Small RNA: mechanism of miRNA biogenesis

MicroRNAs (miRNA) are regulatory small RNAs that have crucial roles in numerous developmental and metabolic processes. MiRNAs are sequentially processed from long primary transcripts (pri-miRNAs) through precursor miRNAs (pre-miRNAs). Then, mature miRNAs are loaded into RNA induced silencing complexes (RISC) which performs miRNA paired target mRNA cleavage or translational inhibition.

 

In plant, Dicer-like protein 1 (DCL1), HYPONASTIC LEAF 1 (HYL1) and SERRATE (SE) are important components for the two stepwise miRNA processing pathway. DCL1 is the major RNase that processes pri-miRNAs into mature miRNAs. HYL1 and SE are crucial proteins which guide DCL1 for precise processing of miRNAs. Our research focuses on the detail mechanisms of the components in miRNA processing. 

 

In addition, we recently found several novel mutant lines which have strong defects in miRNA biogenesis. We defined the genes for mutations those have no linkages to previously reported genes for miRNA biogenesis. To understand their roles in miRNA biogenesis, we are currently investigating the genes with molecular, genetic, and biochemical approaches.

 

 

UNIK synthetic biology projects

 

Expression levels of miRNAs can be used as molecular biomarkers for cell development and differentiation in plants and cancer diagnosis in human. Therefore, innovative detection methods have been developed for high sensitivity and specificity. Due to the stability and bright fluorescent of silver nanoparticle, it has been investigated for cellular imaging and molecular labelling. Despite the increasing number of study reports on DNA/AgNC nano-cluster, their applications are still narrow. Recently, we found a novel mechanism of DNA/AgNC clustering that emitted extremely strong fluorescent in an hour. The mechanism is extraordinary to the previous findings in several view points; intensity, evolution time and structure. Based on this, we are developing a novel method for miRNAs detection in plants by applying the novel DNA/AgNC nano-clustering technique.

 

Current Research

MiRNA research projects
            
1. Mechanism analysis of miRNA biogenesis in Arabidopsis.
Member: Samir ben Chaabane, Master Student
Aim: We have investigated the structural function of HYL1 which has two RNA binding domain. HR1 and HR2 domains are cooperatively responsible for dsRNA binding and HR2 domain is important for protein to protein interaction. With HR2 domain, HYL1 interacts with SE and DCL1 for precise processing of miRNAs. We are investigating how HR1 and HR2 recognize the secondary structure of miRNA stem and loop and what is the determinant for it. 

 

2. Characterization of novel mutants for miRNA biogenesis in Arabidopsis.
Member: Samir ben Chaabane, Master Student, Pratik Shah, Ph.D. Student
Aim: We have identified several mutant lines which have severe defects in miRNA biogenesis. One of them was recently defined as a gene for splicing and stabilization of primary transcripts. Knock out mutant lines showed a dramatic reduction in the accumulation of miRNAs. The mutant plants displayed similar miRNA defective phenotypes to those of hyl1-2 and se-1. Based on these preliminary results, we are studying roles of the novel gene in miRNA biogenesis.

 
UNIK research projects
 
1. Development of innovative detection technique for miRNAs. 
Member: Pratik Shah, Ph.D. Student
Aim: Designing of silver cluster DNA probe for specific miRNA detection. We are currently collaborating with Tom Vosch’s group (Department of Chemistry, University of Copenhagen).
     
2. Development of light switching proteo-liposome.
Member: Parik Shah, Ph.D. Student
Aim: Construction of light gated channel with target channel in liposome. We are currently collaborating with Thomas-Günter Promosky’s group (Department of Plant Biology and Biotechnology, University of Copenhagen).