title: Identification of novel small ncRNAs in pollen of tomato.
abstract: BACKGROUND
  The unprecedented role of sncRNAs in the regulation of pollen biogenesis on both transcriptional and epigenetic levels has been experimentally proven. However, little is known about their global regulation, especially under stress conditions. We used tomato pollen in order to identify pollen stage-specific sncRNAs and their target mRNAs. We further deployed elevated temperatures to discern stress responsive sncRNAs. For this purpose high throughput sncRNA-sequencing as well as Massive Analysis of cDNA Ends (MACE) were performed for three-replicated sncRNAs libraries derived from tomato tetrad, post-meiotic, and mature pollen under control and heat stress conditions.
  
  
  RESULTS
  Using the omiRas analysis pipeline we identified known and predicted novel miRNAs as well as sncRNAs from other classes, responsive or not to heat. Differential expression analysis revealed that post-meiotic and mature pollen react most strongly by regulation of the expression of coding and non-coding genomic regions in response to heat. To gain insight to the function of these miRNAs, we predicted targets and annotated them to Gene Ontology terms. This approach revealed that most of them belong to protein binding, transcription, and Serine/Threonine kinase activity GO categories. Beside miRNAs, we observed differential expression of both tRNAs and snoRNAs in tetrad, post-meiotic, and mature pollen when comparing normal and heat stress conditions.
  
  
  CONCLUSIONS
  Thus, we describe a global spectrum of sncRNAs expressed in pollen as well as unveiled those which are regulated at specific time-points during pollen biogenesis. We integrated the small RNAs into the regulatory network of tomato heat stress response in pollen.
authors.affiliation: GenXPro GmbH, Frankfurt am Main, Germany. kbokszczanin@genxpro.de.
authors.forename: Kamila Lucia
authors.initials: KL
authors.lastname: Bokszczanin
authors.affiliation: GenXPro GmbH, Frankfurt am Main, Germany.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Krezdorn
authors.affiliation: Cluster of Excellence Frankfurt, Centre of Membrane Proteomics, Department of Biosciences, Goethe University, Frankfurt am Main, Germany.
authors.forename: Sotirios
authors.initials: S
authors.lastname: Fragkostefanakis
authors.affiliation: GenXPro GmbH, Frankfurt am Main, Germany.
authors.forename: Sören
authors.initials: S
authors.lastname: Müller
authors.affiliation: GenXPro GmbH, Frankfurt am Main, Germany.
authors.forename: Lukas
authors.initials: L
authors.lastname: Rycak
authors.affiliation: GenXPro GmbH, Frankfurt am Main, Germany.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Chen
authors.affiliation: GenXPro GmbH, Frankfurt am Main, Germany.
authors.forename: Klaus
authors.initials: K
authors.lastname: Hoffmeier
authors.affiliation: GenXPro GmbH, Frankfurt am Main, Germany.
authors.forename: Jutta
authors.initials: J
authors.lastname: Kreutz
authors.affiliation: Department of Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands.
authors.forename: Marine J
authors.initials: MJ
authors.lastname: Paupière
authors.affiliation: Department for Molecular Systems Biology, University of Vienna, Vienna, Austria.
authors.forename: Palak
authors.initials: P
authors.lastname: Chaturvedi
authors.affiliation: ALSIA Research Center Metapontum Agrobios Metaponto (MT), Metaponto, Italy.
authors.forename: Rina
authors.initials: R
authors.lastname: Iannacone
authors.affiliation: Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
authors.forename: Florian
authors.initials: F
authors.lastname: Müller
authors.affiliation: Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy.
authors.forename: Hamed
authors.initials: H
authors.lastname: Bostan
authors.affiliation: Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy.
authors.forename: Maria Luisa
authors.initials: ML
authors.lastname: Chiusano
authors.affiliation: Cluster of Excellence Frankfurt, Centre of Membrane Proteomics, Department of Biosciences, Goethe University, Frankfurt am Main, Germany.
authors.forename: Klaus-Dieter
authors.initials: KD
authors.lastname: Scharf
authors.affiliation: GenXPro GmbH, Frankfurt am Main, Germany.
authors.forename: Björn
authors.initials: B
authors.lastname: Rotter
authors.affiliation: Cluster of Excellence Frankfurt, Centre of Membrane Proteomics, Department of Biosciences, Goethe University, Frankfurt am Main, Germany.
authors.forename: Enrico
authors.initials: E
authors.lastname: Schleiff
authors.affiliation: GenXPro GmbH, Frankfurt am Main, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Winter
mesh_terms: D018551:Solanum lycopersicum / Q000235:genetics*; D011058:Pollen / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*
chemical_list: D058727:RNA, Small Untranslated