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Subcellular Localization of Mirnas and Implications in Cellular Homeostasis

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Subcellular Localization of Mirnas and Implications in Cellular Homeostasis G C A T T A C G G C A T genes Review Subcellular Localization of miRNAs and Implications in Cellular Homeostasis Minwen Jie 1,2,† , Tong Feng 1,3,†, Wei Huang 4, Moran Zhang 5 , Yuliang Feng 6,*,‡, Hao Jiang 1,* and Zhili Wen 5,* 1 Laboratory for Aging and Cancer Research, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China; [email protected] (M.J.); [email protected] (T.F.) 2 Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu 610041, China 3 Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China 4 Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; [email protected] 5 Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China; [email protected] 6 Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, Headington, Oxford OX3 7LD, UK * Correspondence: [email protected] (Y.F.); [email protected] (H.J.); [email protected] (Z.W.) † These authors contributed equally. ‡ Lead Contact. Abstract: MicroRNAs (miRNAs) are thought to act as post-transcriptional regulators in the cytoplasm Citation: Jie, M.; Feng, T.; Huang, W.; by either dampening translation or stimulating degradation of target mRNAs. With the increasing Zhang, M.; Feng, Y.; Jiang, H.; Wen, Z. resolution and scope of RNA mapping, recent studies have revealed novel insights into the subcel- Subcellular Localization of miRNAs and Implications in Cellular lular localization of miRNAs. Based on miRNA subcellular localization, unconventional functions Homeostasis. Genes 2021, 12, 856. and mechanisms at the transcriptional and post-transcriptional levels have been identified. This https://doi.org/10.3390/ minireview provides an overview of the subcellular localization of miRNAs and the mechanisms by genes12060856 which they regulate transcription and cellular homeostasis in mammals, with a particular focus on the roles of phase-separated biomolecular condensates. Academic Editors: Enrique Fuentes-Mattei and Keywords: microRNA; subcellular localization; transcriptional regulation; phase separation; condensate Selvarangan Ponnazhagan Received: 24 February 2021 1. Introduction Accepted: 28 May 2021 Published: 2 June 2021 MicroRNAs (miRNAs), a class of evolutionarily conserved endogenous small noncod- ing RNAs (ncRNAs), contain approximately 20–22 nucleotides. Since their initial discovery, Publisher’s Note: MDPI stays neutral an increasing number of miRNAs have been identified in invertebrates, vertebrates, and with regard to jurisdictional claims in plant genomes [1–3], including ~2000 miRNAs in the human genome [4]. As the most published maps and institutional affil- extensively studied class of ncRNAs, miRNAs play important roles in many cellular bio- iations. logical processes, such as proliferation, differentiation, apoptosis, and stress responses [5,6]. They are key regulators and biomarkers [7–9] of human diseases, such as neurological diseases [10], cardiovascular diseases [11], cancer [12,13], and aging [14]. For example, fragile X syndrome-related miR-125b and miR-132 could modify synaptic strength and regulate synaptic structure [15]. Although miRNAs were initially discovered for their role Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. in cell fate and differentiation decisions during organismal development, they are equally This article is an open access article crucial in modulating different homeostasis, including endothelial [16], bone [17], and distributed under the terms and gut [18]. For instance, miR-876-3p regulates glucose homeostasis and insulin sensitivity by conditions of the Creative Commons targeting the adiponectin system molecules [18]. Attribution (CC BY) license (https:// MiRNA genes could either be located in intragenic regions and share transcriptional creativecommons.org/licenses/by/ regulatory units with host genes [19–21] or be found in intergenic regions of the genome 4.0/). with independent cis-regulatory elements (CREs) [19,22,23]. MiRNA biogenesis typically Genes 2021, 12, 856. https://doi.org/10.3390/genes12060856 https://www.mdpi.com/journal/genes Genes 2021, 12, 856 2 of 16 Genes 2021, 12, x FOR PEER REVIEW 2 of 18 involvesMiRNA processing genes from could primary either be miRNAlocated in transcriptsintragenic regions (pri-miRNAs) and share transcriptional to precursor miRNAs (pre-miRNAs)regulatory units and with mature host miRNAsgenes [19–21] in the or be nuclei found and in intergenic cytoplasm regions (Figure of the1). genome Most miRNAs are canonicallywith independent transcribed cis-regulatory as large elements pri-miRNAs (CREs) [19,22 with,23]. a5 MiRNA0-cap and/or biogenesis poly-A typically tail by RNA polymerasesinvolves processing II or III in from nuclei primary [24]. Pri-miRNAsmiRNA transcripts are long (pri-miRNAs) double-stranded to precursor RNAs miR- composed of anNAs apical (pre-miRNAs) loop, a stem and ofmature ~35 basemiRNAs pairs, in andthe nuclei two flankingand cytoplasm single-stranded (Figure 1). Most nucleotides miRNAs are canonically transcribed as large pri-miRNAs with a 5′-cap and/or poly-A tail (Belt and Wedge) at the basal end [25]. Then, pri-miRNAs are further cleaved into pre- by RNA polymerases II or III in nuclei [24]. Pri-miRNAs are long double-stranded RNAs miRNAscomposed by a of microprocessor an apical loop, a complexstem of ~35 containing base pairs, and the two RNase flanking III enzyme single-stranded DROSHA and RNAnucleotides binding protein(Belt and DiGeorge Wedge) at syndromethe basal end critical [25]. Then, region pri-miRNAs 8 (DGCR8) are further in the cleaved nucleus [25,26]. Duringinto thispre-miRNAs cleavage event,by a microprocessor the DGCR8 double-stranded complex containing RNA the binding RNase domainIII enzyme (dsRBD) in the apicalDROSHA half and and RNA the binding DROSHA protei dsRBDn DiGeorge in the syndrome basal half critical form region a “double-dsRBD” 8 (DGCR8) in the molecular rulernucleus for an [25,26]. ~35 base During pairs this stemcleavage region event, [25 the]. DGCR8 Moreover, double-stranded pre-miRNAs RNA with binding a stem-loop structuredomain are (dsRBD) transported in the apical from half the and nucleus the DROSHA to the cytoplasm dsRBD in the through basal half the form exportin/RanGTP a “dou- ble-dsRBD” molecular ruler for an ~35 base pairs stem region [25]. Moreover, pre-miRNAs complexwith a [ stem-loop27]. Then, structure after theare transported removal of from an the apical nucleus loop to bythe cytoplasm the RNase through III endonuclease the DICERexportin/RanGTP and trans-activation-responsive complex [27]. Then, after RNA the re bindingmoval of protein an apical (TRBP) loop by [the28 ,RNase29], pre-miRNAs III 0 are furtherendonuclease processed DICER into and a miRNA trans-activation duplex-responsive with a phosphorylated RNA binding 5 proteinend and (TRBP) hydroxylated 2 nt[28,29], 30-overhang pre-miRNAs [30]. Next,are further the processed miRNA duplexinto a miRNA is unwound duplex wi andth a thephosphorylated guide strand along with5′ Argonaute end and hydroxylated (AGO) protein 2 nt 3′-overhang form the [30]. miRNA-induced Next, the miRNA duplex silencing is unwound complex and (miRISC), bindingthe guide to the strand target along mRNAs with Argonaute to suppress (AGO gene) protein expression form the miRNA-induced [31]. silencing complex (miRISC), binding to the target mRNAs to suppress gene expression [31]. Figure 1.FigureSchematic 1. Schematic illustration illustration of canonical of canonical biogenesis biogenesis and and function function ofof miRNAs. First, First, large large pri-miRNAs pri-miRNAs are transcribed are transcribed by RNA polymerasesby RNA polymerases II or III in theII nucleusor III in andthe thennucleus converted and then into converted pre-miRNAs into pre-miRNAs after cleavage after using cleavage the DROSHA/DGCR8using the microprocessor complex. Afterwards, the exportin/RanGTP complex exported pre-miRNAs to the cytoplasm. Then, the DICER and TRBP removed the apical loop of pre-miRNAs and unwound the miRNA duplex. After the formation of miRISC, it could suppress the genes by repressing translation or promoting cleavage of target mRNA. Abbreviations: Pri-miRNAs, primary miRNA transcripts. Pre-miRNAs, precursor miRNAs. DGCR8, DiGeorge syndrome critical region 8. TRBP, trans-activation-responsive RNA binding protein. AGO, Argonaute. miRISC, miRNA-induced silencing complex. MiRNAs were initially thought to regulate gene expression in the cytoplasm [3] negatively. Most studies of the gene regulatory functions of miRNAs have focused on Genes 2021, 12, 856 3 of 16 sequence-specific mRNA degradation or 30 UTR “seed-based” translational repression at the post-transcriptional level in the cytoplasm [6]. Nowadays, accumulating data, including small RNA deep sequencing data, has clarified the subcellular location of miRNAs in the nuclei [32] and revealed various novel functions in cellular homeostasis [33]. By unconven- tional methods, miRNAs could encode small peptides, interact with splicing machinery to regulate gene transcription, and even directly activate target gene transcription [33]. Recently, a study reported that inflammatory miRNAs, including miR-146a,
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