Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 1.881
Filter
1.
Int J Biol Sci ; 20(7): 2388-2402, 2024.
Article in English | MEDLINE | ID: mdl-38725844

ABSTRACT

Metastasis is the leading cause of death in colorectal cancer (CRC) patients. By mediating intercellular communication, exosomes exhibit considerable value in regulating tumor metastasis. Long non-coding RNAs (lncRNAs) are abundant in exosomes and participate in regulating tumor progression. However, it is poorly understood how the cancer-secreted exosomal lncRNAs affect CRC proliferation and metastasis. Here, by analyzing the public databases we identified a lncRNA SNHG3 and demonstrated that SNHG3 was delivered through CRC cells-derived exosomes to promote metastasis in CRC. Mechanistically, exosomal SNHG3 was internalized by CRC cells and afterward upregulated the expression of ß-catenin by facilitating the intranuclear transport of hnRNPC. Consequently, the RNA stability of ß-catenin was enhanced which led to the activation of EMT and metastasis of CRC cells. Our findings expand the oncogenic mechanisms of exosomal SNHG3 and identify it as a diagnostic marker for CRC.


Subject(s)
Colorectal Neoplasms , Exosomes , RNA, Long Noncoding , beta Catenin , Humans , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , Colorectal Neoplasms/genetics , RNA, Long Noncoding/metabolism , RNA, Long Noncoding/genetics , beta Catenin/metabolism , Exosomes/metabolism , Cell Line, Tumor , RNA Stability/genetics , Gene Expression Regulation, Neoplastic , Neoplasm Metastasis , Animals , Mice , Cell Proliferation/genetics , Mice, Nude
2.
Hum Mol Genet ; 33(R1): R26-R33, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38779774

ABSTRACT

Mitochondria are vital organelles present in almost all eukaryotic cells. Although most of the mitochondrial proteins are nuclear-encoded, mitochondria contain their own genome, whose proper expression is necessary for mitochondrial function. Transcription of the human mitochondrial genome results in the synthesis of long polycistronic transcripts that are subsequently processed by endonucleases to release individual RNA molecules, including precursors of sense protein-encoding mRNA (mt-mRNA) and a vast amount of antisense noncoding RNAs. Because of mitochondrial DNA (mtDNA) organization, the regulation of individual gene expression at the transcriptional level is limited. Although transcription of most protein-coding mitochondrial genes occurs with the same frequency, steady-state levels of mature transcripts are different. Therefore, post-transcriptional processes are important for regulating mt-mRNA levels. The mitochondrial degradosome is a complex composed of the RNA helicase SUV3 (also known as SUPV3L1) and polynucleotide phosphorylase (PNPase, PNPT1). It is the best-characterized RNA-degrading machinery in human mitochondria, which is primarily responsible for the decay of mitochondrial antisense RNA. The mechanism of mitochondrial sense RNA decay is less understood. This review aims to provide a general picture of mitochondrial genome expression, with a particular focus on mitochondrial RNA (mtRNA) degradation.


Subject(s)
Mitochondria , Polyribonucleotide Nucleotidyltransferase , RNA Stability , RNA, Mitochondrial , Humans , Mitochondria/metabolism , Mitochondria/genetics , RNA Stability/genetics , Polyribonucleotide Nucleotidyltransferase/metabolism , Polyribonucleotide Nucleotidyltransferase/genetics , RNA, Mitochondrial/metabolism , RNA, Mitochondrial/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA, Antisense/genetics , RNA, Antisense/metabolism , DNA, Mitochondrial/genetics , DNA, Mitochondrial/metabolism , RNA Helicases/metabolism , RNA Helicases/genetics , RNA/metabolism , RNA/genetics , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/genetics , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Endoribonucleases , Exoribonucleases , Multienzyme Complexes
3.
Cells ; 13(10)2024 May 16.
Article in English | MEDLINE | ID: mdl-38786074

ABSTRACT

Mammalian oocyte development depends on the temporally controlled translation of maternal transcripts, particularly in the coordination of meiotic and early embryonic development when transcription has ceased. The translation of mRNA is regulated by various RNA-binding proteins. We show that the absence of cytoplasmic polyadenylation element-binding protein 3 (CPEB3) negatively affects female reproductive fitness. CPEB3-depleted oocytes undergo meiosis normally but experience early embryonic arrest due to a disrupted transcriptome, leading to aberrant protein expression and the subsequent failure of embryonic transcription initiation. We found that CPEB3 stabilizes a subset of mRNAs with a significantly longer 3'UTR that is enriched in its distal region with cytoplasmic polyadenylation elements. Overall, our results suggest that CPEB3 is an important maternal factor that regulates the stability and translation of a subclass of mRNAs that are essential for the initiation of embryonic transcription and thus for embryonic development.


Subject(s)
Oocytes , RNA-Binding Proteins , Oocytes/metabolism , Animals , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , Female , Mice , Meiosis/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Embryonic Development/genetics , Gene Expression Regulation, Developmental , 3' Untranslated Regions/genetics , Polyadenylation , RNA Stability/genetics
4.
Mol Cell Biol ; 44(5): 194-208, 2024.
Article in English | MEDLINE | ID: mdl-38769646

ABSTRACT

Cellular senescence is a dynamic biological process triggered by sublethal cell damage and driven by specific changes in gene expression programs. We recently identified ANKRD1 (ankyrin repeat domain 1) as a protein strongly elevated after triggering senescence in fibroblasts. Here, we set out to investigate the mechanisms driving the elevated production of ANKRD1 in the early stages of senescence. Our results indicated that the rise in ANKRD1 levels after triggering senescence using etoposide (Eto) was the result of moderate increases in transcription and translation, and robust mRNA stabilization. Antisense oligomer (ASO) pulldown followed by mass spectrometry revealed a specific interaction of the RNA-binding protein RBMS1 with ANKRD1 mRNA that was confirmed by ribonucleoprotein immunoprecipitation analysis. RBMS1 abundance decreased in the nucleus and increased in the cytoplasm during Eto-induced senescence; in agreement with the hypothesis that RBMS1 may participate in post-transcriptional stabilization of ANKRD1 mRNA, silencing RBMS1 reduced, while overexpressing RBMS1 enhanced ANKRD1 mRNA half-life after Eto treatment. A segment proximal to the ANKRD1 coding region was identified as binding RBMS1 and conferring RBMS1-dependent increased expression of a heterologous reporter. We propose that RBMS1 increases expression of ANKRD1 during the early stages of senescence by stabilizing ANKRD1 mRNA.


Subject(s)
Cellular Senescence , Nuclear Proteins , RNA Stability , RNA, Messenger , RNA-Binding Proteins , Repressor Proteins , Humans , Cellular Senescence/drug effects , Cellular Senescence/genetics , RNA Stability/genetics , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , Nuclear Proteins/metabolism , Nuclear Proteins/genetics , Repressor Proteins/metabolism , Repressor Proteins/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Etoposide/pharmacology , Fibroblasts/metabolism , Fibroblasts/drug effects , Cell Nucleus/metabolism , Cell Line , Muscle Proteins
5.
J Cell Mol Med ; 28(9): e18328, 2024 May.
Article in English | MEDLINE | ID: mdl-38683130

ABSTRACT

Gallbladder cancer is a rare but fatal malignancy. However, the mechanisms underlying gallbladder carcinogenesis and its progression are poorly understood. The function of m6A modification and its regulators was still unclear for gallbladder cancer. The current study seeks to investigate the function of YTH m6A RNA-binding protein 1 (YTHDF1) in gallbladder cancer. Transcriptomic analysis and immunochemical staining of YTHDF1 in gallbladder cancer tissues revealed its upregulation compared to paracancerous tissues. Moreover, YTHDF1 promotes the proliferation assays, Transwell migration assays, and Transwell invasion assays of gallbladder cancer cells in vitro. And it also increased tumour growth in xenograft mouse model and metastases in tail vein injection model in vivo. In vitro, UHRF1 knockdown partly reversed the effects of YTHDF1 overexpression. Mechanistically, dual-luciferase assays proved that YTHDF1 promotes UHRF1 expression via direct binding to the mRNA 3'-UTR in a m6A-dependent manner. Overexpression of YTHDF1 enhanced UHRF1 mRNA stability, as demonstrated by mRNA stability assays, and Co-IP studies confirmed a direct interaction between YTHDF1 and PABPC1. Collectively, these findings provide new insights into the progression of gallbladder cancer as well as a novel post-transcriptional mechanism of YTHDF1 via stabilizing target mRNA.


Subject(s)
Adenosine , Gallbladder Neoplasms , Gene Expression Regulation, Neoplastic , RNA-Binding Proteins , Ubiquitin-Protein Ligases , Animals , Female , Humans , Male , Mice , Adenosine/analogs & derivatives , CCAAT-Enhancer-Binding Proteins/metabolism , CCAAT-Enhancer-Binding Proteins/genetics , Cell Line, Tumor , Cell Movement/genetics , Cell Proliferation/genetics , Disease Progression , Gallbladder Neoplasms/genetics , Gallbladder Neoplasms/pathology , Gallbladder Neoplasms/metabolism , Mice, Nude , RNA Stability/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/genetics
6.
Cell Rep ; 43(4): 114069, 2024 Apr 23.
Article in English | MEDLINE | ID: mdl-38602876

ABSTRACT

The integrated stress response (ISR) is a key cellular signaling pathway activated by environmental alterations that represses protein synthesis to restore homeostasis. To prevent sustained damage, the ISR is counteracted by the upregulation of growth arrest and DNA damage-inducible 34 (GADD34), a stress-induced regulatory subunit of protein phosphatase 1 that mediates translation reactivation and stress recovery. Here, we uncover a novel ISR regulatory mechanism that post-transcriptionally controls the stability of PPP1R15A mRNA encoding GADD34. We establish that the 3' untranslated region of PPP1R15A mRNA contains an active AU-rich element (ARE) recognized by proteins of the ZFP36 family, promoting its rapid decay under normal conditions and stabilization for efficient expression of GADD34 in response to stress. We identify the tight temporal control of PPP1R15A mRNA turnover as a component of the transient ISR memory, which sets the threshold for cellular responsiveness and mediates adaptation to repeated stress conditions.


Subject(s)
3' Untranslated Regions , Protein Phosphatase 1 , Animals , Humans , Mice , 3' Untranslated Regions/genetics , Adaptation, Physiological/genetics , AU Rich Elements/genetics , HEK293 Cells , Protein Phosphatase 1/metabolism , Protein Phosphatase 1/genetics , RNA Stability/genetics , RNA, Messenger/metabolism , RNA, Messenger/genetics , Stress, Physiological/genetics , Tristetraprolin/metabolism , Tristetraprolin/genetics
7.
Adv Sci (Weinh) ; 11(20): e2302379, 2024 May.
Article in Italian | MEDLINE | ID: mdl-38566431

ABSTRACT

The modification and recognition of 5-methylcytosine (m5C) are involved in the initiation and progression of various tumor types. However, the precise role and potential mechanism of Y-box-binding protein 1 (YBX1) in esophageal squamous cell carcinoma (ESCC) remains unclear. Here, it is found that YBX1 is frequently upregulated in ESCC compared with matched nontumor tissues. Gain- and loss-of-function assays show that YBX1 promoted the proliferation and metastasis of ESCC cells both in vitro and in vivo. Functional studies revealed that NOP2/Sun RNA methyltransferase family member 2 (NSUN2) is a critical RNA methyltransferase that facilitates YBX1-mediated ESCC progression. Mechanistically, integrated analysis based on RNA immunoprecipitation sequencing (RIP-seq) and m5C methylated RNA immunoprecipitation and sequencing (MeRIP-seq) assays identified spermine oxidase (SMOX) as a target gene containing an m5C site in its coding sequence (CDS) region, which coincided well with the binding site of YBX1. Overexpression of SMOX-WT but not SMOX-Mut partially restored the proliferation and invasion ability of ESCC cells curbed by YBX1 knockdown. Moreover, YBX1 activated the mTORC1 signaling pathway by stabilizing SMOX mRNA. The study reveals that YBX1 promotes ESCC development by stabilizing SMOX mRNA in an m5C-dependent manner, thus providing a valuable therapeutic target for ESCC.


Subject(s)
Disease Progression , Esophageal Neoplasms , Esophageal Squamous Cell Carcinoma , RNA Stability , Y-Box-Binding Protein 1 , Humans , Y-Box-Binding Protein 1/genetics , Y-Box-Binding Protein 1/metabolism , Esophageal Squamous Cell Carcinoma/genetics , Esophageal Squamous Cell Carcinoma/metabolism , Esophageal Squamous Cell Carcinoma/pathology , Esophageal Neoplasms/genetics , Esophageal Neoplasms/metabolism , Esophageal Neoplasms/pathology , RNA Stability/genetics , Mice , Animals , Cell Line, Tumor , Cell Proliferation/genetics , Gene Expression Regulation, Neoplastic/genetics , Disease Models, Animal , RNA, Messenger/genetics , RNA, Messenger/metabolism , Methyltransferases
8.
Nucleic Acids Res ; 52(9): 4985-5001, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38471816

ABSTRACT

Many microRNA (miRNA)-guided Argonaute proteins can cleave RNA ('slicing'), even though miRNA-mediated target repression is generally cleavage-independent. Here we use Caenorhabditis elegans to examine the role of catalytic residues of miRNA Argonautes in organismal development. In contrast to previous work, mutations in presumed catalytic residues did not interfere with development when introduced by CRISPR. We find that unwinding and decay of miRNA star strands is weakly defective in the catalytic residue mutants, with the largest effect observed in embryos. Argonaute-Like Gene 2 (ALG-2) is more dependent on catalytic residues for unwinding than ALG-1. The miRNAs that displayed the greatest (albeit minor) dependence on catalytic residues for unwinding tend to form stable duplexes with their star strand, and in some cases, lowering duplex stability alleviates dependence on catalytic residues. While a few miRNA guide strands are reduced in the mutant background, the basis of this is unclear since changes were not dependent on EBAX-1, an effector of Target-Directed miRNA Degradation (TDMD). Overall, this work defines a role for the catalytic residues of miRNA Argonautes in star strand decay; future work should examine whether this role contributes to the selection pressure to conserve catalytic activity of miRNA Argonautes across the metazoan phylogeny.


Subject(s)
Argonaute Proteins , Caenorhabditis elegans Proteins , Caenorhabditis elegans , MicroRNAs , Animals , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , MicroRNAs/metabolism , MicroRNAs/genetics , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans Proteins/chemistry , Argonaute Proteins/metabolism , Argonaute Proteins/genetics , Argonaute Proteins/chemistry , RNA Stability/genetics , Mutation , Catalytic Domain/genetics , CRISPR-Cas Systems , RNA-Binding Proteins
9.
J Biol Chem ; 300(4): 107152, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38462165

ABSTRACT

Prostate cancer is a leading cause of cancer-related mortality in males. Dysregulation of RNA adenine N-6 methylation (m6A) contributes to cancer malignancy. m6A on mRNA may affect mRNA splicing, turnover, transportation, and translation. m6A exerts these effects, at least partly, through dedicated m6A reader proteins, including YTH domain-containing family protein 2 (YTHDF2). YTHDF2 is necessary for development while its dysregulation is seen in various cancers, including prostate cancer. However, the mechanism underlying the dysregulation and function of YTHDF2 in cancer remains elusive. Here, we find that the deubiquitinase OUT domain-containing ubiquitin aldehyde-binding protein 1 (OTUB1) increases YTHDF2 protein stability by inhibiting its ubiquitination. With in vivo and in vitro ubiquitination assays, OTUB1 is shown to block ubiquitin transfer to YTHDF2 independent of its deubiquitinase activity. Furthermore, analysis of functional transcriptomic data and m6A-sequencing data identifies PRSS8 as a potential tumor suppressor gene. OTUB1 and YTHDF2 decrease mRNA and protein levels of PRSS8, which is a trypsin-like serine protease. Mechanistically, YTHDF2 binds PRSS8 mRNA and promotes its degradation in an m6A-dependent manner. Further functional study on cellular and mouse models reveals PRSS8 is a critical downstream effector of the OTUB1-YTHDF2 axis in prostate cancer. We find in prostate cancer cells, PRSS8 decreases nuclear ß-catenin level through E-cadherin, which is independent of its protease activity. Collectively, our study uncovers a key regulator of YTHDF2 protein stability and establishes a functional OTUB1-YTHDF2-PRSS8 axis in prostate cancer.


Subject(s)
Cell Proliferation , Deubiquitinating Enzymes , Prostatic Neoplasms , RNA-Binding Proteins , Serine Endopeptidases , Animals , Humans , Male , Mice , Cell Line, Tumor , Cell Proliferation/genetics , Deubiquitinating Enzymes/metabolism , Deubiquitinating Enzymes/genetics , Gene Expression Regulation, Neoplastic , Prostatic Neoplasms/metabolism , Prostatic Neoplasms/genetics , Prostatic Neoplasms/pathology , Protein Stability , RNA Stability/genetics , RNA, Messenger/metabolism , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , Serine Endopeptidases/metabolism , Ubiquitination
10.
Proc Natl Acad Sci U S A ; 121(14): e2308814121, 2024 Apr 02.
Article in English | MEDLINE | ID: mdl-38527194

ABSTRACT

RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in posttranscriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. We developed a hierarchical Bayesian model that corrects for confounding factors in rifampicin RNA stability assays and enables us to identify differentially decaying transcripts transcriptome-wide. Our analysis revealed that the median RNA half-life in Salmonella in early stationary phase is less than 1 min, a third of previous estimates. We found that over half of the 500 most long-lived transcripts are bound by at least one major RBP, suggesting a general role for RBPs in shaping the transcriptome. Integrating differential stability estimates with cross-linking and immunoprecipitation followed by RNA sequencing (CLIP-seq) revealed that approximately 30% of transcripts with ProQ binding sites and more than 40% with CspC/E binding sites in coding or 3' untranslated regions decay differentially in the absence of the respective RBP. Analysis of differentially destabilized transcripts identified a role for ProQ in the oxidative stress response. Our findings provide insights into posttranscriptional regulation by ProQ and CspC/E, and the importance of RBPs in regulating gene expression.


Subject(s)
Gene Expression Profiling , Rifampin , Bayes Theorem , Half-Life , Transcriptome , RNA-Binding Proteins/metabolism , RNA/metabolism , Salmonella/metabolism , RNA Stability/genetics
11.
Nat Commun ; 15(1): 2720, 2024 Mar 28.
Article in English | MEDLINE | ID: mdl-38548718

ABSTRACT

RNA decay is vital for regulating mRNA abundance and gene expression. Existing technologies lack the spatiotemporal precision or transcript specificity to capture the stochastic and transient decay process. We devise a general strategy to inducibly recruit protein factors to modulate target RNA metabolism. Specifically, we introduce a Rapid Inducible Decay of RNA (RIDR) technology to degrade target mRNAs within minutes. The fast and synchronous induction enables direct visualization of mRNA decay dynamics in cells. Applying RIDR to endogenous ACTB mRNA reveals rapid formation and dissolution of RNA granules in pre-existing P-bodies. Time-resolved RNA distribution measurements demonstrate rapid RNA decay inside P-bodies, which is further supported by knocking down P-body constituent proteins. Light and oxidative stress modulate P-body behavior, potentially reconciling the contradictory literature about P-body function. This study reveals compartmentalized RNA decay kinetics, establishing RIDR as a pivotal tool for exploring the spatiotemporal RNA metabolism in cells.


Subject(s)
Processing Bodies , Proteins , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA Stability/genetics
12.
J Cell Biol ; 223(3)2024 03 04.
Article in English | MEDLINE | ID: mdl-38349334

ABSTRACT

The cell cycle is a highly regulated process in which proteins involved in cell cycle progression exhibit periodic expression patterns, controlled by specific mechanisms such as transcription, translation, and degradation. However, the precise mechanisms underlying the oscillations of mRNA levels in cell cycle regulators are not fully understood. In this study, we observed that the stability of cyclin D1 (CCND1) mRNA fluctuates during the cell cycle, with increased stability during interphase and decreased stability during the M phase. Additionally, we identified a key RNA binding protein, positive coactivator 4 (PC4), which plays a crucial role in stabilizing CCND1 mRNA and regulating its periodic expression. Moreover, the binding affinity of PC4 to CCND1 mRNA is modulated by two cell cycle-specific posttranslational modifications: ubiquitination of K68 enhances binding and stabilizes the CCND1 transcript during interphase, while phosphorylation of S17 inhibits binding during the M phase, leading to degradation of CCND1 mRNA. Remarkably, PC4 promotes the transition from G1 to S phase in the cell cycle, and depletion of PC4 enhances the efficacy of CDK4/6 inhibitors in hepatocellular carcinoma, suggesting that PC4 could serve as a potential therapeutic target. These findings provide valuable insights into the intricate regulation of cell cycle dynamics.


Subject(s)
Cell Cycle , Cyclin D1 , RNA Stability , RNA-Binding Proteins , Cell Cycle/genetics , Cell Division , Cyclin D1/genetics , Cyclin-Dependent Kinase Inhibitor Proteins , RNA Stability/genetics , RNA, Messenger/genetics , Male , Animals , Mice , Mice, Inbred BALB C , Humans , Cell Line, Tumor , RNA-Binding Proteins/genetics , Phosphorylation , Ubiquitination
13.
Nucleic Acids Res ; 52(9): 5320-5335, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38366569

ABSTRACT

The σ54-σS sigma factor cascade plays a central role in regulating differential gene expression during the enzootic cycle of Borreliella burgdorferi, the Lyme disease pathogen. In this pathway, the primary transcription of rpoS (which encodes σS) is under the control of σ54 which is activated by a bacterial enhancer-binding protein (EBP), Rrp2. The σ54-dependent activation in B. burgdorferi has long been thought to be unique, requiring an additional factor, BosR, a homologue of classical Fur/PerR repressor/activator. However, how BosR is involved in this σ54-dependent activation remains unclear and perplexing. In this study, we demonstrate that BosR does not function as a regulator for rpoS transcriptional activation. Instead, it functions as a novel RNA-binding protein that governs the turnover rate of rpoS mRNA. We further show that BosR directly binds to the 5' untranslated region (UTR) of rpoS mRNA, and the binding region overlaps with a region required for rpoS mRNA degradation. Mutations within this 5'UTR region result in BosR-independent RpoS production. Collectively, these results uncover a novel role of Fur/PerR family regulators as RNA-binding proteins and redefine the paradigm of the σ54-σS pathway in B. burgdorferi.


Subject(s)
Bacterial Proteins , Borrelia burgdorferi , Gene Expression Regulation, Bacterial , RNA Stability , RNA-Binding Proteins , Sigma Factor , Sigma Factor/metabolism , Sigma Factor/genetics , Borrelia burgdorferi/genetics , Borrelia burgdorferi/metabolism , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , RNA Stability/genetics , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , 5' Untranslated Regions , Lyme Disease/microbiology , Lyme Disease/genetics , Repressor Proteins/metabolism , Repressor Proteins/genetics , RNA, Messenger/metabolism , RNA, Messenger/genetics , RNA Polymerase Sigma 54/metabolism , RNA Polymerase Sigma 54/genetics
14.
Nucleic Acids Res ; 52(9): 5336-5355, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38381904

ABSTRACT

Temporally and spatially controlled accumulation underlies the functions of microRNAs (miRNAs) in various developmental processes. In Caenorhabditis elegans, this is exemplified by the temporal patterning miRNAs lin-4 and let-7, but for most miRNAs, developmental expression patterns remain poorly resolved. Indeed, experimentally observed long half-lives may constrain possible dynamics. Here, we profile miRNA expression throughout C. elegans postembryonic development at high temporal resolution, which identifies dynamically expressed miRNAs. We use mathematical models to explore the underlying mechanisms. For let-7, we can explain, and experimentally confirm, a striking stepwise accumulation pattern through a combination of rhythmic transcription and stage-specific regulation of precursor processing by the RNA-binding protein LIN-28. By contrast, the dynamics of several other miRNAs cannot be explained by regulation of production rates alone. Specifically, we show that a combination of oscillatory transcription and rhythmic decay drive rhythmic accumulation of miR-235, orthologous to miR-92 in other animals. We demonstrate that decay of miR-235 and additional miRNAs depends on EBAX-1, previously implicated in target-directed miRNA degradation (TDMD). Taken together, our results provide insight into dynamic miRNA decay and establish a resource to studying both the developmental functions of, and the regulatory mechanisms acting on, miRNAs.


Subject(s)
Caenorhabditis elegans Proteins , Caenorhabditis elegans , Gene Expression Regulation, Developmental , Larva , MicroRNAs , Animals , MicroRNAs/metabolism , MicroRNAs/genetics , Caenorhabditis elegans/genetics , Caenorhabditis elegans/growth & development , Caenorhabditis elegans/metabolism , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Larva/genetics , Larva/growth & development , Larva/metabolism , RNA Stability/genetics , Transcription Factors/metabolism , Transcription Factors/genetics , Repressor Proteins
15.
Nucleic Acids Res ; 52(7): 4002-4020, 2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38321934

ABSTRACT

Poly(ADP-ribosylation) (PARylation) is a post-translational modification mediated by a subset of ADP-ribosyl transferases (ARTs). Although PARylation-inhibition based therapies are considered as an avenue to combat debilitating diseases such as cancer and myopathies, the role of this modification in physiological processes such as cell differentiation remains unclear. Here, we show that Tankyrase1 (TNKS1), a PARylating ART, plays a major role in myogenesis, a vital process known to drive muscle fiber formation and regeneration. Although all bona fide PARPs are expressed in muscle cells, experiments using siRNA-mediated knockdown or pharmacological inhibition show that TNKS1 is the enzyme responsible of catalyzing PARylation during myogenesis. Via this activity, TNKS1 controls the turnover of mRNAs encoding myogenic regulatory factors such as nucleophosmin (NPM) and myogenin. TNKS1 mediates these effects by targeting RNA-binding proteins such as Human Antigen R (HuR). HuR harbors a conserved TNKS-binding motif (TBM), the mutation of which not only prevents the association of HuR with TNKS1 and its PARylation, but also precludes HuR from regulating the turnover of NPM and myogenin mRNAs as well as from promoting myogenesis. Therefore, our data uncover a new role for TNKS1 as a key modulator of RBP-mediated post-transcriptional events required for vital processes such as myogenesis.


Subject(s)
Muscle Development , Muscle Fibers, Skeletal , Myogenin , RNA, Messenger , Tankyrases , Tankyrases/metabolism , Tankyrases/genetics , Humans , RNA, Messenger/metabolism , RNA, Messenger/genetics , Muscle Development/genetics , Animals , Muscle Fibers, Skeletal/metabolism , Mice , Myogenin/genetics , Myogenin/metabolism , Nucleophosmin , ELAV-Like Protein 1/metabolism , ELAV-Like Protein 1/genetics , RNA Stability/genetics , Poly ADP Ribosylation/genetics , Cell Line , Nuclear Proteins/metabolism , Nuclear Proteins/genetics , Cell Differentiation/genetics , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , HEK293 Cells
16.
Oncogene ; 43(13): 976-991, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38361047

ABSTRACT

Cellular senescence plays a critical role in cancer development, but the underlying mechanisms remain poorly understood. Our recent study uncovered that replicative senescent colorectal cancer (CRC) cells exhibit increased levels of mRNA N6-methyladenosine (m6A) and methyltransferase METTL3. Knockdown of METTL3 can restore the senescence-associated secretory phenotype (SASP) of CRC cells. Our findings, which were confirmed by m6A-sequencing and functional studies, demonstrate that the cyclin-dependent kinase inhibitor 2B (CDKN2B, encoding p15INK4B) is a mediator of METTL3-regulated CRC senescence. Specifically, m6A modification at position A413 in the coding sequence (CDS) of CDKN2B positively regulates its mRNA stability by recruiting IGF2BP3 and preventing binding with the CCR4-NOT complex. Moreover, increased METTL3 methylates and stabilizes the mRNA of E2F1, which binds to the -208 to -198 regions of the CDKN2B promoter to facilitate transcription. Inhibition of METTL3 or specifically targeting CDKN2B methylation can suppress CRC senescence. Finally, the METTL3/CDKN2B axis-induced senescence can facilitate M2 macrophage polarization and is correlated with aging and CRC progression. The involvement of METTL3/CDKN2B in cell senescence provides a new potential therapeutic target for CRC treatment and expands our understanding of mRNA methylation's role in cellular senescence.


Subject(s)
Colorectal Neoplasms , Methyltransferases , Humans , Methyltransferases/metabolism , Cellular Senescence/genetics , Colorectal Neoplasms/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA Stability/genetics
17.
New Phytol ; 241(4): 1636-1645, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38009859

ABSTRACT

Transposable elements (TEs) are mobile genetic elements that can impair the host genome stability and integrity. It has been well documented that activated transposons in plants are suppressed by small interfering (si) RNAs. However, transposon repression by the cytoplasmic RNA surveillance system is unknown. Here, we show that mRNA deadenylation is critical for controlling transposons in Arabidopsis. Trimming of poly(A) tail is a rate-limiting step that precedes the RNA decay and is primarily mediated by the CARBON CATABOLITE REPRESSION 4 (CCR4)-NEGATIVE ON TATA-LESS (NOT) complex. We found that the loss of CCR4a leads to strong derepression and mobilization of TEs in Arabidopsis. Intriguingly, CCR4a regulates a largely distinct set of TEs from those controlled by RNA-dependent RNA Polymerase 6 (RDR6), a key enzyme that produces cytoplasmic siRNAs. This indicates that the cytoplasmic RNA quality control mechanism targets the TEs that are poorly recognized by the previously well-characterized RDR6-mediated pathway, and thereby augments the host genome stability. Our study suggests a hitherto unknown mechanism for transposon repression mediated by RNA deadenylation and unveils a complex nature of the host's strategy to maintain the genome integrity.


Subject(s)
Arabidopsis , Catabolite Repression , Arabidopsis/genetics , Arabidopsis/metabolism , RNA, Small Interfering/metabolism , DNA Transposable Elements/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Genomic Instability , RNA Stability/genetics
18.
RNA Biol ; 21(1): 1-15, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38111129

ABSTRACT

Inhibition of apoptosis is one of the hallmarks of cancer and is a target of various therapeutic interventions. BIRC5 is an inhibitor of apoptosis that is aberrantly expressed in cancer leading to sustained growth of tumours. Post-transcriptional control mechanisms involving RNA-binding proteins and AU-rich elements (AREs) are fundamental to many cellular processes and changes in the expression or function of these proteins can promote an aberrant and pathological phenotype. BIRC5 mRNA has an ARE in its 3' UTR making it a candidate for regulation by the RNA binding proteins tristetraprolin (TTP) and HuR (ELAVL1). In this study, we investigated the binding of TTP and HuR by RNA-immunoprecipitation assays and found that these proteins were associated with BIRC5 mRNA to varying extents. Consequently, BIRC5 expression decreased when TTP was overexpressed and apoptosis was induced. In the absence of TTP, BIRC5 mRNA was stabilized, protein expression increased and the number of apoptotic cells declined. As an ARE-mRNA stabilizing protein, recombinant HuR led to upregulation of BIRC5 expression, whereas HuR silencing was concomitant with downregulation of BIRC5 mRNA and protein and increased cell death. Survival analyses demonstrated that increased TTP and low BIRC5 expression predicted an overall better prognosis compared to dysregulated TTP and high BIRC5. Thus, the results present a novel target of ARE-mediated post-transcriptional regulation.


Subject(s)
Breast Neoplasms , Tristetraprolin , Humans , Female , Tristetraprolin/genetics , Tristetraprolin/metabolism , Survivin/genetics , Survivin/metabolism , Breast Neoplasms/genetics , 3' Untranslated Regions , Apoptosis/genetics , RNA, Messenger/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , RNA Stability/genetics
19.
Sci Rep ; 13(1): 22870, 2023 12 18.
Article in English | MEDLINE | ID: mdl-38129448

ABSTRACT

A mutant deficient in polynucleotide phosphorylase (PNPase) activity was previously constructed in Enterococcus faecalis 14; a strain producing a leaderless two-peptide enterocin DD14 (EntDD14). Here, we examined the impact of the absence of PNPase on the expression and synthesis of EntDD14, at the transcriptional and functional levels. As result, EntDD14 synthesis augmented in line with the growth curve, reaching a two- to fourfold increase in the ΔpnpA mutant compared to the E. faecalis 14 wild-type strain (WT). EntDD14 synthesis has reached its highest level after 9 h of growth in both strains. Notably, high expression level of the ddABCDEFGHIJ cluster was registered in ΔpnpA mutant. Transcriptional and in silico analyses support the existence of ddAB and ddCDEFGHIJ independent transcripts, and analysis of the fate of ddAB and ddCDEFGHIJ mRNAs indicated that the differences in mRNA levels and the high EntDD14 activity are likely due to a better stability of the two transcripts in the ΔpnpA mutant, which should result in a higher translation efficiency of the ddAB EntDD14 structural genes and their other protein determinants. Consequently, this study shows a potential link between the mRNA stability and EntDD14 synthesis, secretion and immunity in a genetic background lacking PNPase.


Subject(s)
Bacteriocins , Bacteriocins/genetics , Bacteriocins/metabolism , Enterococcus faecalis/genetics , Enterococcus faecalis/metabolism , Bridged-Ring Compounds/metabolism , RNA Stability/genetics
20.
Sci Rep ; 13(1): 23103, 2023 12 29.
Article in English | MEDLINE | ID: mdl-38158431

ABSTRACT

Glioma is the most common primary malignant brain tumor in adults and remains an incurable disease at present. Thus, there is an urgent need for progress in finding novel molecular mechanisms that control the progression of glioma which could be used as therapeutic targets for glioma patients. The RNA binding protein cytoplasmic polyadenylate element-binding protein 2 (CPEB2) is involved in the pathogenesis of several tumors. However, the role of CPEB2 in glioma progression is unknown. In this study, the functional characterization of the role and molecular mechanism of CPEB2 in glioma were examined using a series of biological and cellular approaches in vitro and in vivo. Our work shows CPEB2 is significantly downregulated in various glioma patient cohorts. Functional characterization of CPEB2 by overexpression and knockdown revealed that it inhibits glioma cell proliferation and promotes apoptosis. CPEB2 exerts an anti-tumor effect by increasing p21 mRNA stability and inducing G1 cell cycle arrest in glioma. Overall, this work stands as the first report of CPEB2 downregulation and involvement in glioma pathogenesis, and identifies CPEB2 as an important tumor suppressor gene through targeting p21 in glioma, which revealed that CPEB2 may become a promising predictive biomarker for prognosis in glioma patients.


Subject(s)
Gene Expression Regulation, Neoplastic , Glioma , Oncogene Protein p21(ras) , RNA Stability , RNA-Binding Proteins , RNA-Binding Proteins/blood , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Cell Proliferation/genetics , Oncogene Protein p21(ras)/genetics , Oncogene Protein p21(ras)/metabolism , RNA Stability/genetics , Glioma/diagnosis , Glioma/physiopathology , Gene Knockdown Techniques , Apoptosis/genetics , Gene Expression Regulation, Neoplastic/genetics , Cell Cycle Checkpoints/genetics , Biomarkers, Tumor/blood , Down-Regulation/genetics , Cell Line, Tumor , Mice, Inbred BALB C , HEK293 Cells , Humans , Female , Animals , Mice
SELECTION OF CITATIONS
SEARCH DETAIL
...