miR319-regulated TCP4. Molecular Plant. 2014.
- Bologna NG, Schapire AL, Zhai J, Chorostecki U, Boisbouvier J, Meyers BC, et al. Multiple RNA recognition patterns during microRNA biogenesis in plants. Genome Research. 2013.
- “rGRF3 Mutants, Methods and Plants”. Aumento de biomasa y tolerancia a sequía en plantas por medio de factores de transcripción GRF y el microARN miR396. Inventores: Palatnik JF, Rodriguez RE, Mecchia MG, Debernardi JM. (CONICET/UNR) WO/2013/102762, PCT/GB2013/050005,US Patent 9890388.
- “Chimeric proteins which enhance the activity of DNA binding domains (DBD) and transcription factors in plants” Inventores: Palatnik JF, Debernardi JM, Schommer C, Rodriguez RE. (CONICET/UNR) WO2016098027 A1, PCT/IB2015/059696.