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Plant and animal microRNAs: similarities and differences.

Plant and animal microRNAs (miRNAs) are evolutionarily ancient small RNAs, approximately 19-24 nucleotides in length, that are generated by cleavage from larger highly structured precursor molecules. In both plants and animals, miRNAs posttranscriptionally regulate gene expression through interactions with their target mRNAs, and these targets are often genes involved with regulating key developmental events. Despite these similarities, plant and animal miRNAs exert their control in fundamentally different ways. Generally, animal miRNAs repress gene expression by mediating translational attenuation through (multiple) miRNA-binding sites located within the 3' untranslated region of the target gene. In contrast, almost all plant miRNAs regulate their targets by directing mRNA cleavage at single sites in the coding regions. These and other differences suggest that the two systems may have originated independently, possibly as a prerequisite to the development of complex body plans.

Animals↗

miR-2116-5p functions as a tumor suppressor in lung adenocarcinoma by targeting ADAM12 and serves as a prognostic biomarker.

BACKGROUND: MicroRNAs play key roles in tumor progression. miR-2116-5p is downregulated in lung adenocarcinoma (LUAD), and this study investigated its prognostic value and functional role in the disease. MATERIALS AND METHODS: A total of 125 LUAD patients contributed tissue samples. miR-2116-5p and ADAM12 expression in tissues and cell lines were detected by RT&#x2011;qPCR. Clinicopathological correlations of miR-2116-5p were analyzed using the chi-square test. Kaplan&#x2011;Meier and Cox regression were employed to assess prognostic significance. CCK&#x2011;8, Transwell, and dual&#x2011;luciferase reporter assays were performed to investigate miR&#x2011;2116-5p function and its targeting of ADAM12. Rescue experiments validated the functional involvement of ADAM12. RESULTS: Significant downregulation of miR-2116-5p was observed in LUAD tissues and cell lines. Low expression was markedly linked to lymph node metastasis (P&#x2009;=&#x2009;0.013) and advanced TNM stage (P&#x2009;=&#x2009;0.002). Patients exhibiting reduced miR-2116-5p levels showed worse overall survival, and it was identified as an independent prognostic factor (HR&#x2009;=&#x2009;2.521, 95% CI: 1.129-5.628, P&#x2009;=&#x2009;0.020). Functional experiments showed that increasing miR-2116-5p expression suppressed LUAD cell proliferation, migration, and invasion, whereas its knockdown promoted these processes. ADAM12 was confirmed as a direct target, with expression inversely correlated in LUAD tissues (r = -0.749, P&#x2009;<&#x2009;0.001). ADAM12 overexpression effectively counteracted the ability of miR-2116-5p to suppress proliferation, migration, and invasion. CONCLUSION: miR&#x2011;2116-5p suppresses LUAD progression by targeting ADAM12, suggesting it may serve as a prognostic biomarker and therapeutic target.

Humans↗

A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain.

microRNAs (or miRNAs) are small noncoding RNAs (21 to 25 nucleotides) that are processed from longer hairpin RNA precursors and are believed to be involved in a wide range of developmental and cellular processes, by either repressing translation or triggering mRNA degradation (RNA interference). By using a computer-assisted approach, we have identified 46 potential miRNA genes located in the human imprinted 14q32 domain, 40 of which are organized as a large cluster. Although some of these clustered miRNA genes appear to be encoded by a single-copy DNA sequence, most of them are arranged in tandem arrays of closely related sequences. In the mouse, this miRNA gene cluster is conserved at the homologous distal 12 region. In vivo all the miRNAs that we have detected are expressed in the developing embryo (both in the head and in the trunk) and in the placenta, whereas in the adult their expression is mainly restricted to the brain. We also show that the miRNA genes are only expressed from the maternally inherited chromosome and that their imprinted expression is regulated by an intergenic germline-derived differentially methylated region (IG-DMR) located approximately 200 kb upstream from the miRNA cluster. The functions of these miRNAs, which seem only conserved in mammals, are discussed both in terms of epigenetic control and gene regulation during development.

Animals↗

Characterization of an abundant COL9A1 transcript in the cochlea with a novel 3' UTR: Expression studies and detection of miRNA target sequence.

EST N66408 represents one of several large unique clusters expressed in the Morton human fetal cochlear cDNA library. N66408 is 575 bp in size and initial BLAST analysis of this sequence showed no homology to any known genes or expressed sequence tags (ESTs) from other organs or tissues. Sequence of the original cochlear clone from which N66408 was derived revealed that the corresponding cDNA was about 700 bp in size, including 125 bp at its 5' end with homology to the 3' end of COL9A1 in addition to 575 bp of novel sequence. RT-PCR analysis using primers specific to COL9A1 isoforms 1 and 2 detected expression of both isoforms in human fetal cochlea. Tissue in situ hybridization using the novel 3' UTR sequence as probe showed abundant expression in spiral limbus and spiral ligament, and a moderate level of expression in the organ of Corti. dbEST analysis of ESTs specific to the 3' UTR of COL9A1 showed 19 ESTs derived from various tissues; three polyadenylation sites were identified and the majority of these ESTs were derived from overlapping polyadenylation signals at the second site (position 749-758). Comparison of the 3' UTR of human COL9A1 with its orthologs as well as with dbEST uncovered a highly conserved region around the overlapping polyadenylation signals at position 749-758 in mammals. A search of the microRNA database revealed a highly conserved target sequence for miR-9 immediately preceding the overlapping polyadenylation signals in the novel 3' UTR of COL9A1, suggesting its role in posttranscriptional regulation of COL9A1.

3' Untranslated Regions↗

Genetic regulation by non-coding RNAs.

Large scale cDNA sequencing and genome tiling array studies have shown that around 50% of genomic DNA in humans is transcribed, of which 2% is translated into proteins and the remaining 98% is non-coding RNAs (ncRNAs). There is mounting evidence that these ncRNAs play critical roles in regulating DNA structure, RNA expression, protein translation and protein functions through multiple genetic mechanisms, and thus affect normal development of organisms at all levels. Today, we know very little about the regulatory mechanisms and functions of these ncRNAs, which is clearly essential knowledge for understanding the secret of life. To promote this emerging research subject of critical importance, in this paper we review (1) ncRNAs' past and present, (2) regulatory mechanisms and their functions, (3) experimental strategies for identifying novel ncRNAs, (4) experimental strategies for investigating their functions, and (5) methodologies and examples of the application of ncRNAs.

Databases, Nucleic Acid↗

Herpes simplex virus type-1 latency inhibits dendritic growth in sympathetic neurons.

Herpes simplex virus type-1 (HSV-1) initially infects mucoepithelial tissues of the orofacial region, the eye and to a lesser extent the genitalia. Subsequently, the virus is retrogradely transported through the axons of the sensory and sympathetic neurons to their nuclei, where the virus establishes a life-long latent infection. During this latency period, the viral genome is transcriptionally silent except for a single region encoding the latency-associated transcript (LAT). LAT has been shown to affect apoptosis, but little else is known regarding its effects on neurons. To understand how HSV-1 latency might affect dendrites in sympathetic neurons, we transfected primary cultures of sympathetic neurons obtained from rat embryos, with LAT expressing plasmids. LAT inhibited initial dendritic growth and induced dendritic retraction in sympathetic neurons. Latent HSV-1 infection of cultured sympathetic neurons inhibited dendritic growth indicating that this is likely also a consequence of natural infection.

Animals↗

Herpesvirus quiescence (QIF) in neuronal cells VI: Correlative analysis demonstrates usefulness of QIF-PC12 cells to examine HSV-1 latency, reactivation and genes implicated in its regulation.

PURPOSE: To compare the usefulness of the in vitro quiescently infected (QIF)-PC12 cell model(30) with the in vivo rabbit eye model of latency for the study of herpes simplex virus (HSV) genes implicated in reactivation from latency. METHODS: HSV-1 strains 17+/pR20.5/5 and 17+/pR20.5/5/LAT, that were previously constructed by insertion of genes encoding beta-galactosidase, green fluorescent protein (GFP) or the latency associated transcript (LAT) open reading frame in the U(S)5 region,(34) were used to examine viral growth and inducible reactivation in the two models. RESULTS: 17+/pR20.5/5 exhibited diminished reactivation phenotype when compared with wild type 17+ in neuronal cells (i.e., QIF-PC12 cell model) and the rabbit eye model of latency. 17+/pR20.5/5/LAT, which contains the deregulated LAT gene, reactivated at wild type levels. Analysis of growth in neurally differentiated (ND)-PC12 cells demonstrated a low proportion of QIF cells expressed virus-encoded signals during the quiescent infection and a direct relationship between lytic viral growth in neuronal cells and reactivation phenotype. Even though 17+/pR20.5/5/LAT produced a more severe acute infection in the rabbit cornea, the different reactivation efficiency of 17+/pR20.5/5 and 17+/pR20.5/5/LAT in vivo and in vitro was not attributed to different viral genome copy number in the cells harboring cryptic genomes. CONCLUSIONS: We conclude that 1) viral growth in neuronal cells correlates with reactivation phenotype in vivo and in vitro, 2) 17+/pR20.5/5 is attenuated in viral growth and reactivation in both models, and 3) 17+/pR20.5/5/LAT demonstrates wild-type phenotype for reactivation in both models. Attenuation of 17+/pR20.5/5 could be the result of the disruption of U(S)5 or a second site mutation. If the attenuation is the result of U(S)5 disruption, a gene that provides anti-apoptotic functions,( 41,42) this attenuation is more than compensated for by the expression of the LAT ORF. Overall, the findings indicate that the QIF-PC12 cell model is useful for segregating phases of reactivation, and particularly studying the inductive events involved in reactivation of a cryptic viral genome in neurally differentiated cells.

Animals↗

Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing.

Dicer is the enzyme that cleaves double-stranded RNA (dsRNA) into 21-25-nt-long species responsible for sequence-specific RNA-induced gene silencing at the transcriptional, post-transcriptional, or translational level. We disrupted the dicer-1 (dcr-1) gene in mouse embryonic stem (ES) cells by conditional gene targeting and generated Dicer-null ES cells. These cells were viable, despite being completely defective in RNA interference (RNAi) and the generation of microRNAs (miRNAs). However, the mutant ES cells displayed severe defects in differentiation both in vitro and in vivo. Epigenetic silencing of centromeric repeat sequences and the expression of homologous small dsRNAs were markedly reduced. Re-expression of Dicer in the knockout cells rescued these phenotypes. Our data suggest that Dicer participates in multiple, fundamental biological processes in a mammalian organism, ranging from stem cell differentiation to the maintenance of centromeric heterochromatin structure and centromeric silencing.

Animals↗

Predicting diagnostic gene biomarkers associated with immune infiltration in patients with diabetes.

Diabetes is a global public health problem with various complications, which can lead to disability and mortality. This study identified potential diagnostic markers for diabetes and explored the immunometabolic mechanisms in the pathological process. The gene expression of 17 diabetes cases and 16 normal controls were obtained from the Gene Expression Omnibus (GEO) database. The "limma" package was employed for screening differentially expressed genes (DEGs). Gene functions and enriched pathways of DEGs were analyzed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Candidate key genes were screened using the least absolute shrinkage and selection operator (LASSO) regression model and support vector machine recursive feature elimination (SVM-RFE) analysis. The diagnostic effectiveness of identified markers was further verified via the receiver operating characteristic (ROC) curve. The compositional patterns of immune cell infiltration and signaling pathway enrichment associated with key genes were explored via single sample Gene Set Enrichment Analysis (ssGSEA) and GSEA analysis, respectively. Possible miRNAs interacting with key genes were predicted via miRcode database. B2M, FTL, SH3BGRL3, and SOD2 were recognized as diagnostic markers for diabetes based on LASSO regression and the support vector machine recursive feature elimination (SVM-RFE) feature selection algorithm. Analysis of immune cell infiltration demonstrated that the four key genes were related to B cells, neutrophils, macrophages, and CD8+ T cells. The diagnostic value of B2M, FTL, and SOD2 for diabetes was higher than that of SH3BGRL3 according to the ROC curve. Validation experiments indicated that the mRNA expression of B2M and FTL was increased in liver tissues of diabetic mice. B2M and FTL can act as diagnostic markers for diabetes and contribute to new understandings of the disease's molecular mechanisms.

Humans↗

Screening of biomarkers related to lung adenocarcinoma based on construction of ceRNA regulation network.

BACKGROUND: Lung adenocarcinoma (LUAD) is a common malignant tumor with a poor prognosis and limited effective therapeutic targets. The underlying molecular regulatory mechanisms driving its progression remain largely unclear. The study objectives were to build a circRNA-miRNA-mRNA ceRNA regulation network of LUAD and to identify miRNAs and mRNAs significantly related to the prognosis . METHODS: The gene expression data and GSE101684 were downloaded from the UCSC Xene and NCBI-GEO databases, respectively. The differentially expressed RNAs (DEcircRNAs, DEmiRNAs, and DEmRNAs; DERs) were obtained by the Limma package in R. Then, the differential LUAD-related genes were identified, and the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the differential LUAD-related genes were analyzed. Moreover, the circRNA-miRNA-mRNA ceRNA network of LUAD was built. The Kaplan-Meier (K-M) survival curve analysis of ceRNA network nodes was performed. In addition, the proliferation-related ceRNA network was built. RESULTS: A total of 382 DEcircRNAs, 1907 DEmRNAs and 156 DEmiRNAs were acquired. A total of 245 differential LUAD-related genes were acquired, which were significantly associated with 189 GO biological processes (BP) and 17 KEGG pathways. Moreover, the ceRNA network of LUAD was built. The K-M survival curve analysis of ceRNA network nodes revealed that a total of 2 miRNAs (hsa-miR-96-5p and hsa-miR-125b-2-3p) and 22 mRNAs (CGNL1, CTHRC1, TK1, etc) were significantly related to the prognosis. mRNAs were significantly enriched in 92 GO BPs (such as cell division, cell adhesion) and 9 KEGG pathways (such as cell cycle, HTLV-1 infection). In addition, the proliferation-related ceRNA network was built. CONCLUSION: This research built a ceRNA regulation network of LUAD and is of great significance for identifying biomarkers related to the prognosis in LUAD.

Humans↗

Viruses, microRNAs and cancer.

Viruses represent one of the main factors that cause normal cells to proliferate and to become malignant: up to 15% of all human cancers are associated with single or multiple virus infections, and several viruses have been recognized as causal agents of specific types of cancer. Viruses have evolved many strategies to prevent infected cells from becoming apoptotic and to evade the innate and adaptive immune responses of their hosts. The recent discovery that Epstein-Barr virus and other herpesviruses produce their own sets of micro (mi)RNAs brings an additional layer of complexity in this ongoing host-virus arms race and changes our initial views of the antiviral roles of RNA silencing in plants and insects. It seems that, rather than being inhibited by this process, many mammalian viruses can usurp or divert the host RNA silencing machinery to their advantage. Viral-encoded miRNAs can act both in cis, to ensure accurate expression of viral genomes, and in trans, to modify the expression of host transcripts. Here, we review the current knowledge on viral miRNAs and discuss how mammalian viruses can also perturb host miRNA expression. Those recent findings provide new insights into the role of viruses and miRNAs in cancer development.

Animals↗

Numerous microRNPs in neuronal cells containing novel microRNAs.

Spinal muscular atrophy (SMA) is a common neurodegenerative disease that is caused by deletions or loss-of-function mutations in the Survival of Motor Neuron (SMN) protein. SMN is part of a large complex that functions in the assembly/restructuring of ribonucleoprotein (RNP) complexes. We recently showed in HeLa cells that two components of the SMN complex, Gemin3 and Gemin4, together with the argonaute protein eIF2C2, also associate with microRNAs (miRNAs) as part of a novel class of RNPs termed miRNPs. Here we report on miRNPs isolated from neuronal cell lines of mouse and human, and describe 53 novel miRNAs. Several of these miRNAs are conserved in divergent organisms, including rat, zebrafish, pufferfish, and the nematode Caenorhabditis elegans. The chromosomal locations of most of the novel miRNAs were identified and indicate some phylogenetic conservation of the likely precursor structures. Interestingly the gene locus of one miRNA, miR-175, is a candidate region for two neurologic diseases: early-onset parkinsonism (Waisman syndrome) and X-linked mental retardation (MRX3). Also, several miRNAs identified as part of miRNPs in these cells appear to constitute two distinct subfamilies. These subfamilies comprise multiple copies of miRNAs on different chromosomes, suggesting an important function in the regulation of gene expression.

Animals↗

MicroRNA: fine-tunes the function of genes in zebrafish.

MicroRNAs (miRNAs), 18-25 nt single-stranded RNAs, act as regulators in fine-tuning gene function. The absence of miRNAs is not life-threatening in early embryonic development of Dicer-knockout zebrafish and mice, which may account for genetic expression of various traits as a result of miRNA complexity in higher animals during natural evolution. The Pol-II-mediated intronic miRNA is a useful tool to validate the function of computer-predicated miRNAs in zebrafish and mice.

Animals↗

The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae.

Quorum-sensing bacteria communicate with extracellular signal molecules called autoinducers. This process allows community-wide synchronization of gene expression. A screen for additional components of the Vibrio harveyi and Vibrio cholerae quorum-sensing circuits revealed the protein Hfq. Hfq mediates interactions between small, regulatory RNAs (sRNAs) and specific messenger RNA (mRNA) targets. These interactions typically alter the stability of the target transcripts. We show that Hfq mediates the destabilization of the mRNA encoding the quorum-sensing master regulators LuxR (V. harveyi) and HapR (V. cholerae), implicating an sRNA in the circuit. Using a bioinformatics approach to identify putative sRNAs, we identified four candidate sRNAs in V. cholerae. The simultaneous deletion of all four sRNAs is required to stabilize hapR mRNA. We propose that Hfq, together with these sRNAs, creates an ultrasensitive regulatory switch that controls the critical transition into the high cell density, quorum-sensing mode.

Amino Acid Sequence↗

Two alphaherpesvirus latency-associated gene products influence calcitonin gene-related peptide levels in rat trigeminal neurons.

Herpes simplex virus type-1 (HSV-1) initially infects mucoepithelial tissues of the eye and the orofacial region. Subsequently, the virus is retrogradely transported through the axons of the trigeminal sensory neurons. HSV-1 establishes a life-long latent infection in these neurons, during which the transcription of the viral genome is silent, except for the sequences encoding the latency-associated transcript (LAT). To determine if HSV-1 latency might affect calcitonin gene-related peptide (CGRP) expression in trigeminal sensory neurons, we transfected primary neuronal cultures of trigeminal ganglia from rat embryos with plasmids expressing LAT. In the presence of Bone Morphogenetic Protein-7 (BMP7), CGRP was expressed in 49% of sensory neurons. However, this percentage was reduced to 19% in neurons transfected with LAT expressing plasmids. We also found that transfection of the IE63 gene of varicella-zoster virus (VZV) reduced the percentage of trigeminal neurons containing CGRP. However, the observed effect of IE63 in contrast to that of LAT was completely reversed by treatment of cultures with MgCl2, which indicates that the effect of IE63 was due to increased release of CGRP from trigeminal neurons. We provide here the first evidence that HSV-1 LAT decreases the level of CGRP in trigeminal neurons. These effects may be important for reducing the neuroinflammatory response, thus protecting host neuronal cells during HSV-1 latency in trigeminal neurons. In contrast, increased release of CGRP in the presence of IE63 protein may contribute to the neuralgias associated with VZV infection.

Animals↗

Small RNAs just got bigger: Piwi-interacting RNAs (piRNAs) in mammalian testes.

Small RNAs constitute a large family of regulatory molecules with diverse functions in eukaryotes. Hallmarks of small RNAs are their dependence on double-stranded RNAs (dsRNA)-specific RNase III-type enzymes for biogenesis and their association with Argonaute family proteins for the silencing process. At least two classes of small RNAs have previously been described: microRNAs (miRNAs) derived from hairpin-shaped precursors and small interfering RNAs (siRNAs) generated from long dsRNAs. Recent articles reported a novel class of small RNAs that are expressed specifically and abundantly in the spermatogenic cells of mice. These RNAs are bigger (26-31 nucleotides [nt]) than most previously described small RNAs (21-23 nt) and are associated with Piwi-subclade members of the Argonaute protein family. Although the biogenesis and function of these RNAs are yet to be determined, these findings may add new dimensions in small RNA biology and germline cell biology.

Animals↗