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Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions

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Abstract

MicroRNAs negatively regulate the accumulation of mRNAs therefore when they are expressed in the same cells their expression profiles show an inverse correlation. We previously described one positively correlated miRNA/target pair, but it is not known how widespread this phenomenon is. Here, we investigated the correlation between the expression profiles of differentially expressed miRNAs and their targets during tomato fruit development using deep sequencing, Northern blot and RT-qPCR. We found an equal number of positively and negatively correlated miRNA/target pairs indicating that positive correlation is more frequent than previously thought. We also found that the correlation between microRNA and target expression profiles can vary between mRNAs belonging to the same gene family and even for the same target mRNA at different developmental stages. Since microRNAs always negatively regulate their targets, the high number of positively correlated microRNA/target pairs suggests that mutual exclusion could be as widespread as temporal regulation. The change of correlation during development suggests that the type of regulatory circuit directed by a microRNA can change over time and can be different for individual gene family members. Our results also highlight potential problems for expression profiling-based microRNA target identification/validation.

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Abbreviations

AGO1:

Argonaute 1

DCL1:

Dicer-like 1

miRNA:

MicroRNA

PARE:

Parallel analysis of RNA ends

PCC:

Pearson correlation coefficient

RT-qPCR:

Reverse transcription followed by quantitative polymerase chain reaction

sRNA:

Small RNA

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Acknowledgments

This work was supported by the BBSRC (grant numbers: BB/G008078/1, BB/H023895/1 and BB/I00016X/1). The authors also thank Dr. Matt Box and Dr. Ruben Alvarez-Fernandez for their helpful advice and technical suggestions. S.L-G. was supported by the Spanish Ministerio de Ciencia e Innovacion and by Ibercaja Obra Social.

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Authors and Affiliations

  1. School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK

    Sara Lopez-Gomollon, Gyorgy Szittya & Tamas Dalmay

  2. School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK

    Irina Mohorianu & Vincent Moulton

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  1. Sara Lopez-Gomollon
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  2. Irina Mohorianu
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  3. Gyorgy Szittya
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  4. Vincent Moulton
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  5. Tamas Dalmay
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Corresponding author

Correspondence to Tamas Dalmay.

Additional information

S. Lopez-Gomollon and I. Mohorianu contributed equally to this work.

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425_2012_1734_MOESM4_ESM.xls

Target mRNAs identified by degradome/PARE analysis. Deagradome/PARE libraries from flower and green fruits were analysed using CleaveLand and the identified targets are shown in the table. (XLS 60 kb)

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Lopez-Gomollon, S., Mohorianu, I., Szittya, G. et al. Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions. Planta 236, 1875–1887 (2012). https://doi.org/10.1007/s00425-012-1734-7

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  • DOI: https://doi.org/10.1007/s00425-012-1734-7

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