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Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis.

Guimbellot JS, Erickson SW, Mehta T, Wen H, Page GP, Sorscher EJ, Hong JS - BMC Med Genomics (2009)

Bottom Line: To date, few studies have investigated an environmental perturbation for effects on genome-wide miRNA levels, or their consequent influence on mRNA output.Target prediction programs and expression profiling techniques do not yet adequately represent the complexity of miRNA-mediated gene repression, and new methods may be required to better elucidate these pathways.Our data suggest the physiologic impact of miRNAs on cellular transcription results from a multifaceted network of miRNA and mRNA relationships, working together in an interconnected system and in context of hundreds of RNA species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA. jsguimbellot@uasom.uab.edu

ABSTRACT

Background: Low levels of oxygen in tissues, seen in situations such as chronic lung disease, necrotic tumors, and high altitude exposures, initiate a signaling pathway that results in active transcription of genes possessing a hypoxia response element (HRE). The aim of this study was to investigate whether a change in miRNA expression following hypoxia could account for changes in the cellular transcriptome based on currently available miRNA target prediction tools.

Methods: To identify changes induced by hypoxia, we conducted mRNA- and miRNA-array-based experiments in HT29 cells, and performed comparative analysis of the resulting data sets based on multiple target prediction algorithms. To date, few studies have investigated an environmental perturbation for effects on genome-wide miRNA levels, or their consequent influence on mRNA output.

Results: Comparison of miRNAs with predicted mRNA targets indicated a lower level of concordance than expected. We did, however, find preliminary evidence of combinatorial regulation of mRNA expression by miRNA.

Conclusion: Target prediction programs and expression profiling techniques do not yet adequately represent the complexity of miRNA-mediated gene repression, and new methods may be required to better elucidate these pathways. Our data suggest the physiologic impact of miRNAs on cellular transcription results from a multifaceted network of miRNA and mRNA relationships, working together in an interconnected system and in context of hundreds of RNA species. The methods described here for comparative analysis of cellular miRNA and mRNA will be useful for understanding genome wide regulatory responsiveness and refining miRNA predictive algorithms.

No MeSH data available.


Related in: MedlinePlus

Differentially expressed mRNAs. Comparison of changes in HT29 mRNA levels under hypoxic vs. normoxic conditions. Unique genes that were differentially expressed 1.5 fold or greater are shown on the log-scale scatter plot. Upper cloud indicates transcripts at increased levels under hypoxic conditions and lower cloud indicates those decreased under hypoxic conditions.
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Figure 1: Differentially expressed mRNAs. Comparison of changes in HT29 mRNA levels under hypoxic vs. normoxic conditions. Unique genes that were differentially expressed 1.5 fold or greater are shown on the log-scale scatter plot. Upper cloud indicates transcripts at increased levels under hypoxic conditions and lower cloud indicates those decreased under hypoxic conditions.

Mentions: Data analysis was performed using three replicates of array data per group (within group Mean r2 = 0.996, range 0.004–0.998). Genes were considered differentially expressed between normoxic and hypoxic conditions if absolute expression changes were 1.5-fold or greater, a lower than 0.1% false discovery rate (FDR) was observed, and the p-value from a Welch two-sample t-test was less than 0.001. Over 8% of all probes satisfied these criteria (1999 probes up-regulated and 2099 down-regulated, see Figure 1). These probe sets map on to 1476 up- and 1649 down-regulated genes with a HUGO gene symbol, along with 208 probe sets that did not map to a HUGO identifier. Table 1 provides examples of selected genes known to be regulated by hypoxia with a broad biological significance, which are also predicted to contain target sites (in the 3'UTR) for miRNAs, according to the miRanda(microrna.org) target prediction database (for complete dataset of all genes altered by oxygen restriction in our studies, see GEO series GSE9234). Interestingly, the miRanda(mirorna.org) Target Database predicted that every 3'UTR in this set had target sites for between 4 and 69 miRNAs, although only 30% of the genome has been suggested to be regulated by miRNA-based mechanisms[1,4,5].


Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis.

Guimbellot JS, Erickson SW, Mehta T, Wen H, Page GP, Sorscher EJ, Hong JS - BMC Med Genomics (2009)

Differentially expressed mRNAs. Comparison of changes in HT29 mRNA levels under hypoxic vs. normoxic conditions. Unique genes that were differentially expressed 1.5 fold or greater are shown on the log-scale scatter plot. Upper cloud indicates transcripts at increased levels under hypoxic conditions and lower cloud indicates those decreased under hypoxic conditions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2667434&req=5

Figure 1: Differentially expressed mRNAs. Comparison of changes in HT29 mRNA levels under hypoxic vs. normoxic conditions. Unique genes that were differentially expressed 1.5 fold or greater are shown on the log-scale scatter plot. Upper cloud indicates transcripts at increased levels under hypoxic conditions and lower cloud indicates those decreased under hypoxic conditions.
Mentions: Data analysis was performed using three replicates of array data per group (within group Mean r2 = 0.996, range 0.004–0.998). Genes were considered differentially expressed between normoxic and hypoxic conditions if absolute expression changes were 1.5-fold or greater, a lower than 0.1% false discovery rate (FDR) was observed, and the p-value from a Welch two-sample t-test was less than 0.001. Over 8% of all probes satisfied these criteria (1999 probes up-regulated and 2099 down-regulated, see Figure 1). These probe sets map on to 1476 up- and 1649 down-regulated genes with a HUGO gene symbol, along with 208 probe sets that did not map to a HUGO identifier. Table 1 provides examples of selected genes known to be regulated by hypoxia with a broad biological significance, which are also predicted to contain target sites (in the 3'UTR) for miRNAs, according to the miRanda(microrna.org) target prediction database (for complete dataset of all genes altered by oxygen restriction in our studies, see GEO series GSE9234). Interestingly, the miRanda(mirorna.org) Target Database predicted that every 3'UTR in this set had target sites for between 4 and 69 miRNAs, although only 30% of the genome has been suggested to be regulated by miRNA-based mechanisms[1,4,5].

Bottom Line: To date, few studies have investigated an environmental perturbation for effects on genome-wide miRNA levels, or their consequent influence on mRNA output.Target prediction programs and expression profiling techniques do not yet adequately represent the complexity of miRNA-mediated gene repression, and new methods may be required to better elucidate these pathways.Our data suggest the physiologic impact of miRNAs on cellular transcription results from a multifaceted network of miRNA and mRNA relationships, working together in an interconnected system and in context of hundreds of RNA species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA. jsguimbellot@uasom.uab.edu

ABSTRACT

Background: Low levels of oxygen in tissues, seen in situations such as chronic lung disease, necrotic tumors, and high altitude exposures, initiate a signaling pathway that results in active transcription of genes possessing a hypoxia response element (HRE). The aim of this study was to investigate whether a change in miRNA expression following hypoxia could account for changes in the cellular transcriptome based on currently available miRNA target prediction tools.

Methods: To identify changes induced by hypoxia, we conducted mRNA- and miRNA-array-based experiments in HT29 cells, and performed comparative analysis of the resulting data sets based on multiple target prediction algorithms. To date, few studies have investigated an environmental perturbation for effects on genome-wide miRNA levels, or their consequent influence on mRNA output.

Results: Comparison of miRNAs with predicted mRNA targets indicated a lower level of concordance than expected. We did, however, find preliminary evidence of combinatorial regulation of mRNA expression by miRNA.

Conclusion: Target prediction programs and expression profiling techniques do not yet adequately represent the complexity of miRNA-mediated gene repression, and new methods may be required to better elucidate these pathways. Our data suggest the physiologic impact of miRNAs on cellular transcription results from a multifaceted network of miRNA and mRNA relationships, working together in an interconnected system and in context of hundreds of RNA species. The methods described here for comparative analysis of cellular miRNA and mRNA will be useful for understanding genome wide regulatory responsiveness and refining miRNA predictive algorithms.

No MeSH data available.


Related in: MedlinePlus