scholarly journals Codon Bias Confers Stability to mRNAs via ILF2 in Humans

2019 ◽  
Author(s):  
Fabian Hia ◽  
Sheng Fan Yang ◽  
Yuichi Shichino ◽  
Masanori Yoshinaga ◽  
Yasuhiro Murakawa ◽  
...  
Keyword(s):  
Mrna Stability ◽  
Codon Bias ◽  
Rna Binding ◽  
Rna Stability ◽  
Gc Content ◽  
Ribosome Profiling ◽  
The Third ◽  
Base Position ◽  
Major Factors

AbstractCodon bias has been implicated as one of the major factors contributing to mRNA stability in yeast. However, the effects of codon-bias on mRNA stability remain unclear in humans. Here we show that human cells possess a mechanism to modulate RNA stability through a unique codon bias different from that of yeast. Bioinformatics analysis showed that codons could be clustered into two distinct groups – codons with G or C at the third base position (GC3) and codons with either A or T at the third base position (AT3); the former stabilizing while the latter destabilizing mRNA. Quantification of codon bias showed that increased GC3 content entails proportionately higher GC content. Through bioinformatics, ribosome profiling andin vitroanalysis, we show that decoupling of the effects of codon bias reveals two modes of mRNA regulation, GC3- and GC-content dependent. Employing an immunoprecipitation-based strategy, we identified ILF2 as an RNA binding protein that differentially regulates global mRNA abundances based on codon bias. Our results demonstrate that codon bias is a two-pronged system that governs mRNA abundance.

scholarly journals RALYL increases hepatocellular carcinoma stemness by sustaining the mRNA stability of TGF-β2

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Xia Wang ◽  
Jin Wang ◽  
Yu-Man Tsui ◽  
Chaoran Shi ◽  
Ying Wang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Mrna Stability ◽  
Rna Binding ◽  
Embryonic Stem ◽  
Molecular Characteristics ◽  
Specific Gene ◽  
Functional Studies ◽  
Poor Differentiation ◽  
Development In Vitro

AbstractGrowing evidences suggest that cancer stem cells exhibit many molecular characteristics and phenotypes similar to their ancestral progenitor cells. In the present study, human embryonic stem cells are induced to differentiate into hepatocytes along hepatic lineages to mimic liver development in vitro. A liver progenitor specific gene, RALY RNA binding protein like (RALYL), is identified. RALYL expression is associated with poor prognosis, poor differentiation, and metastasis in clinical HCC patients. Functional studies reveal that RALYL could promote HCC tumorigenicity, self-renewal, chemoresistance, and metastasis. Moreover, molecular mechanism studies show that RALYL could upregulate TGF-β2 mRNA stability by decreasing N6-methyladenosine (m6A) modification. TGF-β signaling and the subsequent PI3K/AKT and STAT3 pathways, upregulated by RALYL, contribute to the enhancement of HCC stemness. Collectively, RALYL is a liver progenitor specific gene and regulates HCC stemness by sustaining TGF-β2 mRNA stability. These findings may inspire precise therapeutic strategies for HCC.

scholarly journals An Interaction between Two RNA Binding Proteins, Nab2 and Pub1, Links mRNA Processing/Export and mRNA Stability

2007 ◽  
Vol 27 (18) ◽  
pp. 6569-6579 ◽  
Author(s):  
Luciano H. Apponi ◽  
Seth M. Kelly ◽  
Michelle T. Harreman ◽  
Alexander N. Lehner ◽  
Anita H. Corbett ◽  
...  
Keyword(s):  
Mrna Stability ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Tail Length ◽  
Functional Link ◽  
Mrna Binding Protein ◽  
Mrna Binding

ABSTRACT mRNA stability is modulated by elements in the mRNA transcript and their cognate RNA binding proteins. Poly(U) binding protein 1 (Pub1) is a cytoplasmic Saccharomyces cerevisiae mRNA binding protein that stabilizes transcripts containing AU-rich elements (AREs) or stabilizer elements (STEs). In a yeast two-hybrid screen, we identified nuclear poly(A) binding protein 2 (Nab2) as being a Pub1-interacting protein. Nab2 is an essential nucleocytoplasmic shuttling mRNA binding protein that regulates poly(A) tail length and mRNA export. The interaction between Pub1 and Nab2 was confirmed by copurification and in vitro binding assays. The interaction is mediated by the Nab2 zinc finger domain. Analysis of the functional link between these proteins reveals that Nab2, like Pub1, can modulate the stability of specific mRNA transcripts. The half-life of the RPS16B transcript, an ARE-like sequence-containing Pub1 target, is decreased in both nab2-1 and nab2-67 mutants. In contrast, GCN4, an STE-containing Pub1 target, is not affected. Similar results were obtained for other ARE- and STE-containing Pub1 target transcripts. Further analysis reveals that the ARE-like sequence is necessary for Nab2-mediated transcript stabilization. These results suggest that Nab2 functions together with Pub1 to modulate mRNA stability and strengthen a model where nuclear events are coupled to the control of mRNA turnover in the cytoplasm.

scholarly journals RNA-Binding Protein IGF2BP1 Enhances mRNA Stability and Translation Efficiency of INHBA to Promote the Invasion and Migration of Esophageal Squamous Cancer Cells

2021 ◽  
Author(s):  
Juan-Juan Wang ◽  
Ding-Xiong Chen ◽  
Yu Zhang ◽  
Xin Xu ◽  
Yan Cai ◽  
...  
Keyword(s):  
Mrna Stability ◽  
Rna Binding ◽  
Binding Protein ◽  
Mrna Level ◽  
Rna Stability ◽  
Translation Efficiency ◽  
Invasion And Migration ◽  
Squamous Cancer ◽  
And Migration

Abstract BackgroundMetastasis are mainly responsible for the death of patients with advanced esophageal squamous cell carcinoma (ESCC). At present, there is no targeted drug for the treatment of ESCC in clinic practice. The present study aims to investigate the roles and implication of IGF2BP1 overexpression in ESCC.MethodsIGF2BP1 protein expression was assessed by immunohistochemistry (IHC), and the mRNA abundance of IGF2BP1 and INHBA were analyzed with TCGA datasets and by RNA in situ hybridization (RISH). Cell viability, migration, invasion and in vivo metastasis assays were performed to explore the roles of IGF2BP1 in ESCC. RNA immunoprecipitation sequencing (RIP-seq) and mass spectrometry were applied to identify the targets and interacting proteins of IGF2BP1, respectively. RIP-PCR, RNA-pulldown, immunofluorescence (IF), gene specific m6A PCR and RNA stability assay were used to uncover the molecular mechanism of IGF2BP1 dysregulation. The methylation level of IGF2BP1 promoter region was detected by MSP-PCR. BTYNB, a small molecular inhibitor which could block the binding of IGF2BP1 to c-Myc mRNA, was evaluated for the inhibition effect on the malignant phenotypes of ESCC cells.ResultsIGF2BP1 overexpression was detected in ESCC tissues and associated with depth of tumor invasion. Knockdown of IGF2BP1 inhibited ESCC cell invasion and migration as well as tumor metastasis. Importantly, INHBA was identified as a direct target of IGF2BP1 in ESCC cells, which had a role in promoting the malignant phenotypes. TCGA data and RISH analyses showed that the mRNA level of INHBA was upregaluted in ESCC tissues as well. Mechanistically, IGF2BP1 bound and stabilized INHBA mRNA and then enhanced its translation, leading to an activation of Smad2/3 signaling. Ras GTPase-activating protein-binding protein 1 (G3BP1) was recruited by IGF2BP1 to participate in activating the signaling process, which was inhibited by the IGF2BP1 inhibitor BTYNB. Of note, IGF2BP1 mRNA expression in ESCC cells was negatively correlated with the level of its promoter methylation.ConclusionsIGF2BP1 overexpression promotes the invasion and migration of ESCC cells by up-regulating TGF-β-Smad2/3 pathway through enhancing INHBA mRNA stability and translation, providing a potential therapeutic target for ESCC treatment.

scholarly journals A Nascent Peptide Code for Translational Control of mRNA Stability in Human Cells

2021 ◽  
Author(s):  
Phillip C. Burke ◽  
Heungwon Park ◽  
Arvind Rasi Subramaniam
Keyword(s):  
Amino Acids ◽  
Mrna Stability ◽  
Translational Control ◽  
Gc Content ◽  
Human Cells ◽  
Sequence Motifs ◽  
Coding Sequence ◽  
Ribosome Stalling ◽  
Nascent Peptide

AbstractStability of eukaryotic mRNAs is associated with their codon, amino acid, and GC content. Yet, coding sequence motifs that predictably alter mRNA stability in human cells remain poorly defined. Here, we develop a massively parallel assay to measure mRNA effects of thousands of synthetic and endogenous coding sequence motifs in human cells. We identify several families of simple dipeptide repeats whose translation triggers acute mRNA instability. Rather than individual amino acids, specific combinations of bulky and positively charged amino acids are critical for the destabilizing effects of dipeptide repeats. Remarkably, dipeptide sequences that form extended β strands in silico and in vitro drive ribosome stalling and mRNA instability in vivo. The resulting nascent peptide code underlies ribosome stalling and mRNA-destabilizing effects of hundreds of endogenous peptide sequences in the human proteome. Our work reveals an intrinsic role for the ribosome as a selectivity filter against the synthesis of bulky and aggregation-prone peptides.

scholarly journals FMRP links optimal codons to mRNA stability in neurons

2020 ◽  
Vol 117 (48) ◽  
pp. 30400-30411
Author(s):  
Huan Shu ◽  
Elisa Donnard ◽  
Botao Liu ◽  
Suna Jung ◽  
Ruijia Wang ◽  
...  
Keyword(s):  
Mrna Stability ◽  
Cortical Neurons ◽  
Rna Binding ◽  
Fragile X ◽  
Transcript Abundance ◽  
Ribosome Profiling ◽  
Metabolic Labeling ◽  
Genetic Rescue ◽  
Translational Machinery ◽  
Optimal Codons

Fragile X syndrome (FXS) is caused by inactivation of theFMR1gene and loss of encoded FMRP, an RNA binding protein that represses translation of some of its target transcripts. Here we use ribosome profiling and RNA sequencing to investigate the dysregulation of translation in the mouse brain cortex. We find that most changes in ribosome occupancy on hundreds of mRNAs are largely driven by dysregulation in transcript abundance. Many down-regulated mRNAs, which are mostly responsible for neuronal and synaptic functions, are highly enriched for FMRP binding targets. RNA metabolic labeling demonstrates that, in FMRP-deficient cortical neurons, mRNA down-regulation is caused by elevated degradation and is correlated with codon optimality. Moreover, FMRP preferentially binds mRNAs with optimal codons, suggesting that it stabilizes such transcripts through direct interactions via the translational machinery. Finally, we show that the paradigm of genetic rescue of FXS-like phenotypes in FMRP-deficient mice by deletion of theCpeb1gene is mediated by restoration of steady-state RNA levels and consequent rebalancing of translational homeostasis. Our data establish an essential role of FMRP in codon optimality-dependent mRNA stability as an important factor in FXS.

scholarly journals Structural and Functional Analysis of an mRNP Complex That Mediates the High Stability of Human β-Globin mRNA

2001 ◽  
Vol 21 (17) ◽  
pp. 5879-5888 ◽  
Author(s):  
Jia Yu ◽  
J. Eric Russell
Keyword(s):  
Mrna Stability ◽  
Rna Binding ◽  
Assembly Sequence ◽  
Regulatory Pathway ◽  
Globin Mrna ◽  
Mrnp Complex ◽  
The Stability ◽  
High Level

ABSTRACT Human globins are encoded by mRNAs exhibiting high stabilities in transcriptionally silenced erythrocyte progenitors. Unlike α-globin mRNA, whose stability is enhanced by assembly of a specific messenger RNP (mRNP) α complex on its 3′ untranslated region (UTR), neither the structure(s) nor the mechanism(s) that effects the high-level stability of human β-globin mRNA has been identified. The present work describes an mRNP complex assembling on the 3′ UTR of the β-globin mRNA that exhibits many of the properties of the stability-enhancing α complex. The β-globin mRNP complex is shown to contain one or more factors homologous to αCP, a 39-kDa RNA-binding protein that is integral to α-complex assembly. Sequence analysis implicates a specific 14-nucleotide pyrimidine-rich track within its 3′ UTR as the site of β-globin mRNP assembly. The importance of this track to mRNA stability is subsequently verified in vivo using mice expressing human β-globin transgenes that contain informative mutations in this region. In combination, the in vitro and in vivo analyses indicate that the high stabilities of the α- and β-globin mRNAs are maintained through related mRNP complexes that may share a common regulatory pathway.

scholarly journals Pan-cancer analysis of mRNA stability for decoding tumour post-transcriptional programs

2021 ◽  
Author(s):  
Gabrielle Perron ◽  
Pouria Jandaghi ◽  
Maryam Rajaee ◽  
Rached Alkallas ◽  
Yasser Riazalhosseini ◽  
...  
Keyword(s):  
Mrna Stability ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Rna Stability ◽  
Cancer Type ◽  
Multiple Cancers ◽  
Transcriptional Changes ◽  
Potential Factors ◽  
Pan Cancer

AbstractRNA stability is a crucial and often overlooked determinant of gene expression. Some of the regulators of mRNA stability are long known as key oncogenic or tumour suppressor factors. Nonetheless, the extent to which mRNA stability contributes to transcriptome remodeling in cancer is unknown, and the factors that modulate mRNA stability during cancer development and progression are largely uncharacterized. Here, by decoupling transcriptional and post-transcriptional effects in RNA-seq data of 7760 samples from 18 cancer types, we present a pan-cancer view of the mRNA stability changes that accompany tumour development and progression. We show that thousands of genes are dysregulated at the mRNA stability level, and identify the potential factors that drive these changes, including >80 RNA-binding proteins (RBPs) and microRNAs (miRNAs). Most RBPs and miRNAs have cancer type-specific activities, but a few show recurrent inactivation across multiple cancers, including the RBFOX family of RBPs and miR-29. Analysis of cell lines with phenotypic activation or inhibition of RBFOX1 and miR-29 confirms their role in modulation of genes that are dysregulated across multiple cancers, with functions in calcium signaling, extracellular matrix organization, and stemness. Overall, our study highlights the critical role of mRNA stability in shaping the tumour transcriptome, with recurrent post-transcriptional changes that are ~30% as frequent as transcriptional events. These results provide a resource for systematic interrogation of cancer-associated stability drivers and pathways.

scholarly journals Rbm24a Is Necessary for Hair Cell Development Through Regulating mRNA Stability in Zebrafish

2020 ◽  
Vol 8 ◽  
Author(s):  
Yan Zhang ◽  
Yanfei Wang ◽  
Xuebo Yao ◽  
Changquan Wang ◽  
Fangyi Chen ◽  
...  
Keyword(s):  
Hair Cell ◽  
Inner Ear ◽  
Mrna Stability ◽  
Target Genes ◽  
Rna Binding ◽  
Rna Stability ◽  
Vestibular Function ◽  
Cell Development ◽  
Binding Motif ◽  
Lateral Lines

Hair cells in the inner ear and lateral lines are mechanosensitive receptor cells whose development and function are tightly regulated. Several transcription factors as well as splicing factors have been identified to play important roles in hair cell development, whereas the role of RNA stability in this process is poorly understood. In the present work, we report that RNA-binding motif protein 24a (Rbm24a) is indispensable for hair cell development in zebrafish. Rbm24a expression is detected in the inner ear as well as lateral line neuromasts. Albeit rbm24a deficient zebrafish do not survive beyond 9 days post fertilization (dpf) due to effects outside of the inner ear, rbm24a deficiency does not affect the early development of inner ear except for delayed otolith formation and semicircular canal fusion. However, hair cell development is severely affected and hair bundle is disorganized in rbm24a mutants. As a result, the auditory and vestibular function of rbm24a mutants are compromised. RNAseq analyses identified several Rbm24a-target mRNAs that are directly bound by Rbm24a and are dysregulated in rbm24a mutants. Among the identified Rbm24a-target genes, lrrc23, dfna5b, and smpx are particularly interesting as their dysregulation might contribute to the inner ear phenotypes in rbm24a mutants. In conclusion, our data suggest that Rbm24a affects hair cell development in zebrafish through regulating mRNA stability.

scholarly journals A Nucleolin-Binding 3′ Untranslated Region Element Stabilizes β-Globin mRNA In Vivo

2006 ◽  
Vol 26 (6) ◽  
pp. 2419-2429 ◽  
Author(s):  
Yong Jiang ◽  
Xiang-Sheng Xu ◽  
J. Eric Russell
Keyword(s):  
Mrna Stability ◽  
Untranslated Region ◽  
Rna Binding ◽  
Critical Role ◽  
Specific Interaction ◽  
Globin Mrna ◽  
Intact Cells ◽  
Normal Expression

ABSTRACT The normal expression of human β globin is critically dependent upon the constitutively high stability of its encoding mRNA. Unlike with α-globin mRNA, the specific cis-acting determinants and trans-acting factors that participate in stabilizing β-globin mRNA are poorly described. The current work uses a linker-scanning strategy to identify a previously unknown determinant of mRNA stability within the β-globin 3′ untranslated region (3′UTR). The new determinant is positioned on an mRNA half-stem opposite a pyrimidine-rich sequence targeted by αCP/hnRNP-E, a factor that plays a critical role in stabilizing human α-globin mRNA. Mutations within the new determinant destabilize β-globin mRNA in intact cells while also ablating its 3′UTR-specific interaction with the polyfunctional RNA-binding factor nucleolin. We speculate that 3′UTR-bound nucleolin enhances mRNA stability by optimizing αCP access to its functional binding site. This model is favored by in vitro evidence that αCP binding is enhanced both by cis-acting stem-destabilizing mutations and by the trans-acting effects of supplemental nucleolin. These studies suggest a mechanism for β-globin mRNA stability that is related to, but distinct from, the mechanism that stabilizes human α-globin mRNA.

scholarly journals Staufen1 Protein Participates Positively in the Viral RNA Replication of Enterovirus 71

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 142 ◽  
Author(s):  
Young-Mao Chen ◽  
Bo-Ting Ou ◽  
Chao-Ying Chen ◽  
Han-Hsiang Chan ◽  
Chih-Jung Chen ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Virus ◽  
Rna Stability ◽  
Enterovirus 71 ◽  
Viral Rna ◽  
Viral Translation ◽  
Rna Translation ◽  
Rna Accumulation

The double-stranded RNA-binding protein Staufen1 (Stau1) has multiple functions during RNA virus infection. In this study, we investigated the role of Stau1 in viral translation by using a combination of enterovirus 71 (EV-A71) infection, RNA reporter transfection, and in vitro functional and biochemical assays. We demonstrated that Stau1 specifically binds to the 5′-untranslated region of EV-A71 viral RNA. The RNA-binding domain 2-3 of Stau1 is responsible for this binding ability. Subsequently, we created a Stau1 knockout cell line using the CRISPR/Cas9 approach to further characterize the functional role of Stau1’s interaction with viral RNA in the EV-A71-infected cells. Both the viral RNA accumulation and viral protein expression were downregulated in the Stau1 knockout cells compared with the wild-type naïve cells. Moreover, dysregulation of viral RNA translation was observed in the Stau1 knockout cells using ribosome fractionation assay, and a reduced RNA stability of 5′-UTR of the EV-A71 was also identified using an RNA stability assay, which indicated that Stau1 has a role in facilitating viral translation during EV-A71 infection. In conclusion, we determined the functional relevance of Stau1 in the EV-A71 infection cycle and herein describe the mechanism of Stau1 participation in viral RNA translation through its interaction with viral RNA. Our results suggest that Stau1 is an important host factor involved in viral translation and influential early in the EV-A71 replication cycle.

Sign in / Sign up

Export Citation Format

Share Document