scholarly journals Identification of cellular mRNA targets for RNA-binding protein Sam68

2002 ◽  
Vol 30 (24) ◽  
pp. 5452-5464 ◽  
Author(s):  
M. Itoh
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Mrna Targets

scholarly journals The RNA-binding protein Sam68 modulates the alternative splicing of Bcl-x

2007 ◽  
Vol 176 (7) ◽  
pp. 929-939 ◽  
Author(s):  
Maria Paola Paronetto ◽  
Tilman Achsel ◽  
Autumn Massiello ◽  
Charles E. Chalfant ◽  
Claudio Sette
Keyword(s):  
Alternative Splicing ◽  
Tyrosine Phosphorylation ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Live Cells ◽  
Hnrnp A1 ◽  
Splice Site Selection ◽  
Subnuclear Localization ◽  
Mrna Targets

The RNA-binding protein Sam68 is involved in apoptosis, but its cellular mRNA targets and its mechanism of action remain unknown. We demonstrate that Sam68 binds the mRNA for Bcl-x and affects its alternative splicing. Depletion of Sam68 by RNA interference caused accumulation of antiapoptotic Bcl-x(L), whereas its up-regulation increased the levels of proapoptotic Bcl-x(s). Tyrosine phosphorylation of Sam68 by Fyn inverted this effect and favored the Bcl-x(L) splice site selection. A point mutation in the RNA-binding domain of Sam68 influenced its splicing activity and subnuclear localization. Moreover, coexpression of ASF/SF2 with Sam68, or fusion with an RS domain, counteracted Sam68 splicing activity toward Bcl-x. Finally, Sam68 interacted with heterogenous nuclear RNP (hnRNP) A1, and depletion of hnRNP A1 or mutations that impair this interaction attenuated Bcl-x(s) splicing. Our results indicate that Sam68 plays a role in the regulation of Bcl-x alternative splicing and that tyrosine phosphorylation of Sam68 by Src-like kinases can switch its role from proapoptotic to antiapoptotic in live cells.

scholarly journals Phosphoregulation provides specificity to biomolecular condensates in the cell cycle and cell polarity

2020 ◽  
Vol 219 (7) ◽  
Author(s):  
Therese M. Gerbich ◽  
Grace A. McLaughlin ◽  
Katelyn Cassidy ◽  
Scott Gerber ◽  
David Adalsteinsson ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Nucleic Acids ◽  
Cell Polarity ◽  
Filamentous Fungus ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Ashbya Gossypii ◽  
Mrna Targets ◽  
Functional Identities

Biomolecular condensation is a way of organizing cytosol in which proteins and nucleic acids coassemble into compartments. In the multinucleate filamentous fungus Ashbya gossypii, the RNA-binding protein Whi3 regulates the cell cycle and cell polarity through forming macromolecular structures that behave like condensates. Whi3 has distinct spatial localizations and mRNA targets, making it a powerful model for how, when, and where specific identities are established for condensates. We identified residues on Whi3 that are differentially phosphorylated under specific conditions and generated mutants that ablate this regulation. This yielded separation of function alleles that were functional for either cell polarity or nuclear cycling but not both. This study shows that phosphorylation of individual residues on molecules in biomolecular condensates can provide specificity that gives rise to distinct functional identities in the same cell.

scholarly journals RNA-Binding Protein Khd1 and Ccr4 Deadenylase Play Overlapping Roles in the Cell Wall Integrity Pathway in Saccharomyces cerevisiae

2011 ◽  
Vol 10 (10) ◽  
pp. 1340-1347 ◽  
Author(s):  
Wataru Ito ◽  
Xia Li ◽  
Kaoru Irie ◽  
Tomoaki Mizuno ◽  
Kenji Irie
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Wall ◽  
Rna Binding ◽  
Binding Protein ◽  
Mrna Level ◽  
Rna Binding Protein ◽  
Cell Lysis ◽  
Cell Wall Integrity ◽  
Nucleotide Exchange ◽  
Mrna Targets

ABSTRACT The Saccharomyces cerevisiae RNA-binding protein Khd1/Hek2 associates with hundreds of potential mRNA targets preferentially, including the mRNAs encoding proteins localized to the cell wall and plasma membrane. We have previously revealed that Khd1 positively regulates expression of MTL1 mRNA encoding a membrane sensor in the cell wall integrity (CWI) pathway. However, a khd1 Δ mutation has no detectable phenotype on cell wall synthesis. Here we show that the khd1 Δ mutation causes a severe cell lysis when combined with the deletion of the CCR4 gene encoding a cytoplasmic deadenylase. We identified the ROM2 mRNA, encoding a guanine nucleotide exchange factor (GEF) for Rho1, as a target for Khd1 and Ccr4. The ROM2 mRNA level was decreased in the khd1 Δ ccr4 Δ mutant, and ROM2 overexpression suppressed the cell lysis of the khd1 Δ ccr4 Δ mutant. We also found that Ccr4 negatively regulates expression of the LRG1 mRNA encoding a GTPase-activating protein (GAP) for Rho1. The LRG1 mRNA level was increased in the ccr4 Δ and khd1 Δ ccr4 Δ mutants, and deletion of LRG1 suppressed the cell lysis of the khd1 Δ ccr4 Δ mutant. Our results presented here suggest that Khd1 and Ccr4 modulate a signal from Rho1 in the CWI pathway by regulating the expression of RhoGEF and RhoGAP.

scholarly journals CLIP-Seq and massively parallel functional analysis of the CELF6 RNA binding protein reveals a role in destabilizing synaptic gene mRNAs through interaction with 3’UTR elements in vivo

2018 ◽  
Author(s):  
Michael A. Rieger ◽  
Dana M. King ◽  
Barak A. Cohen ◽  
Joseph D. Dougherty
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Synaptic Proteins ◽  
Massively Parallel ◽  
Sequence Motifs ◽  
Mrna Targets ◽  
The Brain

AbstractCELF6 is a RNA-binding protein in a family of proteins with roles in human health and disease, however little is known about the mRNA targets or in vivo function of this protein. We utilized CLIP-Seq to identify, for the first time, in vivo targets of CELF6 and identify hundreds of transcripts bound by CELF6 in the brain. We found these are disproportionately mRNAs coding for synaptic proteins. We then conducted functional validation of these targets, testing greater than 400 CELF6 bound sequence elements for their activity, applying a massively parallel reporter assay framework to evaluation of the CLIP data. We also mutated potential binding motifs within these elements and tested their impact. This comprehensive analysis led us to ascribe a previously unknown function to CELF6: we found bound elements were generally repressive of translation, that CELF6 further enhances this repression via decreasing RNA abundance, and this process was dependent on UGU-rich sequence motifs. This greatly extends the known role for CELF6, which had previously been defined only as a splicing factor. We further extend these findings by demonstrating the same function for CELF3, CELF4, and CELF5. Finally, we demonstrate that the CELF6 targets are derepressed in CELF6 mutant mice in vivo, confirming this new role in the brain. Thus, our study demonstrates that CELF6 and other sub-family members are repressive CNS RNA-binding proteins, and CELF6 downregulates specific mRNAs in vivo.

scholarly journals The mTOR regulated RNA-binding protein LARP1 requires PABPC1 for guided mRNA interaction

2020 ◽  
Author(s):  
Ewan M Smith ◽  
Nour El Houda Benbahouche ◽  
Katherine Morris ◽  
Ania Wilczynska ◽  
Sarah Gillen ◽  
...  
Keyword(s):  
Cell Growth ◽  
Rna Binding ◽  
Binding Protein ◽  
Mammalian Target Of Rapamycin ◽  
Rna Binding Protein ◽  
Mtor Inhibition ◽  
Growth And Survival ◽  
Mrna Targets ◽  
Terminal Oligopyrimidine ◽  
Rna Interaction

Abstract The mammalian target of rapamycin (mTOR) is a critical regulator of cell growth, integrating multiple signalling cues and pathways. Key among the downstream activities of mTOR is the control of the protein synthesis machinery. This is achieved, in part, via the co-ordinated regulation of mRNAs that contain a terminal oligopyrimidine tract (TOP) at their 5′ends, although the mechanisms by which this occurs downstream of mTOR signalling are still unclear. We used RNA-binding protein (RBP) capture to identify changes in the protein-RNA interaction landscape following mTOR inhibition. Upon mTOR inhibition, the binding of LARP1 to a number of mRNAs, including TOP-containing mRNAs, increased. Importantly, non-TOP-containing mRNAs bound by LARP1 are in a translationally-repressed state, even under control conditions. The mRNA interactome of the LARP1-associated protein PABPC1 was found to have a high degree of overlap with that of LARP1 and our data show that PABPC1 is required for the association of LARP1 with its specific mRNA targets. Finally, we demonstrate that mRNAs, including those encoding proteins critical for cell growth and survival, are translationally repressed when bound by both LARP1 and PABPC1.

scholarly journals Phosphoregulation provides functional specificity to biomolecular condensates in the cell cycle and cell polarity

2019 ◽  
Author(s):  
Therese M. Gerbich ◽  
Amy S. Gladfelter
Keyword(s):  
Cell Cycle ◽  
Cell Polarity ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Ashbya Gossypii ◽  
Functional Specificity ◽  
Molecular Identity ◽  
Mrna Targets ◽  
Functional Identities

AbstractCytoplasmic patterning is a feature of many cells from embryos to neurons and fungi. Biomolecular condensation is a way of organizing cytosol in which proteins and nucleic acids coassemble into compartments. How molecular identity of condensates is achieved is not well understood. In the multinucleate, filamentous fungus Ashbya gossypii, the RNA-binding protein Whi3 regulates the cell cycle and cell polarity through forming macromolecular structures that behave like condensates. Whi3 has distinct spatial localizations and mRNA targets making it a powerful model for how, when and where specific identities are established for condensates. Using mass-spectrometry, we identified residues on Whi3 that are differentially phosphorylated under specific conditions and generated mutants which ablate this regulation. This yielded separation of function alleles that were functional for either cell polarity or nuclear cycling but not both. This study shows that phosphorylation of individual residues on molecules in biomolecular condensates can provide specificity that give rise to distinct functional identities in the same cell.SummaryResidue specific phosphorylation of the RNA-binding protein Whi3 is used to specifically regulate subsets of functionally distinct condensates in the multinucleate fungus Ashbya gossypii.

235: The RNA-Binding Protein IMP3: A Novel Molecular Marker Predicts Progression of Superficial (TA and T1) Urothelial Carcinomas of Bladder

2007 ◽  
Vol 177 (4S) ◽  
pp. 78-79
Author(s):  
Lioudmila Sitnikova ◽  
Gary Mendese ◽  
Qin Lui ◽  
Bruce A. Woda ◽  
Di Lu ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Urothelial Carcinomas
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