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

Molecular Cancer

Research

Francesca M Buffa¹  Adrian L Harris¹  José Afonso Guerra-Assunção²  Harpreet K Saini²  Anton J Enright²  Ya-Min Tian³  David R Mole³  Martin Reczko⁴  Artemis G Hatzigeorgiou⁴  Carme Camps⁵  Hani Choudhry⁶  Jiannis Ragoussis⁷ 

[1] Cancer Research UK Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom;EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom;Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford, United Kingdom;Institute of Molecular Oncology, Biomedical Sciences Research Center “Alexander Fleming”, 34 Fleming Street, 16672, Vari, Greece;The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom;The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom;Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia;The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom;Institute of Molecular Oncology, Biomedical Sciences Research Center “Alexander Fleming”, 34 Fleming Street, 16672, Vari, Greece;McGill University and Genome Quebec Innovation Centre, 740 DR Penfield Ave, H3A 0G1, Montreal, Canada;

关键词: MicroRNA;    Hypoxia;    HIF;    Transcription factor;    Gene regulation;   

DOI  :  10.1186/1476-4598-13-28

 received in 2013-09-14, accepted in 2014-02-05,  发布年份 2014

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© Camps et al.; licensee BioMed Central Ltd. 2014