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| Status |
Public on Feb 13, 2014 |
| Title |
Integrated analysis of microRNA and mRNA expression and association with HIF binding in MCF-7 cells under hypoxia [miRNA] |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by array
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| Summary |
Purpose: We aimed 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: microRNA sequencing data and gene expression microarray data were generated from MCF-7 cells submitted to an hypoxia timecourse (16h, 32h and 48h at 1% Oxygen). Data was integrated to 500 published high-stringency HIF binding sites identified in MCF-7 cells.
Results: We identified 41 microRNAs significantly up- and 28 down- regulated, of which 38 mature and 20 star forms are reported in conjunction with hypoxia for the first time. HIF-1α and HIF-2α binding sites within 50kb distance of microRNA loci were found by integration of HIF ChIP-seq data, showing overall association between binding sites and up-regulation. Gene expression profiling analysis showed no full coordination between pri-miRNA and microRNA expression, pointing towards additional levels of regulation. Several transcripts playing a role in microRNA processing were found regulated by hypoxia, of which two were HIF dependent.
Conclusions: The data support the hypothesis that microRNA expression under hypoxia is regulated at transcriptional and post-transcriptional level. HIF is involved at both levels, regulating the transcription of certain microRNAs and also the expression of key elements of the microRNA processing pathway.
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| Overall design |
MicroRNA expression profiles of MCF-7 exposed to hypoxia (1% Oxygen) for 16h (2 replicates), 32h (3 replicates) and 48h (3 replicates) and to normoxia (3 replicates) were generated using Agilent miRNA microarrays. This data was used to validate the microRNA-seq data included in this study.
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| Contributor(s) |
Camps C, Ragoussis J |
| Citation(s) |
24517586 |
| Submission date |
May 30, 2013 |
| Last update date |
May 07, 2014 |
| Contact name |
Carme Camps |
| Organization name |
Wellcome Trust Centre for Human Genetics/ U. of Oxford
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| Street address |
Roosevelt Drive
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| City |
Oxford |
| ZIP/Postal code |
OX37BN |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL8227 |
Agilent-019118 Human miRNA Microarray 2.0 G4470B (miRNA ID version) |
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| Samples (11)
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| This SubSeries is part of SuperSeries: |
| GSE47534 |
Integrated analysis of microRNA and mRNA expression and association with HIF binding in MCF-7 cells under hypoxia |
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| Relations |
| BioProject |
PRJNA205987 |
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