Cell density regulates turnover of microRNAs

Mature microRNAs (miRNAs) are stabilized in growth-retarded mammalian cells owing to increased sequestration with poly ribosomes (polysome) which results in increased levels of functionally inactive miRNPs. Polysomal arrest also leads to reduced export of these miRNAs via exosomes thereby restricting turnover of these regulatory molecules.

HFSP Career Development Award holder Suvendra Bhattacharyya and colleagues
authored on Tue, 19 May 2015

miRNAs are tiny post-transcriptional regulators of gene expression in metazoan cells. These 20-22 nucleotide long RNAs form complexes with AGO proteins (miRNPs) and by imperfect base pairing with the 3’UTR of target messenger RNAs induce translation repression followed by degradation of the targeted messages.  Steady state levels of mature miRNAs in metazoans are controlled by their biogenesis and turnover. Regulated turnover of these regulatory RNAs is crucial to optimize cellular response to external stimuli.

With increasing cell density in monolayer culture, we documented an increase in mature miRNA levels in human cells due to stabilization of its mature form. However, the increased pool of miRNPs was functionally incompetent to induce translation repression of its target messages. Analysis of subcellular distribution of the miRNPs resolved the apparent discrepancy between the miRNP levels and activity in cells grown to high density. miRNPs associated with target mRNAs were found to be predominantly polysomal in distribution in high density cells. Therefore, it is rational to conclude that sequestration with polysomes results in loss of activity of miRNPs in cells cultured to high density. Boosting translation of polysome associated mRNAs in an in vitro system restored miRNA activity confirming that retention of miRNPs with polysomes restricts its recruitment to new target mRNAs contributing to the apparent loss of activity.

Extracellular miRNA has lately received a lot of attention due to its potential usage as easy to detect biomarkers for several diseases. Exosomes form one such vesicle for extracellular content of RNA which are derived from the multi vesicular bodies inside the cell. Our experiments indicated that with an increase of cellular density, the net miRNA export into exosomes was curtailed without affecting the biogenesis of exosomes per se. This illustrates that miRNA export is a regulated process which is possibly relevant in the cell-cell communication mechanisms.  

In a nutshell, our study showed that the cell to cell contact influences miRNA-mediated gene regulation pathways by influencing cellular miRNA content. It also highlights how differential distribution of miRNA within the cell can be an effective tool to control functioning of key biomolecules like miRNAs.


Polysome arrest restricts miRNA turnover by preventing exosomal export of miRNA in growth-retarded mammalian cells. Ghosh S, Bose M, Ray A, Bhattacharyya SN. (2015) Molecular Biololgy of the Cell. 26:1072-83.

Pubmed link