Biological Basis of miRNA Action when Their Targets Are Located in Human Protein Coding Region

<div><p>Recent analyses have revealed many functional microRNA (miRNA) targets in mammalian protein coding regions. But, the mechanisms that ensure miRNA function when their target sites are located in protein coding regions of mammalian mRNA transcripts are largely unknown. In this paper, we investigate some potential biological factors, such as target site accessibility and local translation efficiency. We computationally analyze these two factors using experimentally identified miRNA targets in human protein coding region. We find site accessibility is significantly increased in miRNA target region to facilitate miRNA binding. At the mean time, local translation efficiency is also selectively decreased near miRNA target region. GC-poor codons are preferred in the flank region of miRNA target sites to ease the access of miRNA targets. Within-genome analysis shows substantial variations of site accessibility and local translation efficiency among different miRNA targets in the genome. Further analyses suggest target gene’s GC content and conservation level could explain some of the differences in site accessibility. On the other hand, target gene’s functional importance and conservation level can affect local translation efficiency near miRNA target region. We hence propose both site accessibility and local translation efficiency are important in miRNA action when miRNA target sites are located in mammalian protein coding regions.</p></div

Comparison of the mean between miRNA targets in genes at different conservation levels.

<p>Comparison of the mean between miRNA targets in genes at different conservation levels.</p

Comparison of the mean between miRNA targets in genes with the highest 5% and lowest 5% protein complex size.

<p>Comparison of the mean between miRNA targets in genes with the highest 5% and lowest 5% protein complex size.</p

Comparison of the mean between miRNA targets in genes with the highest 5% and the lowest 5% GC content.

<p>Comparison of the mean between miRNA targets in genes with the highest 5% and the lowest 5% GC content.</p

Comparison of the mean between miRNA targets in genes at different conservation levels.

<p>Comparison of the mean between miRNA targets in genes at different conservation levels.</p

in miRNA target region as a function of in that region.

<p>Each point represents a miRNA target in human protein coding sequences.</p

The mean and standard error of of each sliding window near miRNA target region in the human genome.

<p>The mean and standard error of of each sliding window near miRNA target region in the human genome.</p

<i>VDAC1</i> and its interacting genes.

<p>(A) <i>VDAC1</i> is up-regulated in tumor tissues in breast, colon, liver, lung, pancreatic, and thyroid cancers. Paired normal and tumor tissues were included in the comparison. Y-axis: log₂-transformed expression values. (B) The top 10 GO biological process terms associated with dysregulated <i>VDAC1</i> interacting genes. Forty-four <i>VDAC1</i> interacting genes were identified as being commonly differentially expressed between normal and tumor tissues in human carcinomas. The <i>P</i>-values were calculated by Fisher’s exact test. The red dash line denotes the significance level of 0.05. (C) The top ten PANTHER pathway terms associated with dysregulated <i>VDAC1</i> interacting genes. The <i>P</i>-values were calculated by Fisher’s exact test. The red dash line denotes the significance level of 0.05.</p

Kaplan-Meier curves for colon cancer patients from the validation cohort stratified by stage.

<p>Red curves are for VAG-positive patients while blue curves are for VAG-negative patients. VAG-positive patients were defined as those having a risk score greater than the group median. <i>P</i>-values were calculated by log-rank tests for the differences in survival between VAG-positive and -negative groups.</p

Cox proportional hazards regression of survival by VAG status in breast, colon, and lung cancers.

<p>Cox proportional hazards regression of survival by VAG status in breast, colon, and lung cancers.</p