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MMP1 bimodal expression and differential response to inflammatory mediators is linked to promoter polymorphisms.

Affara M, Dunmore BJ, Sanders DA, Johnson N, Print CG, Charnock-Jones DS - BMC Genomics (2011)

Bottom Line: Identifying the functional importance of the millions of single nucleotide polymorphisms (SNPs) in the human genome is a difficult challenge.In this study, we used a novel but straightforward method based on agglomerative hierarchical clustering to identify bimodally expressed transcripts in human umbilical vein endothelial cell (HUVEC) microarray data from 15 individuals.We describe a simple method to identify putative bimodally expressed RNAs from transcriptome data that is effective yet easy for non-statisticians to understand and use.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.

ABSTRACT

Background: Identifying the functional importance of the millions of single nucleotide polymorphisms (SNPs) in the human genome is a difficult challenge. Therefore, a reverse strategy, which identifies functionally important SNPs by virtue of the bimodal abundance across the human population of the SNP-related mRNAs will be useful. Those mRNA transcripts that are expressed at two distinct abundances in proportion to SNP allele frequency may warrant further study. Matrix metalloproteinase 1 (MMP1) is important in both normal development and in numerous pathologies. Although much research has been conducted to investigate the expression of MMP1 in many different cell types and conditions, the regulation of its expression is still not fully understood.

Results: In this study, we used a novel but straightforward method based on agglomerative hierarchical clustering to identify bimodally expressed transcripts in human umbilical vein endothelial cell (HUVEC) microarray data from 15 individuals. We found that MMP1 mRNA abundance was bimodally distributed in un-treated HUVECs and showed a bimodal response to inflammatory mediator treatment. RT-PCR and MMP1 activity assays confirmed the bimodal regulation and DNA sequencing of 69 individuals identified an MMP1 gene promoter polymorphism that segregated precisely with the MMP1 bimodal expression. Chromatin immunoprecipitation (ChIP) experiments indicated that the transcription factors (TFs) ETS1, ETS2 and GATA3, bind to the MMP1 promoter in the region of this polymorphism and may contribute to the bimodal expression.

Conclusions: We describe a simple method to identify putative bimodally expressed RNAs from transcriptome data that is effective yet easy for non-statisticians to understand and use. This method identified bimodal endothelial cell expression of MMP1, which appears to be biologically significant with implications for inflammatory disease. (271 Words).

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Sequencing of the -1607 MMP-1 promoter polymorphism, illustrating the homozygous and heterozygous genotypes. Insertion of an additional G creates the consensus sequence for the ETS binding site, GGA (indicated by blue shading).
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Figure 6: Sequencing of the -1607 MMP-1 promoter polymorphism, illustrating the homozygous and heterozygous genotypes. Insertion of an additional G creates the consensus sequence for the ETS binding site, GGA (indicated by blue shading).

Mentions: A 1G/2G deletion/insertion polymorphism at position -1607 in the MMP-1 promoter has been associated with differential expression of this gene in fibroblast and melanoma cells, with the 2G genotype associated with higher basal levels of MMP1 mRNA [16]. This polymorphism occurs within a consensus binding site for the ETS family of transcription factors [16,18]. Therefore, direct DNA sequencing of the MMP1 promoter was carried out to determine whether the MMP1 mRNA abundance and activity profiles segregated with this promoter polymorphism. We determined MMP1 mRNA level, MMP1 enzymatic activity and MMP1 promoter genotypes in HUVECs from 69 different individuals. Figure 6 and Table 1 illustrate the three genotypes observed in these individuals. Of the 69 individuals, 76% were heterozygous at the site of the promoter polymorphism, 15% were homozygous for the 1G allele, while only 9% were homozygous for the 2G allele. All 1G homozygous individuals segregated with low basal expression and activity of MMP1, whereas all but one of the heterozygotes and homozygous 2G individuals segregated with high basal expression and activity of MMP1.


MMP1 bimodal expression and differential response to inflammatory mediators is linked to promoter polymorphisms.

Affara M, Dunmore BJ, Sanders DA, Johnson N, Print CG, Charnock-Jones DS - BMC Genomics (2011)

Sequencing of the -1607 MMP-1 promoter polymorphism, illustrating the homozygous and heterozygous genotypes. Insertion of an additional G creates the consensus sequence for the ETS binding site, GGA (indicated by blue shading).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3040839&req=5

Figure 6: Sequencing of the -1607 MMP-1 promoter polymorphism, illustrating the homozygous and heterozygous genotypes. Insertion of an additional G creates the consensus sequence for the ETS binding site, GGA (indicated by blue shading).
Mentions: A 1G/2G deletion/insertion polymorphism at position -1607 in the MMP-1 promoter has been associated with differential expression of this gene in fibroblast and melanoma cells, with the 2G genotype associated with higher basal levels of MMP1 mRNA [16]. This polymorphism occurs within a consensus binding site for the ETS family of transcription factors [16,18]. Therefore, direct DNA sequencing of the MMP1 promoter was carried out to determine whether the MMP1 mRNA abundance and activity profiles segregated with this promoter polymorphism. We determined MMP1 mRNA level, MMP1 enzymatic activity and MMP1 promoter genotypes in HUVECs from 69 different individuals. Figure 6 and Table 1 illustrate the three genotypes observed in these individuals. Of the 69 individuals, 76% were heterozygous at the site of the promoter polymorphism, 15% were homozygous for the 1G allele, while only 9% were homozygous for the 2G allele. All 1G homozygous individuals segregated with low basal expression and activity of MMP1, whereas all but one of the heterozygotes and homozygous 2G individuals segregated with high basal expression and activity of MMP1.

Bottom Line: Identifying the functional importance of the millions of single nucleotide polymorphisms (SNPs) in the human genome is a difficult challenge.In this study, we used a novel but straightforward method based on agglomerative hierarchical clustering to identify bimodally expressed transcripts in human umbilical vein endothelial cell (HUVEC) microarray data from 15 individuals.We describe a simple method to identify putative bimodally expressed RNAs from transcriptome data that is effective yet easy for non-statisticians to understand and use.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.

ABSTRACT

Background: Identifying the functional importance of the millions of single nucleotide polymorphisms (SNPs) in the human genome is a difficult challenge. Therefore, a reverse strategy, which identifies functionally important SNPs by virtue of the bimodal abundance across the human population of the SNP-related mRNAs will be useful. Those mRNA transcripts that are expressed at two distinct abundances in proportion to SNP allele frequency may warrant further study. Matrix metalloproteinase 1 (MMP1) is important in both normal development and in numerous pathologies. Although much research has been conducted to investigate the expression of MMP1 in many different cell types and conditions, the regulation of its expression is still not fully understood.

Results: In this study, we used a novel but straightforward method based on agglomerative hierarchical clustering to identify bimodally expressed transcripts in human umbilical vein endothelial cell (HUVEC) microarray data from 15 individuals. We found that MMP1 mRNA abundance was bimodally distributed in un-treated HUVECs and showed a bimodal response to inflammatory mediator treatment. RT-PCR and MMP1 activity assays confirmed the bimodal regulation and DNA sequencing of 69 individuals identified an MMP1 gene promoter polymorphism that segregated precisely with the MMP1 bimodal expression. Chromatin immunoprecipitation (ChIP) experiments indicated that the transcription factors (TFs) ETS1, ETS2 and GATA3, bind to the MMP1 promoter in the region of this polymorphism and may contribute to the bimodal expression.

Conclusions: We describe a simple method to identify putative bimodally expressed RNAs from transcriptome data that is effective yet easy for non-statisticians to understand and use. This method identified bimodal endothelial cell expression of MMP1, which appears to be biologically significant with implications for inflammatory disease. (271 Words).

Show MeSH
Related in: MedlinePlus