scholarly journals Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires a Bicc1-Ccr4 RNA degradation complex

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Katsura Minegishi ◽  
Benjamin Rothé ◽  
Kaoru R. Komatsu ◽  
Hiroki Ono ◽  
Yayoi Ikawa ◽  
...  
Keyword(s):  
Fluid Flow ◽  
Mouse Embryo ◽  
Untranslated Region ◽  
Mrna Decay ◽  
Rna Binding ◽  
Specific Binding ◽  
Flow Direction ◽  
Rna Degradation ◽  
Immotile Cilia ◽  
Necessary And Sufficient

AbstractMolecular left-right (L-R) asymmetry is established at the node of the mouse embryo as a result of the sensing of a leftward fluid flow by immotile cilia of perinodal crown cells and the consequent degradation of Dand5 mRNA on the left side. We here examined how the fluid flow induces Dand5 mRNA decay. We found that the first 200 nucleotides in the 3′ untranslated region (3′-UTR) of Dand5 mRNA are necessary and sufficient for the left-sided decay and to mediate the response of a 3′-UTR reporter transgene to Ca2+, the cation channel Pkd2, the RNA-binding protein Bicc1 and their regulation by the flow direction. We show that Bicc1 preferentially recognizes GACR and YGAC sequences, which can explain the specific binding to a conserved GACGUGAC motif located in the proximal Dand5 3′-UTR. The Cnot3 component of the Ccr4-Not deadenylase complex interacts with Bicc1 and is also required for Dand5 mRNA decay at the node. These results suggest that Ca2+ currents induced by leftward fluid flow stimulate Bicc1 and Ccr4-Not to mediate Dand5 mRNA degradation specifically on the left side of the node.

scholarly journals Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires Bicc1-Ccr4 RNA degradation complex

2020 ◽  
Author(s):  
Katsura Minegishi ◽  
Benjamin Rothé ◽  
Kaoru R. Komatsu ◽  
Hiroki Ono ◽  
Yayoi Ikawa ◽  
...  
Keyword(s):  
Fluid Flow ◽  
Mouse Embryo ◽  
Untranslated Region ◽  
Mrna Decay ◽  
Rna Binding ◽  
Flow Direction ◽  
Rna Degradation ◽  
Immotile Cilia ◽  
Necessary And Sufficient ◽  
Nucleotide Region

SUMMARYMolecular left-right (L-R) asymmetry is established at the node of the mouse embryo as a result of the sensing of a leftward fluid flow by immotile cilia of perinodal crown cells and the consequent degradation of Dand5 mRNA on the left side. We here examined how the fluid flow induces Dand5 mRNA decay. We found that the 3’ untranslated region (3’-UTR) of Dand5 mRNA is necessary and sufficient for the left-sided decay and is responsive to the flow direction, loss of the cation channel Pkd2, and Ca2+. The 200-nucleotide proximal-most portion of the 3’-UTR, which is conserved among mammals, is essential for the asymmetric mRNA decay and binds Bicc1, an RNA binding protein specifically expressed at the node. Bicc1 preferentially recognizes GAC and GACR sequences in RNA, and these motifs are enriched in the 200-nucleotide region of the Dand5 3’-UTR. The Cnot3 component of the Ccr4-Not deadenylase complex interacts with Bicc1 and is also required for Dand5 mRNA decay at the node. Our results thus suggest that leftward fluid flow induces binding of Bicc1 to the 3’-UTR of Dand5 mRNA in crown cells on the left side of the node, and that consequent recruitment of Ccr4-Not mediates mRNA degradation.

scholarly journals Changes in mRNA abundance drive shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Sarah Gilbertson ◽  
Joel D Federspiel ◽  
Ella Hartenian ◽  
Ileana M Cristea ◽  
Britt Glaunsinger
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Mrna Decay ◽  
Binding Proteins ◽  
Rna Binding ◽  
Nuclear Translocation ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Protein Localization ◽  
Rna Degradation

Alterations in global mRNA decay broadly impact multiple stages of gene expression, although signals that connect these processes are incompletely defined. Here, we used tandem mass tag labeling coupled with mass spectrometry to reveal that changing the mRNA decay landscape, as frequently occurs during viral infection, results in subcellular redistribution of RNA binding proteins (RBPs) in human cells. Accelerating Xrn1-dependent mRNA decay through expression of a gammaherpesviral endonuclease drove nuclear translocation of many RBPs, including poly(A) tail-associated proteins. Conversely, cells lacking Xrn1 exhibited changes in the localization or abundance of numerous factors linked to mRNA turnover. Using these data, we uncovered a new role for relocalized cytoplasmic poly(A) binding protein in repressing recruitment of TATA binding protein and RNA polymerase II to promoters. Collectively, our results show that changes in cytoplasmic mRNA decay can directly impact protein localization, providing a mechanism to connect seemingly distal stages of gene expression.

scholarly journals p53 Binds Selectively to the 5′ Untranslated Region ofcdk4, an RNA Element Necessary and Sufficient for Transforming Growth Factor β- and p53-Mediated Translational Inhibition of cdk4

2000 ◽  
Vol 20 (22) ◽  
pp. 8420-8431 ◽  
Author(s):  
Susan J. Miller ◽  
Tuangporn Suthiphongchai ◽  
Gerard P. Zambetti ◽  
Mark E. Ewen
Keyword(s):  
Growth Factor ◽  
Translational Control ◽  
Untranslated Region ◽  
Rna Binding ◽  
Transforming Growth Factor ◽  
Transforming Growth Factor Β ◽  
Wild Type ◽  
Translational Inhibition ◽  
Wild Type P53 ◽  
Necessary And Sufficient

ABSTRACT One consequence of transforming growth factor β (TGF-β) treatment is inhibition of Cdk4 synthesis, and this is dependent on p53. Here, we show that the 5′ untranslated region (UTR) of thecdk4 mRNA is both necessary and sufficient for wild-type p53-dependent TGF-β-regulated translational inhibition of cdk4. Wild-type p53 bound selectively to the 5′ UTR of the cdk4 mRNA and inhibited translation of RNAs that contain this region. RNA binding and translational control are two genetically separable functions of p53, as are specific and nonspecific RNA binding. Moreover, transactivation-defective mutants of p53 retain the ability to regulate cdk4 translation. Our findings suggest that p53 functions as a regulator of translation in response to TGF-β in vivo.

scholarly journals Notch/Her12 signalling modulates, motile/immotile cilia ratio downstream of Foxj1a in zebrafish left-right organizer

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Barbara Tavares ◽  
Raquel Jacinto ◽  
Pedro Sampaio ◽  
Sara Pestana ◽  
Andreia Pinto ◽  
...  
Keyword(s):  
Fluid Flow ◽  
Notch Signalling ◽  
Normal Fluid ◽  
Two Photon ◽  
Notch Intracellular Domain ◽  
Immotile Cilia ◽  
Flow Intensity ◽  
Dynein Arms ◽  
Motile Cilia ◽  
Necessary And Sufficient

Foxj1a is necessary and sufficient to specify motile cilia. Using transcriptional studies and slow-scan two-photon live imaging capable of identifying the number of motile and immotile cilia, we now established that the final number of motile cilia depends on Notch signalling (NS). We found that despite all left-right organizer (LRO) cells express foxj1a and the ciliary axonemes of these cells have dynein arms, some cilia remain immotile. We identified that this decision is taken early in development in the Kupffer’s Vesicle (KV) precursors the readout being her12 transcription. We demonstrate that overexpression of either her12 or Notch intracellular domain (NICD) increases the number of immotile cilia at the expense of motile cilia, and leads to an accumulation of immotile cilia at the anterior half of the KV. This disrupts the normal fluid flow intensity and pattern, with consequent impact on dand5 expression pattern and left-right (L-R) axis establishment.

scholarly journals tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector

2021 ◽  
Author(s):  
Ekaterina Semenova ◽  
Ishita Jain ◽  
Matvey Kolesnik ◽  
Leonid Minakhin ◽  
Natalia Morozova ◽  
...  
Keyword(s):  
Defense Mechanism ◽  
Specific Binding ◽  
Rna Degradation ◽  
Host Population ◽  
Bacterial Toxin ◽  
Rna Recognition ◽  
Trna Species ◽  
Necessary And Sufficient ◽  
Cell Dormancy ◽  
Target Rna

Abstract Type VI CRISPR-Cas systems are the only CRISPR variety that cleaves exclusively RNA1,2. In addition to the CRISPR RNA (crRNA)-guided, sequence-specific binding and cleavage of target RNAs, such as phage transcripts, the type VI effector, Cas13, causes collateral RNA cleavage, which induces bacterial cell dormancy, thus protecting the host population from phage spread3,4. We show here that the principal form of collateral RNA degradation elicited by Cas13a protein from Leptotrichia shahii upon target RNA recognition is the cleavage of anticodons of multiple tRNA species, primarily those with anticodons containing uridines. This tRNA cleavage is necessary and sufficient for bacterial dormancy induction by Cas13a. In addition, Cas13a activates the RNases of bacterial toxin-antitoxin modules, thus indirectly causing mRNA and rRNA cleavage, which could provide a back-up defense mechanism. The identified mode of action of Cas13a resembles that of bacterial anticodon nucleases involved in antiphage defense5, which is compatible with the hypothesis that type VI effectors evolved from an abortive infection module6,7 encompassing an anticodon nuclease.

scholarly journals A Yeast Homologue of Hsp70, Ssa1p, Regulates Turnover of the MFA2 Transcript through Its AU-Rich 3′ Untranslated Region

2003 ◽  
Vol 23 (8) ◽  
pp. 2623-2632 ◽  
Author(s):  
Radharani Duttagupta ◽  
Shobha Vasudevan ◽  
Carol J. Wilusz ◽  
Stuart W. Peltz
Keyword(s):  
Untranslated Region ◽  
Mrna Decay ◽  
Critical Role ◽  
Temperature Sensitive ◽  
Rich Region ◽  
Rapid Decay ◽  
Chaperone Protein ◽  
Eukaryotic Mrnas ◽  
Necessary And Sufficient ◽  
Dependent Mechanism

ABSTRACT Many eukaryotic mRNAs exhibit regulated decay in response to cellular signals. AU-rich elements (AREs) identified in the 3′ untranslated region (3′-UTR) of several such mRNAs play a critical role in controlling the half-lives of these transcripts. The yeast ARE-containing mRNA, MFA2, has been studied extensively and is degraded by a deadenylation-dependent mechanism. However, the trans-acting factors that promote the rapid decay of MFA2 have not been identified. Our results suggest that the chaperone protein Hsp70, encoded by the SSA family of genes, is involved in modulating MFA2 mRNA decay. MFA2 is specifically stabilized in a strain bearing a temperature-sensitive mutation in the SSA1 gene. Furthermore, an AU-rich region within the 3′-UTR of the message is both necessary and sufficient to confer this regulation. Stabilization occurs as a result of slower deadenylation in the ssa1ts strain, suggesting that Hsp70 is required for activation of the turnover pathway.

scholarly journals Role of Ca2+ transients at the node of the mouse embryo in breaking of left-right symmetry

2020 ◽  
Vol 6 (30) ◽  
pp. eaba1195 ◽  
Author(s):  
Katsutoshi Mizuno ◽  
Kei Shiozawa ◽  
Takanobu A. Katoh ◽  
Katsura Minegishi ◽  
Takahiro Ide ◽  
...  
Keyword(s):  
Fluid Flow ◽  
Symmetry Breaking ◽  
Mouse Embryo ◽  
Extracellular Signals ◽  
Flow Sensing ◽  
Immotile Cilia ◽  
Left Posterior ◽  
R Symmetry

Immotile cilia sense extracellular signals such as fluid flow, but whether Ca2+ plays a role in flow sensing has been unclear. Here, we examined the role of ciliary Ca2+ in the flow sensing that initiates the breaking of left-right (L-R) symmetry in the mouse embryo. Intraciliary and cytoplasmic Ca2+ transients were detected in the crown cells at the node. These Ca2+ transients showed L-R asymmetry, which was lost in the absence of fluid flow or the PKD2 channel. Further characterization allowed classification of the Ca2+ transients into two types: cilium-derived, L-R-asymmetric transients (type 1) and cilium-independent transients without an L-R bias (type 2). Type 1 intraciliary transients occurred preferentially at the left posterior region of the node, where L-R symmetry breaking takes place. Suppression of intraciliary Ca2+ transients delayed L-R symmetry breaking. Our results implicate cilium-derived Ca2+ transients in crown cells in initiation of L-R symmetry breaking in the mouse embryo.

scholarly journals Assembly of the α-Globin mRNA Stability Complex Reflects Binary Interaction between the Pyrimidine-Rich 3′ Untranslated Region Determinant and Poly(C) Binding Protein αCP

1999 ◽  
Vol 19 (7) ◽  
pp. 4572-4581 ◽  
Author(s):  
Alexander N. Chkheidze ◽  
Dmitry L. Lyakhov ◽  
Alexander V. Makeyev ◽  
Julia Morales ◽  
Jian Kong ◽  
...  
Keyword(s):  
Mrna Stability ◽  
Untranslated Region ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Specific Binding ◽  
Direct Interaction ◽  
Binary Interaction ◽  
Globin Mrna ◽  
Hnrnp K

ABSTRACT Globin mRNAs accumulate to 95% of total cellular mRNA during terminal erythroid differentiation, reflecting their extraordinary stability. The stability of human α-globin mRNA is paralleled by formation of a sequence-specific RNA-protein (RNP) complex at a pyrimidine-rich site within its 3′ untranslated region (3′UTR), the α-complex. The proteins of the α-complex are widely expressed. The α-complex or a closely related complex also assembles at pyrimidine-rich 3′UTR segments of other stable mRNAs. These data suggest that the α-complex may constitute a general determinant of mRNA stability. One or more αCPs, members of a family of hnRNP K-homology domain poly(C) binding proteins, are essential constituents of the α-complex. The ability of αCPs to homodimerize and their reported association with additional RNA binding proteins such as AU-rich binding factor 1 (AUF1) and hnRNP K have suggested that the α-complex is a multisubunit structure. In the present study, we have addressed the composition of the α-complex. An RNA titration recruitment assay revealed that αCPs were quantitatively incorporated into the α-complex in the absence of associated AUF1 and hnRNP K. A high-affinity direct interaction between each of the three major αCP isoforms and the α-globin 3′UTR was detected, suggesting that each of these proteins might be sufficient for α-complex assembly. This sufficiency was further supported by the sequence-specific binding of recombinant αCPs to a spectrum of RNA targets. Finally, density sedimentation analysis demonstrated that the α-complex could accommodate only a single αCP. These data established that a single αCP molecule binds directly to the α-globin 3′UTR, resulting in a simple binary structure for the α-complex.

scholarly journals RasGAP-Associated Endoribonuclease G3BP: Selective RNA Degradation and Phosphorylation-Dependent Localization

2001 ◽  
Vol 21 (22) ◽  
pp. 7747-7760 ◽  
Author(s):  
Hélène Tourrière ◽  
Imed-eddine Gallouzi ◽  
Karim Chebli ◽  
Jean Paul Capony ◽  
John Mouaikel ◽  
...  
Keyword(s):  
Mrna Decay ◽  
Rna Binding ◽  
Specific Interaction ◽  
Rna Degradation ◽  
Binding Motif ◽  
Quiescent Cells ◽  
Carboxyl Terminal ◽  
A Site ◽  
Binding Sequence ◽  
Mitogen Activation

ABSTRACT Mitogen activation of mRNA decay pathways likely involves specific endoribonucleases, such as G3BP, a phosphorylation-dependent endoribonuclease that associates with RasGAP in dividing but not quiescent cells. G3BP exclusively cleaves between cytosine and adenine (CA) after a specific interaction with RNA through the carboxyl-terminal RRM-type RNA binding motif. Accordingly, G3BP is tightly associated with a subset of poly(A)+ mRNAs containing its high-affinity binding sequence, such as the c-myc mRNA in mouse embryonic fibroblasts. Interestingly, c-myc mRNA decay is delayed in RasGAP-deficient fibroblasts, which contain a defective isoform of G3BP that is not phosphorylated at serine 149. A G3BP mutant in which this serine is changed to alanine remains exclusively cytoplasmic, whereas a glutamate for serine substitution that mimics the charge of a phosphorylated serine is translocated to the nucleus. Thus, a growth factor-induced change in mRNA decay may be modulated by the nuclear localization of a site-specific endoribonuclease such as G3BP.

scholarly journals tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector

2021 ◽  
Author(s):  
Ishita Jain ◽  
Matvey Kolesnik ◽  
Leonid Minakhin ◽  
Natalia Morozova ◽  
Anna Shiriaeva ◽  
...  
Keyword(s):  
Defense Mechanism ◽  
Specific Binding ◽  
Rna Degradation ◽  
Host Population ◽  
Bacterial Toxin ◽  
Rna Recognition ◽  
Trna Species ◽  
Necessary And Sufficient ◽  
Cell Dormancy ◽  
Target Rna

Type VI CRISPR-Cas systems are the only CRISPR variety that cleaves exclusively RNA. In addition to the CRISPR RNA (crRNA)-guided, sequence-specific binding and cleavage of target RNAs, such as phage transcripts, the type VI effector, Cas13, causes collateral RNA cleavage, which induces bacterial cell dormancy, thus protecting the host population from phage spread. We show here that the principal form of collateral RNA degradation elicited by Cas13a protein from Leptotrichia shahii upon target RNA recognition is the cleavage of anticodons of multiple tRNA species, primarily those with anticodons containing uridines. This tRNA cleavage is necessary and sufficient for bacterial dormancy induction by Cas13a. In addition, Cas13a activates the RNases of bacterial toxin-antitoxin modules, thus indirectly causing mRNA and rRNA cleavage, which could provide a back-up defense mechanism. The identified mode of action of Cas13a resembles that of bacterial anticodon nucleases involved in antiphage defense, which is compatible with the hypothesis that type VI effectors evolved from an abortive infection module encompassing an anticodon nuclease.

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