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Physcomitrella patens Small RNA Pathways

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Non Coding RNAs in Plants

Part of the book series: RNA Technologies ((RNATECHN))

Abstract

Small, non coding RNAs (sRNAs) are a distinct class of regulatory RNAs in plants and animals controlling a variety of biological processes. Given the great impact of sRNAs in biology, recent studies in model seed-plant species, particularly in Arabidopsis thaliana, focused on the identification, biogenesis and functional analysis of sRNAs. In seed plants, several classes of sRNAs with specific sizes and dedicated functions have evolved through a series of pathways, namely, microRNAs (miRNAs), repeat-associated small interfering RNAs (ra-siRNAs), natural antisense transcript-derived small interfering RNAs (nat-siRNAs) and trans-acting small interfering RNAs (ta-siRNAs). In the last few years, the analysis of plant sRNA pathways has been extended to the bryophyte Physcomitrella patens, a non-flowering, non-vascular ancient land plant, that diverged from the lineage of seed plants approximately 450 million years ago. Based on a number of characteristic features and its phylogenetic key position in land-plant evolution, P. patens emerged as a plant model species to address basic as well as applied topics in plant biology. The analysis of P. patens sRNA pathways has been recently advanced by the deep sequencing of sRNA libraries, the release of the P. patens genome that allowed the mapping of sRNA producing loci and first molecular analyses of P. patens mutants with targeted disruption of genes encoding essential components of endogenous sRNA pathways. Even though the major sRNA pathways are evolutionarily conserved in P. patens, there are particular differences in the functional components of sRNA pathways and the biological function of sRNAs. These include a specific amplification of initial miRNA and ta-siRNA signals by the generation of transitive siRNAs, deviating functions and specificities of DICER-LIKE proteins and an epigenetic gene silencing pathway that is triggered by miRNAs. Further, the conservation of miRNA biogenesis in P. patens was used to establish specific gene silencing by the expression of artificial miRNAs suited for functional gene analysis by reverse genetics approaches. These findings underline that P. patens serves as a valuable model system to study the evolution, diversity and function of plant sRNAs. Here, we summarise the current knowledge on different sRNA biogenesis pathways, their biological relevance and the expression of artificial miRNAs in P. patens.

Muhammad Asif Arif, Isam Fattash and Basel Khraiwesh contributed equally to this work.

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Acknowledgements

We gratefully acknowledge financial support to our work on small RNA pathways by the Landesstiftung Baden-Württemberg (P-LS-RNS/40 to W.F.), the German Federal Ministry of Education and Research (BMBF; FRISYS 0313921 to W.F.), the German Research Foundation (DFG; FR 1677/3-1 to W.F.) and the German Academic Exchange Service (DAAD; Ph.D. fellowships to M.A.A. and I.F.).

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Authors and Affiliations

  1. Department of Plant Biotechnology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany

    Isam Fattash & Wolfgang Frank

  2. Institute for Genetics, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany

    Muhammad Asif Arif

  3. Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Flanders, Belgium

    Basel Khraiwesh

  4. Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, 9052, Gent, Belgium

    Basel Khraiwesh

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  1. Muhammad Asif Arif
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  2. Isam Fattash
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  3. Basel Khraiwesh
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  4. Wolfgang Frank
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Correspondence to Wolfgang Frank .

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Editors and Affiliations

  1. Institute of Chemistry/Biochemistry, Free University Berlin, Thielallee 63, Berlin, 14195, Berlin, Germany

    Volker A. Erdmann

  2. Inst. Bioorganic Chemistry, PAN Poznan, ul. Z. Noskowskiego 12/14, Poznan, 61-704, Poland

    Jan Barciszewski

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Arif, M.A., Fattash, I., Khraiwesh, B., Frank, W. (2011). Physcomitrella patens Small RNA Pathways. In: Erdmann, V., Barciszewski, J. (eds) Non Coding RNAs in Plants. RNA Technologies. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19454-2_10

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