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

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Affara, Muna 
Dunmore, Benjamin J 
Sanders, Deborah A 
Johnson, Nicola 
Print, Cristin G 


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).



Cells, Cultured, Chromatin Immunoprecipitation, Female, GATA3 Transcription Factor, Humans, Immunoblotting, Inflammation Mediators, Interleukin-1beta, Interleukin-8, Matrix Metalloproteinase 1, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Protein Binding, Proto-Oncogene Protein c-ets-1, Proto-Oncogene Protein c-ets-2, Reverse Transcriptase Polymerase Chain Reaction, Tumor Necrosis Factor-alpha

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BMC Genomics

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Springer Science and Business Media LLC