scholarly journals From life to death: microRNAs in the fine tuning of the heart

2014 ◽  
Vol 1 (1) ◽  
Author(s):  
Sayantan Nath ◽  
S I Rizvi ◽  
Munish Kumar

AbstractThe heart is one of the most important vital organs, and any malfunctioning of the heart and its blood vessels may contribute to cardiovascular disorders. Diseases of the cardiovascular system represent the most common cause of human morbidity and mortality around the globe. Thus, there is always a need for innovative new therapies and diagnostics for cardiovascular disorders. In the past decades, a plethora of tiny, endogenous, singlestranded RNA sequences called microRNAs (miRNAs) has been studied meticulously in cardiovascular development and pathophysiology, providing a new dimension to the heart’s biology. miRNAs posttranscriptional inhibit the gene expression of specific mRNA targets through Watson– Crick base pairing between the miRNA “seed region” and the 3′ untranslated regions (UTRs) of target mRNAs. Better recognized as “master switches”, miRNAs are emerging as vital regulators of mammalian cardiovascular development and disease and thus are helpful in understanding therapeutic targets and diagnostics for a variety of cardiovascular disorders. In this review, a detailed discussion of the roles of various microRNAs in cardiovascular development and pathophysiology with potential therapeutics is considered.

2014 ◽  
Vol 42 (15) ◽  
pp. 10050-10060 ◽  
Author(s):  
Hideaki Kume ◽  
Kimihiro Hino ◽  
Josephine Galipon ◽  
Kumiko Ui-Tei

Abstract Hydrolytic deamination of adenosine to inosine (A-to-I) by adenosine deaminases acting on RNA (ADARs) is a post-transcriptional modification which results in a discrepancy between genomic DNA and the transcribed RNA sequence, thus contributing to the diversity of the transcriptome. Inosine preferentially base pairs with cytidine, meaning that A-to-I modifications in the mRNA sequences may be observed as A-to-G substitutions by the protein-coding machinery. Genome-wide studies have revealed that the majority of editing events occur in non-coding RNA sequences, but little is known about their functional meaning. MiRNAs are small non-coding RNAs that regulate the expression of target mRNAs with complementarities to their seed region. Here, we confirm that A-to-I editing in the miRNA seed duplex globally reassigns their target mRNAs in vivo, and reveal that miRNA containing inosine in the seed region exhibits a different degree of silencing efficiency compared to the corresponding miRNA with guanosine at the same position. The difference in base-pairing stability, deduced by melting temperature measurements, between seed-target duplexes containing either C:G or I:C pairs may account for the observed silencing efficiency. These findings unequivocally show that C:G and I:C pairs are biologically different in terms of gene expression regulation by miRNAs.


Blood ◽  
2012 ◽  
Vol 119 (17) ◽  
pp. 4034-4046 ◽  
Author(s):  
Giuseppe Zardo ◽  
Alberto Ciolfi ◽  
Laura Vian ◽  
Linda M. Starnes ◽  
Monia Billi ◽  
...  

Abstract Epigenetic modifications regulate developmental genes involved in stem cell identity and lineage choice. NFI-A is a posttranscriptional microRNA-223 (miR-223) target directing human hematopoietic progenitor lineage decision: NFI-A induction or silencing boosts erythropoiesis or granulopoiesis, respectively. Here we show that NFI-A promoter silencing, which allows granulopoiesis, is guaranteed by epigenetic events, including the resolution of opposing chromatin “bivalent domains,” hypermethylation, recruitment of polycomb (PcG)–RNAi complexes, and miR-223 promoter targeting activity. During granulopoiesis, miR-223 localizes inside the nucleus and targets the NFI-A promoter region containing PcGs binding sites and miR-223 complementary DNA sequences, evolutionarily conserved in mammalians. Remarkably, both the integrity of the PcGs-RNAi complex and DNA sequences matching the seed region of miR-223 are required to induce NFI-A transcriptional silencing. Moreover, ectopic miR-223 expression in human myeloid progenitors causes heterochromatic repression of NFI-A gene and channels granulopoiesis, whereas its stable knockdown produces the opposite effects. Our findings indicate that, besides the regulation of translation of mRNA targets, endogenous miRs can affect gene expression at the transcriptional level, functioning in a critical interface between chromatin remodeling complexes and the genome to direct fate lineage determination of hematopoietic progenitors.


1980 ◽  
Vol 87 (1) ◽  
pp. 6-13 ◽  
Author(s):  
B A Brennessel ◽  
D K Biswas

Prolactin (PRL) gene expression in three strains of GH cells (rat pituitary tumor cells) has been quantitated by measurement of: (a) intracellular and extracellular PRL, (b) cytoplasmic translatable PRL-specific mRNA (mRNAPRL), and (c) molecular hybridization of cytoplasmic poly(A) RNA to cDNAPRL (DNA complementary to mRNAPRL). Three GH cell lines utilized in this investigation were a PRL-producing (PRL+) strain, GH4C1, a PRL nonproducing 5-bromo-deoxyuridine resistnat (PRL- BrdUrdr) strain, F1BGH12C1, and a new strain, 928-9b, derived by fusion of PRL+ cells with a nuclear monolayer of the PRL-, BrdUrdr GH cell strain. PRL production is a characteristic of 928-9b cells, but the level of PRL production (2-4 micrograms/mg protein/24 h) is much lower than that of the PRL+ strain, GH4C1 (15-25 micrograms/mg protein/24 h). Levels of cytoplasmic translatable mRNAPRL and cytoplasmic PRL-RNA sequences quantitated with a cDNAPRL probe were also much lower in 928-9b as compared to the PRL+ parent. PRL-RNA sequences could not be detected in the PRL- strain. Thyrotopin-releasing hormone (TRH) stimulates PRL synthesis about threefold and inhibit a growth hormone (GH) synthesis 72% in the PRL+ strain. TRH has no effect on the synthesis of either PRL or GH in the 928-9b strain, although TRH receptors could be detected in these cells. Stimulation of PRL synthesis in the PRL+ strain by TRH could be correlated with increases in levels of cytoplasmic translatable mRNAPRL and increases in cytoplasmic PRL-RNA sequences. These results demonstrate that the graded expression of the PRL gene at the basal level, and in response to TRH, is caused by the regulated production of specific mRNA, i.e., mRNAPRL in these three GH cell strains.


2021 ◽  
Vol 22 (18) ◽  
pp. 9980
Author(s):  
Ganesh R. Koshre ◽  
Feba Shaji ◽  
Neeraja K. Mohanan ◽  
Nimmy Mohan ◽  
Jamshaid Ali ◽  
...  

Star-PAP is a non-canonical poly(A) polymerase that selects mRNA targets for polyadenylation. Yet, genome-wide direct Star-PAP targets or the mechanism of specific mRNA recognition is still vague. Here, we employ HITS-CLIP to map the cellular Star-PAP binding landscape and the mechanism of global Star-PAP mRNA association. We show a transcriptome-wide association of Star-PAP that is diminished on Star-PAP depletion. Consistent with its role in the 3′-UTR processing, we observed a high association of Star-PAP at the 3′-UTR region. Strikingly, there is an enrichment of Star-PAP at the coding region exons (CDS) in 42% of target mRNAs. We demonstrate that Star-PAP binding de-stabilises these mRNAs indicating a new role of Star-PAP in mRNA metabolism. Comparison with earlier microarray data reveals that while UTR-associated transcripts are down-regulated, CDS-associated mRNAs are largely up-regulated on Star-PAP depletion. Strikingly, the knockdown of a Star-PAP coregulator RBM10 resulted in a global loss of Star-PAP association on target mRNAs. Consistently, RBM10 depletion compromises 3′-end processing of a set of Star-PAP target mRNAs, while regulating stability/turnover of a different set of mRNAs. Our results establish a global profile of Star-PAP mRNA association and a novel role of Star-PAP in the mRNA metabolism that requires RBM10-mRNA association in the cell.


2018 ◽  
Author(s):  
Thidathip Wongsurawat ◽  
Piroon Jenjaroenpun ◽  
Trudy M. Wassenaar ◽  
Taylor D Wadley ◽  
Visanu Wanchai ◽  
...  

AbstractSequencing of native RNA and corresponding cDNA was performed using Oxford Nanopore Technology. The % Error of Specific Bases (%ESB) was higher for native RNA than for cDNA, which enabled detection of ribonucleotide modification sites. Based on %ESB differences of the two templates, a bioinformatic tool ELIGOS was developed and applied to rRNAs of E. coli, yeast and human cells. ELIGOS captured 91%, 95%, ∼75%, respectively, of the known variety of RNA methylation sites in these rRNAs. Yeast transcriptomes from different growth conditions were also compared, which identified an association between metabolic adaptation and inferred RNA modifications. ELIGOS was further applied to human transcriptome datasets, which identified the well-known DRACH motif containing N6-methyadenine being located close to 3’-untranslated regions of mRNA. Moreover, the RNA G-quadruplex motif was uncovered by ELIGOS. In summary, we have developed an experimental method coupled with bioinformatic software to uncover native RNA modifications and secondary-structures within transcripts.


Author(s):  
Hua Jin ◽  
Daxiang Na ◽  
Reazur Rahman ◽  
Weijin Xu ◽  
Allegra Fieldsend ◽  
...  

Abstract4E-BP (eIF4E-BP) represses translation initiation by binding to the 5’cap-binding protein eIF4E and inhibiting its activity. Although 4E-BP has been shown to be important in growth control, stress response, cancer, neuronal activity and mammalian circadian rhythms, it is not understood how it preferentially represses a subset of mRNAs. We successfully used hyperTRIBE (Targets of RNA-binding proteins identified by editing) to identify in vivo 4E-BP mRNA targets in both Drosophila and mammals under conditions known to activate 4E-BP. The protein associates with specific mRNAs, and ribosome profiling data show that mTOR inhibition changes the translational efficiency of 4E-BP TRIBE targets compared to non-targets. In both systems, these targets have specific motifs and are enriched in translation-related pathways, which correlate well with the known activity of 4E-BP and suggest that it modulates the binding specificity of eIF4E and contributes to mTOR translational specificity.


2019 ◽  
Vol 40 (4) ◽  
pp. 1152-1162 ◽  
Author(s):  
Sandra Handgraaf ◽  
Jacques Philippe

AbstractSex steroid estrogens, androgens, and progesterone, produced by the gonads, which have long been considered as endocrine glands, are implicated in sexual differentiation, puberty, and reproduction. However, the impact of sex hormones goes beyond these effects through their role on energy metabolism. Indeed, sex hormones are important physiological regulators of glucose homeostasis and, in particular, of the enteroinsular axis. In this review, we describe the roles of estrogens, androgens, and progesterone on glucose homeostasis through their effects on pancreatic α- and β-cells, as well as on enteroendocrine L-cells, and their implications in hormonal biosynthesis and secretion. The analysis of their mechanisms of action with the dissection of the receptors implicated in the several protective effects could provide some new aspects of the fine-tuning of hormonal secretion under the influence of the sex. This knowledge paves the way to the understanding of transgender physiology and new potential therapeutics in the field of type 2 diabetes.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. SCI-39-SCI-39
Author(s):  
Paul F. Bray

Abstract Abstract SCI-39 Alterations in gene expression are at the heart of both megakaryocytopoiesis and interindividual variation in platelet reactivity. Over the past decade there has been an increasing awareness of the important role played by microRNAs (miRNAs) in these diverse cell biologic and physiologic processes. MiRNAs are noncoding RNAs that target complementary sequences in mRNAs, leading to mRNA degradation or inhibition of translation. More than 1000 miRNAs have been identified, which are estimated to regulate 30%-90% of all coding genes. Expression of miRNAs is cell and developmental stage specific. MiRNAs regulate hematopoietic lineage commitment, as well as B lymphopoiesis, granulopoiesis, erythropoiesis and monocytopoiesis. Recent data also demonstrate a clear role for miRNAs in megakaryocytopoiesis (Meg-poiesis). The molecular genetic basis for the transition from one stage of Meg-poiesis to another requires fine-tuning of the various control elements, and miRNAs act as “rheostats” in this process. MiRNA-150 has a strong effect on Meg-erythroid progenitor cells, inducing commitment to the Meg lineage at the expense of erythropoiesis. MiRNA-150 directly down-regulates MYB, a transcription factor important in thrombopoiesis. Over-expressed miRNA-146a knocks down CXCR4 (receptor for SDF-1), reducing Meg proliferation and maturation. MiR-146a gene expression is negatively regulated by the promyelocytic zinc finger protein, PLZF. Thus, miRNAs act as intermediaries of transcription factors that control Meg-poiesis. An increasing number of genetic diseases are being described due to mutations in miRNA genes or their mRNA targets. Deletion of miR-145 and miR-146a on 5q is sufficient to cause the 5q- phenotype; miR-125b-2 up-regulates Meg-poiesis and may be involved in megakaryoblastic leukemia. Platelets appear to be a particularly rich source of miRNAs, many of which are expressed at very high levels. Notably, platelets contain Dicer, TRBP2 and Ago2, and are capable of synthesizing miRNAs from pre-miRNAs. MiRNAs regulate Bcl-xL and Bak, raising the possibility that platelet miRNAs affect platelet lifespan. Because miRNAs are very stable, they also represent a potential biomarker, and we have found sets of miRNAs that appear to classify platelet reactivity to epinephrine. Using bioinformatic approaches, we have identified miRNA-mRNA pairs differentially expressed in platelets with differing phenotypes. This approach permits functional characterization of novel platelet mRNAs, and elucidation of a potential genetic mechanism for adjusting megakaryocyte/platelet mRNA expression. Thus, information extracted from these RNA networks continue to provide insights into systems biology of higher organisms. Disclosures: No relevant conflicts of interest to declare.


eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Vikram Agarwal ◽  
George W Bell ◽  
Jin-Wu Nam ◽  
David P Bartel

MicroRNA targets are often recognized through pairing between the miRNA seed region and complementary sites within target mRNAs, but not all of these canonical sites are equally effective, and both computational and in vivo UV-crosslinking approaches suggest that many mRNAs are targeted through non-canonical interactions. Here, we show that recently reported non-canonical sites do not mediate repression despite binding the miRNA, which indicates that the vast majority of functional sites are canonical. Accordingly, we developed an improved quantitative model of canonical targeting, using a compendium of experimental datasets that we pre-processed to minimize confounding biases. This model, which considers site type and another 14 features to predict the most effectively targeted mRNAs, performed significantly better than existing models and was as informative as the best high-throughput in vivo crosslinking approaches. It drives the latest version of TargetScan (v7.0; targetscan.org), thereby providing a valuable resource for placing miRNAs into gene-regulatory networks.


2018 ◽  
Vol 2018 ◽  
pp. 1-4 ◽  
Author(s):  
Sha He ◽  
Haiyan Ou ◽  
Cunyou Zhao ◽  
Jian Zhang

miRNAs are a class of noncoding RNAs important in posttranscriptional repressors and involved in the regulation of almost every biological process by base paring with target genes through sequence in their seed regions. Genetic variations in the seed regions have vital effects on gene expression, phenotypic variation, and disease susceptibility in humans. The distribution pattern of genetic variation in miRNA seed regions might be related to miRNA function and is worth paying more attention to. We here employed computational analyses to explore the clustering pattern and functional effect of SNPs in human miRNA seed regions. A total of 1879 SNPs were mapped to 1226 human miRNA seed regions. We found that miRNAs with SNPs in their seed region are significantly enriched in miRNA clusters. We also found that SNPs in clustered miRNA seed regions have a lower functional effect than have SNPs in nonclustered miRNA seed regions. Additionally, we found that clustered miRNAs with SNPs in seed regions are involved in more pathways. Overall, our results demonstrate that SNPs in clustered miRNA seed regions can take part in more intricate and complex gene-regulating networks with lower functional cost by functional complementarity. Moreover, our results also broaden current knowledge on the genetic variation in human miRNA seed regions.


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