Possible miRNA coregulation of target genes in brain regions by both differential miRNA expression and miRNA-targeting-specific promoter methylation
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.
IntroductionEpigenetic regulation of gene expression isknown to be important nowadays.e.g.- Development and Cellular Differentiation- Diseases including Cancer- Aging
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
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?)
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)
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]
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)
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
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
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
Bold : appear more than twiceunderline : previously reported to be related to brain non- reciprocalReciprocal Selected miRNAs are diverse. Biological meaning?
KEGG pathway analysis for the union oftarget genes (DIANA-mirpath v2.0) In contrast to selected m iRNAs, KEGG pathways are com m on
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.
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).
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