Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis

Ivett Baksa, Tibor Nagy, Endre Barta, Zoltán Havelda, Éva Várallyay, Dániel Silhavy, J. Burgyán, György Szittya

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Background: Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for protein expression and purification. To discover and characterize the miRNAs and their cleaved target mRNAs in N. benthamiana, we sequenced small RNA transcriptomes and degradomes of two N. benthamiana accessions and validated them by Northern blots. Results: We used a comprehensive molecular approach to detect and to experimentally validate N. benthamiana miRNAs and their target mRNAs from various tissues. We identified 40 conserved miRNA families and 18 novel microRNA candidates and validated their target mRNAs with a genomic scale approach. The accumulation of thirteen novel miRNAs was confirmed by Northern blot analysis. The conserved and novel miRNA targets were found to be involved in various biological processes including transcription, RNA binding, DNA modification, signal transduction, stress response and metabolic process. Among the novel miRNA targets we found the mRNA of REPRESSOR OF SILENCING (ROS1). Regulation of ROS1 by a miRNA provides a new regulatory layer to reinforce transcriptional gene silencing by a post-transcriptional repression of ROS1 activity. Conclusions: The identified conserved and novel miRNAs along with their target mRNAs also provides a tissue specific atlas of known and new miRNA expression and their cleaved target mRNAs of N. benthamiana. Thus this study will serve as a valuable resource to the plant research community that will be beneficial well into the future.

Original languageEnglish
Article number1025
JournalBMC Genomics
Volume16
Issue number1
DOIs
Publication statusPublished - Dec 1 2015

Fingerprint

MicroRNAs
Tobacco
Messenger RNA
Northern Blotting
RNA
Biological Phenomena
Atlases
RNA Interference
Transcriptome
Research
Signal Transduction
Proteins
DNA

Keywords

  • Degradome
  • High throughput sequencing
  • MicroRNA
  • Nicotiana benthamiana
  • Non-coding RNAs
  • Small RNA

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Baksa, I., Nagy, T., Barta, E., Havelda, Z., Várallyay, É., Silhavy, D., ... Szittya, G. (2015). Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis. BMC Genomics, 16(1), [1025]. https://doi.org/10.1186/s12864-015-2209-6

Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis. / Baksa, Ivett; Nagy, Tibor; Barta, Endre; Havelda, Zoltán; Várallyay, Éva; Silhavy, Dániel; Burgyán, J.; Szittya, György.

In: BMC Genomics, Vol. 16, No. 1, 1025, 01.12.2015.

Research output: Contribution to journalArticle

Baksa, Ivett ; Nagy, Tibor ; Barta, Endre ; Havelda, Zoltán ; Várallyay, Éva ; Silhavy, Dániel ; Burgyán, J. ; Szittya, György. / Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis. In: BMC Genomics. 2015 ; Vol. 16, No. 1.
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AB - Background: Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for protein expression and purification. To discover and characterize the miRNAs and their cleaved target mRNAs in N. benthamiana, we sequenced small RNA transcriptomes and degradomes of two N. benthamiana accessions and validated them by Northern blots. Results: We used a comprehensive molecular approach to detect and to experimentally validate N. benthamiana miRNAs and their target mRNAs from various tissues. We identified 40 conserved miRNA families and 18 novel microRNA candidates and validated their target mRNAs with a genomic scale approach. The accumulation of thirteen novel miRNAs was confirmed by Northern blot analysis. The conserved and novel miRNA targets were found to be involved in various biological processes including transcription, RNA binding, DNA modification, signal transduction, stress response and metabolic process. Among the novel miRNA targets we found the mRNA of REPRESSOR OF SILENCING (ROS1). Regulation of ROS1 by a miRNA provides a new regulatory layer to reinforce transcriptional gene silencing by a post-transcriptional repression of ROS1 activity. Conclusions: The identified conserved and novel miRNAs along with their target mRNAs also provides a tissue specific atlas of known and new miRNA expression and their cleaved target mRNAs of N. benthamiana. Thus this study will serve as a valuable resource to the plant research community that will be beneficial well into the future.

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