scholarly journals Impact of Methods on the Measurement of mRNA Turnover

2017 ◽  
Author(s):  
Takeo Wada ◽  
Attila Becskei
Keyword(s):  
Mrna Stability ◽  
Rna Degradation ◽  
Mrna Turnover ◽  
Gene Control ◽  
Cellular Activity ◽  
Transcription Inhibition ◽  
Rna Molecules ◽  
Metabolic Labelling ◽  
Differential Stability ◽  
Made In

The turnover of the RNA molecules is determined by the rates of transcription and RNA degradation. Several methods have been developed to study mRNA turnover since the beginnings of molecular biology. Here we summarize the main methods to measure RNA half-life: transcription inhibition, gene control and metabolic labelling. These methods were used to detect the cellular activity of the mRNAs degradation machinery, including the exo-ribonuclease Xrn1 and the exosome. Less progress has been made in the study of the differential stability of mature RNAs because the different methods have often yielded inconsistent results so that an mRNA considered to be stable can be classified as unstable by another method. Recent advances in the systematic comparison of different method variants in yeast have permitted the identification of the least invasive methodologies that reflect half-lives the most faithfully, which is expected to open the way for a consistent quantitative analysis of the determinants of mRNA stability.

scholarly journals Ribozymes of the hepatitis delta virus: recent findings on their structure, mechanism of catalysis and possible applications.

2001 ◽  
Vol 48 (2) ◽  
pp. 409-418 ◽  
Author(s):  
J Ciesiolka ◽  
J Wrzesinski ◽  
M Legiewicz ◽  
B Smólska ◽  
M Dutkiewicz
Keyword(s):  
Hepatitis Delta Virus ◽  
Catalytic Properties ◽  
Rna Degradation ◽  
Base Catalysis ◽  
Rna Catalysis ◽  
X Ray ◽  
Rna Molecules ◽  
Mechanism Of Catalysis ◽  
Made In ◽  
Delta Virus

Although the delta ribozymes have been studied for more than ten years the most important information concerning their structure and mechanism of catalysis were only obtained very recently. The crystal structure of the genomic delta ribozyme turns out to be an excellent example of the extraordinary properties of RNA molecules to fold into uniquely compact structures. Details of the X-ray structure have greatly stimulated further studies on the folding of the ribozymes into functionally active molecules as well as on the mechanism of RNA catalysis. The ability of the delta ribozymes to carry out general acid-base catalysis by nucleotide side chains has been assumed in two proposed mechanisms of self-cleavage. Recently, considerable progress has been also made in characterizing the catalytic properties of trans-acting ribozyme variants that are potentially attractive tools in the strategy of directed RNA degradation.

scholarly journals Multiplexed gene control reveals rapid mRNA turnover

2017 ◽  
Vol 3 (7) ◽  
pp. e1700006 ◽  
Author(s):  
Antoine Baudrimont ◽  
Sylvia Voegeli ◽  
Eduardo Calero Viloria ◽  
Fabian Stritt ◽  
Marine Lenon ◽  
...  
Keyword(s):  
Mrna Turnover ◽  
Gene Control

Regulated and quality-control mRNA turnover pathways in eukaryotes

2010 ◽  
Vol 38 (6) ◽  
pp. 1506-1510 ◽  
Author(s):  
Boris Reznik ◽  
Jens Lykke-Andersen
Keyword(s):  
Quality Control ◽  
Rna Processing ◽  
Rna Localization ◽  
Rna Degradation ◽  
Eukaryotic Cells ◽  
Mrna Turnover ◽  
Surveillance Systems ◽  
Rna Turnover ◽  
Rna Surveillance ◽  
Multiple Levels

Gene expression can be regulated at multiple levels, including transcription, RNA processing, RNA localization, translation and, finally, RNA turnover. RNA degradation may occur at points along the processing pathway or during translation as it undergoes quality control by RNA surveillance systems. Alternatively, mRNAs may be subject to regulated degradation, often mediated by cis-encoded determinants in the mRNA sequence that, through the recruitment of trans factors, determine the fate of the mRNA. The aim of the present review is to highlight mechanisms of regulated and quality-control RNA degradation in eukaryotic cells, with an emphasis on mammals.

scholarly journals Characterizing the Effect of the Staphylococcus aureus Virulence Factor Regulator, SarA, on Log-Phase mRNA Half-Lives

2006 ◽  
Vol 188 (7) ◽  
pp. 2593-2603 ◽  
Author(s):  
Corbette Roberts ◽  
Kelsi L. Anderson ◽  
Ellen Murphy ◽  
Steven J. Projan ◽  
William Mounts ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Virulence Factor ◽  
Mrna Stability ◽  
Transcription Initiation ◽  
Target Gene ◽  
Dependent Manner ◽  
Reading Frame ◽  
Rna Molecules ◽  
Regulatory Systems ◽  
Small Stable Rna

ABSTRACT Bacterial pathogens regulate virulence factor expression at both the level of transcription initiation and mRNA processing/turnover. Within Staphylococcus aureus, virulence factor transcript synthesis is regulated by a number of two-component regulatory systems, the DNA binding protein SarA, and the SarA family of homologues. However, little is known about the factors that modulate mRNA stability or influence transcript degradation within the organism. As our entree to characterizing these processes, S. aureus GeneChips were used to simultaneously determine the mRNA half-lives of all transcripts produced during log-phase growth. It was found that the majority of log-phase transcripts (90%) have a short half-life (<5 min), whereas others are more stable, suggesting that cis- and/or trans-acting factors influence S. aureus mRNA stability. In support of this, it was found that two virulence factor transcripts, cna and spa, were stabilized in a sarA-dependent manner. These results were validated by complementation and real-time PCR and suggest that SarA may regulate target gene expression in a previously unrecognized manner by posttranscriptionally modulating mRNA turnover. Additionally, it was found that S. aureus produces a set of stable RNA molecules with no predicted open reading frame. Based on the importance of the S. aureus agr RNA molecule, RNAIII, and small stable RNA molecules within other pathogens, it is possible that these RNA molecules influence biological processes within the organism.

scholarly journals Natural Antisense Transcripts in Plants: A Review and Identification in Soybean Infected withPhakopsora pachyrhiziSuperSAGE Library

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
Suzana de Aragão Britto-Kido ◽  
José Ribamar Costa Ferreira Neto ◽  
Valesca Pandolfi ◽  
Francismar Corrêa Marcelino-Guimarães ◽  
Alexandre Lima Nepomuceno ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Mrna Stability ◽  
In Silico ◽  
Target Genes ◽  
Plant Response ◽  
Phakopsora Pachyrhizi ◽  
Antisense Transcripts ◽  
Rna Molecules ◽  
Coding Capacity ◽  
Different Levels

Natural antisense ranscripts (NAT) are RNA molecules complementary to other endogenous RNAs. They are capable of regulating the expression of target genes at different levels (transcription, mRNA stability, translation, etc.). Such a property makes them ideal for interventions in organisms' metabolism. The present study reviewed plant NAT aspects, including features, availability and genesis, conservation and distribution, coding capacity, NAT pair expression, and functions. Besides, anin silicoidentification of NATs pairs was presented, using deepSuperSAGE libraries of soybean infected or not withPhakopsora pachyrhizi. Results showed that around 1/3 of the 77,903 predictedtrans-NATs (by PlantsNATsDB database) detected had unitags mapped in both sequences of each pair. The same 1/3 of the 436 foreseencis-NATs showed unitags anchored in both sequences of the related pairs. For those unitags mapped in NAT pairs, a modulation expression was assigned as upregulated, downregulated, or constitutive, based on the statistical analysis (P<0.05). As a result, the infected treatment promoted the expression of 2,313trans-NATs pairs comprising unitags exclusively from that library (1,326 pairs had unitags only found in the mock library). To understand the regulation of these NAT pairs could be a key aspect in the ASR plant response.

Viroid-induced DNA methylation in plants

2013 ◽  
Vol 4 (6) ◽  
pp. 557-565 ◽  
Author(s):  
Athanasios Dalakouras ◽  
Elena Dadami ◽  
Michael Wassenegger
Keyword(s):  
Dna Methylation ◽  
Small Rnas ◽  
Rna Silencing ◽  
De Novo ◽  
Rna Degradation ◽  
Double Stranded Rna ◽  
Methyl Group ◽  
Rna Molecules ◽  
Cumulative Data

AbstractIn eukaryotes, DNA methylation refers to the addition of a methyl group to the fifth atom in the six-atom ring of cytosine residues. At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). RdDM was first discovered in viroid-infected plants. Viroids are pathogenic circular, non-coding, single-stranded RNA molecules. Members of the Pospiviroidae family replicate in the nucleus through double-stranded RNA intermediates, attracting the host RNA silencing machinery. The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. Here, we provide an overview of the cumulative data on the field of viroid-induced RdDM and discuss three possible scenarios concerning the mechanistic details of its establishment.

Tumor protein D52 expression is post-transcriptionally regulated by T-cell intercellular antigen (TIA) 1 and TIA-related protein via mRNA stability

2017 ◽  
Vol 474 (10) ◽  
pp. 1669-1687
Author(s):  
Hiromi Motohashi ◽  
Yoshiki Mukudai ◽  
Chihiro Ito ◽  
Kosuke Kato ◽  
Toshikazu Shimane ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
T Cell ◽  
Growth Factor ◽  
Mrna Stability ◽  
Rna Binding ◽  
Rna Degradation ◽  
Related Protein ◽  
Binding Ability ◽  
Cis Acting ◽  
Post Transcriptional Regulation

Although tumor protein D52 (TPD52) family proteins were first identified nearly 20 years ago, their molecular regulatory mechanisms remain unclear. Therefore, we investigated the post-transcriptional regulation of TPD52 family genes. An RNA immunoprecipitation (RIP) assay showed the potential binding ability of TPD52 family mRNAs to several RNA-binding proteins, and an RNA degradation assay revealed that TPD52 is subject to more prominent post-transcriptional regulation than are TPD53 and TPD54. We subsequently focused on the 3′-untranslated region (3′-UTR) of TPD52 as a cis-acting element in post-transcriptional gene regulation. Several deletion mutants of the 3′-UTR of TPD52 mRNA were constructed and ligated to the 3′-end of a reporter green fluorescence protein gene. An RNA degradation assay revealed that a minimal cis-acting region, located in the 78-280 region of the 5′-proximal region of the 3′-UTR, stabilized the reporter mRNA. Biotin pull-down and RIP assays revealed specific binding of the region to T-cell intracellular antigen 1 (TIA-1) and TIA-1-related protein (TIAR). Knockdown of TIA-1/TIAR decreased not only the expression, but also the stability of TPD52 mRNA; it also decreased the expression and stability of the reporter gene ligated to the 3′-end of the 78-280 fragment. Stimulation of transforming growth factor-β and epidermal growth factor decreased the binding ability of these factors, resulting in decreased mRNA stability. These results indicate that the 78-280 fragment and TIA-1/TIAR concordantly contribute to mRNA stability as a cis-acting element and trans-acting factor(s), respectively. Thus, we here report the specific interactions between these elements in the post-transcriptional regulation of the TPD52 gene.

Decapping the message: a beginning or an end

2006 ◽  
Vol 34 (1) ◽  
pp. 35-38 ◽  
Author(s):  
H. Liu ◽  
M. Kiledjian
Keyword(s):  
Mrna Stability ◽  
Mrna Turnover ◽  
Decapping Enzyme ◽  
Decapping Enzymes

Removal of the mRNA 5′ cap is an important step in the regulation of mRNA stability. mRNAs are degraded by at least two distinct exonucleolytic decay pathways, one from the 5′ end, and the second from the 3′ end. Two major cellular decapping enzymes have been identified, and each primarily functions in one of the two decay pathways. The Dcp2 decapping enzyme utilizes capped mRNA as substrate and hydrolyses the cap to release m7GDP (N7-methyl GDP), while a scavenger decapping enzyme, DcpS, utilizes cap dinucleotides or capped oligonucleotides as substrate and releases m7GMP (N7-methyl GMP). In this review, we will highlight the function of different decapping enzymes and their role in mRNA turnover.

scholarly journals Conceptual Advances in Control of Inflammation by the RNA-Binding Protein Tristetraprolin

2021 ◽  
Vol 12 ◽  
Author(s):  
Pavel Kovarik ◽  
Annika Bestehorn ◽  
Jeanne Fesselet
Keyword(s):  
Immune Responses ◽  
Mrna Stability ◽  
Binding Sites ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Degradation ◽  
Decay Rates ◽  
Mrna Destabilization

Regulated changes in mRNA stability are critical drivers of gene expression adaptations to immunological cues. mRNA stability is controlled mainly by RNA-binding proteins (RBPs) which can directly cleave mRNA but more often act as adaptors for the recruitment of the RNA-degradation machinery. One of the most prominent RBPs with regulatory roles in the immune system is tristetraprolin (TTP). TTP targets mainly inflammation-associated mRNAs for degradation and is indispensable for the resolution of inflammation as well as the maintenance of immune homeostasis. Recent advances in the transcriptome-wide knowledge of mRNA expression and decay rates together with TTP binding sites in the target mRNAs revealed important limitations in our understanding of molecular mechanisms of TTP action. Such orthogonal analyses lead to the discovery that TTP binding destabilizes some bound mRNAs but not others in the same cell. Moreover, comparisons of various immune cells indicated that an mRNA can be destabilized by TTP in one cell type while it remains stable in a different cell linage despite the presence of TTP. The action of TTP extends from mRNA destabilization to inhibition of translation in a subset of targets. This article will discuss these unexpected context-dependent functions and their implications for the regulation of immune responses. Attention will be also payed to new insights into the role of TTP in physiology and tissue homeostasis.

scholarly journals Computational prediction of nonenzymatic RNA degradation patterns

2017 ◽  
Vol 63 (4) ◽  
Author(s):  
Agnieszka Rybarczyk ◽  
Paulina Jackowiak ◽  
Marek Figlerowicz ◽  
Jacek Blazewicz
Keyword(s):  
Regulation Of Gene Expression ◽  
Computational Prediction ◽  
Rna Degradation ◽  
Branch And Cut ◽  
Structural Factors ◽  
Rna Molecules ◽  
Small Regulatory Rnas ◽  
Rna Fragments ◽  
Regulatory Rnas

Since the beginning of XXI century, the increasing interest in the research of ribonucleic acids has been observed in response to a surprising discovery of the role that RNA molecules play in the biological systems. It was demonstrated that they do not only take part in the protein synthesis (mRNA, rRNA, tRNA) but also are involved in the regulation of gene expression. Several classes of small regulatory RNAs have been discovered (e.g. microRNA, small interfering RNA, piwiRNA). Most of them are excised from specific double-stranded RNA precursors by enzymes that belong to the RNaseIII family (Drosha, Dicer or Dicer-like proteins). More recently, it has been shown that small regulatory RNAs are also generated as stable intermediates of RNA degradation (so called RNA fragments originating from tRNA, snRNA, snoRNA etc.). Unfortunately, the mechanisms underlying biogenesis of the RNA fragments remain unclear. It is thought that several factors may be involved in the formation of the RNA fragments. The most important are specific RNases, RNA-protein interactions and RNA structure.  In this work, we focus on RNA primary and secondary structures as factors influencing RNA stability and consequently the pattern of RNA fragmentation. Earlier, we identified major structural factors affecting non-enzymatic RNA degradation. Now based on these data we developed a new branch-and-cut algorithm that is able to predict the products of large RNA molecules hydrolysis in vitro. We also present the experimental data that verify the results generated using this algorithm.

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