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Conserved microRNAs and their targets in model grass species Brachypodium distachyon

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Abstract

MicroRNAs are small, non-protein-coding RNAs playing regulatory functions in many organisms. Using computational approaches 26 new Brachypodium distachyon miRNAs belonging to 19 miRNA families were identified in expressed sequence tags (EST) and genomic survey sequence databases. EST revealed that predicted miRNAs are expressed in B. distachyon. Detailed nucleotide analyses showed that pre-miRNAs in B. distachyon are in the range of 63–180 nucleotides. Mature miRNAs located in the different positions of precursor RNAs are varied from 19 to 24 nucleotides in length. Quantifying RNAs using realtime PCR (qRT-PCR) analyses validated expression level differences of selected B. distachyon miRNAs. In this study, we detected that the expression level of some of the predicted miRNAs are distinct and some of them are similar in the leaf tissues. In addition, using these miRNAs as queries 27 potential target mRNAs were predicted in B. distachyon NCBI EST database and 246 target mRNA were predicted in NCBI protein-coding nucleotide (mRNA) database of all plant species. The majority of the target mRNAs encode transcription factors regulating plant development, morphology and flowering time. Other newly identified miRNAs target the mRNAs involving metabolic processes, signal transduction and stress response.

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Abbreviations

ΔG:

Folding-free energies

AGO1:

Argonaute-1

Ap2:

APETALA2

ARF:

Auxin response transcription factor

DCL1:

Dicer-like protein

GSS:

Genomic survey sequence

miRNA:

MicroRNA

RT:

Real time

EST:

Expressed sequence tag

DCL1:

Dicer-like protein

EREBPs:

Ethylene-responsive element-binding proteins

MFE:

Minimal folding-free energy

MFEI:

Minimal folding-free energy index

miRNA*:

Opposite miRNA sequence

NCBI:

National Center of Biotechnology Information

Nt:

Nucleotide(s)

pre-miRNA:

MicroRNA precursor

pri-miRNAs:

MicroRNA primary

RISC:

RNA-induced silencing complex

qRT-PCR:

Quantitative real-time PCR

SBP:

Squamosa promoter-binding proteins

Ser:

Serine

SPL:

SBP-like proteins

Thr:

Threonine

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Acknowledgment

We would like to thank Mine Bakar for technical assistance in performing qRT-PCR experiments.

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Authors and Affiliations

  1. Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey

    Turgay Unver & Hikmet Budak

  2. Kocaeli University, Arslanbey MYO, Izmit, Turkey

    Turgay Unver

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  1. Turgay Unver
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  2. Hikmet Budak
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Correspondence to Hikmet Budak.

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Unver, T., Budak, H. Conserved microRNAs and their targets in model grass species Brachypodium distachyon . Planta 230, 659–669 (2009). https://doi.org/10.1007/s00425-009-0974-7

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  • DOI: https://doi.org/10.1007/s00425-009-0974-7

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