The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum

BMC Genomics

Angela Falciatore⁵  Wolfgang R Hess³  Alessandra Carbone⁴  Lionel Navarro⁶  Raphaël Champeimont⁵  Soizic Cheminant Navarro⁵  Björn Voss³  Alexis Sarazin²  Hugues Richard⁵  Alessandra Rogato¹ 

[1] Institute of Biosciences and Bioresources, CNR, Naples, Italy;Swiss Federal Institute of Technology Zürich (ETH-Z), Department of Biology, Zürich, Switzerland;Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany;Institut Universitaire de France, Paris, France;CNRS UMR7238, LCQB, F-75006 Paris, France;Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique UMR8197, Institut National de la Santé et de la Recherche Médicale, U1024 Paris, France

关键词: Periodic small RNAs distribution;    DNA methylation;    Transposable Elements;    U2 snRNA;    tRNAs;    Small RNAs;    Phaeodactylum tricornutum;    Diatoms;   

Others  :  1216253
DOI  :  10.1186/1471-2164-15-698

 received in 2014-02-11, accepted in 2014-07-30,  发布年份 2014

【 摘 要 】

Background

Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations of genes acquired from bacterial, animal and plant ancestors. Furthermore, they display both DNA methylation and gene silencing activities. Yet, the biogenesis and regulatory function of small RNAs (sRNAs) remain ill defined in diatoms.

Results

Here we report the first comprehensive characterization of the sRNA landscape and its correlation with genomic and epigenomic information in Phaeodactylum tricornutum. The majority of sRNAs is 25 to 30 nt-long and maps to repetitive and silenced Transposable Elements marked by DNA methylation. A subset of this population also targets DNA methylated protein-coding genes, suggesting that gene body methylation might be sRNA-driven in diatoms. Remarkably, 25-30 nt sRNAs display a well-defined and unprecedented 180 nt-long periodic distribution at several highly methylated regions that awaits characterization. While canonical miRNAs are not detectable, other 21-25 nt sRNAs of unknown origin are highly expressed. Besides, non-coding RNAs with well-described function, namely tRNAs and U2 snRNA, constitute a major source of 21-25 nt sRNAs and likely play important roles under stressful environmental conditions.

Conclusions

P. tricornutum has evolved diversified sRNA pathways, likely implicated in the regulation of largely still uncharacterized genetic and epigenetic processes. These results uncover an unexpected complexity of diatom sRNA population and previously unappreciated features, providing new insights into the diversification of sRNA-based processes in eukaryotes.

【 授权许可】

   
2014 Rogato et al.; licensee BioMed Central Ltd.

【 图 表 】

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