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Genome-wide associations between genetic and epigenetic variation influence mRNA expression and insulin secretion in human pancreatic islets.

Olsson AH, Volkov P, Bacos K, Dayeh T, Hall E, Nilsson EA, Ladenvall C, Rönn T, Ling C - PLoS Genet. (2014)

Bottom Line: CpGs of significant cis-mQTLs were overrepresented in the gene body and outside of CpG islands.Follow-up analyses further identified mQTLs associated with gene expression and insulin secretion in human islets.Finally, we found direct correlations between DNA methylation of 22,773 (4.9%) CpGs with mRNA expression of 4,876 genes, where 90% of the correlations were negative when CpGs were located in the region surrounding transcription start site.

View Article: PubMed Central - PubMed

Affiliation: Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Malmö, Sweden.

ABSTRACT
Genetic and epigenetic mechanisms may interact and together affect biological processes and disease development. However, most previous studies have investigated genetic and epigenetic mechanisms independently, and studies examining their interactions throughout the human genome are lacking. To identify genetic loci that interact with the epigenome, we performed the first genome-wide DNA methylation quantitative trait locus (mQTL) analysis in human pancreatic islets. We related 574,553 single nucleotide polymorphisms (SNPs) with genome-wide DNA methylation data of 468,787 CpG sites targeting 99% of RefSeq genes in islets from 89 donors. We identified 67,438 SNP-CpG pairs in cis, corresponding to 36,783 SNPs (6.4% of tested SNPs) and 11,735 CpG sites (2.5% of tested CpGs), and 2,562 significant SNP-CpG pairs in trans, corresponding to 1,465 SNPs (0.3% of tested SNPs) and 383 CpG sites (0.08% of tested CpGs), showing significant associations after correction for multiple testing. These include reported diabetes loci, e.g. ADCY5, KCNJ11, HLA-DQA1, INS, PDX1 and GRB10. CpGs of significant cis-mQTLs were overrepresented in the gene body and outside of CpG islands. Follow-up analyses further identified mQTLs associated with gene expression and insulin secretion in human islets. Causal inference test (CIT) identified SNP-CpG pairs where DNA methylation in human islets is the potential mediator of the genetic association with gene expression or insulin secretion. Functional analyses further demonstrated that identified candidate genes (GPX7, GSTT1 and SNX19) directly affect key biological processes such as proliferation and apoptosis in pancreatic β-cells. Finally, we found direct correlations between DNA methylation of 22,773 (4.9%) CpGs with mRNA expression of 4,876 genes, where 90% of the correlations were negative when CpGs were located in the region surrounding transcription start site. Our study demonstrates for the first time how genome-wide genetic and epigenetic variation interacts to influence gene expression, islet function and potential diabetes risk in humans.

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Genomic distribution of CpG sites of significantly identified mQTLs in human pancreatic islets.(A) Chromosomal distribution of CpG sites of significant cis- and trans-mQTLs in comparison to all analyzed CpG sites on the Infinium Human Methylation450 BeadChip. (B) All analyzed CpG sites on the Infinium Human Methylation450 BeadChip have been annotated to genomic regions based on their relation to the nearest gene (TSS: proximal promoter, defined as 200 bp or 1500 bp upstream of transcription start site; UTR: untranslated region) or in relation to the nearest CpG island (CpG island: DNA stretch of 200 bp or more with a C+G content of >50% and an observed CpG/expected CpG in excess of 0.6; Shore: the flanking region of CpG islands, 0–2000 bp; Shelf: regions flanking island shores, i.e., covering 2000–4000 bp distant from the CpG island). Distribution of CpG sites of significant mQTLs in relation to (C) the nearest gene and (D) in relation to CpG islands. *Significantly different distribution (P<0.05) of CpGs of significant cis- or trans-mQTLs from what is expected by chance based on a Chi-squared-test when compared with all analyzed CpG sites on the Infinium HumanMethylation450 BeadChip.
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pgen-1004735-g003: Genomic distribution of CpG sites of significantly identified mQTLs in human pancreatic islets.(A) Chromosomal distribution of CpG sites of significant cis- and trans-mQTLs in comparison to all analyzed CpG sites on the Infinium Human Methylation450 BeadChip. (B) All analyzed CpG sites on the Infinium Human Methylation450 BeadChip have been annotated to genomic regions based on their relation to the nearest gene (TSS: proximal promoter, defined as 200 bp or 1500 bp upstream of transcription start site; UTR: untranslated region) or in relation to the nearest CpG island (CpG island: DNA stretch of 200 bp or more with a C+G content of >50% and an observed CpG/expected CpG in excess of 0.6; Shore: the flanking region of CpG islands, 0–2000 bp; Shelf: regions flanking island shores, i.e., covering 2000–4000 bp distant from the CpG island). Distribution of CpG sites of significant mQTLs in relation to (C) the nearest gene and (D) in relation to CpG islands. *Significantly different distribution (P<0.05) of CpGs of significant cis- or trans-mQTLs from what is expected by chance based on a Chi-squared-test when compared with all analyzed CpG sites on the Infinium HumanMethylation450 BeadChip.

Mentions: Although previous cancer studies have described the genomic location of CpG sites that exhibit differential DNA methylation in tumor versus normal cells [34], [35], to our knowledge, no previous study has examined the genomic distribution of CpG sites in genome-wide mQTLs. Moreover, while there is an accumulation of genetic variation on certain chromosomes associated with disease [23], [36], it remains unknown if there is an over- or underrepresentation of significant mQTLs on certain chromosomes linked to islet function. Here, we describe the genomic distribution of significant mQTLs in human pancreatic islets. When analyzing the chromosomal distribution of CpG sites among significant cis-mQTLs, an overrepresentation of CpG sites on chromosomes 6, 7, 8 and 21 together with an underrepresentation of CpG sites on chromosomes 1, 2, 3, 12, 14, 15, 16, 17, 19 and 20 were found in comparison to the chromosomal distribution of all analyzed sites on the Infinium HumanMethylation450 BeadChip based on chi-squared-tests (Figure 3A and Table S4A). In the trans-mQTL analysis, an overrepresentation of CpGs was found on chromosomes 6 and 17 together with an underrepresentation on chromosomes 1, 9 and 14 (Figure 3A and Table S4A). Chromosome 6, which possess the HLA region – a gene region known to be involved in diabetes and autoimmune reaction [37], [38], was found to show the highest enrichment when comparing the chromosomal distribution of CpG sites among significant mQTLs for both the cis- and trans-analysis compared with all analyzed CpG sites (Figure 3A and Table S4A).


Genome-wide associations between genetic and epigenetic variation influence mRNA expression and insulin secretion in human pancreatic islets.

Olsson AH, Volkov P, Bacos K, Dayeh T, Hall E, Nilsson EA, Ladenvall C, Rönn T, Ling C - PLoS Genet. (2014)

Genomic distribution of CpG sites of significantly identified mQTLs in human pancreatic islets.(A) Chromosomal distribution of CpG sites of significant cis- and trans-mQTLs in comparison to all analyzed CpG sites on the Infinium Human Methylation450 BeadChip. (B) All analyzed CpG sites on the Infinium Human Methylation450 BeadChip have been annotated to genomic regions based on their relation to the nearest gene (TSS: proximal promoter, defined as 200 bp or 1500 bp upstream of transcription start site; UTR: untranslated region) or in relation to the nearest CpG island (CpG island: DNA stretch of 200 bp or more with a C+G content of >50% and an observed CpG/expected CpG in excess of 0.6; Shore: the flanking region of CpG islands, 0–2000 bp; Shelf: regions flanking island shores, i.e., covering 2000–4000 bp distant from the CpG island). Distribution of CpG sites of significant mQTLs in relation to (C) the nearest gene and (D) in relation to CpG islands. *Significantly different distribution (P<0.05) of CpGs of significant cis- or trans-mQTLs from what is expected by chance based on a Chi-squared-test when compared with all analyzed CpG sites on the Infinium HumanMethylation450 BeadChip.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222689&req=5

pgen-1004735-g003: Genomic distribution of CpG sites of significantly identified mQTLs in human pancreatic islets.(A) Chromosomal distribution of CpG sites of significant cis- and trans-mQTLs in comparison to all analyzed CpG sites on the Infinium Human Methylation450 BeadChip. (B) All analyzed CpG sites on the Infinium Human Methylation450 BeadChip have been annotated to genomic regions based on their relation to the nearest gene (TSS: proximal promoter, defined as 200 bp or 1500 bp upstream of transcription start site; UTR: untranslated region) or in relation to the nearest CpG island (CpG island: DNA stretch of 200 bp or more with a C+G content of >50% and an observed CpG/expected CpG in excess of 0.6; Shore: the flanking region of CpG islands, 0–2000 bp; Shelf: regions flanking island shores, i.e., covering 2000–4000 bp distant from the CpG island). Distribution of CpG sites of significant mQTLs in relation to (C) the nearest gene and (D) in relation to CpG islands. *Significantly different distribution (P<0.05) of CpGs of significant cis- or trans-mQTLs from what is expected by chance based on a Chi-squared-test when compared with all analyzed CpG sites on the Infinium HumanMethylation450 BeadChip.
Mentions: Although previous cancer studies have described the genomic location of CpG sites that exhibit differential DNA methylation in tumor versus normal cells [34], [35], to our knowledge, no previous study has examined the genomic distribution of CpG sites in genome-wide mQTLs. Moreover, while there is an accumulation of genetic variation on certain chromosomes associated with disease [23], [36], it remains unknown if there is an over- or underrepresentation of significant mQTLs on certain chromosomes linked to islet function. Here, we describe the genomic distribution of significant mQTLs in human pancreatic islets. When analyzing the chromosomal distribution of CpG sites among significant cis-mQTLs, an overrepresentation of CpG sites on chromosomes 6, 7, 8 and 21 together with an underrepresentation of CpG sites on chromosomes 1, 2, 3, 12, 14, 15, 16, 17, 19 and 20 were found in comparison to the chromosomal distribution of all analyzed sites on the Infinium HumanMethylation450 BeadChip based on chi-squared-tests (Figure 3A and Table S4A). In the trans-mQTL analysis, an overrepresentation of CpGs was found on chromosomes 6 and 17 together with an underrepresentation on chromosomes 1, 9 and 14 (Figure 3A and Table S4A). Chromosome 6, which possess the HLA region – a gene region known to be involved in diabetes and autoimmune reaction [37], [38], was found to show the highest enrichment when comparing the chromosomal distribution of CpG sites among significant mQTLs for both the cis- and trans-analysis compared with all analyzed CpG sites (Figure 3A and Table S4A).

Bottom Line: CpGs of significant cis-mQTLs were overrepresented in the gene body and outside of CpG islands.Follow-up analyses further identified mQTLs associated with gene expression and insulin secretion in human islets.Finally, we found direct correlations between DNA methylation of 22,773 (4.9%) CpGs with mRNA expression of 4,876 genes, where 90% of the correlations were negative when CpGs were located in the region surrounding transcription start site.

View Article: PubMed Central - PubMed

Affiliation: Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Malmö, Sweden.

ABSTRACT
Genetic and epigenetic mechanisms may interact and together affect biological processes and disease development. However, most previous studies have investigated genetic and epigenetic mechanisms independently, and studies examining their interactions throughout the human genome are lacking. To identify genetic loci that interact with the epigenome, we performed the first genome-wide DNA methylation quantitative trait locus (mQTL) analysis in human pancreatic islets. We related 574,553 single nucleotide polymorphisms (SNPs) with genome-wide DNA methylation data of 468,787 CpG sites targeting 99% of RefSeq genes in islets from 89 donors. We identified 67,438 SNP-CpG pairs in cis, corresponding to 36,783 SNPs (6.4% of tested SNPs) and 11,735 CpG sites (2.5% of tested CpGs), and 2,562 significant SNP-CpG pairs in trans, corresponding to 1,465 SNPs (0.3% of tested SNPs) and 383 CpG sites (0.08% of tested CpGs), showing significant associations after correction for multiple testing. These include reported diabetes loci, e.g. ADCY5, KCNJ11, HLA-DQA1, INS, PDX1 and GRB10. CpGs of significant cis-mQTLs were overrepresented in the gene body and outside of CpG islands. Follow-up analyses further identified mQTLs associated with gene expression and insulin secretion in human islets. Causal inference test (CIT) identified SNP-CpG pairs where DNA methylation in human islets is the potential mediator of the genetic association with gene expression or insulin secretion. Functional analyses further demonstrated that identified candidate genes (GPX7, GSTT1 and SNX19) directly affect key biological processes such as proliferation and apoptosis in pancreatic β-cells. Finally, we found direct correlations between DNA methylation of 22,773 (4.9%) CpGs with mRNA expression of 4,876 genes, where 90% of the correlations were negative when CpGs were located in the region surrounding transcription start site. Our study demonstrates for the first time how genome-wide genetic and epigenetic variation interacts to influence gene expression, islet function and potential diabetes risk in humans.

Show MeSH
Related in: MedlinePlus