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Open Access Research article

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

Muna Affara1, Benjamin J Dunmore2, Deborah A Sanders2, Nicola Johnson1, Cristin G Print13 and D Stephen Charnock-Jones124*

  • * Corresponding author: D S Charnock-Jones dscj1@cam.ac.uk

  • † Equal contributors

Author Affiliations

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

2 Department of Obstetrics and Gynaecology, University of Cambridge. The Rosie Hospital, Robinson Way, Cambridge CB2 0SW, UK

3 Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Private bag 92019, Auckland, New Zealand

4 National Institute for Health Research, Cambridge Comprehensive Biomedical Centre, Box 277, Hills Road, Cambridge, CB2 0QQ, UK

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BMC Genomics 2011, 12:43  doi:10.1186/1471-2164-12-43

Published: 19 January 2011

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 immunoprecipation (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-statisticans 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)