Post on 16-Jul-2015
Inference of target gene regulation via miRNAs during cell senescence by MiRaGE Server
Y-h. TaguchiDepartment of Physics
Chuo University
1. What is cell senescence?
2. What is miRNA?
3. Previous works (wet)
4. MiRaGE Method
5. Correlation between target gene regulation by miRNA and miRNA expression change during cell senescence
6. Summary & Conclusion
The cell division cannot continue forever for incubated cell lines. It must stop after several rounds of proliferation.
⇓This is called “cell senescence”, which is believed to be related to agingaging.
1. What is cell senescence?
Thus, cell senescence is caused by the interruption of cell divisions, typically by cell cycle arrests.
2. What is miRNA?
miRNA is a kind of non-coding RNA. miRNAs are believed to suppress target gene expression by degradation of mRNAs. Important features:
・ Typically, there are hundreds kinds of miRNAs found for each species (c.a., 1000 for human).≧
・ Each miRNA targets more than hundreds of genes. ・ miRNA mainly contributes to cell type change
(e.g., cancer, defferentiation, diseases) ・Infulence to target gene expression by miRNA is subtle (〜10%) and contexts dependent.・In spite of that, miRNA critically contributes to the related processesmiRNA critically contributes to the related processes (e.g., induction of cell cycle arrest)
3. Previous works (wet)
Several researches suggest the contribution of miRNAs to cell senescence.
Upregulation of miRNAs during cell senescencemiR-34a,miR-486-5p,miR-494,miR-210...
Downregulation of miRNAs during cell senescencemiR-15a/b,miR-20a,miR-92,miR-16b....
Induction of cell senescence by suppression of miRNA downregulated during cell senescence.
It is likely true that miRNAs contribute to cell senescence.
However, which one?
Dhahbi et al (2011) recently reported the upregulaton of
141(!) miRNAs and the downregulation of 131(!!) miRNAs during cell senescence by deep sequencing.
The reason why limited number of miRNAs revealed significant expression change during cell senescence seems to be due to less sensitivity of microarray analysis.Is it truly critical the down/upregulation of such large number of miRNAs for cell senescence?
4. MiRaGE Method
In order to select “Critical ” miRNAs during cell senescence, regulation of target genes by miRNAs is inferred by MiRaGE Server.
For details, see
SIGBIO-25-5: Search of miRNAs critical for medulloblastoma formation using MiRaGE method○Y-h. Taguchi(Chuo Univ.) , Jun Yasuda(Tohoku Univ.)
SIGBIO-25-30:Gene expression regulation during differentiation from murine ES cells due to microRNA○Masato Yoshizawa,Y-h. Taguchi(Chuo Univ.)
significantly up/downregulated?
(t test, Wilcoxon test, KS test)
MiRaGE :MiRNA Ranking by Gene Expression
miRNA
target gene
target gene
VS
gene
considered miRNA
5. Correlation between target gene regulation by miRNA and miRNA expression change during cell senescenceA) Confirmation of independence of cell line
Two Cell Lines:IMR90 : young (PD 30) vs senescent (PD 48) vsMRC5 : young (PDL 28) vs senescent (PDL 63)
mRNA expression change (during cell senescence)
MiRaGE Server⇓
P-values attributed to each miRNA
Intersection between N top-ranked significant miRNAs based upon P-values (t test) IMR90 vs MRC5
downregulation
upregulation
10
10
30%
100%
20%
100%
500 1500N 500 1500N0
4
% o
f com
mo
n miR
NA
s
random
random
P=0.05
binomial: -log
10 P
P=0.05Thus, the results are cell line independent (possibly robust)
miRDeep2:genome alignment program for miRNA-seq
B) Confirmation of reciprocal relationship between miRNA expression change and Pvalue (upregulation of target genes)
Co
rrela
tion C
oe
fficient
# o
f miR
NA
s-log
10 P
quality score(miRDeep2)
1 102 104
2
1
quality score quality score
100
700
0.05
0.35
Threshold Value
IMR90,NGS
P=0.050
Candidates of miRNAs downregulaed(target genes are upreglated)
NMRC : Normalied miRNA Read CountsSCORE : miRDeeps scoreP-value : upregulation of target genesRFC : Reciprocal Fold Change : young/senescent
P<0.05 RFC>1.0
P<0.05 FC>1.0NMRC : Normalied miRNA Read CountsSCORE : miRDeeps scoreP-value : downregulation of target genesFC : Fold Change : senescent/young
Candidates of miRNAs upregulaed(target genes are downreglated)
FC>1.0P<0.05NMRC : Normalied miRNA Read CountsSCORE : miRDeeps scoreP-value : downregulation of targe genesFC : Fold Change : senescent/young
Candidates of miRNAs upregulaed(target genes are downreglated) continued