Nuclear and cytoplasmic localization of neural stem cell microRNAs

Abstract

Although generally regarded as functional in the cytoplasm, a number of microRNAs (miRNAs) have been found in the nucleus, possibly with a role in gene regulation. Here we report that, in fact, a substantial fraction of all human miRNAs are present in the nucleus of neural stem cells. Further, subsets of these miRNAs display consistently higher standardized rank in the nucleus than in the cytoplasm of these cells, as identified with an RT-qPCR technology and confirmed by microarray analysis. Likewise, other miRNAs display higher cytoplasmic standardized ranks. Three samples were partitioned into nuclear and cytoplasmic fractions in six assays for 373 miRNAs. From the 100 most highly expressed miRNAs, standard scores of nuclear and cytoplasmic concentrations were determined. Among those, 21 miRNAs had all three nuclear standard scores higher than all three cytoplasmic scores; likewise, 31 miRNAs had consistently higher cytoplasmic scores. Random concentrations would result in only five in each set. Remarkably, if one miRNA has a high standard score in a compartment, then other miRNAs having the same 59 seeds and certain similar 39 end patterns are also highly scored in the same way. That is, in addition to the seed sequence, 39 sequence similarity criteria identify families of mature miRNAs with consistently high nuclear or cytoplasmic expression.

Cellular microRNAs up-regulate transcription via interaction with promoter TATA-box motifs

“…The nuclear/cytoplasmic ratio of miRNAs is not very consistent among different reports, which may be due to the different cell lines or tissues used for the examinations. For instance, Jeffries et al (2011) used neural stem cells, while Liao et al (2010) used human nasopharyngeal carcinoma cells to investigate the nucleus-enriched miRNAs, but their top nucleus-localized miRNAs lists have little overlap. These observations also reflect the cell-or tissue-specific preferential expression of miRNAs.…”

Human TNRC6A is an Argonaute-navigator protein for microRNA-mediated gene silencing in the nucleus

“…The components of miRISC containing miRNAs, Ago and GW182 family proteins are localized in the cytoplasm, but several instances of evidence indicating their nuclear 1 localization were reported recently (Meister et al 2004;Hwang et al 2007;Till et al 2007;Rüdel et al 2008;Politz et al 2009;Liao et al 2010;Taft et al 2010;Yoo et al 2010;Jeffries et al 2011). In addition, several reports demonstrated that miRISC components are functional in the nucleus as well.…”

Nuclear microRNAs and their unconventional role in regulating non-coding RNAs

“…Thus, according to this canonical model, miRNAs only exert their post-transcriptional regulatory roles in the cytoplasmic compartment. However, evidence has accumulated demonstrating that certain mature miRNAs can re-enter the nucleus, and, in some cases, are even more abundant in the nucleus than in the cytoplasm (Meister et al, 2004;Politz et al, 2006;Hwang et al, 2007;Foldes-Papp et al, 2009;Liao et al, 2010;Jeffries et al, 2011).…”

“…Their results indicated that miR-206 was not only distributed throughout the cytoplasm but also concentrated in the nucleus (Politz et al, 2006). Using high-throughput profi ling technology, such as microarrays and deep sequencing, researchers compared the levels of mature miRNAs in both cytoplasmic and nuclear fractions and reported that many miRNAs were located in both the cytoplasm and the nucleus (Liao et al, 2010;Jeffries et al, 2011). These results indicated that the presence of mature miRNAs in the nucleus is a general phenomenon in mammalian cells.…”

“…The fi nding that significant amounts of mature miRNAs are localized in the nucleus (Meister et al, 2004;Politz et al, 2006;Hwang et al, 2007;Foldes-Papp et al, 2009;Liao et al, 2010;Jeffries et al, 2011) raises the interesting possibility that miRNAs may function as gene regulators in the nucleus, through a mechanism other than classic post-transcriptional repression. Indeed, recent studies by our (Tang et al, 2012) and other research groups (Hansen et al, 2011;Zisoulis et al, 2012) demonstrate that some miRNAs can act in an unconventional manner to regulate the biogenesis and function of ncRNAs, including miRNAs and long ncRNAs.…”