Competitive target gene regulation by promoter methylation and miRNA
Competitive target gene regulation bypromoter methylation and miRNAY-h. Taguchi, Chuo University
0. What is miRNA?1. Introduction2. Promoter Methylation3. MiRaGE Method4. Competitive target gene regulation bypromoter methylation and miRNA5. Conclusion
0. What is miRNA?・miRNA = microRNA・non-coding RNA・regulate (suppress) target gene expression viaeitherdegradation or translation interruptionof target genes
1. IntroductionEpigenetic gene expression regulation iscurrent central topics ingenomics/bioinformatics because ….A) Cell types (development, diseases, tumorformation etc... ) are often decided byepigentic regulationB)Control of epigenetic regulation can altercell types (suppression of cancer, inductionof pluripotency....)
Epigenetic gene regulation =gene expression regulation without modification of DNAsequencesExample・promoter methylation・histon modification・transcription factor binding to promoter region・miRNA regulation of target genes..... How these two regulate gene expression cooperatively is unknown.
3. MiRaGE MethodMiRaGE :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)
4. Competitive target gene regulation bypromoter methylation and miRNAResult 1:hyper(heypo)methyaletion ⇔ less(more) regulated by miRNAs suppressive suppressive
GSE30653Nazor KL, Altun G, Lynch C, Tran H et al.Recurrent variations in DNA methylation in humanpluripotent stem cells and their differentiatedderivatives.Cell Stem Cell 2012 May 4;10(5):620-34.numbed of cell lines : 271Promoter methylation is measured by microarraymethylation:raw value (raw signal)β-value (normalized value)271 cell lines vs 1921 miRNAs = 520591 casesP-values of miRNA target specific promoterhypomethylation is computed by MiRaGE methodhypoSignificance : adjusted P-value <0.05
Amount of methylation Number of casesStatistical 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 casessStatistical tests Not significant Significant t-test 39390 481201 92% Wilcoxon test 45188 475403 91% KS test 41952 478639 92%
P-values are highly cell type independentMean Pearsons correlation coefficients of P-value betweenpairs 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
Result 2:Genes with hypomethyaled promoter aredownregulated during cell senescence
Result 3:Genes with hypomethyaled promoter areupregulated during differentiation from EScell
IMR90 and MRC5 (cell senescence)BG02 and BG03 (differentiation from ES cell)P-values of miRNA regulation of targe genes arecomputed by MiRaGE methodCorrelation 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 genesmiRNA regulation of target genes and promotermethylation are competitive
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 ＊ ＊ ＊
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 ＊ ＊
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 promotermethylation of target gene may assist miRNA-548 to regulate target genes.
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.