1. MicroRNA regulation in Arabidopsis thaliana
Diane Guo
CUHK
6th IncoB, Aug.29, 2007

2. Outline Background Characterization of miRNA targets
Interactions between miRNAs and various cellular pathways
Coordinated regulation by miRNAs and transcription factors
Summary

3. microRNA
miRNAs are small endogenous RNA molecules (~22nt) found in plant and animals
Regulate gene expression through targeted mRNA cleavage or translational repression
Play critical roles in a variety of cellular processes such as development, cell proliferation, apoptosis, and stress response, etc

4. MiRNA processing and activity
(borrowed from Ambion)

5. Mode of miRNA action in plants and animals
(borrowed from Ambion)

6. Table 1 GO terms of miRNA targets (molecular function)
GO ID
GO Term
Target
P-value
GO:
GO:
GO:
GO:
GO:
GO:
GO:
GO:
GO:
transcription factor activity
other enzyme activity
DNA or RNA binding
hydrolase activity
protein binding
nucleotide binding
kinase activity
molecular function unknown
139 9 89 14 17 10 44 58
333
0.0002
0.0006
0.0013
0.0026
0.0032
0.0076
0.01 1

7. Table 2 Feature of miRNA target
Target Type
Target Number
High-link (>5) 78
Low-link (<=4) 45
Total
123

8. Table 2 Feature of miRNA target
Role of target
Positive regulation
Negative regulation
Total
Regulating 27 28 55
Being regulated 21 14 35 48 42 90

9. MiRNAs more frequently target genes with less transcription factor binding site

10. Summary
We systematically analyzed the characteristics of miRNA targets. MiRNAs with multi-gene families are more likely to target TFs, and miRNAs represented by single gene tend to target non-TFs.
To systematically investigate the interactions between miRNAs and various cellular pathways, we analyzed the miRNA targets distribution in the pathways and found that miRNAs regulate the pathway through selectively interacting with positive regulatory modules and highly connected nodes.
We found that miRNA preferentially target genes bearing less TFBSs. This suggests that the post-transcriptional regulation by miRNAs is coordinated with regulation at the transcriptional level by transcription factors.

11. Acknowledgement
CUHK:
Zhang Qing
NEAU:
Li Yong
Zhu Yanming