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Application Stories


Changes in Gene Expression in Response to Starvation 

MicroRNA Array Services 

Dr. Tom Hamborg Nielsen
Dr. Maria Lundmark
Tom Hamborg Nielsen, Associate Professor and group leader, and Maria Lundmark, Post Doctoral researcher, both work at Plant Molecular Biology Laboratory, Faculty of Life Sciences, Copenhagen University, Denmark.

1. What is the current research going on in your lab?

We are interested in understanding how plants respond to phosphate starvation by changing their gene expression. Phosphate is a major nutrient, required for growth of plants and all other living organisms. On a global scale phosphate availability is an important factor in plant productivity and ecosystems balance. Recent research in this field has revealed that the regulation of gene expression in response to P-stavation in plants involves several mechanisms forming an intricate network, where microRNAs play a key role. It is an exiting challenge to unravel these mechanisms, as it may allow new strategies for developing improved crops. We focus on the role of a group of transcription factors which are central to this regulatory system.

2. How did your research lead you to the study of microRNAs?

A key element in P-starvation dependent gene expression in plants is a specific MYB-related transcription factors called PHR1. The regulation mediated by PHR1 and its homologs is one of our main research interests. It was recently discovered that PHR1 regulates a family of microRNA, miR399. This miRNA family targets a ubiquitin ligase, which influences protein turnover, and, by a yet unknown mechanism, regulates the expression of genes encoding P-transport proteins, essential to the cellular uptake of P. Other non-coding RNAs act as mimicry, antagonizing the effect of miR399s. Clearly, miRNAs are essential to the response and we need to understand how they are involved in nutrient dependent gene expression. Data obtained by the array based miRNA analysis designed by Exiqon has now revealed that more families of miRNA are involved in this response.

3. What were the key factors for you in choosing a microRNA supplier and partner?

The novel miRCURY™ LNA Arrays were specifically designed for miRNA profiling in the model plant Arabidopsis, which serves as our experimental system. This opened new and unique possibility to discover all the miRNAs involved in the biological processes that we are studying. The miRNA Profiling Services at Exiqon has performed the technical aspects of the analysis, a task which requires time and specialised knowledge. This has allowed us to focus on the quality of biological aspects of the experiment. We find that this has provided a highly efficient approach.

4. What made you choose Exiqon?

The Arabidopsis microarrays designed by Exiqon are presently one-of-a-kind, and offered us a unique opportunity to analyze a biological problem by sensitive and specific detection of mature miRNA. Also the good personal contact to the company furthered the choice.

5. What were some specific challenges in your project?

The major challenge is to obtain high quality plant material to analyze and high quality RNA preparations. During P-starvation plants increase their activity of RNAses and the overall levels of RNA in the cells may be low in the P-starved plant material.

6. How did you overcome them?

Further biological characterization verified the quality of the analyzed experiments. We have good experience in purifying good quality RNA and the quality RNA was verified by appropriate analysis.

7. What advice would you give to researchers who want to get started in microRNA research?

This is a field developing fast and it is recommendable to keep track of the technological developments within the field. For us, the new facilities developed by Exiqon have greatly facilitated an analysis in a broader perspective. It is really important to verify the microarray data by alternative methods. Using LNA-primers offers an attactive way to achieve this.

8. What would you tell a colleague about why they should work with Exiqon?

We have experienced the collaboration with Exiqon as very good and highly qualified.

9. Where will your research be showcased next? (Articles, conferences, posters, etc.)

We have presented the data as a poster on an international plant biology conference (ASPB annual meeting, 2009) and we are next planning a method oriented paper in a scientific journal.

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