title: The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum.
abstract: 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.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Rogato
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Laboratory of Computational and Quantitative Biology, F-75006 Paris, France. hugues.richard@upmc.fr.
authors.forename: Hugues
authors.initials: H
authors.lastname: Richard
authors.forename: Alexis
authors.initials: A
authors.lastname: Sarazin
authors.forename: Björn
authors.initials: B
authors.lastname: Voss
authors.forename: Soizic
authors.initials: S
authors.lastname: Cheminant Navarro
authors.forename: Raphaël
authors.initials: R
authors.lastname: Champeimont
authors.forename: Lionel
authors.initials: L
authors.lastname: Navarro
authors.forename: Alessandra
authors.initials: A
authors.lastname: Carbone
authors.forename: Wolfgang R
authors.initials: WR
authors.lastname: Hess
authors.forename: Angela
authors.initials: A
authors.lastname: Falciatore
mesh_terms: D002874:Chromosome Mapping; D019295:Computational Biology; D019175:DNA Methylation; D004251:DNA Transposable Elements; D017377:Diatoms / Q000235:genetics* / Q000378:metabolism*; D005786:Gene Expression Regulation; D016678:Genome; D055106:Genome-Wide Association Study; D023281:Genomics; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D012342:RNA, Small Nuclear / Q000235:genetics / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*
chemical_list: D004251:DNA Transposable Elements; D012342:RNA, Small Nuclear; D058727:RNA, Small Untranslated; C405484:U2 small nuclear RNA