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Insm1 cooperates with Neurod1 and Foxa2 to maintain mature pancreatic β-cell function.

Jia S, Ivanov A, Blasevic D, Müller T, Purfürst B, Sun W, Chen W, Poy MN, Rajewsky N, Birchmeier C - EMBO J. (2015)

Bottom Line: We defined Insm1, Neurod1 and Foxa2 binding sites associated with genes deregulated in Insm1 mutant β-cells.Human genomic sequences corresponding to the murine sites occupied by Insm1/Neurod1/Foxa2 were enriched in single nucleotide polymorphisms associated with glycolytic traits.Thus, our data explain part of the mechanisms by which β-cells maintain maturity: Combinatorial Insm1/Neurod1/Foxa2 binding identifies regulatory sequences that maintain the mature gene expression program in β-cells, and disruption of this network results in functional failure.

View Article: PubMed Central - PubMed

Affiliation: Developmental Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany cbirch@mdc-berlin.de jshiqi@mdc-berlin.de.

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Sites co-occupied by Insm1, Neurod1 and Foxa2 correspond to a functionally important subclass of Insm1 sitesA Proportions of all expressed and deregulated genes containing sites bound by Insm1/Neurod1/Foxa2 within ±10 kb and ±50 kb of the transcription start site (left). Proportions of all expressed and deregulated genes with sites occupied by Insm1 only ±10 kb and ±50 kb of the transcription start site (right). P-values for the enrichment of genes are indicated. NS: P-value > 0.01; ***P-value ≤ 10−10.B, C SNPs with genome-wide association for 14 traits in European individuals overlapping with Insm1/Neurod1/Foxa2 and Insm1 only sites; note that SNPs associated with fasting glucose levels are significantly enriched in Insm1/Neurod1/Foxa2 but not in sites bound by Insm1 only.D SNPs with genome-wide association for glycolytic traits in European individuals that overlap with different combinations of Insm1, Neurod1 and Foxa2 binding sites; P-values are displayed as −log10 values. Thus, SNPs associated with Insm1/Neurod1/Foxa2 binding sites are highly enriched for glycolytic traits.
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fig08: Sites co-occupied by Insm1, Neurod1 and Foxa2 correspond to a functionally important subclass of Insm1 sitesA Proportions of all expressed and deregulated genes containing sites bound by Insm1/Neurod1/Foxa2 within ±10 kb and ±50 kb of the transcription start site (left). Proportions of all expressed and deregulated genes with sites occupied by Insm1 only ±10 kb and ±50 kb of the transcription start site (right). P-values for the enrichment of genes are indicated. NS: P-value > 0.01; ***P-value ≤ 10−10.B, C SNPs with genome-wide association for 14 traits in European individuals overlapping with Insm1/Neurod1/Foxa2 and Insm1 only sites; note that SNPs associated with fasting glucose levels are significantly enriched in Insm1/Neurod1/Foxa2 but not in sites bound by Insm1 only.D SNPs with genome-wide association for glycolytic traits in European individuals that overlap with different combinations of Insm1, Neurod1 and Foxa2 binding sites; P-values are displayed as −log10 values. Thus, SNPs associated with Insm1/Neurod1/Foxa2 binding sites are highly enriched for glycolytic traits.

Mentions: Transcription factors typically bind to many thousand sites in the genome. It has remained a challenge to identify among these sites the ones functionally important for regulating gene expression. We related Insm1 binding and changes in gene expression in coInsm1 mutant islets. In comparison to all expressed genes, combinatorial Insm1/Neurod1/Foxa2 binding sites were significantly enriched in deregulated genes (P-value = 2.2 × 10−19 and 8.0 × 10−22 for sequences 10 kb or 50 kb around the genes, respectively, for FC > 1.2). For instance, 16% of all expressed genes and 32% of deregulated genes (FC > 1.4) contained an Insm1/Neurod1/Foxa2 binding site within 10 kb (P-value = 4.3 × 10−13). Sites occupied by ‘Insm1 only’ did not correlate with changed gene expression (Fig 8A). Additional computational analysis of other categories of single and combinatorial binding sites confirmed that sites co-occupied by Insm1/Neurod1/Foxa2 correlate best with changes in Insm1-dependent gene expression (Supplementary Table S5). Similar numbers of genes associated with Insm1/Neurod1/Foxa2 binding sites were up- and down-regulated (Supplementary Table S6), indicating that these sites regulate transcription in a context-dependent manner to activate or repress genes. Many deregulated genes associated with combinatorial Insm1/Neurod1/Foxa2 binding sites participate in insulin secretion, among them all deregulated genes whose expression was verified by qPCR in Fig 3B (see Supplementary Table S3 for a list of deregulated genes implicated in insulin secretion associated with Insm1/Neurod1/Foxa2 sites). Finally, we defined the presence of Insm1/Neurod1/Foxa2 binding sites in genes deregulated in both, immature islets and coInsm1, and observed again a significant enrichment (P-value = 1.0 × 10−10 and 4.2 × 10−15 for sequences 10 kb and 50 kb around deregulated genes, respectively). We conclude that the presence of sites characterized by triple Insm1/Neurod1/Foxa2 binding is a predictor of Insm1-dependent gene expression.


Insm1 cooperates with Neurod1 and Foxa2 to maintain mature pancreatic β-cell function.

Jia S, Ivanov A, Blasevic D, Müller T, Purfürst B, Sun W, Chen W, Poy MN, Rajewsky N, Birchmeier C - EMBO J. (2015)

Sites co-occupied by Insm1, Neurod1 and Foxa2 correspond to a functionally important subclass of Insm1 sitesA Proportions of all expressed and deregulated genes containing sites bound by Insm1/Neurod1/Foxa2 within ±10 kb and ±50 kb of the transcription start site (left). Proportions of all expressed and deregulated genes with sites occupied by Insm1 only ±10 kb and ±50 kb of the transcription start site (right). P-values for the enrichment of genes are indicated. NS: P-value > 0.01; ***P-value ≤ 10−10.B, C SNPs with genome-wide association for 14 traits in European individuals overlapping with Insm1/Neurod1/Foxa2 and Insm1 only sites; note that SNPs associated with fasting glucose levels are significantly enriched in Insm1/Neurod1/Foxa2 but not in sites bound by Insm1 only.D SNPs with genome-wide association for glycolytic traits in European individuals that overlap with different combinations of Insm1, Neurod1 and Foxa2 binding sites; P-values are displayed as −log10 values. Thus, SNPs associated with Insm1/Neurod1/Foxa2 binding sites are highly enriched for glycolytic traits.
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fig08: Sites co-occupied by Insm1, Neurod1 and Foxa2 correspond to a functionally important subclass of Insm1 sitesA Proportions of all expressed and deregulated genes containing sites bound by Insm1/Neurod1/Foxa2 within ±10 kb and ±50 kb of the transcription start site (left). Proportions of all expressed and deregulated genes with sites occupied by Insm1 only ±10 kb and ±50 kb of the transcription start site (right). P-values for the enrichment of genes are indicated. NS: P-value > 0.01; ***P-value ≤ 10−10.B, C SNPs with genome-wide association for 14 traits in European individuals overlapping with Insm1/Neurod1/Foxa2 and Insm1 only sites; note that SNPs associated with fasting glucose levels are significantly enriched in Insm1/Neurod1/Foxa2 but not in sites bound by Insm1 only.D SNPs with genome-wide association for glycolytic traits in European individuals that overlap with different combinations of Insm1, Neurod1 and Foxa2 binding sites; P-values are displayed as −log10 values. Thus, SNPs associated with Insm1/Neurod1/Foxa2 binding sites are highly enriched for glycolytic traits.
Mentions: Transcription factors typically bind to many thousand sites in the genome. It has remained a challenge to identify among these sites the ones functionally important for regulating gene expression. We related Insm1 binding and changes in gene expression in coInsm1 mutant islets. In comparison to all expressed genes, combinatorial Insm1/Neurod1/Foxa2 binding sites were significantly enriched in deregulated genes (P-value = 2.2 × 10−19 and 8.0 × 10−22 for sequences 10 kb or 50 kb around the genes, respectively, for FC > 1.2). For instance, 16% of all expressed genes and 32% of deregulated genes (FC > 1.4) contained an Insm1/Neurod1/Foxa2 binding site within 10 kb (P-value = 4.3 × 10−13). Sites occupied by ‘Insm1 only’ did not correlate with changed gene expression (Fig 8A). Additional computational analysis of other categories of single and combinatorial binding sites confirmed that sites co-occupied by Insm1/Neurod1/Foxa2 correlate best with changes in Insm1-dependent gene expression (Supplementary Table S5). Similar numbers of genes associated with Insm1/Neurod1/Foxa2 binding sites were up- and down-regulated (Supplementary Table S6), indicating that these sites regulate transcription in a context-dependent manner to activate or repress genes. Many deregulated genes associated with combinatorial Insm1/Neurod1/Foxa2 binding sites participate in insulin secretion, among them all deregulated genes whose expression was verified by qPCR in Fig 3B (see Supplementary Table S3 for a list of deregulated genes implicated in insulin secretion associated with Insm1/Neurod1/Foxa2 sites). Finally, we defined the presence of Insm1/Neurod1/Foxa2 binding sites in genes deregulated in both, immature islets and coInsm1, and observed again a significant enrichment (P-value = 1.0 × 10−10 and 4.2 × 10−15 for sequences 10 kb and 50 kb around deregulated genes, respectively). We conclude that the presence of sites characterized by triple Insm1/Neurod1/Foxa2 binding is a predictor of Insm1-dependent gene expression.

Bottom Line: We defined Insm1, Neurod1 and Foxa2 binding sites associated with genes deregulated in Insm1 mutant β-cells.Human genomic sequences corresponding to the murine sites occupied by Insm1/Neurod1/Foxa2 were enriched in single nucleotide polymorphisms associated with glycolytic traits.Thus, our data explain part of the mechanisms by which β-cells maintain maturity: Combinatorial Insm1/Neurod1/Foxa2 binding identifies regulatory sequences that maintain the mature gene expression program in β-cells, and disruption of this network results in functional failure.

View Article: PubMed Central - PubMed

Affiliation: Developmental Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany cbirch@mdc-berlin.de jshiqi@mdc-berlin.de.

Show MeSH