Changes in nuclear and cytoplasmic microRNA distribution in response to hypoxic stress

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that have well-characterized roles in cytoplasmic gene regulation, where they act by binding to mRNA transcripts and inhibiting their translation (i.e. post-transcriptional gene silencing, PTGS). However, miRNAs have also been implicated in transcriptional gene regulation and alternative splicing, events that are restricted to the cell nucleus. Here we performed nuclear-cytoplasmic fractionation in a mouse endothelial cell line and characterized the localization of miRNAs in response to hypoxia using small RNA sequencing. A highly diverse population of abundant miRNA species was detected in the nucleus, of which the majority (56%) was found to be preferentially localized in one compartment or the other. Induction of hypoxia resulted in changes in miRNA levels in both nuclear and cytoplasmic compartments, with the majority of changes being restricted to one location and not the other. Notably, the classical hypoxamiR (miR-210-3p) was highly up-regulated in the nuclear compartment after hypoxic stimulus. These findings reveal a previously unappreciated level of molecular complexity in the physiological response occurring in ischemic tissue. Furthermore, widespread differential miRNA expression in the nucleus strongly suggests that these small RNAs are likely to perform extensive nuclear regulatory functions in the general case.

Nutrition in Cancer Therapy in the Elderly—An Epigenetic Connection?

“…The third main element of epigenetic regulation, non-coding RNAs, with broad two categories, short non-coding RNAs (sncRNA) and long non-coding RNAs (lncRNAs), is reported to display some disrupted functions with aging [74][75][76][77]. Mainly, micro RNAs (miRNA) and lncRNAs were studied for their age-related aspects and, in fact, the majority of miRNAs were shown to be downregulated with age [78][79][80].…”

Advances in oligonucleotide drug delivery

“…2i). Similarly, there is a growing appreciation of the importance of endogenous small RNAs in the nucleus that function as natural mediators of such transcriptional gene activation or silencing events, and may themselves constitute targets for oligonucleotide therapeutics 85,86 .…”

Deciphering miRNAs’ Action through miRNA Editing

“…There are two major consequences associated with these properties: (1) various miRNAs and other factors may compete for binding sites on a particular mRNA (e.g., on the 3 -UTR); (2) variations in the stoichiometry of targets for a specific miRNA, and localization of these targets within distinct cell compartments, can deeply affect the expected interaction between the miRNA and a particular mRNA. In this regard, miRNAs can also traffic between various intracellular compartments (e.g., nucleus, cytoplasm, stress granules and mitochondria) under stress conditions (e.g., starvation or hypoxia), thereby either modulating transcriptional/translational rates of target mRNAs within specific intracellular compartments or being secreted as paracrine factors mediating intercellular communication [4,17,[21][22][23]. In addition, expression of other endogenous competing RNAs (ceRNAs), such as pseudogenes, circular RNAs and long ncRNAs (lncRNAs), can act as "sponges" and impair specific miRNA-mRNA interactions (Figure 1d) [20].…”

“…Among those new regulatory mechanisms, the relevance of miRNA editing for their functions is highly debated, but progressions in our understanding of these mechanisms are currently restricted by technological limitations specifically related to bioinformatic analyses of high-throughput RNA-seq approaches. Convincing evidence has been provided showing that a single nucleotide change on a primary miRNA molecule can greatly influence its stability and maturation, or can alter its activity by retargeting miRNAs towards other messenger RNAs (mRNAs), as shown in the context of several cancers or cellular stresses; e.g., hypoxia or endoplasmic reticulum (ER) stress [3,4].…”