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Physcomitrella patens small RNA pathways

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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, particu-larly in A. 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 microR-NAs (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 years, the analysis of plant sRNA pathways was extended to the bryophyte P. patens, a non-flowering, non-vascular ancient land plant, that diverged from the lineage of seed plants approxi-mately 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 was 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 expres-sion of artificial miRNAs in P. patens.
Keywords
Physcomitrella patens, small non-coding RNA, development, gene silencing, DICER-LIKE

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Chicago
Arif, Muhammad Asif, Isam Fattash, Basel Khraiwesh, and Wolfgang Frank. 2011. “Physcomitrella Patens Small RNA Pathways.” In Non Coding RNAs in Plants, ed. VA Erdmann and J Barciszewski, 139–173. Berlin, Germany: Springer.
APA
Arif, M. A., Fattash, I., Khraiwesh, B., & Frank, W. (2011). Physcomitrella patens small RNA pathways. In V. Erdmann & J. Barciszewski (Eds.), Non coding RNAs in plants (pp. 139–173). Berlin, Germany: Springer.
Vancouver
1.
Arif MA, Fattash I, Khraiwesh B, Frank W. Physcomitrella patens small RNA pathways. In: Erdmann V, Barciszewski J, editors. Non coding RNAs in plants. Berlin, Germany: Springer; 2011. p. 139–73.
MLA
Arif, Muhammad Asif, Isam Fattash, Basel Khraiwesh, et al. “Physcomitrella Patens Small RNA Pathways.” Non Coding RNAs in Plants. Ed. VA Erdmann & J Barciszewski. Berlin, Germany: Springer, 2011. 139–173. Print.
@incollection{1057766,
  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, particu-larly in A. 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 microR-NAs (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 years, the analysis of plant sRNA pathways was extended to the bryophyte P. patens, a non-flowering, non-vascular ancient land plant, that diverged from the lineage of seed plants approxi-mately 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 was 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 expres-sion of artificial miRNAs in P. patens.},
  author       = {Arif, Muhammad Asif and Fattash, Isam and Khraiwesh, Basel and Frank, Wolfgang},
  booktitle    = {Non coding RNAs in plants},
  editor       = {Erdmann, VA and Barciszewski, J},
  isbn         = {9783642194542},
  keywords     = {Physcomitrella patens,small non-coding RNA,development,gene silencing,DICER-LIKE},
  language     = {eng},
  pages        = {139--173},
  publisher    = {Springer},
  series       = {RNA Technologies},
  title        = {Physcomitrella patens small RNA pathways},
  url          = {http://dx.doi.org/10.1007/978-3-642-19454-2_10},
  year         = {2011},
}

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