SIGBIO31

1. Competitive target gene regulation by
promoter methylation and miRNA
Y-h. Taguchi, Chuo University

2. 0. What is miRNA?
1. Introduction
2. Promoter Methylation
3. MiRaGE Method
4. Competitive target gene regulation by
promoter methylation and miRNA
5. Conclusion

3. 0. What is miRNA?
・miRNA = microRNA
・non-coding RNA
・regulate (suppress) target gene expression via
either
degradation or translation interruption
of target genes

4. 1. Introduction
Epigenetic gene expression regulation is
current central topics in
genomics/bioinformatics because ….
A) Cell types (development, diseases, tumor
formation etc... ) are often decided by
epigentic regulation
B)Control of epigenetic regulation can alter
cell types (suppression of cancer, induction
of pluripotency....)

5. Epigenetic gene regulation =
gene expression regulation without modification of DNA
sequences
Example
・promoter methylation
・histon modification
・transcription factor binding to promoter region
・miRNA regulation of target genes.....
How these two regulate gene expression
cooperatively is unknown.

6. 2. Promoter Methylation
Methylated
promoter
⇓
expression
suppression
unmethylated
promoter
⇓
no expression
suppression

7. 3. MiRaGE Method
MiRaGE :
MiRNA Ranking by Gene Expression
Promoter Methylation
considered
miRNA target
miRNA gene
VS
target
gene
significantly
gene up/downregulated?
hypo/hypermethylated?
(t test, Wilcoxon test, KS test)

8. 4. Competitive target gene regulation by
promoter methylation and miRNA
Result 1:
hyper(heypo)methyaletion ⇔ less(more) regulated by miRNAs
suppressive suppressive

9. GSE30653
Nazor KL, Altun G, Lynch C, Tran H et al.
Recurrent variations in DNA methylation in human
pluripotent stem cells and their differentiated
derivatives.
Cell Stem Cell 2012 May 4;10(5):620-34.
numbed of cell lines : 271
Promoter methylation is measured by microarray
methylation:
raw value (raw signal)
β-value (normalized value)
271 cell lines vs 1921 miRNAs = 520591 cases
P-values of miRNA target specific promoter
hypomethylation is computed by MiRaGE method
hypo
Significance : adjusted P-value <0.05

10. Amount of methylation
Number of cases
Statistical tests Not significant Significant
t-test 136054 384537 74%
Wilcoxon rank
144572 376019 72%
sum test
Kolmogorov-
129998 390593 75%
Smirnov test
β-values
Number of casess
Statistical tests Not significant Significant
t-test 39390 481201 92%
Wilcoxon test 45188 475403 91%
KS test 41952 478639 92%

11. P-values are highly cell type independent
Mean Pearson's correlation coefficients of P-value between
pairs of cell lines.
Statistical test Averaged correlation coefficients
Amount of methylation
t-test 0.9112043
Wilcoxon rank 0.8981256
sum test
Kolmogorov- 0.8263153
Smirnov test
β-values
t-test 0.8919359
Wilcoxon test 0.8832241
K-Stest 0.8257556

12. Result 2:
Genes with hypomethyaled promoter are
downregulated during cell senescence

13. Result 3:
Genes with hypomethyaled promoter are
upregulated during differentiation from ES
cell

14. IMR90 and MRC5 (cell senescence)
BG02 and BG03 (differentiation from ES cell)
P-values of miRNA regulation of targe genes are
computed by MiRaGE method
Correlation coefficients between
P-vales for promoter hypomethylation
and
P-values of miRNA downregulation of target genes
are computed
Hypomethylation : gene expression : expressive
vs
downregulation of miRNA target genes
miRNA regulation of target genes and promoter
methylation are competitive

15. Cell senescence Pm:methy = Pm> vs. Pm:regul = Pm>
IMR90
t test 0.33 0.4 0.41
P -values ＊(<2E-16) ＊ ＊
Wilcoxon test 0.28 0.35 0.33
P -values ＊ ＊ ＊
K-S test 0.31 0.72 0.61
P -values ＊ ＊ ＊
MRC5
t test 0.22 0.23 0.25
P -values ＊ ＊ ＊
Wilcoxon test 0.53 0.76 0.73
P -values ＊ ＊ ＊
K-S test 0.38 0.82 0.67
P -values ＊ ＊ ＊

16. Differentiation Pm:methy = Pm> vs. Pm:regul = １− Pm<
BG02
t test ー0.25 ー0.68 ー0.67
P -values ＊(<2E-16) ＊ ＊
Wilcoxon test ー0.13 ー0.52 ー0.53
P -values 2.4E-9 ＊ ＊
K-S test ー0.16 ー0.7 ー0.69
P -values 2.8 E-12 ＊ ＊
BG03
t test ー0.31 ー0.57 ー0.53
P -values ＊ ＊ ＊
Wilcoxon test ー0.14 ー0.23 ー0.23
P -values 8.9 E-11 ＊ ＊
K-S test ー0.14 ー0.21 ー0.19
P -values 1.3E-10 ＊ ＊

17. Result 4:
Especially, genes with hypomethylated
promoters are targeted by miR-548, which
is primate-specific and generally not
expressive miRNAs.
Cooperative miRNA regulation with promoter
methylation of target gene may assist miRNA-
548 to regulate target genes.

18. 5. Conclusion
・Promoter methylation is related to
miRNA targeting
・Genes with hypo(hyper)methylated
promoters are more(less) frequently
targeted by miRNAs
・miR-548 targeting specific promoter
methylation may help miR-548 to regulate
target genes.