Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxiaReport as inadecuate

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Molecular Cancer

, 13:28

First Online: 11 February 2014Received: 14 September 2013Accepted: 05 February 2014DOI: 10.1186-1476-4598-13-28

Cite this article as: Camps, C., Saini, H.K., Mole, D.R. et al. Mol Cancer 2014 13: 28. doi:10.1186-1476-4598-13-28


BackgroundIn mammalians, HIF is a master regulator of hypoxia gene expression through direct binding to DNA, while its role in microRNA expression regulation, critical in the hypoxia response, is not elucidated genome wide. Our aim is to investigate in depth the regulation of microRNA expression by hypoxia in the breast cancer cell line MCF-7, establish the relationship between microRNA expression and HIF binding sites, pri-miRNA transcription and microRNA processing gene expression.

MethodsMCF-7 cells were incubated at 1% Oxygen for 16, 32 and 48 h. SiRNA against HIF-1α and HIF-2α were performed as previously published. MicroRNA and mRNA expression were assessed using microRNA microarrays, small RNA sequencing, gene expression microarrays and Real time PCR. The Kraken pipeline was applied for microRNA-seq analysis along with Bioconductor packages. Microarray data was analysed using Limma Bioconductor, ChIP-seq data were analysed using Gene Set Enrichment Analysis and multiple testing correction applied in all analyses.

ResultsHypoxia time course microRNA sequencing data analysis identified 41 microRNAs significantly up- and 28 down-regulated, including hsa-miR-4521, hsa-miR-145-3p and hsa-miR-222-5p reported in conjunction with hypoxia for the first time. Integration of HIF-1α and HIF-2α ChIP-seq data with expression data showed overall association between binding sites and microRNA up-regulation, with hsa-miR-210-3p and microRNAs of miR-27a-23a-24-2 and miR-30b-30d clusters as predominant examples. Moreover the expression of hsa-miR-27a-3p and hsa-miR-24-3p was found positively associated to a hypoxia gene signature in breast cancer. Gene expression analysis showed no full coordination between pri-miRNA and microRNA expression, pointing towards additional levels of regulation. Several transcripts involved in microRNA processing were found regulated by hypoxia, of which DICER down-regulated and AGO4 up-regulated were HIF dependent. DICER expression was found inversely correlated to hypoxia in breast cancer.

ConclusionsIntegrated analysis of microRNA, mRNA and ChIP-seq data in a model cell line supports the hypothesis that microRNA expression under hypoxia is regulated at transcriptional and post-transcriptional level, with the presence of HIF binding sites at microRNA genomic loci associated with up-regulation. The identification of hypoxia and HIF regulated microRNAs relevant for breast cancer is important for our understanding of disease development and design of therapeutic interventions.

KeywordsMicroRNA Hypoxia HIF Transcription factor Gene regulation AbbreviationsAGOArgonaute

ChIPChromatin immunoprecipitation

ChIP-seqChromatin immunoprecipitation sequencing

GSEAGene set enrichment analysis

HIFHypoxia inducible factor

HUVECHuman umbilical vein endothelial cells

PASMCPulmonary artery smooth muscle cells

Pre-miRNAPrecursor microRNA

Pri-miRNAPrimary microRNA

qPCRReal time PCR or quantitative PCR

RISCRNA induced silencing complex

ROSReactive oxygen species

siRNAShort interfering RNA

VHLVon Hippel Lindau.

Electronic supplementary materialThe online version of this article doi:10.1186-1476-4598-13-28 contains supplementary material, which is available to authorized users.

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Author: Carme Camps - Harpreet K Saini - David R Mole - Hani Choudhry - Martin Reczko - José Afonso Guerra-Assunção - Ya-Min 


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