scholarly journals Exon Selection in α-Tropomyosin mRNA Is Regulated by the Antagonistic Action of RBM4 and PTB

2005 ◽  
Vol 25 (22) ◽  
pp. 10111-10121 ◽  
Author(s):  
Jung-Chun Lin ◽  
Woan-Yuh Tarn
Keyword(s):  
Skeletal Muscle ◽  
Rna Binding ◽  
Binding Motif ◽  
Splicing Regulators ◽  
Polypyrimidine Tract Binding Protein ◽  
Muscle Cell Type ◽  
Differential Display Analysis ◽  
Splicing Regulator ◽  
Mrna Isoform

ABSTRACT RNA-binding motif protein 4 (RBM4) has been implicated in the regulation of precursor mRNA splicing. Using differential display analysis, we identified mRNAs that associate with RBM4-containing messenger RNPs in vivo. Among these mRNAs, α-tropomyosin (α-TM) is known to exhibit a muscle cell type-specific splicing pattern. The level of the skeletal muscle-specific α-TM mRNA isoform partially correlated with that of RBM4 in human tissues examined and could be modulated by ectopic overexpression or suppression of RBM4. These results indicated that RBM4 directly influences the expression of the skeletal muscle-specific α-TM isoform. Using minigenes, we demonstrated that RBM4 can activate the selection of skeletal muscle-specific exons, possibly via binding to intronic pyrimidine-rich elements. By contrast, the splicing regulator polypyrimidine tract binding protein (PTB) excluded these exons; moreover, RBM4 antagonized this PTB-mediated exon exclusion likely by competing with PTB for binding to a CU-rich element. This study suggests a possible mechanism underlying the regulated alternative splicing of α-TM by the antagonistic splicing regulators RBM4 and PTB.

scholarly journals RBMX suppresses tumorigenicity and progression of bladder cancer by interacting with the hnRNP A1 protein to regulate PKM alternative splicing

Oncogene ◽  
2021 ◽  
Author(s):  
Qiuxia Yan ◽  
Peng Zeng ◽  
Xiuqin Zhou ◽  
Xiaoying Zhao ◽  
Runqiang Chen ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Alternative Splicing ◽  
Rna Binding ◽  
Aerobic Glycolysis ◽  
Histological Grade ◽  
Migration And Invasion ◽  
Binding Motif ◽  
Hnrnp A1

AbstractThe prognosis for patients with metastatic bladder cancer (BCa) is poor, and it is not improved by current treatments. RNA-binding motif protein X-linked (RBMX) are involved in the regulation of the malignant progression of various tumors. However, the role of RBMX in BCa tumorigenicity and progression remains unclear. In this study, we found that RBMX was significantly downregulated in BCa tissues, especially in muscle-invasive BCa tissues. RBMX expression was negatively correlated with tumor stage, histological grade and poor patient prognosis. Functional assays demonstrated that RBMX inhibited BCa cell proliferation, colony formation, migration, and invasion in vitro and suppressed tumor growth and metastasis in vivo. Mechanistic investigations revealed that hnRNP A1 was an RBMX-binding protein. RBMX competitively inhibited the combination of the RGG motif in hnRNP A1 and the sequences flanking PKM exon 9, leading to the formation of lower PKM2 and higher PKM1 levels, which attenuated the tumorigenicity and progression of BCa. Moreover, RBMX inhibited aerobic glycolysis through hnRNP A1-dependent PKM alternative splicing and counteracted the PKM2 overexpression-induced aggressive phenotype of the BCa cells. In conclusion, our findings indicate that RBMX suppresses BCa tumorigenicity and progression via an hnRNP A1-mediated PKM alternative splicing mechanism. RBMX may serve as a novel prognostic biomarker for clinical intervention in BCa.

scholarly journals Translational induction of ATF4 during integrated stress response requires noncanonical initiation factors eIF2D and DENR

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Deepika Vasudevan ◽  
Sarah D. Neuman ◽  
Amy Yang ◽  
Lea Lough ◽  
Brian Brown ◽  
...  
Keyword(s):  
Stress Response ◽  
Er Stress ◽  
Stress Responses ◽  
Rna Binding ◽  
Open Reading Frames ◽  
Binding Motif ◽  
Integrated Stress Response ◽  
Developmental Defects ◽  
Initiation Factors

Abstract The Integrated Stress Response (ISR) helps metazoan cells adapt to cellular stress by limiting the availability of initiator methionyl-tRNA for translation. Such limiting conditions paradoxically stimulate the translation of ATF4 mRNA through a regulatory 5′ leader sequence with multiple upstream Open Reading Frames (uORFs), thereby activating stress-responsive gene expression. Here, we report the identification of two critical regulators of such ATF4 induction, the noncanonical initiation factors eIF2D and DENR. Loss of eIF2D and DENR in Drosophila results in increased vulnerability to amino acid deprivation, susceptibility to retinal degeneration caused by endoplasmic reticulum (ER) stress, and developmental defects similar to ATF4 mutants. eIF2D requires its RNA-binding motif for regulation of 5′ leader-mediated ATF4 translation. Consistently, eIF2D and DENR deficient human cells show impaired ATF4 protein induction in response to ER stress. Altogether, our findings indicate that eIF2D and DENR are critical mediators of ATF4 translational induction and stress responses in vivo.

scholarly journals Severe muscle wasting and denervation in mice lacking the RNA-binding protein ZFP106

2016 ◽  
Vol 113 (31) ◽  
pp. E4494-E4503 ◽  
Author(s):  
Douglas M. Anderson ◽  
Jessica Cannavino ◽  
Hui Li ◽  
Kelly M. Anderson ◽  
Benjamin R. Nelson ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Motor Neurons ◽  
Knockout Mice ◽  
Muscle Wasting ◽  
Rna Binding ◽  
Neuromuscular Junctions ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Binding Motif ◽  
Nerve Muscle

Innervation of skeletal muscle by motor neurons occurs through the neuromuscular junction, a cholinergic synapse essential for normal muscle growth and function. Defects in nerve–muscle signaling cause a variety of neuromuscular disorders with features of ataxia, paralysis, skeletal muscle wasting, and degeneration. Here we show that the nuclear zinc finger protein ZFP106 is highly enriched in skeletal muscle and is required for postnatal maintenance of myofiber innervation by motor neurons. Genetic disruption of Zfp106 in mice results in progressive ataxia and hindlimb paralysis associated with motor neuron degeneration, severe muscle wasting, and premature death by 6 mo of age. We show that ZFP106 is an RNA-binding protein that associates with the core splicing factor RNA binding motif protein 39 (RBM39) and localizes to nuclear speckles adjacent to spliceosomes. Upon inhibition of pre-mRNA synthesis, ZFP106 translocates with other splicing factors to the nucleolus. Muscle and spinal cord of Zfp106 knockout mice displayed a gene expression signature of neuromuscular degeneration. Strikingly, altered splicing of the Nogo (Rtn4) gene locus in skeletal muscle of Zfp106 knockout mice resulted in ectopic expression of NOGO-A, the neurite outgrowth factor that inhibits nerve regeneration and destabilizes neuromuscular junctions. These findings reveal a central role for Zfp106 in the maintenance of nerve–muscle signaling, and highlight the involvement of aberrant RNA processing in neuromuscular disease pathogenesis.

scholarly journals Therapeutic modulation of RNA-binding protein Rbm38 facilitates re-endothelialization after arterial injury

2019 ◽  
Vol 115 (12) ◽  
pp. 1804-1810 ◽  
Author(s):  
Kristina Sonnenschein ◽  
Jan Fiedler ◽  
Angelika Pfanne ◽  
Annette Just ◽  
Saskia Mitzka ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Balloon Angioplasty ◽  
Carotid Arteries ◽  
Rna Binding ◽  
Luciferase Reporter ◽  
Binding Motif ◽  
Cell Functions ◽  
Endothelial Regeneration

Abstract Aims Delayed re-endothelialization after balloon angioplasty in patients with coronary or peripheral artery disease impairs vascular healing and leads to neointimal proliferation. In the present study, we examined the effect of RNA-binding motif protein 38 (Rbm38) during re-endothelialization in a murine model of experimental vascular injury. Methods and results Left common carotid arteries of C57BL/6 mice were electrically denudated and endothelial regeneration was evaluated. Profiling of RNA-binding proteins revealed dysregulated expression of Rbm38 in the denudated and regenerated areas. We next tested the importance of Rbm38 in human umbilical vein endothelial cells (HUVECS) and analysed its effects on cellular proliferation, migration and apoptosis. Rbm38 silencing in vitro demonstrated important beneficial functional effects on migratory capacity and proliferation of endothelial cells. In vivo, local silencing of Rbm38 also improved re-endothelialization of denuded carotid arteries. Luciferase reporter assay identified miR-98 and let-7f to regulate Rbm38 and the positive proliferative properties of Rbm38 silencing in vitro and in vivo were mimicked by therapeutic overexpression of these miRNAs. Conclusion The present data identified Rbm38 as an important factor of the regulation of various endothelial cell functions. Local inhibition of Rbm38 as well as overexpression of the upstream regulators miR-98 and let-7f improved endothelial regeneration in vivo and thus may be a novel therapeutic entry point to avoid endothelial damage after balloon angioplasty.

scholarly journals Identification of RBPMS as a smooth muscle master splicing regulator via proximity of its gene with super-enhancers

2019 ◽  
Author(s):  
Erick E. Nakagaki-Silva ◽  
Clare Gooding ◽  
Miriam Llorian ◽  
Aishwarya Griselda Jacob ◽  
Frederick Richards ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Control Cell ◽  
Phenotypic Switching ◽  
Regulatory Rna ◽  
Splicing Regulators ◽  
Its Gene ◽  
Splicing Regulator ◽  
Transcription Regulators

AbstractAlternative splicing (AS) programs are primarily controlled by regulatory RNA binding proteins (RBPs). It has been proposed that a small number of master splicing regulators might control cell-specific splicing networks and that these RBPs could be identified by proximity of their genes to transcriptional super-enhancers. Using this approach we identified RBPMS as a critical splicing regulator in differentiated vascular smooth muscle cells (SMCs). RBPMS is highly down-regulated during phenotypic switching of SMCs from a contractile to a motile and proliferative phenotype and is responsible for 20% of the AS changes during this transition. RBPMS directly regulates AS of numerous components of the actin cytoskeleton and focal adhesion machineries whose activity is critical for SMC function in both phenotypes. RBPMS also regulates splicing of other splicing, post-transcriptional and transcription regulators including the key SMC transcription factor Myocardin, thereby matching many of the criteria of a master regulator of AS in SMCs.

scholarly journals Unravelling the Stability and Capsid Dynamics of the Three Virions of Brome Mosaic Virus Assembled Autonomously In Vivo

2019 ◽  
Author(s):  
Antara Chakravarty ◽  
Christian Beren ◽  
Rees Garmann ◽  
A.L.N. Rao
Keyword(s):  
Mosaic Virus ◽  
Transient Expression ◽  
Rna Binding ◽  
Conformational Dynamics ◽  
Brome Mosaic Virus ◽  
Crystallographic Structure ◽  
Binding Motif ◽  
Genomic Rnas ◽  
Viral Capsids

ABSTRACTViral capsids are dynamic assemblies that undergo controlled conformational transitions to perform various biological functions. The replicated three-molecule RNA progeny of Brome mosaic virus (BMV) are packaged by a single capsid protein (CP) into three types of morphologically indistinguishable icosahedral virions with T=3 quasi-symmetry. Type 1 (B1v) and type 2 (B2v) virions respectively package genomic RNA1 or RNA2, while type 3 (B3+4v) co-packages genomic RNA3 (B3) and its sub-genomic RNA4 (B4). In this study, the application of a robust Agrobacterium-mediated transient expression system allowed us to assemble each virion type separately in planta. Physical and biochemical approaches analyzing the morphology, size, and electrophoretic mobility failed to distinguish between the virion types, so protease-based mapping experiments were used to analyze the conformational dynamics of the individual virions. The crystallographic structure of the BMV capsid shows four trypsin-cleavage sites (K65, R103, K111 and K165 on the A, B and C subunits) exposed on the exterior of the capsid. Irrespective of the digestion time, while retaining their capsid structural integrity, B1v and B2v released only two peptides involving amino acids 2-8 and 16-22 from the N-proximal arginine-rich RNA binding motif. In contrast, B3+4v capsids are unstable to trypsin, releasing several peptides in addition to the four sites predicted to be exposed on the capsid exterior. These results, demonstrating qualitatively different dynamics for the three types of BMV virions, suggest that the different RNA genes they contain may have different translational timing and efficiency and may even impart different structures to their capsids.IMPORTANCEThe majority of viruses contain RNA genomes protected by a shell of capsid proteins. Although crystallographic studies show that viral capsids are static structures, accumulating evidence suggests that in solution virions are highly dynamic assemblies. The three genomic RNAs (RNAs 1, 2 and 3) and a single subgenomic RNA (RNA4) of Brome mosaic virus (BMV), an RNA virus pathogenic to plants, are distributed among three physically homogeneous virions. This study examines the capsid dynamics by MALDI-TOF analyses following trypsin digestion of the three virions assembled separately in vivo using the Agrobacterium-mediated transient expression approach. The results provide compelling evidence that virions packaging genomic RNAs1 and 2 are more stable and dynamically distinct from those co-packaging RNA3 and 4, suggesting that RNA-dependent capsid dynamics play an important biological role in the viral life cycle.

scholarly journals Circ-CTNNB1 Drives Aerobic Glycolysis and Osteosarcoma Progression via m6A Modification Through Interacting With RBM15

2021 ◽  
Author(s):  
Hucheng Liu ◽  
Jun Xiao ◽  
Bo Li ◽  
Yajun Chen ◽  
Jin Zeng ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Rna Binding ◽  
Aerobic Glycolysis ◽  
Ectopic Expression ◽  
Phosphoglycerate Kinase ◽  
Binding Motif ◽  
Mobility Shift ◽  
Underlying Mechanisms

Abstract Background In a previous study, we have identified that circ-CTNNB1 (a circular RNA derived from CTNNB1) drives cancer progression through the activation of the Wnt/β-catenin signaling pathway in various tumors. However, the functions of circ-CTNNB1 in regulating osteosarcoma (OS, a highly malignant bone tumor in children and adolescents) remain unclear. In this study, we aimed to assess the role of circ-CTNNB1 in OS and identify the underlying mechanisms, which may contribute to the exploration of a potential therapeutic strategy for OS. Methods Circ-CTNNB1 was analyzed by qRT-PCR, and the results were confirmed by Sanger sequencing. The interaction and effects between circ-CTNNB1 and RNA binding motif protein 15 (RBM15) were analyzed through biotin-labeled RNA pull-down and mass spectrometry, in vitro binding, and RNA electrophoretic mobility shift assays. In vitro and in vivo experiments were performed to evaluate the biological functions and underlying mechanisms of circ-CTNNB1 and RBM15 in OS cells. Results Circ-CTNNB1 was highly expressed in OS tissues and predominantly detected in the nucleus of OS cells. Ectopic expression of circ-CTNNB1 promoted the growth, invasion, and metastasis of OS cells in vitro and in vivo. Mechanistically, circ-CTNNB1 interacted with RBM15 and subsequently promoted the expression of hexokinase 2 (HK2), glucose-6-phosphate isomerase (GPI), and phosphoglycerate kinase 1 (PGK1) through N6-methyladenosine (m6A) modification to facilitate the glycolysis process and activate OS progression. Conclusions These results indicate that oncogenic circ-CTNNB1 drives aerobic glycolysis and OS progression by facilitating RBM15-mediated m6A modification.

Tristetraprolin and LPS-inducible CXC chemokine are rapidly induced in presumptive satellite cells in response to skeletal muscle injury

2002 ◽  
Vol 115 (13) ◽  
pp. 2701-2712 ◽  
Author(s):  
Chetana Sachidanandan ◽  
Ramkumar Sambasivan ◽  
Jyotsna Dhawan
Keyword(s):  
Skeletal Muscle ◽  
Satellite Cells ◽  
Cell Biology ◽  
Muscle Injury ◽  
Rna Binding ◽  
C2c12 Myoblasts ◽  
Adult Skeletal Muscle ◽  
Cxc Chemokine

Myogenic precursor cells known as satellite cells persist in adult skeletal muscle and are responsible for its ability to regenerate after injury. Quiescent satellite cells are activated by signals emanating from damaged muscle. Here we describe the rapid activation of two genes in response to muscle injury; these transcripts encode LPS-inducible CXC chemokine (LIX), a neutrophil chemoattractant, and Tristetraprolin (TTP), an RNA-binding protein implicated in the regulation of cytokine expression. Using a synchronized cell culture model we show that C2C12 myoblasts arrested in G0 exhibit some molecular attributes of satellite cells in vivo: suppression of MyoD and Myf5 expression during G0 and their reactivation in G1. Synchronization also revealed cell cycle dependent expression of CD34, M-cadherin, HGF and PEA3, genes implicated in satellite cell biology. To identify other genes induced in synchronized C2C12 myoblasts we used differential display PCR and isolated LIX and TTP cDNAs. Both LIX and TTP mRNAs are short-lived, encode molecules implicated in inflammation and are transiently induced during growth activation in vitro. Further, LIX and TTP are rapidly induced in response to muscle damage in vivo. TTP expression precedes that of MyoD and is detected 30 minutes after injury. The spatial distribution of LIX and TTP transcripts in injured muscle suggests expression by satellite cells. Our studies suggest that in addition to generating new cells for repair, activated satellite cells may be a source of signaling molecules involved in tissue remodeling during regeneration.

scholarly journals Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse

2018 ◽  
Vol 115 (47) ◽  
pp. E11061-E11070 ◽  
Author(s):  
Kyu-Hyeon Yeom ◽  
Simon Mitchell ◽  
Anthony J. Linares ◽  
Sika Zheng ◽  
Chia-Ho Lin ◽  
...  
Keyword(s):  
Neuronal Differentiation ◽  
Rna Binding ◽  
Binding Protein ◽  
Embryonic Stem ◽  
Specific Expression ◽  
Stem Loop ◽  
Polypyrimidine Tract Binding Protein ◽  
Precursor Rna

MicroRNA (miRNA)-124 is expressed in neurons, where it represses genes inhibitory for neuronal differentiation, including the RNA binding protein PTBP1. PTBP1 maintains nonneuronal splicing patterns of mRNAs that switch to neuronal isoforms upon neuronal differentiation. We find that primary (pri)-miR-124-1 is expressed in mouse embryonic stem cells where mature miR-124 is absent. PTBP1 binds to this precursor RNA upstream of the miRNA stem–loop to inhibit mature miR-124 expression in vivo and DROSHA cleavage of pri-miR-124-1 in vitro. This function for PTBP1 in repressing miR-124 biogenesis defines an additional regulatory loop in the already intricate interplay between these two molecules. Applying mathematical modeling to examine the dynamics of this regulation, we find that the pool of pri-miR-124 whose maturation is blocked by PTBP1 creates a robust and self-reinforcing transition in gene expression as PTBP1 is depleted during early neuronal differentiation. While interlocking regulatory loops are often found between miRNAs and transcriptional regulators, our results indicate that miRNA targeting of posttranscriptional regulators also reinforces developmental decisions. Notably, induction of neuronal differentiation observed upon PTBP1 knockdown likely results from direct derepression of miR-124, in addition to indirect effects previously described.

scholarly journals Robust RBM3 and β-klotho expression in developing neurons in the human brain

2019 ◽  
Vol 39 (12) ◽  
pp. 2355-2367 ◽  
Author(s):  
Travis C Jackson ◽  
Keri Janesko-Feldman ◽  
Shaun W Carlson ◽  
Shawn E Kotermanski ◽  
Patrick M Kochanek
Keyword(s):  
Cortical Neurons ◽  
Rna Binding ◽  
Transmembrane Protein ◽  
Adult Brain ◽  
Human Infant ◽  
Fibroblast Growth Factor 21 ◽  
Binding Motif ◽  
Dependent Manner ◽  
Neuroprotective Effects

RNA binding motif 3 (RBM3) is a powerful neuroprotectant that inhibits neurodegenerative cell death in vivo and is a promising therapeutic target in brain ischemia. RBM3 is increased by the hormone fibroblast growth factor 21 (FGF21) in an age- and temperature-dependent manner in rat cortical neurons. FGF21 receptor binding is controlled by the transmembrane protein β-klotho, which is mostly absent in the adult brain. We discovered that RBM3/β-klotho is unexpectedly high in the human infant vs. adult brain (hippocampus/prefrontal cortex). The use of tissue homogenates in that study precluded a comparison of RBM3/β-klotho expression among different CNS cell-types, thus, omitted key evidence (i.e. confirmation of neuronal expression) that would otherwise provide a critical link to support their possible direct neuroprotective effects in humans. This report addresses that knowledge gap. High-quality fixed human hippocampus, cortex, and hypothalamic tissues were acquired from the NIH Neurobiobank (<1 yr (premature born) infants, 1 yr, 4 yr, and 34 yr). Dual labeling of cell-type markers vs. RBM3/β-klotho revealed enriched staining of targets in neurons in the developing brain. Identifying that RBM3/β-klotho is abundant in neurons in the immature brain is fundamentally important to guide protocol design and conceptual frameworks germane to future testing of these neuroprotective pathways in humans.

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