Transcript MicroRNA regulation in Arabidopsis thaliana

MicroRNA regulation in
Arabidopsis thaliana
Diane Guo
CUHK
6th IncoB, Aug.29, 2007
Outline
• Background
• Characterization of miRNA targets
• Interactions between miRNAs and various
cellular pathways
• Coordinated regulation by miRNAs and
transcription factors
• Summary
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
MiRNA processing and activity
(borrowed from Ambion)
Mode of miRNA action in plants and animals
(borrowed from Ambion)
Table 1 GO terms of miRNA targets
(molecular function)
GO ID
GO Term
GO:0003700
GO:0004386
GO:0003677
GO:0008234
GO:0004842
GO:0051082
GO:0005524
GO:0016301
GO:0005554
transcription factor activity
other enzyme activity
DNA or RNA binding
hydrolase activity
other enzyme activity
protein binding
nucleotide binding
kinase activity
molecular function
unknown
Target P-value
139
9
89
14
17
10
44
58
333
0
0.0002
0.0006
0.0013
0.0026
0.0032
0.0076
0.01
1
Table 2 Feature of miRNA target
Target Type
Target Number
High-link (>5)
78
Low-link (<=4)
45
Total
123
Table 2 Feature of miRNA target
Role of
target
Positive
regulation
Negative
regulation
Total
Regulating
27
28
55
Being
regulated
21
14
35
Total
48
42
90
MiRNAs more frequently target genes with
less transcription factor binding site
miRNA ratio
0.08
0.07
0.06
0.05
0.04
0.03
0.02
0.01
0
10
12
14
16
18
20
TFBS-count
22
24
26
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.
Acknowledgement
CUHK:
Zhang Qing
NEAU:
Li Yong
Zhu Yanming