scholarly journals The deadenylation conferred by the 3' untranslated region of a developmentally controlled mRNA in Xenopus embryos is switched to polyadenylation by deletion of a short sequence element.

1994 ◽  
Vol 14 (3) ◽  
pp. 1893-1900 ◽  
Author(s):  
P Bouvet ◽  
F Omilli ◽  
Y Arlot-Bonnemains ◽  
V Legagneux ◽  
C Roghi ◽  
...  
Keyword(s):  
Untranslated Region ◽  
Mature Oocyte ◽  
Sequence Information ◽  
Cellular Mechanisms ◽  
Sequence Element ◽  
Cis Acting ◽  
Xenopus Embryos ◽  
Chimeric Rnas ◽  
Chimeric Transcripts ◽  
Developmental Switch

The maternal Xenopus Eg mRNAs are adenylated and translated in the mature oocyte and then, after fertilization, are deadenylated and released from polysomes. Therefore, after fertilization, a change occurs in the cellular mechanisms that control mRNA adenylation. In the study reported here, we show that the 3' untranslated region of Eg2 mRNA contains a cis-acting element that is required for the deadenylation of chimeric RNAs after fertilization. This cis-acting element is contained within a single 17-nucleotide portion of the Eg2 mRNA. Disruption of this deadenylation element allows adenylation of the chimeric transcripts in the embryo. Therefore, this cis-acting element is part of the sequence information required for the developmental switch from adenylation to deadenylation of the maternal Eg2 mRNA in Xenopus embryos.

The deadenylation conferred by the 3' untranslated region of a developmentally controlled mRNA in Xenopus embryos is switched to polyadenylation by deletion of a short sequence element

1994 ◽  
Vol 14 (3) ◽  
pp. 1893-1900
Author(s):  
P Bouvet ◽  
F Omilli ◽  
Y Arlot-Bonnemains ◽  
V Legagneux ◽  
C Roghi ◽  
...  
Keyword(s):  
Untranslated Region ◽  
Mature Oocyte ◽  
Sequence Information ◽  
Cellular Mechanisms ◽  
Sequence Element ◽  
Cis Acting ◽  
Xenopus Embryos ◽  
Chimeric Rnas ◽  
Chimeric Transcripts ◽  
Developmental Switch

The maternal Xenopus Eg mRNAs are adenylated and translated in the mature oocyte and then, after fertilization, are deadenylated and released from polysomes. Therefore, after fertilization, a change occurs in the cellular mechanisms that control mRNA adenylation. In the study reported here, we show that the 3' untranslated region of Eg2 mRNA contains a cis-acting element that is required for the deadenylation of chimeric RNAs after fertilization. This cis-acting element is contained within a single 17-nucleotide portion of the Eg2 mRNA. Disruption of this deadenylation element allows adenylation of the chimeric transcripts in the embryo. Therefore, this cis-acting element is part of the sequence information required for the developmental switch from adenylation to deadenylation of the maternal Eg2 mRNA in Xenopus embryos.

scholarly journals Postfertilization deadenylation of mRNAs in Xenopus laevis embryos is sufficient to cause their degradation at the blastula stage.

1997 ◽  
Vol 17 (1) ◽  
pp. 209-218 ◽  
Author(s):  
Y Audic ◽  
F Omilli ◽  
H B Osborne
Keyword(s):  
Xenopus Laevis ◽  
Untranslated Region ◽  
Sequence Information ◽  
Blastula Stage ◽  
Cytoplasmic Polyadenylation ◽  
Cis Acting ◽  
Stage Of Development ◽  
Chimeric Rnas ◽  
Xenopus Laevis Embryos

Although the maternal Xenopus laevis Eg mRNAs are deadenylated after fertilization, they are not immediately degraded and they persist in the embryos as poly(A)- transcripts. The degradation of these RNAs is not detected until the blastula stage of development (6 to 7 h postfertilization). To understand the basis for this delay between deadenylation and degradation, it is necessary to identify the cis-acting element(s) required to trigger degradation in blastula stage embryos. To this end, several chimeric RNAs containing different portions of the 3' untranslated region of Eg2 mRNA were injected into two-cell X. laevis embryos. We observed that only the RNAs that contained the cis-acting elements that confer rapid deadenylation were subsequently degraded at the blastula stage. This suggested that deadenylation may be sufficient to trigger degradation. By injecting chimeric RNAs devoid of Eg sequence information, we further showed that only deadenylated RNAs were degraded in X. laevis embryos. Last, introduction of a functional cytoplasmic polyadenylation element into a poly(A)- RNA, thereby causing its polyadenylation after injection into embryos, protected the RNA from degradation. Hence, in X. laevis embryos, the postfertilization deadenylation of maternal Eg mRNAs is sufficient to cause the degradation of an mRNA, which, however, only becomes apparent at the blastula stage. Possible causes for this delay between deadenylation and degradation are discussed in the light of these results.

scholarly journals The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1473
Author(s):  
Junxing Zhao ◽  
Jianming Qiu ◽  
Sadikshya Aryal ◽  
Jennifer L. Hackett ◽  
Jingxin Wang
Keyword(s):  
Untranslated Region ◽  
Dimethyl Sulfate ◽  
Nonstructural Proteins ◽  
Stem Loop ◽  
Cis Acting ◽  
Chemical Probing ◽  
Mutational Profiling ◽  
Genome Transcription ◽  
Polymerase Binding ◽  
Transcription And Replication

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. The 3′ untranslated region (UTR) of this β-CoV contains essential cis-acting RNA elements for the viral genome transcription and replication. These elements include an equilibrium between an extended bulged stem-loop (BSL) and a pseudoknot. The existence of such an equilibrium is supported by reverse genetic studies and phylogenetic covariation analysis and is further proposed as a molecular switch essential for the control of the viral RNA polymerase binding. Here, we report the SARS-CoV-2 3′ UTR structures in cells that transcribe the viral UTRs harbored in a minigene plasmid and isolated infectious virions using a chemical probing technique, namely dimethyl sulfate (DMS)-mutational profiling with sequencing (MaPseq). Interestingly, the putative pseudoknotted conformation was not observed, indicating that its abundance in our systems is low in the absence of the viral nonstructural proteins (nsps). Similarly, our results also suggest that another functional cis-acting element, the three-helix junction, cannot stably form. The overall architectures of the viral 3′ UTRs in the infectious virions and the minigene-transfected cells are almost identical.

scholarly journals Dendritic Transport and Localization of Protein Kinase Mζ mRNA

2004 ◽  
Vol 279 (50) ◽  
pp. 52613-52622 ◽  
Author(s):  
Ilham Aliagaevich Muslimov ◽  
Volker Nimmrich ◽  
Alejandro Ivan Hernandez ◽  
Andrew Tcherepanov ◽  
Todd Charlton Sacktor ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Translational Control ◽  
Untranslated Region ◽  
Functional Integration ◽  
Long Term Potentiation ◽  
Memory Storage ◽  
Reading Frame ◽  
Cis Acting ◽  
Translational Repressor ◽  
Protein Kinase Mζ

Protein kinase Mζ (PKMζ) is an atypical protein kinase C isoform that has been implicated in the protein synthesis-dependent maintenance of long term potentiation and memory storage in the brain. Synapse-associated kinases are uniquely positioned to promote enduring consolidation of structural and functional modifications at the synapse, provided that kinase mRNA is available on site for local input-specific translation. We now report that the mRNA encoding PKMζ is rapidly transported and specifically localized to synaptodendritic neuronal domains. Transport of PKMζ mRNA is specified by two cis-acting dendritic targeting elements (Mζ DTEs). Mζ DTE1, located at the interface of the 5′-untranslated region and the open reading frame, directs somato-dendritic export of the mRNA. Mζ DTE2, in contrast, is located in the 3′-untranslated region and is required for delivery of the mRNA to distal dendritic segments. Colocalization with translational repressor BC1 RNA in hippocampal dendrites suggests that PKMζ mRNA may be subject to translational control in local domains. Dendritic localization of PKMζ mRNA provides a molecular basis for the functional integration of synaptic signal transduction and translational control pathways.

cis-acting elements involved in the alternative translation initiation process of human basic fibroblast growth factor mRNA

1992 ◽  
Vol 12 (10) ◽  
pp. 4796-4805
Author(s):  
A C Prats ◽  
S Vagner ◽  
H Prats ◽  
F Amalric
Keyword(s):  
Growth Factor ◽  
Fibroblast Growth Factor ◽  
Basic Fibroblast Growth Factor ◽  
Untranslated Region ◽  
Specific Effect ◽  
Regulatory Elements ◽  
Fibroblast Growth ◽  
Cis Acting ◽  
Initiation Of Translation ◽  
Alternative Translation

Four forms of basic fibroblast growth factor (bFGF) are synthesized from the same mRNA, resulting from alternative initiations of translation at three CUG start codons and one AUG start codon. The CUG- and AUG-initiated forms have distinct intracellular localizations and can modify cell phenotypes differently, indicating that control of the alternative expression of the different forms of bFGF has an important impact on the cell. In this study, we investigated the roles of the mRNA 5' untranslated region and the alternatively translated region located between the CUG and AUG codons in the regulation of alternative translation of the different forms of bFGF. Deletions and site-directed mutagenesis were carried out in bFGF mRNA leader, and translation was studied in vitro and in vivo. The results enabled us to identify five cis-acting RNA elements (two in the 5' untranslated region and three in the alternatively translated region) involved in the regulation of either global or alternative initiation of translation. Each of these elements had a specific effect on the level of synthesis of the different forms of bFGF. Furthermore, we showed that the 5' untranslated region regulatory elements had different effects on bFGF translation, depending on the translation system used. These results suggest that bFGF translation is modulated by cis-acting elements corresponding to secondary or tertiary RNA structures, which could be the targets of cell-specific trans-acting factors.

Identification of a signal transduction response sequence element necessary for induction of a Dictyostelium discoideum gene by extracellular cyclic AMP

1989 ◽  
Vol 9 (11) ◽  
pp. 4660-4669
Author(s):  
J Pavlovic ◽  
B Haribabu ◽  
R P Dottin
Keyword(s):  
Signal Transduction ◽  
Cyclic Amp ◽  
Dictyostelium Discoideum ◽  
Regulatory Element ◽  
Response Sequence ◽  
Base Pairs ◽  
Camp Response Element ◽  
Sequence Element ◽  
Cis Acting ◽  
Gene Coding

The signal transduction pathways that lead to gene induction are being intensively investigated in Dictyostelium discoideum. We have identified by deletion and transformation analysis a sequence element necessary for induction of a gene coding for uridine diphosphoglucose pyrophosphorylase (UDPGP1) of D. discoideum in response to extracellular cyclic AMP (cAMP). This regulatory element is located 380 base pairs upstream of the transcription start site and contains a G+C-rich partially palindromic sequence. It is not required for transcription per se but is required for induction of the gene in response to the stimulus of extracellular cAMP. The cAMP response sequence is also required for induction of the gene during normal development. A second A+T-rich cis-acting region located immediately downstream of the cAMP response sequence appears to be essential for the basal level of expression of the UDPGP1 gene. The position of the cAMP response element coincides with a DNase I-hypersensitive site that is observed when the UDPGP1 gene is actively transcribed.

scholarly journals Control of yeast gene expression by transposable elements: maximum expression requires a functional Ty activator sequence and a defective Ty promoter.

1988 ◽  
Vol 8 (10) ◽  
pp. 4009-4017 ◽  
Author(s):  
L R Coney ◽  
G S Roeder
Keyword(s):  
Gene Expression ◽  
Adjacent Gene ◽  
Multiple Sequence ◽  
Sequence Element ◽  
Cis Acting ◽  
Ty Elements ◽  
The Relationship ◽  
Maximum Expression ◽  
Modest Effect

Integration of a transposable element adjacent to a gene frequently results in an alteration in expression of the nearby gene. The purpose of our experiments was to identify cis-acting sequences within a yeast transposon (Ty) that are important for expression of the adjacent gene. The role of these sequences in Ty transcription was also analyzed in order to examine the relationship between Ty and adjacent gene expression. Three naturally occurring Ty elements located at the HIS4 locus were examined. These Ty elements differed by multiple sequence changes and had different effects on HIS4 expression. To determine which sequences were important to Ty and HIS4 expression, Ty::lacZ and Ty::HIS4::lacZ fusion genes were constructed and analyzed. Results of these experiments indicated that a sequence element is present in the Ty epsilon region that is necessary for HIS4 expression but which has only a modest effect on Ty transcription. Additionally, a mutation in the Ty promoter region decreased Ty transcription and increased HIS4 expression. The opposite effects of this mutation on Ty and adjacent gene expression were probably caused by promoter competition.

scholarly journals A presumptive helicase (MOT1 gene product) affects gene expression and is required for viability in the yeast Saccharomyces cerevisiae.

1992 ◽  
Vol 12 (4) ◽  
pp. 1879-1892 ◽  
Author(s):  
J L Davis ◽  
R Kunisawa ◽  
J Thorner
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Product ◽  
Essential Gene ◽  
Single Gene ◽  
Temperature Sensitive ◽  
Yeast Saccharomyces Cerevisiae ◽  
Sequence Element ◽  
Cis Acting ◽  
Upstream Activating Sequence ◽  
Identical Manner

Exposure of a haploid yeast cell to mating pheromone induces transcription of a set of genes. Induction is mediated through a cis-acting DNA sequence found upstream of all pheromone-responsive genes. Although the STE12 gene product binds specifically to this sequence element and is required for maximum levels of both basal and induced transcription, not all pheromone-responsive genes are regulated in an identical manner. To investigate whether additional factors may play a role in transcription of these genes, a genetic screen was used to identify mutants able to express pheromone-responsive genes constitutively in the absence of Ste12. In this way, we identified a recessive, single gene mutation (mot1, for modifier of transcription) which increases the basal level of expression of several, but not all, pheromone-responsive genes. The mot1-1 allele also relaxes the requirement for at least one other class of upstream activating sequence and enhances the expression of another gene not previously thought to be involved in the mating pathway. Cells carrying mot1-1 grow slowly at 30 degrees C and are inviable at 38 degrees C. The MOT1 gene was cloned by complementation of this temperature-sensitive lethality. Construction of a null allele confirmed that MOT1 is an essential gene. MOT1 residues on chromosome XVI and encodes a large protein of 1,867 amino acids which contains all seven of the conserved domains found in known and putative helicases. The product of MOT1 is strikingly homologous to the Saccharomyces cerevisiae SNF2/SW12 and RAD54 gene products over the entire helicase region.

Temporal regulation of the Xenopus FGF receptor in development: a translation inhibitory element in the 3′ untranslated region

Development ◽  
1995 ◽  
Vol 121 (6) ◽  
pp. 1775-1785 ◽  
Author(s):  
E.P. Robbie ◽  
M. Peterson ◽  
E. Amaya ◽  
T.J. Musci
Keyword(s):  
Protein Interactions ◽  
Translational Control ◽  
Untranslated Region ◽  
Rna Stability ◽  
Immature Oocyte ◽  
Translational Repression ◽  
Meiotic Maturation ◽  
Fgf Receptor ◽  
Cis Acting ◽  
Maternal Mrna

Early frog embryogenesis depends on a maternal pool of mRNA to execute critical intercellular signalling events. FGF receptor-1, which is required for normal development, is stored as a stable, untranslated maternal mRNA transcript in the fully grown immature oocyte, but is translationally activated at meiotic maturation. We have identified a short cis-acting element in the FGF receptor 3′ untranslated region that inhibits translation of synthetic mRNA. This inhibitory element is sufficient to inhibit translation of heterologous reporter mRNA in the immature oocyte without changing RNA stability. Deletion of the poly(A) tract or polyadenylation signal sequences does not affect translational inhibition by this element. At meiotic maturation, we observe the reversal of translational repression mediated by the inhibitory element, mimicking that seen with endogenous maternal FGF receptor mRNA at meiosis. In addition, the activation of synthetic transcripts at maturation does not appear to require poly(A) lengthening. We also show that an oocyte cytoplasmic protein specifically binds the 3′ inhibitory element, suggesting that translational repression of Xenopus FGF receptor-1 maternal mRNA in the oocytes is mediated by RNA-protein interactions. These data describe a mechanism of translational control that appears to be independent of poly(A) changes.

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