In Vivo Regulation by Estradiol of the Messenger RNAs Encoding LH and FSH Subunits and the Secretion of Gonadotropins

DEGRADATION OF MESSENGER RNA IN MAMMALIAN CELLS

Acta Endocrinologica ◽

10.1530/acta.0.071s369 ◽

1972 ◽

Vol 71 (2_Suppla) ◽

pp. S369-S380 ◽

Cited By ~ 7

Author(s):

Francis T. Kenney ◽

Kai-Lin Lee ◽

Charles D. Stiles

Keyword(s):

Messenger Rna ◽

Mammalian Cells ◽

Messenger Rnas ◽

Tyrosine Transaminase

ABSTRACT Analyses of the response of hydrocortisone-induced tyrosine transaminase in cultured H-35 cells to inhibitors of translation (cycloheximide, puromycin) suggest: (1) that bound ribosomes stabilize messenger RNA in vivo; (2) that messenger is degraded at a rate determined by the rate of translation. Since specific messenger RNAs of mammalian cells are degraded at quite different rates, there may be extensive heterogeneity either in the rate at which ribosomes traverse different messengers or in the number of ribosomes which translate specific messenger RNAs.

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Transcriptome Changes in Mycoplasma hyopneumoniae during Infection

Infection and Immunity ◽

10.1128/iai.01291-07 ◽

2007 ◽

Vol 76 (2) ◽

pp. 658-663 ◽

Cited By ~ 34

Author(s):

Melissa L. Madsen ◽

Supraja Puttamreddy ◽

Eileen L. Thacker ◽

Michael D. Carruthers ◽

F. Chris Minion

Keyword(s):

Elongation Factor ◽

Mycoplasma Hyopneumoniae ◽

Trna Synthetase ◽

Messenger Rnas ◽

Reading Frame ◽

Polymerase Beta ◽

Glycerol Transport ◽

Transcriptional Changes ◽

Bronchial Alveolar Lavage

ABSTRACT Mycoplasma hyopneumoniae causes swine pneumonia and contributes significantly to the porcine respiratory disease complex. The mechanisms of pathogenesis are difficult to address, since there is a lack of genetic tools, but microarrays are available and can be used to study transcriptional changes that occur during disease as a way to identify important virulence-related genes. Mycoplasmas were collected from bronchial alveolar lavage samples and compared to broth-grown cells using microarrays. Bronchial alveolar lavage was performed on pigs 28 days postinfection, and mycoplasmas were isolated by differential centrifugation. Mycoplasma RNA-enriched preparations were then obtained from total RNA by subtracting eucaryotic ribosomal and messenger RNAs. Labeled cDNAs were generated with mycoplasma open reading frame-specific primers. Nine biological replicates were analyzed. During lung infection, our analysis indicated that 79 M. hyopneumoniae genes were differentially expressed (P < 0.01), at a false-discovery rate of <2.7%. Of the down-regulated genes, 28 of 46 (61%) lacked an assigned function, in comparison to 21 of 33 (63%) of up-regulated genes. Four down-regulated genes and two up-regulated genes encoded putative lipoproteins. secA (mhp295) (P = 0.003) and two glycerol transport permease genes (potA [mhp380; P = 0.006] and ugpA [mhp381; P = 0.003]) were up-regulated in vivo. Elongation factor EF-G (fusA [mhp083]) (P = 0.002), RNA polymerase beta chain (rpoC [mhp635]) (P = 0.003), adenylate kinase (adk [mhp208]) (P = 0.001), prolyl aminoacyl tRNA synthetase (proS [mhp397]) (P = 0.009), and cysteinyl-tRNA synthetase (cysS [mhp661]) (P < 0.001) were down-regulated in vivo.

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Genetic identification of the functional surface for RNA binding by Escherichia coli ProQ

Nucleic Acids Research ◽

10.1093/nar/gkaa144 ◽

2020 ◽

Vol 48 (8) ◽

pp. 4507-4520 ◽

Cited By ~ 6

Author(s):

Smriti Pandey ◽

Chandra M Gravel ◽

Oliver M Stockert ◽

Clara D Wang ◽

Courtney L Hegner ◽

...

Keyword(s):

Escherichia Coli ◽

Molecular Mechanisms ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Site Directed Mutagenesis ◽

Genetic Identification ◽

Messenger Rnas ◽

Functional Surface

Abstract The FinO-domain-protein ProQ is an RNA-binding protein that has been known to play a role in osmoregulation in proteobacteria. Recently, ProQ has been shown to act as a global RNA-binding protein in Salmonella and Escherichia coli, binding to dozens of small RNAs (sRNAs) and messenger RNAs (mRNAs) to regulate mRNA-expression levels through interactions with both 5′ and 3′ untranslated regions (UTRs). Despite excitement around ProQ as a novel global RNA-binding protein, and its potential to serve as a matchmaking RNA chaperone, significant gaps remain in our understanding of the molecular mechanisms ProQ uses to interact with RNA. In order to apply the tools of molecular genetics to this question, we have adapted a bacterial three-hybrid (B3H) assay to detect ProQ’s interactions with target RNAs. Using domain truncations, site-directed mutagenesis and an unbiased forward genetic screen, we have identified a group of highly conserved residues on ProQ’s NTD as the primary face for in vivo recognition of two RNAs, and propose that the NTD structure serves as an electrostatic scaffold to recognize the shape of an RNA duplex.

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Significantly Improved Recovery of Recombinant Sonchus Yellow Net Rhabdovirus by Expressing the Negative-Strand Genomic RNA

Viruses ◽

10.3390/v12121459 ◽

2020 ◽

Vol 12 (12) ◽

pp. 1459

Author(s):

Xiaonan Ma ◽

Zhenghe Li

Keyword(s):

Matrix Protein ◽

Plant Viruses ◽

Biologically Active ◽

Messenger Rnas ◽

Genomic Rna ◽

Genomic Rnas ◽

Double Stranded Rna ◽

Core Proteins ◽

Negative Sense

Generation of recombinant negative-stranded RNA viruses (NSVs) from plasmids involves in vivo reconstitution of biologically active nucleocapsids and faces a unique antisense problem where the negative-sense viral genomic RNAs can hybridize to viral messenger RNAs. To overcome this problem, a positive-sense RNA approach has been devised through expression of viral antigenomic (ag)RNA and core proteins for assembly of antigenomic nucleocapsids. Although this detour strategy works for many NSVs, the process is still inefficient. Using Sonchus yellow net rhabdovirus (SYNV) as a model; here, we develop a negative-sense genomic RNA-based approach that increased rescue efficiency by two orders of magnitude compared to the conventional agRNA approach. The system relied on suppression of double-stranded RNA induced antiviral responses by co-expression of plant viruses-encoded RNA silencing suppressors or animal viruses-encoded double-stranded RNA antagonists. With the improved approach, we were able to recover a highly attenuated SYNV mutant with a deletion in the matrix protein gene which otherwise could not be rescued via the agRNA approach. Reverse genetics analyses of the generated mutant virus provided insights into SYNV virion assembly and morphogenesis. This approach may potentially be applicable to other NSVs of plants or animals.

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In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs

Nucleic Acids Research ◽

10.1093/nar/gkz318 ◽

2019 ◽

Vol 47 (13) ◽

pp. 7003-7017 ◽

Cited By ~ 15

Author(s):

Lisa Marie Simon ◽

Edoardo Morandi ◽

Anna Luganini ◽

Giorgio Gribaudo ◽

Luis Martinez-Sobrido ◽

...

Keyword(s):

Secondary Structure ◽

Influenza A ◽

Host Cells ◽

Messenger Rnas ◽

Infected Cells ◽

In Vivo Analysis ◽

First Time ◽

Negative Sense

AbstractThe influenza A virus (IAV) is a continuous health threat to humans as well as animals due to its recurring epidemics and pandemics. The IAV genome is segmented and the eight negative-sense viral RNAs (vRNAs) are transcribed into positive sense complementary RNAs (cRNAs) and viral messenger RNAs (mRNAs) inside infected host cells. A role for the secondary structure of IAV mRNAs has been hypothesized and debated for many years, but knowledge on the structure mRNAs adopt in vivo is currently missing. Here we solve, for the first time, the in vivo secondary structure of IAV mRNAs in living infected cells. We demonstrate that, compared to the in vitro refolded structure, in vivo IAV mRNAs are less structured but exhibit specific locally stable elements. Moreover, we show that the targeted disruption of these high-confidence structured domains results in an extraordinary attenuation of IAV replicative capacity. Collectively, our data provide the first comprehensive map of the in vivo structural landscape of IAV mRNAs, hence providing the means for the development of new RNA-targeted antivirals.

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The TWIST1-centered competing endogenous RNA network promotes proliferation, invasion, and migration of lung adenocarcinoma

Oncogenesis ◽

10.1038/s41389-019-0167-6 ◽

2019 ◽

Vol 8 (11) ◽

Cited By ~ 4

Author(s):

Wenjie Xia ◽

Qixing Mao ◽

Bing Chen ◽

Lin Wang ◽

Weidong Ma ◽

...

Keyword(s):

Lung Adenocarcinoma ◽

Migration And Invasion ◽

Circular Rnas ◽

Messenger Rnas ◽

Competing Endogenous Rna ◽

Invasion And Migration ◽

Non Coding Rnas ◽

And Migration

Abstract The proposed competing endogenous RNA (ceRNA) mechanism suggested that diverse RNA species, including protein-coding messenger RNAs and non-coding RNAs such as long non-coding RNAs, pseudogenes and circular RNAs could communicate with each other by competing for binding to shared microRNAs. The ceRNA network (ceRNET) is involved in tumor progression and has become a hot research topic in recent years. To date, more attention has been paid to the role of non-coding RNAs in ceRNA crosstalk. However, coding transcripts are more abundant and powerful than non-coding RNAs and make up the majority of miRNA targets. In this study, we constructed a mRNA-mRNA related ceRNET of lung adenocarcinoma (LUAD) and identified the highlighted TWIST1-centered ceRNET, which recruits SLC12A5 and ZFHX4 as its ceRNAs. We found that TWIST1/SLC12A5/ZFHX4 are all upregulated in LUAD and are associated with poorer prognosis. SLC12A5 and ZFHX4 facilitated proliferation, migration, and invasion in vivo and in vitro, and their effects were reversed by miR-194–3p and miR-514a-3p, respectively. We further verified that SLC12A5 and ZFHX4 affected the function of TWIST1 by acting as ceRNAs. In summary, we constructed a mRNA-mRNA related ceRNET for LUAD and highlighted the well-known oncogene TWIST1. Then we verified that SLC12A5 and ZFHX4 exert their oncogenic function by regulating TWIST1 expression through a ceRNA mechanism.

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Intronic MicroRNA (miRNA)

Journal of Biomedicine and Biotechnology ◽

10.1155/jbb/2006/26818 ◽

2006 ◽

Vol 2006 ◽

pp. 1-13 ◽

Cited By ~ 65

Author(s):

Shi-Lung Lin ◽

Joseph D. Miller ◽

Shao-Yao Ying

Keyword(s):

Rna Interference ◽

Gene Silencing ◽

Regulatory System ◽

Fine Tuning ◽

Messenger Rnas ◽

Noncoding Dna ◽

Protein Coding ◽

C Elegans ◽

Adult Mice

Nearly 97% of the human genome is composed of noncoding DNA, which varies from one species to another. Changes in these sequences often manifest themselves in clinical and circumstantial malfunction. Numerous genes in these non-protein-coding regions encode microRNAs, which are responsible for RNA-mediated gene silencing through RNA interference (RNAi)-like pathways. MicroRNAs (miRNAs), small single-stranded regulatory RNAs capable of interfering with intracellular messenger RNAs (mRNAs) with complete or partial complementarity, are useful for the design of new therapies against cancer polymorphisms and viral mutations. Currently, many varieties of miRNA are widely reported in plants, animals, and even microbes. Intron-derived microRNA (Id-miRNA) is a new class of miRNA derived from the processing of gene introns. The intronic miRNA requires type-II RNA polymerases (Pol-II) and spliceosomal components for their biogenesis. Several kinds of Id-miRNA have been identified inC elegans, mouse, and human cells; however, neither function nor application has been reported. Here, we show for the first time that intron-derived miRNAs are able to induce RNA interference in not only human and mouse cells, but in also zebrafish, chicken embryos, and adult mice, demonstrating the evolutionary preservation of intron-mediated gene silencing via functional miRNA in cell and in vivo. These findings suggest an intracellular miRNA-mediated gene regulatory system, fine-tuning the degradation of protein-coding messenger RNAs.

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SMG-1 Is a Phosphatidylinositol Kinase-Related Protein Kinase Required for Nonsense-Mediated mRNA Decay in Caenorhabditis elegans

Molecular and Cellular Biology ◽

10.1128/mcb.24.17.7483-7490.2004 ◽

2004 ◽

Vol 24 (17) ◽

pp. 7483-7490 ◽

Cited By ~ 73

Author(s):

Andrew Grimson ◽

Sean O'Connor ◽

Carrie Loushin Newman ◽

Philip Anderson

Keyword(s):

Protein Kinase ◽

Mammalian Cells ◽

Mrna Decay ◽

Null Alleles ◽

Dependent Manner ◽

Messenger Rnas ◽

Phosphatidylinositol Kinase ◽

Nonsense Mediated Mrna Decay

ABSTRACT Eukaryotic messenger RNAs containing premature stop codons are selectively and rapidly degraded, a phenomenon termed nonsense-mediated mRNA decay (NMD). Previous studies with both Caenohabditis elegans and mammalian cells indicate that SMG-2/human UPF1, a central regulator of NMD, is phosphorylated in an SMG-1-dependent manner. We report here that smg-1, which is required for NMD in C. elegans, encodes a protein kinase of the phosphatidylinositol kinase superfamily of protein kinases. We identify null alleles of smg-1 and demonstrate that SMG-1 kinase activity is required in vivo for NMD and in vitro for SMG-2 phosphorylation. SMG-1 and SMG-2 coimmunoprecipitate from crude extracts, and this interaction is maintained in smg-3 and smg-4 mutants, both of which are required for SMG-2 phosphorylation in vivo and in vitro. SMG-2 is located diffusely through the cytoplasm, and its location is unaltered in mutants that disrupt the cycle of SMG-2 phosphorylation. We discuss the role of SMG-2 phosphorylation in NMD.

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Mutation in the Trapα/Ssr1 Gene, Encoding Translocon-Associated Protein α, Results in Outflow Tract Morphogenetic Defects

Molecular and Cellular Biology ◽

10.1128/mcb.00913-06 ◽

2006 ◽

Vol 26 (20) ◽

pp. 7760-7771 ◽

Cited By ~ 15

Author(s):

K. Mesbah ◽

A. Camus ◽

C. Babinet ◽

J. Barra

Keyword(s):

Heart Development ◽

Proximal Part ◽

Double Outlet Right Ventricle ◽

Outflow Tract ◽

Endoplasmic Reticulum Membrane ◽

Messenger Rnas ◽

Endocardial Cushions ◽

Gene Encoding ◽

Mutant Cells

ABSTRACT Translocon-associated protein complex (TRAP) is thought to be required for efficient protein-specific translocation across the endoplasmic reticulum membrane. We created a mutation in the Trapα gene that leads to the synthesis of a truncated TRAPα protein fused to ShBle-β-galactosidase. Analysis of Trapα cDNAs reveals that among three different messenger RNAs expressed in the mouse, one of them encodes a slightly larger protein that differs in its C-terminal end. This mRNA, specific for skeletal muscle and heart, is only expressed after birth. Homozygous Trapα mutant pups die at birth, likely as a result of severe cardiac defects. Indeed, the septation of the proximal part of the outflow tract is absent, resulting in a double-outlet right ventricle. Studies of protein secretion in transfected embryonic fibroblasts reveal that the TRAP complex does not function properly in homozygous mutant cells and confirm, in vivo, the involvement of TRAP in substrate-specific translocation. Our results provide the first in vivo demonstration that a member of the TRAP complex plays a crucial role in mammalian heart development and suggest that TRAPα could be involved in translocation of factors necessary for maturation of endocardial cushions.

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