RBFOX2 protein domains and cellular activities

RBFOX2 (RNA-binding protein, Fox-1 homologue 2)/RBM9 (RNA-binding-motif protein 9)/RTA (repressor of tamoxifen action)/HNRBP2 (hexaribonucleotide-binding protein 2) encodes an RNA-binding protein involved in tissue specific alternative splicing regulation and steroid receptors transcriptional activity. Its ability to regulate specific splicing profiles depending on context has been related to different expression levels of the RBFOX2 protein itself and that of other splicing regulatory proteins involved in the shared modulation of specific genes splicing. However, this cannot be the sole explanation as to why RBFOX2 plays a widespread role in numerous cellular mechanisms from development to cell survival dependent on cell/tissue type. RBFOX2 isoforms with altered protein domains exist. In the present article, we describe the main RBFOX2 protein domains, their importance in the context of splicing and transcriptional regulation and we propose that RBFOX2 isoform distribution may play a fundamental role in RBFOX2-specific cellular effects.

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Region-specific alternative splicing in the nervous system: Implications for regulation by the RNA-binding protein NAPOR

RNA ◽

10.1017/s1355838202027036 ◽

2002 ◽

Vol 8 (5) ◽

pp. 671-685 ◽

Cited By ~ 60

Author(s):

WENQING ZHANG ◽

HAIYING LIU ◽

KYOUNGHA HAN ◽

PAULA J. GRABOWSKI

Keyword(s):

Nervous System ◽

Alternative Splicing ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Specific Alternative

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

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1608423113 ◽

2016 ◽

Vol 113 (31) ◽

pp. E4494-E4503 ◽

Cited By ~ 16

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.

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The Nuclear RNA-binding Protein Sam68 Translocates to the Cytoplasm and Associates with the Polysomes in Mouse Spermatocytes

Molecular Biology of the Cell ◽

10.1091/mbc.e05-06-0548 ◽

2006 ◽

Vol 17 (1) ◽

pp. 14-24 ◽

Cited By ~ 60

Author(s):

Maria Paola Paronetto ◽

Francesca Zalfa ◽

Flavia Botti ◽

Raffaele Geremia ◽

Claudia Bagni ◽

...

Keyword(s):

Translational Control ◽

Rna Binding ◽

Rna Binding Proteins ◽

Binding Protein ◽

Rna Binding Protein ◽

Male Meiosis ◽

Binding Motif ◽

Mitogen Activated Protein ◽

Pachytene Spermatocytes ◽

And Function

Translational control plays a crucial role during gametogenesis in organisms as different as worms and mammals. Mouse knockout models have highlighted the essential function of many RNA-binding proteins during spermatogenesis. Herein we have investigated the expression and function during mammalian male meiosis of Sam68, an RNA-binding protein implicated in several aspects of RNA metabolism. Sam68 expression and localization within the cells is stage specific: it is expressed in the nucleus of spermatogonia, it disappears at the onset of meiosis (leptotene/zygotene stages), and it accumulates again in the nucleus of pachytene spermatocytes and round spermatids. During the meiotic divisions, Sam68 translocates to the cytoplasm where it is found associated with the polysomes. Translocation correlates with serine/threonine phosphorylation and it is blocked by inhibitors of the mitogen activated protein kinases ERK1/2 and of the maturation promoting factor cyclinB-cdc2 complex. Both kinases associate with Sam68 in pachytene spermatocytes and phosphorylate the regulatory regions upstream and downstream of the Sam68 RNA-binding motif. Molecular cloning of the mRNAs associated with Sam68 in mouse spermatocytes reveals a subset of genes that might be posttranscriptionally regulated by this RNA-binding protein during spermatogenesis. We also demonstrate that Sam68 shuttles between the nucleus and the cytoplasm in secondary spermatocytes, suggesting that it may promote translation of specific RNA targets during the meiotic divisions.

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Loss of the multifunctional RNA-binding protein RBM47 as a source of selectable metastatic traits in breast cancer

eLife ◽

10.7554/elife.02734 ◽

2014 ◽

Vol 3 ◽

Cited By ~ 57

Author(s):

Sakari Vanharanta ◽

Christina B Marney ◽

Weiping Shu ◽

Manuel Valiente ◽

Yilong Zou ◽

...

Keyword(s):

Breast Cancer ◽

Cancer Progression ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Wnt Signaling Pathway ◽

Experimental Models ◽

Breast Cancer Progression ◽

Binding Motif ◽

Clinical Breast

The mechanisms through which cancer cells lock in altered transcriptional programs in support of metastasis remain largely unknown. Through integrative analysis of clinical breast cancer gene expression datasets, cell line models of breast cancer progression, and mutation data from cancer genome resequencing studies, we identified RNA binding motif protein 47 (RBM47) as a suppressor of breast cancer progression and metastasis. RBM47 inhibited breast cancer re-initiation and growth in experimental models. Transcriptome-wide HITS-CLIP analysis revealed widespread RBM47 binding to mRNAs, most prominently in introns and 3′UTRs. RBM47 altered splicing and abundance of a subset of its target mRNAs. Some of the mRNAs stabilized by RBM47, as exemplified by dickkopf WNT signaling pathway inhibitor 1, inhibit tumor progression downstream of RBM47. Our work identifies RBM47 as an RNA-binding protein that can suppress breast cancer progression and demonstrates how the inactivation of a broadly targeted RNA chaperone enables selection of a pro-metastatic state.

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Comprehensive comparative analysis and identification of RNA-binding protein domains: Multi-class classification and feature selection

Journal of Theoretical Biology ◽

10.1016/j.jtbi.2012.07.013 ◽

2012 ◽

Vol 312 ◽

pp. 65-75 ◽

Cited By ~ 8

Author(s):

Samad Jahandideh ◽

Vinodh Srinivasasainagendra ◽

Degui Zhi

Keyword(s):

Feature Selection ◽

Comparative Analysis ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Protein Domains ◽

Multi Class Classification

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Aberrant DJ-1 expression underlies L-type calcium channel hypoactivity in tuberous sclerosis complex and Alzheimer’s disease

10.1101/2020.08.26.267260 ◽

2020 ◽

Author(s):

Farr Niere ◽

Luisa P. Cacheaux ◽

Ayse Uneri ◽

Sanjeev Namjoshi ◽

Cameron Reynoldson ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Tuberous Sclerosis ◽

Neurological Disorders ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Cellular Mechanisms ◽

Mtorc1 Signaling ◽

Voltage Dependent

AbstractL-type voltage-dependent Ca2+ channels (L-VDCC) integrate synaptic signals to facilitate a plethora of cellular mechanisms. L-VDCC dysfunction is implicated in several neurological and psychiatric diseases. Despite their importance, signals upstream of L-VDCC activity that regulate their channel density, however, are poorly defined. In disease models with overactive mammalian target of rapamycin complex 1 (mTORC1) signaling (or mTORopathies), including tuberous sclerosis (TS) and Alzheimer’s disease (AD), we report a novel mechanism downstream of mTORC1 signaling that results in a deficit in dendritic L-VDCC activity. Deficits in L-VDCC activity are associated with increased expression of the mTORC1-regulated RNA-binding protein DJ-1. DJ-1 binds the mRNA coding the auxiliary Ca2+ channel subunit α2δ2 responsible for shuttling L-VDCC to the membrane and represses its expression. Moreover, this novel DJ-1/α2δ2/L-VDCC pathway is disrupted in human AD and preclinical models of AD and TS. Our discovery that DJ-1 directs L-VDCC activity and L-VDCC-associated protein α2δ2 at the synapse suggests that DJ-1/α2δ2/L-VDCC is a common, fundamental pathway disrupted in TS and AD that can be targeted in clinical mTORopathies.Significance StatementMany neurological disorders share symptoms, despite disparity among diseases. Treatments are prescribed based on diagnosis rather than individual symptoms. While only treating symptoms may obscure the disease, mechanism-based drug development allows the two approaches to converge. Hub proteins, those that coordinate the expression of proteins that mediate specific cellular functions, may be dysregulated across a broad range of disorders. Herein, we show that the RNA-binding protein DJ-1 controls the activity of L-type voltage-dependent calcium channels (L-VDCC), via the expression of its auxiliary subunit alpha2delta2 (α2δ2). Importantly, we demonstrate that this novel DJ-1/α2δ2/L-VDCC pathway is commonly disrupted among neurological disorders, namely Alzheimer’s disease (AD) and Tuberous Sclerosis (TS). Collectively, these data rationalize mechanism-based drug therapy to treat disease.

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HPV shapes tumor transcriptome by globally modifying the pool of RNA binding protein-binding motif

Aging ◽

10.18632/aging.101927 ◽

2019 ◽

Vol 11 (8) ◽

pp. 2430-2446 ◽

Cited By ~ 4

Author(s):

Yingcheng Wu ◽

Hao Chen ◽

Yuyan Chen ◽

Lishuai Qu ◽

Erhao Zhang ◽

...

Keyword(s):

Protein Binding ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Binding Motif

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Elucidation of RNA binding protein Rbms1 (RNA binding motif single stranded interacting protein 1) role in neocortical brain development

IBRO Reports ◽

10.1016/j.ibror.2019.07.669 ◽

2019 ◽

Vol 6 ◽

pp. S214

Author(s):

Khadija Habib ◽

Ali Sarda ◽

Sung-Oh Huh

Keyword(s):

Brain Development ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Binding Motif ◽

Interacting Protein

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Purification and characterization of infectious myonecrosis virus of penaeid shrimp

Journal of General Virology ◽

10.1099/vir.0.81127-0 ◽

2006 ◽

Vol 87 (4) ◽

pp. 987-996 ◽

Cited By ~ 113

Author(s):

Bonnie T. Poulos ◽

Kathy F. J. Tang ◽

Carlos R. Pantoja ◽

Jean Robert Bonami ◽

Donald V. Lightner

Keyword(s):

Capsid Protein ◽

Rna Binding ◽

Binding Protein ◽

Buoyant Density ◽

Rna Binding Protein ◽

Binding Motif ◽

Coding Region ◽

Virus Family ◽

Infectious Myonecrosis Virus ◽

Viral Particles

The causative agent of myonecrosis affecting cultured Penaeus vannamei in Brazil was demonstrated to be a virus after purification of the agent from infected shrimp tissues. Purified viral particles were injected into specific pathogen-free P. vannamei, resulting in a disease that displayed the same characteristics as those found in the original shrimp used for purification. The virus was named infectious myonecrosis virus (IMNV). The viral particles were icosahedral in shape and 40 nm in diameter, with a buoyant density of 1·366 g ml−1 in caesium chloride. The genome consisted of a single, double-stranded (dsRNA) molecule of 7560 bp. Sequencing of the viral genome revealed two non-overlapping open reading frames (ORFs). The 5′ ORF (ORF 1, nt 136–4953) encoded a putative RNA-binding protein and a capsid protein. The coding region of the RNA-binding protein was located in the first half of ORF 1 and contained a dsRNA-binding motif in the first 60 aa. The second half of ORF 1 encoded a capsid protein, as determined by amino acid sequencing, with a molecular mass of 106 kDa. The 3′ ORF (ORF 2, nt 5241–7451) encoded a putative RNA-dependent RNA polymerase (RdRp) with motifs characteristic of totiviruses. Phylogenetic analysis based on the RdRp clustered IMNV with Giardia lamblia virus, a member of the family Totiviridae. Based on these findings, IMNV may be a unique member of the Totiviridae or may represent a new dsRNA virus family that infects invertebrate hosts.

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