title: Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize.
abstract: BACKGROUND
  Small RNA (sRNA) has been described as a regulator of gene expression. In order to understand the role of maize sRNA (Zea mays-hybrid UENF 506-8) during association with endophytic nitrogen-fixing bacteria, we analyzed the sRNA regulated by its association with two diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense.
  
  
  RESULTS
  Deep sequencing analysis was done with RNA extracted from plants inoculated with H. seropedicae, allowing the identification of miRNA and siRNA. A total of 25 conserved miRNA families and 15 novel miRNAs were identified. A dynamic regulation in response to inoculation was also observed. A hypothetical model involving copper-miRNA is proposed, emphasizing the fact that the up-regulation of miR397, miR398, miR408 and miR528, which is followed by inhibition of their targets, can facilitate association with diazotrophic bacteria. Similar expression patterns were observed in samples inoculated with A. brasilense. Moreover, novel miRNA and siRNA were classified in the Transposable Elements (TE) database, and an enrichment of siRNA aligned with TE was observed in the inoculated samples. In addition, an increase in 24-nt siRNA mapping to genes was observed, which was correlated with an increase in methylation of the coding regions and a subsequent reduction in transcription.
  
  
  CONCLUSIONS
  Our results show that maize has RNA-based silencing mechanisms that can trigger specific responses when plants interact with beneficial endophytic diazotrophic bacteria. Our findings suggest important roles for sRNA regulation in maize, and probably in other plants, during association with diazotrophic bacteria, emphasizing the up-regulation of Cu-miRNA.
authors.forename: Flávia
authors.initials: F
authors.lastname: Thiebaut
authors.forename: Cristian A
authors.initials: CA
authors.lastname: Rojas
authors.forename: Clícia
authors.initials: C
authors.lastname: Grativol
authors.forename: Mariana Romeiro
authors.initials: MR
authors.lastname: Motta
authors.forename: Tauan
authors.initials: T
authors.lastname: Vieira
authors.forename: Michael
authors.initials: M
authors.lastname: Regulski
authors.forename: Robert A
authors.initials: RA
authors.lastname: Martienssen
authors.forename: Laurent
authors.initials: L
authors.lastname: Farinelli
authors.forename: Adriana S
authors.initials: AS
authors.lastname: Hemerly
authors.affiliation: Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Cidade Universitária, Avenida Carlos Chagas Filho, 373, CCS, Bl,L-29ss, Rio de Janeiro RJ 21941-599, Brazil. paulof@bioqmed.ufrj.br.
authors.forename: Paulo C G
authors.initials: PC
authors.lastname: Ferreira
mesh_terms: D001419:Bacteria / Q000378:metabolism; D002874:Chromosome Mapping; D019295:Computational Biology; D004251:DNA Transposable Elements; D030561:Databases, Nucleic Acid; D060026:Endophytes / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D055106:Genome-Wide Association Study; D008745:Methylation; D035683:MicroRNAs / Q000235:genetics*; D009586:Nitrogen Fixation; D010641:Phenotype; D012326:RNA Splicing; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D013559:Symbiosis; D003313:Zea mays / Q000235:genetics* / Q000254:growth & development / Q000382:microbiology*
chemical_list: D004251:DNA Transposable Elements; D035683:MicroRNAs; D018749:RNA, Plant; D034741:RNA, Small Interfering