Ribonucleic Acid Regulation Research Articles

The Role of MicroRNA, Long Non-Coding RNA and Circular RNA in the Pathogenesis of Polycystic Ovary Syndrome: A Literature Review.

Polycystic ovary syndrome (PCOS) is the most common endocrine-metabolic disease in females of reproductive age, affecting 4-20% of pre-menopausal women worldwide. MicroRNAs (miRNAs) are endogenous, single-stranded, non-coding, regulatory ribonucleic acid molecules found in eukaryotic cells. Abnormal miRNA expression has been associated with several diseases and could possibly explain their underlying pathophysiology. MiRNAs have been extensively studied for their potential diagnostic, prognostic, and therapeutic uses in many diseases, such as type 2 diabetes, obesity, cardiovascular disease, PCOS, and endometriosis. In women with PCOS, miRNAs were found to be abnormally expressed in theca cells, follicular fluid, granulosa cells, peripheral blood leukocytes, serum, and adipose tissue when compared to those without PCOS, making miRNAs a useful potential biomarker for the disease. Key pathways involved in PCOS, such as folliculogenesis, steroidogenesis, and cellular adhesion, are regulated by miRNA. This also highlights their importance as potential prognostic markers. In addition, recent evidence suggests a role for miRNAs in regulating the circadian rhythm (CR). CR is crucial for regulating reproduction through the various functions of the hypothalamic-pituitary-gonadal (HPG) axis and the ovaries. A disordered CR affects reproductive outcomes by inducing insulin resistance, oxidative stress, and systemic inflammation. Moreover, miRNAs were demonstrated to interact with lncRNA and circRNAs, which are thought to play a role in the pathogenesis of PCOS. This review discusses what is currently understood about miRNAs in PCOS, the cellular pathways involved, and their potential role as biomarkers and therapeutic targets.

N6 -methyladenosine Steers RNA Metabolism and Regulation in Cancer.

As one of the most studied ribonucleic acid (RNA) modifications in eukaryotes, N6‐methyladenosine (m6A) has been shown to play a predominant role in controlling gene expression and influence physiological and pathological processes such as oncogenesis and tumor progression. Writer and eraser proteins, acting opposite to deposit and remove m6A epigenetic marks, respectively, shape the cellular m6A landscape, while reader proteins preferentially recognize m6A modifications and mediate fate decision of the methylated RNAs, including RNA synthesis, splicing, exportation, translation, and stability. Therefore, RNA metabolism in cells is greatly influenced by these three classes of m6A regulators. Aberrant expression of m6A regulators has been widely reported in various types of cancer, leading to cancer initiation, progression, and drug resistance. The close links between m6A and cancer shed light on the potential use of m6A methylation and its regulators as prognostic biomarkers and drug targets for cancer therapy. Given the notable effects of m6A in reversing chemoresistance and enhancing immune therapy, it is a promising target for combined therapy. Herein, we summarize the recent discoveries on m6A and its regulators, emphasizing their influences on RNA metabolism, their dysregulation and impacts in diverse malignancies, and discuss the clinical implications of m6A modification in cancer.

Epigenetik Düzenlemenin Kanser Üzerine Etkileri

Epigenetics is the science of biology that studies gene expression changes, which are not caused by changes in DNA sequence, but are also inherited. The molecular basis of epigenetics is a complex phenomenon and determines when and how certain genes are activated. Cancer is characterized as a disease in which cells reproduce uncontrollably and then spread. Cancer is a multifactorial complex disease caused by the accumulation of genetic and/or epigenetic changes. Epigenetic mechanisms include DNA methylation, histone modifications, and noncoding ribonucleic acid regulation. Epigenetic mechanisms affect the tumor behavior and thus the clinical course. Being a biomarker that will determine the diagnosis, treatment and prognosis will enable its use in the diagnosis and treatment of many cancers in the future. We believe that future studies on the relationship between epigenetic mechanisms and cancer will be hope for cancer treatment.

RNA Ensembles from Solvent Accessibility Data: Application to the SAM-I Riboswitch Aptamer Domain

Riboswitches are regulatory ribonucleic acid (RNA) elements that act as ligand-dependent conformational switches that recognize their cognate ligand via a binding pocket located in their aptamer domain. In the apo form, the aptamer domain is dynamic, requiring an ensemble representation of its structure. Here, as a proof-of-concept, we used solvent accessibility information to construct a pair of dynamical ensembles of the aptamer domain of the well-studied S-adenosylmethionine (SAM) class-I riboswitch in the absence (-SAM) and presence (+SAM) of SAM. To achieve this, we first generated a large conformational library and then reweighted conformers in the library using solvent-accessible surface area (SASA) data derived from recently reported light-activated structural examination of RNA (LASER) reactivities measured in the -SAM and +SAM states of the riboswitch. The differences in the resulting -SAM and +SAM ensembles are consistent with a SAM-dependent reshaping of the free-energy landscape of the aptamer domain. Within our -SAM ensemble, we identified a "transient" state that is missing a critical long-range contact, leading us to speculate that it may be representative of a folding intermediate. Further structural analysis also revealed that the transient state harbors a hidden binding pocket that is distinct from the SAM-binding pocket and is predicted by docking calculations to selectively bind small-molecule ligands. The SASA-based method we applied to the SAM-I riboswitch aptamer domain is general and could be used to construct dynamical ensembles for other riboswitch aptamer domains and, more broadly, other classes of structured RNAs.

Differential Expression of Urinary Exosomal MicroRNAs miR-21-5p and miR-30b-5p in Individuals with Diabetic Kidney Disease

Biomarkers for the identification of diabetic kidney disease (DKD) are needed as current tests lack sensitivity for detecting early kidney damage. MicroRNAs (miRNAs) are short, non-coding regulatory ribonucleic acid (RNA) molecules commonly found in urinary exosomes differentially expressed as renal function declines. We evaluated urinary exosomal miRNA expression in persons with type 2 diabetes mellitus and DKD (T2DKD). 87 human urinary exosomal miRNAs were profiled in a discovery cohort of patients with T2DKD (n = 14) and age and gender matched controls with type 2 diabetes mellitus and normal renal function (T2DNRF; n = 15). Independent validation of differentially expressed target miRNAs was performed in a second cohort with T2DKD (n = 22) and two control groups: T2DNRF (n = 15) and controls with chronic kidney disease (CCKD) and poor renal function without diabetes (n = 18). In the discovery cohort, urinary miR-21-5p, let-7e-5p and miR-23b-3p were significantly upregulated in T2DKD compared to T2DNRF (p < 0.05). Conversely, miR-30b-5p and miR-125b-5p expression was significantly lower in T2DKD (p < 0.05). Independent validation confirmed up-regulation of miR-21-5p in the replication cohort in T2DKD (2.13-fold, p = 0.006) and in CCKD (1.73-fold, p = 0.024). In contrast, miR-30b-5p was downregulated in T2DKD (0.82-fold, p = 0.006) and in CCKD (0.66-fold, p < 0.002). This study identified differential expression of miR-21-5p and miR-30b-5p in individuals with diabetic kidney disease and poor renal function. These miRNAs represent potential biomarkers associated with the pathogenesis of renal dysfunction.

RNA-mediated pathogenic mechanisms in polyglutamine diseases and amyotrophic lateral sclerosis.

Gene transcription produces a wide variety of ribonucleic acid (RNA) species in eukaryotes. Individual types of RNA, such as messenger, structural and regulatory RNA, are known to play distinct roles in the cell. Recently, researchers have identified a large number of RNA-mediated toxicity pathways that play significant pathogenic roles in numerous human disorders. In this article, we describe various common RNA toxicity pathways, namely epigenetic gene silencing, nucleolar stress, nucleocytoplasmic transport, bi-directional gene transcription, repeat-associated non-ATG translation, RNA foci formation and cellular protein sequestration. We emphasize RNA toxicity mechanisms that involve nucleotide repeat expansion, such as those related to polyglutamine (polyQ) disorders and frontotemporal lobar degeneration-amyotrophic lateral sclerosis.

Simulated Flight, Muscle Genetics, and Inflammatory Indicators in Mice

Skeletal muscle discomfort commonly occurs during long-distance air travel. Although the effects of high altitude on muscle have been well-studied, the effects of short-term exposure to the altitude at which aircraft cabins are pressurized, 2438 m, have not. The primary aim of this study was to examine global gene expression in the gastrocnemius muscle after simulated flight. Inflammatory indicators were also assessed in the muscle. Thirty-five mice were evenly exposed to normobaria or hypobaria (2438 m) for -8-9 h. Microarray and ribonucleic acid (RNA) analyses were performed. Additionally, macrophage and neutrophil presence was examined. Fourteen genes were downregulated in females after hypobaria. These genes included those related to epithelial homeostasis, such as the keratins, and genes activated by cellular insult. In contrast, four noncoding, regulatory RNAs were upregulated in males. No difference in proinflammatory cytokine gene and messenger RNA (mRNA) expression was detected between normobaria and hypobaria. The mean number of CD68-positive leukocytes per mm2 and mean area percentage of the CD68 antigen in muscle of normobaric (NB) and hypobaric (HB) mice were 53-54 and -0.2%, respectively. Simulated flight does not activate a proinflammatory response in healthy muscle. However, epithelial and cellular defense genes may be downregulated in females, whereas regulatory RNAs may be upregulated in males.

Synergistic Effect of Auto-Activation and Small RNA Regulation on Gene Expression

Auto-activation and small ribonucleic acid (RNA)-mediated regulation are two important mechanisms in controlling gene expression. We study the synergistic effect of these two regulations on gene expression. It is found that under this combinatorial regulation, gene expression exhibits bistable behaviors at the transition regime, while each of these two regulations, if working solely, only leads to monostability. Within the stochastic framework, the base pairing strength between sRNA and mRNA plays an important role in controlling the transition time between on and off states. The noise strength of protein number in the off state approaches 1 and is smaller than that in the on state. The noise strength also depends on which parameters, the feedback strength or the synthesis rate of small RNA, are tuned in switching the gene expression on and off. Our findings may provide a new insight into gene-regulation mechanism and can be applied in synthetic biology.

Cardiac-targeted delivery of regulatory RNA molecules and genes for the treatment of heart failure.

Ribonucleic acid (RNA) in its many facets of structure and function is becoming more fully understood, and, therefore, it is possible to design and use RNAs as valuable tools in molecular biology and medicine. Understanding of the role of RNAs within the cell has changed dramatically during the past few years. Therapeutic strategies based on non-coding regulatory RNAs include RNA interference (RNAi) for the silencing of specific genes, and microRNA (miRNA) modulations to alter complex gene expression patterns. Recent progress has allowed the targeting of therapeutic RNAi to the heart for the treatment of heart failure, and we discuss current strategies in this field. Owing to the peculiar biochemical properties of small RNA molecules, the actual therapeutic translation of findings in vitro or in cell cultures is more demanding than with small molecule drugs or proteins. The critical requirement for animal studies after pre-testing of RNAi tools in vitro likewise applies for miRNA modulations, which also have complex consequences for the recipient that are dependent on stability and distribution of the RNA tools. Problems in the field that are not yet fully solved are the prediction of targets and specificity of the RNA tools as well as their tissue-specific and regulatable expression. We discuss analogies and differences between regulatory RNA therapy and classical gene therapy, since recent breakthroughs in vector technology are of importance for both. Recent years have witnessed parallel progress in the fields of gene-based and regulatory RNA-based therapies that are likely to significantly expand the cardiovascular therapeutic repertoire within the next decade.

Molecular cloning of cytochrome P4501A cDNA of medaka (Oryzias latipes) and messenger ribonucleic acid regulation by environmental pollutants.

The sequence of cytochrome P4501A (CYP1A) cDNA of medaka (Oryzias latipes) was determined, and its messenger ribonucleic acid (mRNA) regulation by beta-naphthoflavone (betaNF) was evaluated. The determined cDNA sequence contained 2,349 base pairs (bp), and the open reading frame contained a total of 1,563 bp encoding 521 predicted amino acids. The induction of CYP1A mRNA in medaka was evaluated using reverse transcription-polymerase chain reaction. The concentration-dependent induction of CYP1A mRNA in the liver was observed after exposure to betaNF at nominal concentrations of 20, 100, and 500 microg/L for 2 d. Time-dependent changes of CYP1A mRNA levels were also observed in the liver, gill, gut, and caudal fin tissues of medaka exposed to 100 microg/L of betaNF for 7 d. Our results showed that the degree of CYP1A mRNA induction in the gill, gut, and caudal fin after exposure to betaNF was relatively higher than that in the liver, possibly because of low basal levels of CYP1A mRNA in the gill, gut, and caudal fin of nonexposed fish. The induction of medaka CYP1A mRNA was also observed after exposure to an environmental sample, landfill leachate. The CYP1A mRNA inductions in the gill, gut, and caudal fin were also higher than that in the liver as shown in the betaNF-treated groups. These results show that CYP1A mRNA determination in the gill, gut, and caudal fin, which are in direct contact with the polluted water, may become a useful method for monitoring CYP1A-inducible chemicals.

Sex differences in estrogen and progesterone receptor messenger ribonucleic acid regulation in the brain of little striped whiptail lizards.

Sex differences in the regulation of steroid hormone receptors in brain areas controlling female- and male-typical sexual behavior may be important in determining sex differences in the display of these behaviors. This study examined sex differences in estrogenic effects on the relative abundance of messenger RNA for estrogen receptor (ER) and progesterone receptor (PR) in discrete brain areas of whiptail lizards, Cnemidophorus inornatus, by in situ hybridization with radiolabeled riboprobes. Gonadectomized females and males received an estradiol benzoate (EB) injection (0.5 microgram) which effectively induces receptive behavior in females; controls received vehicle alone. Sex and regional differences in estrogenic effects on ER- and PR-mRNA abundance were found. Females responded to EB treatment with increases in ER- and PR-mRNA relative abundance in the ventromedial nucleus of the hypothalamus (VMH). Males had similar relative mRNA abundances to females in gonadectomized controls, but did not exhibit increases with EB treatment. EB treatment increased ER-mRNA abundance in the dorsal hypothalamus of females, but not males. ER-mRNA decreases in the lateral septum and PR-mRNA increases in the posterior hypothalamus with hormone treatment were also found, but did not differ by sex. Neither sex nor treatment effects were definitively shown for ER- or PR-mRNA abundance in the anterior hypothalamus-preoptic area. The VMH controls female-typical receptive behavior in this species. Sex differences in the response to estrogen in this nucleus may therefore underlie sex differences in the display of receptive behavior.(ABSTRACT TRUNCATED AT 250 WORDS)

Ribonucleic acid regulation in amino acid-limited cultures of Escherichia coli grown in a chemostat.

The regulation of ribonucleic acid (RNA) synthesis was examined in cultures of bacteria whose growth was limited in the chemostat by the supply of a required amino acid. Strains possessing the relaxed (relA) mutation accumulated excess RNA (relative to protein) at low growth rates when growth was limited by arginine, histidine, or cysteine but not when limited by methionine. In contrast, stringent (relA(+)) strains maintained a constant RNA/protein ratio with decreasing growth rate regardless of the amino acid used to limit growth. The presence of excess RNA in relaxed strains was accompanied by an absence of increase in RNA production upon addition of chloramphenicol, a lag upon shift-up in growth by addition of excess of the limiting amino acid, and a decreased rate of production of beta-galactosidase upon induction. Analysis of the RNA accumulated in relaxed strains indicated it was present as transfer RNA as well as 50S and 30S ribosomal subunits. Microscope examination of the relaxed strains during histidine-, arginine-, or cysteine-limited growth in the chemostat showed them to be 10 to 20 times longer in size than the stringent strains. Also, cell density was reduced to one-tenth when the increased size was observed. An analysis of the amount of ppGpp present in all slow-growing amino acid-limited cultures (relaxed and stringent) demonstrated that only basal levels of ppGpp were made. These data are consistent with the hypothesis that when growth is limited in the chemostat by an initiation event in protein synthesis, i.e., limited methionine, RNA regulation occurs in relaxed as well as stringent strains. Also, when other amino acids are limiting in concentration during translation, errors occur in relaxed strains, resulting in misread proteins.

Ribonucleic acid regulation in premeabilized cells of Escherichia coli capable of ribonucleic acid and protein synthesis.

A cell permeabilization procedure is described that reduces viability less than 10% and does not significantly reduce the rates of ribonucleic acid and protein synthesis when appropriately supplemented. Permeabilization abolishes the normal stringent coupling of protein and ribonucleic acid synthesis.

Temperature-sensitive relaxed Phenotype in a stringent strain of Escherichia coli.

A temperature-sensitive elongation factor G (EF-G) mutation carried by a rel strain of Escherichia coli was transferred to a rel(+) strain. The recombinant (AA-10) was found to be temperature-sensitive "relaxed" for ribonucleic acid (RNA) regulation. However, when a temperature-sensitive EF-G is present in a strain temperature-sensitive for valyl-transfer RNA (tRNA) synthetase, this new strain (AA-16) is no longer temperature-sensitive "relaxed" for RNA regulation. In strain AA-10, all tRNAs remain fully charged, and in AA-16 tRNA(val) becomes completely discharged at the nonpermissive growth temperature. Also, synthesis of ppGpp is not observed in strain AA-10 at 42 C but is observed at 42 C in strain AA-16.

Characterization of mutants of Escherichia coli temperature-sensitive for ribonucleic acid regulation: an unusual phenotype associated with a phenylalanyl transfer ribonucleic acid synthetase mutant.

A mutant strain AA-522, temperature-sensitive for protein synthesis, was isolated from a stringent strain (CP-78) of Escherichia coli K-12. The mutant strain has a relaxed phenotype at the nonpermissive growth temperature. Protein synthesis stops completely at 42 C, whereas the rate of ribonucleic acid (RNA) synthesis is maintained at 20% of the 30 C rate. Sucrose-gradient centrifugation analysis of RNA-containing particles formed at 42 C indicated the presence of "relaxed particles." These particles possess 16S and 23S RNA and are precursors to normal 50S and 30S ribosomal subunits. A search for the temperature-sensitive protein responsible for the halt in protein synthesis implicated phenylalanyl transfer RNA (tRNA) synthetase. Essentially no enzyme activity is detected in vitro at 30 or 40 C. Analysis of phenylalanyl tRNA synthetase activity in revertants of strain AA-522 indicated the presence of intragenic suppressor mutations. Revertants of strain AA-522 analyzed for the relaxed response at 42 C were all stringent; strain AA-522 was stringent at 30 C. These data indicate that a single mutation in phenylalanyl tRNA synthetase is responsible for both a block in protein synthesis and the relaxed phenotype at 42 C.