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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia
Molecular Cancer, Volume 13, No. 1, Article 28, Year 2014
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Description
Background: In 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. Methods: MCF-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. Results: Hypoxia 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. Conclusions: Integrated 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. © 2014 Camps et al.; licensee BioMed Central Ltd.
Authors & Co-Authors
Camps, Carme
United Kingdom, Oxford
The Wellcome Centre for Human Genetics
Saini, Harpreet K.
United Kingdom, London
Wellcome Trust
Mole, David Robert
United Kingdom, Oxford
Nuffield Department of Medicine
Choudhry, Hani M.Z.
United Kingdom, Oxford
The Wellcome Centre for Human Genetics
Saudi Arabia, Jeddah
King Abdulaziz University
Reczko, Martin
Greece, Vari
Biomedical Sciences Research Center Alexander Fleming
Guerra-Assunção, José Afonso
United Kingdom, London
Wellcome Trust
Tian, Ya Min
United Kingdom, Oxford
Nuffield Department of Medicine
Buffa, Francesca Meteora
United Kingdom, Oxford
Mrc Weatherall Institute of Molecular Medicine
Harris, Adrian L.
United Kingdom, Oxford
Mrc Weatherall Institute of Molecular Medicine
Hatzigeorgiou, Artemis G.
Greece, Vari
Biomedical Sciences Research Center Alexander Fleming
Enright, Anton J.
United Kingdom, London
Wellcome Trust
Ragoussis, Ioannis
United Kingdom, Oxford
The Wellcome Centre for Human Genetics
Greece, Vari
Biomedical Sciences Research Center Alexander Fleming
Canada, Montreal
Université Mcgill
Statistics
Citations: 145
Authors: 12
Affiliations: 7
Identifiers
Doi:
10.1186/1476-4598-13-28
e-ISSN:
14764598
Research Areas
Cancer
Genetics And Genomics