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Characterization of regulatory roles of SWI/SNF-type chromatin remodelling complexes in the control of development and hormonal, biotic and abiotic stress responses in Arabidopsis

Final Report Summary - SWI/SNF-CRCS (Characterization of regulatory roles of SWI/SNF-type chromatin remodelling complexes in the control of development and hormonal, biotic and abiotic stress responses in Arabidopsis)

In Eukaryotes, chromatin remodelling complexes (CRCs) of the SWI/SNF family are implicated in numerous regulatory processes including growth, differentiation and development. The increase of the number of genes encoding SNF2-type ATPase and SWI3-type SWI/SNF CRC subunits in Arabidopsis compared to animals, suggests that plant CRCs carry different combinations of these core components. During our previous yeast two-hybrid screens, we have identified potential auxiliary proteins of the Arabidopsis SWI/SNF CRCs. We subsequently confirmed their in vivo interactions with CRC core components using FRET or BiFC assays. Additionally, we found that mutations inactivating SWI3C and BRM genes cause similar phenotypic changes, prompting the conclusion that the BRM ATPase and ATSWI3C subunits occur in common SWI/SNF complexes.
The European- Reintegration grant was based on a focused multidisciplinary approach aiming at precise definition of the regulatory functions of SWI/SNF CRCs. Complementary tasks of the experimental work plan included: i) identification of primary regulatory targets of SWI/SNF CRCs using transcriptome analysis in combination with inducible knock-down of the SWI3 subunits; ii) mapping of SWI/SNF-binding domains in target genes using chromatin precipitation; iii) analysis of SWI/SNF regulated functions in stress and pathogen signaling pathways. The project was expected to provide novel insight into regulatory mechanisms by which distinct classes of SWI/SNF CRCs participate in control of physiological and developmental responses in Arabidopsis.
During Re-Integration Fellowship at the Institute of Biochemistry and Biophysics PAS in Warsaw, the fellow constructed and verified functionality of conditionally inducible mutants inactivating SWI3A and SWI3B genes (mutations in these genes are normally embryolethal). The completion of the project resulted in precise description of somatic phenotypes caused by conditionally induced mutations in SWI3A and SWI3B genes. During his Marie Curie ERG project, the fellow has also found that the above mutations resulted in phenotypic changes similar to those observed upon inactivation of genes involved in the control of cellular homeostasis.
During further studies the fellow identified SWI/SNF targeted domains in promoter regions of genes regulated in hormone-dependent manner. The extended investigation led to identification of novel SWI/SNF function in the GA biosynthesis and perception pathways. Further, the inactivation of SWI/SNF core subunits led to aberrations in biosynthesis of most of the major hormones indicative of SWI/SNF complex acting in hormonal crosstalk. These data were summarized in two publications: 1. Sarnowska EA, Rolicka AT, Bucior E, Cwiek P, Tohge T, Fernie AR, Jikumaru Y, Kamiya Y, Franzen R, Schmelzer E, Porri A, Sacharowski S, Gratkowska DM, Zugaj DL, Taff A, Zalewska A, Archacki R, Davis SJ, Coupland G, Koncz C, Jerzmanowski A, Sarnowski T.J. (2013) DELLA-Interacting SWI3C Core Subunit of Switch/Sucrose Nonfermenting Chromatin Remodeling Complex Modulates Gibberellin Responses and Hormonal Cross Talk in Arabidopsis. Plant Physiology163(1):305-17; and, 2. Archacki R, Buszewicz D, Sarnowski TJ, Sarnowska E, Rolicka AT, Tohge T, Fernie AR, Jikumaru Y, Kotlinski M, Iwanicka-Nowicka R, et al (2013) BRAHMA ATPase of the SWI/SNF chromatin remodeling complex acts as a positive regulator of gibberellin – mediated responses in Arabidopsis. PLoS ONE 8: e58588
During his Marie Curie ERG project, the fellow has strengthened collaborative research interactions between Laboratory Plant Molecular Biology at Institute of Biochemistry and Biophysics PAS, Poland and laboratories at Max-Planck Institute for Plant Breeding Research which resulted in the efficient transfer of knowledge to post-docs, Ph.D. and master’s students of the Polish Laboratory and initiated new collaboration with the Max-Planck Institute for Molecular Plant Physiology in Potsdam-Golm, Germany. The fellow organized several short scientific visits in Cologne of the Ph.D. students and post-docs from Warsaw that allowed them to get familiar with methods used in this Institute, which were subsequently successfully adopted in the Polish Laboratory. This collaboration will soon result in additional joined scientific publications and reports, which will be presented during international conferences and meetings. The Marie Curie ERG fellowship resulted in professional maturation and increase of the fellow’s scientific skills. He received complementary and multidirectional training in writing of scientific manuscripts, communication and constructing grant applications. During the ERG fellowship, the fellow has established his own nearly independent research team composed of post-docs, PhD and undergraduate students.
The ERG fellowship allowed the fellow to gain new scientific skills comparable to those that can be obtained upon completion of training in best universities and research institutes in Europe and USA, and allowed him to start the habilitation procedure.
Finally, the fellow has also benefited from excellent contacts established between IBB PAS and the Marie-Curie Memorial Cancer Center in Warsaw. This greatly increased his interdisciplinary scientific skills. During and after finishing of this fellowship the fellow has been and will continue to be employed in the tenure position in Laboratory of Plant Molecular Biology Polish Academy of Sciences, Pawinskiego 5A 02-106 Warsaw, Poland (E-mail address;