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Possible miRNA coregulation of  target genes in brain regions  by both differential miRNA expression and miRNA-targeting-specific promoter methylation
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Possible miRNA coregulation of target genes in brain regions by both differential miRNA expression and miRNA-targeting-specific promoter methylation

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SIGBIO33 …

SIGBIO33
Full paper published at
http://www.biodatamining.org/content/6/1/11/abstract


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  • 1. Possible miRNA coregulation of target genes in brain regions by both differential miRNA expression andmiRNA-targeting-specific promoter methylation Y-h. Taguchi Dept. Phys. Chuo Univ.
  • 2. IntroductionEpigenetic regulation of gene expression isknown to be important nowadays.e.g.- Development and Cellular Differentiation- Diseases including Cancer- Aging
  • 3. Example of Epigenetic regulation of genes- Transcription Factor Bindings topromoter region- Histon modification- Promoter Methylation- miRNA regulation of target genes. Interactionetc. etc. Rarely Discussed Both gene suppression
  • 4. Methylation Gene Promoter 3UTR cell nucleus cytoplasm miRNAMethylation ↔ cell nucleus miRNA ↔ cytoplasm
  • 5. Previous Research Su et al (2011, BMC Genomics) “miRNAs tended to target the genes with a low DNA methylation level in their promoter regions” Promoter methylation ↔ miRNA targetingPurpose of my study:Promoter methylation is miRNA-targeting-specific or not?(In other words, promoter methylation is affected by beingtargeted by individual miRNA or not?)
  • 6. 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)
  • 7. My Previous Results“Substantial number of miRNAs have targetgenes with significantlyhyper/hypomethylated promoters”References:- Y-h. Taguchi (2012) IPSJ SIG Tech. Rep.2012-BIO-31(1) pp.1-6- Y-h. Taguchi, (2013) F1000Research[v1; ref status: approved 1, approved withreservations 1, http://f1000r.es/wv]
  • 8. This StudyComparison between miRNA, mRNA andpromoter methylation among distinct brainregions (Frontal Cortex [FCTX], TemporalCortex [TCTX], Cerebellum [CRBLM], Pons[PONS]) in miRNA-centric manner.150 subject vs 4 regions = 600 samples(We exclude samples without all four regions)
  • 9. Calculation- Number of miRNAs whose target genes aresignificantly(*) up/downregulated among 1921 miRNAs- Number of miRNAs with significantly (*)hypo/hypermethylated promoters among 1921 miRNAs- Correlation coefficients of mean ranks between miRNAregulation of target genes and miRNA-targeting-specificpromoter methylationfor all six pairs of FCTX, TCTX, CRBLM, and PONS(*) BH adjusted P <0.05
  • 10. Corr. Coef. of Rank Number of miRNAs with up/downregulated target genes (or SD) 183 < +0.26 < 173 Number of miRNAs with target genes with (0.36) hyper/hypomethylated promoters < 280 889 < 221 870 TCTX FCTX upregulated > > > +0 .49> 128 .4 3 +0 > (0 . 3 .3 ) hypermethylated (0 279 7) 608 1 267 > > > 60 234 241 CRBLM 129 804 >1038 168 450 > > > > - 0. . 51 ) > -0 5 +0.09 (0. 41 0. 3 42 ( 490 ) > (0.48) 439 > > 1120 65 45 > > > 108 PONS
  • 11. Present Results- Substantial number of miRNAs have significantlyup/downregulated target genes.- Substantial number of miRNAs have target genes withsignificantly hyper/hypomethylated promoters.- miRNA regulation of target genes and miRNA-targeting-specific promoter methylation are significantlycorrelated- Correlation coefficients are not always negative→ This indicates correlations between miRNAregulation of target genes and miRNA-targeting-specificpromoter methylation are not bi-products of directcorrelation between gene expression and promotermethylation
  • 12. Selection of miRNAs that regulate target genes significantly Liner regression analysis x mjl log P l, l , mRNA l.l . Methyl m , j,> =log P m , j, > +log +a g e j +g e n d e r j x mjl + AIC based feature selectionPl, l j, ,mRNA : P-value of mth miRNAs target genes of jth m, > sample is upregulated between lth and lth regionPl, l, j, ,Methyl : P-value of mth miRNAs target genes promoters m > of jth sample is hypermethylated between lth and lth region x m j l : expression of mth miRNA of jth sample of lth region Significant regulation by miRNAs of target genes
  • 13. Bold : appear more than twiceunderline : previously reported to be related to brain non- reciprocalReciprocal Selected miRNAs are diverse. Biological meaning?
  • 14. KEGG pathway analysis for the union oftarget genes (DIANA-mirpath v2.0) In contrast to selected m iRNAs, KEGG pathways are com m on
  • 15. Relation to Brain related facts - TGFβ: relation to bipolar disorder TGFβ - MAPK: neuronal apoptosis MAPK - Wnt: Amyloid Wnt - ErbB: development of the nervous system ErbB …..Many brain related KEGG pathways areenriched by the union of miRNAs target genes.
  • 16. Q : Why can different set of miRNAstarget common KEGG pathways?A : Target genes overlapExample : TGFβ (CRBLM vs FCTX)reciprocal vs non-reciprocalno overlaped miRNAs (by definition)share 36 mRNAs in TGFβ pathway....Among 36 mRNAs, 25 mRNAs (RefSeq) aredifferently expressed between CRBLM andFTCX (see the next slide).
  • 17. mRNAs expresseddifferentlybetween FTCX andCRBLM, targetedby miRNAsselected by presentstudy,in TGFβ pathway
  • 18. Conclusions- numerous miRNAs have target genes withhyper/hypomethylated promoter methylation- miRNA-targeting-specific promotermethylation is correlated with miRNAregulation of target genes- miRNAs that regulate target genes areselected excluding contribution throughpromoter methylation- In spite of diverse selection of miRNAs,KEGG pathway enrichments are largelycommon