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Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments.

ABSTRACT: BACKGROUND:MicroRNA (miRNA) target genes tend to have relatively long and conserved 3' untranslated regions (UTRs), but to what degree these characteristics contribute to miRNA targeting is poorly understood. Different high-throughput experiments have, for example, shown that miRNAs preferentially regulate genes with both short and long 3' UTRs and that target site conservation is both important and irrelevant for miRNA targeting. RESULTS:We have analyzed several gene context-dependent features, including 3' UTR length, 3' UTR conservation, and messenger RNA (mRNA) expression levels, reported to have conflicting influence on miRNA regulation. By taking into account confounding factors such as technology-dependent experimental bias and competition between transfected and endogenous miRNAs, we show that two factors - target gene expression and competition - could explain most of the previously reported experimental differences. Moreover, we find that these and other target site-independent features explain about the same amount of variation in target gene expression as the target site-dependent features included in the TargetScan model. CONCLUSIONS:Our results show that it is important to consider confounding factors when interpreting miRNA high throughput experiments and urge special caution when using microarray data to compare average regulatory effects between groups of genes that have different average gene expression levels.

SUBMITTER: Saito T

PROVIDER: S-EPMC3293725 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature

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Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments.

Saito Takaya T Sætrom Pål P

Silence 20120210

<h4>Background</h4>MicroRNA (miRNA) target genes tend to have relatively long and conserved 3' untranslated regions (UTRs), but to what degree these characteristics contribute to miRNA targeting is poorly understood. Different high-throughput experiments have, for example, shown that miRNAs preferentially regulate genes with both short and long 3' UTRs and that target site conservation is both important and irrelevant for miRNA targeting.<h4>Results</h4>We have analyzed several gene context-depe ...[more]

PMID: 22325809

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Project description:Assessing algal nutrient limitation is critical for understanding the interaction of primary production and nutrient cycling in streams, and nutrient diffusing substrate (NDS) experiments are often used to determine limiting nutrients such as nitrogen (N) and phosphorus (P). Unexpectedly, many experiments have also shown decreased algal biomass on NDS P treatments compared to controls. To address whether inhibition of algal growth results from direct P toxicity, NDS preparation artifacts, or environmental covariates, we first quantified the frequency of nutrient inhibition in published experiments. We also conducted a meta-analysis to determine whether heterotrophic microbial competition or selective grazing could explain decreases in algal biomass with P additions. We then deployed field experiments to determine whether P-inhibition of algal growth could be explained by P toxicity, differences in phosphate cation (K vs. Na), differences in phosphate form (monobasic vs. dibasic), or production of H2O2 during NDS preparation. We found significant inhibition of algal growth in 12.9% of published NDS P experiments as compared to 4.7% and 3.6% of N and NP experiments. The meta-analysis linear models did not show enhanced heterotrophy on NDS P treatments or selective grazing of P-rich algae. Our field experiments did not show inhibition of autotrophic growth with P additions, but we found significantly lower gross primary productivity (GPP) and biomass-specific GPP of benthic algae on monobasic phosphate salts as compared to dibasic phosphate salts, likely because of reduced pH levels. Additionally, we note that past field experiments and meta-analyses support the plausibility of direct P toxicity or phosphate form (monobasic vs. dibasic) leading to inhibition of algal growth, particularly when other resources such as N or light are limiting. Given that multiple mechanisms may be acting simultaneously, we recommend practical, cost-effective steps to minimize the potential for P- inhibition of algal growth as an artifact of NDS experimental design.

Dataset Information

Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments.

Publications

Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments.

Similar Datasets

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