Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize

BMC Genomics

Paulo CG Ferreira³  Adriana S Hemerly³  Laurent Farinelli¹  Robert A Martienssen⁴  Michael Regulski⁴  Tauan Vieira³  Mariana Romeiro Motta³  Clícia Grativol³  Cristian A Rojas²  Flávia Thiebaut³ 

[1] Fasteris SA, 1228-Plan-les-Ouates, Genève, Switzerland;Universidade Federal da INTEGRAÇÃO Latino-Americana, Av. Tancredo Neves, 6731, Bl.4, Foz do Iguaçu PR 85867-970, Brazil;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;Howard Hughes Medical Institute and Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA

关键词: Epigenetics;    Azospirillum brasilense;    siRNA;    miRNA;    Herbaspirillum seropedicae;   

Others  :  1140806
DOI  :  10.1186/1471-2164-15-766

 received in 2014-01-08, accepted in 2014-08-22,  发布年份 2014

【 摘 要 】

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.

Conclusion

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.

【 授权许可】

   
2014 Thiebaut et al.; licensee BioMed Central Ltd.

【 图 表 】

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