There are a growing number of reports on the sub-physiological temperature culturing of mammalian cells for increased recombinant protein yields. However, the effect varies and the reasons for the enhancement are not fully elucidated. Expression of cold-inducible RNA-binding protein (cirp, also called cirbp or hnRNP A18) is known to be induced in response to mild, but not severe, hypothermia in mammalian cells. To clarify the molecular mechanism underlying the induction and to exploit this to improve the productivity of recombinant proteins, we tried to identify the regulatory sequence(s) in the 5′ flanking region of the mouse cirp gene. By transiently transfecting HEK293 cells with plasmids expressing chloramphenicol acetyltransferase as a reporter, we found that the cirp 5′ flanking region octanucleotide 5′-TCCCCGCC-3′ is a mild-cold responsive element (MCRE). When 3 copies of MCRE were placed upstream of the CMV promoter and used in transient transfection, reporter gene expression was
Shop RNA-binding motif protein ELISA Kit, Recombinant Protein and RNA-binding motif protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
TY - JOUR. T1 - Serine 195 phosphorylation in the RNA-binding protein Rbm38 increases p63 expression by modulating Rbm38s interaction with the Ago2-miR203 complex. AU - Zhang, Yanhong. AU - Feng, Xiuli. AU - Sun, Wenqiang. AU - Zhang, Jin. AU - Chen, Xinbin. PY - 2019/1/1. Y1 - 2019/1/1. N2 - The p63 transcription factor, a p53 family protein, regulates genes involved in various cellular processes, including cell growth and differentiation. We previously showed that RNA-binding motif protein (Rbm38) is a p63 target and, in turn, regulates p63 mRNA stability by binding to the AU/U-rich element in its 3UTR. Interestingly, Rbm38 can be phosphorylated at serine 195, altering its ability to regulate mRNA translation. However, whether the Ser-195 phosphorylation affects Rbm38s ability to destabilize p63 mRNA remains unclear. Here, using MCF7 and HaCaT cells, we showed that ectopic expression of phosphomimetic Rbm38-S195D increases, whereas WT Rbm38 and nonphosphorylatable Rbm38-S195A decrease p63 ...
RNA-binding proteins have diverse functions in the regulation of gene expression. This is the first report, to our knowledge, that a KH motif RNA-binding protein is regulated by p53 and that it serves as a mediator in inducing apoptosis and cell cycle arrest in G2-M. We have demonstrated that deletion of either of the KH domains or a point mutation in the C-terminal KH domain of MCG10as abrogates or severely diminishes the activity of MCG10 and MCG10as in binding RNA. As a result, the MCG10 and MCG10as mutants defective in RNA binding are also defective in inducing apoptosis and cell cycle arrest. These results indicate that, like other RNA-binding proteins, the RNA-binding activity is critical for the function of MCG10 and MCG10as. Interestingly, a 55-amino-acid insertion in the N-terminal KH domain does not interfere with the RNA-binding activity of MCG10.. Previously, we and others have shown that p53 cellular target genes are differentially regulated by p73 (21, 50, 107). We found that the ...
RNA-binding proteins are a critical component of the cellular machinery that dictate the fate of RNA molecules. As RNA virus genomes are small, they rely on host RNA-binding proteins to control the life of the viral RNA. However, which of these host proteins are required for virus infection remains largely unknown. Alfredos group developed a novel technique called comparative RNA interactome capture to interrogate which RNA-binding proteins are involved in the infection of a model virus called Sindbis (SINV). This work uncovered that SINV infection alters the activity of more than 200 cellular RNA-binding proteins, thus rewiring cellular RNA metabolism (Figure 1). ...
BACKGROUND: Low nuclear expression of the RNA-binding motif protein 3 (RBM3) has previously been found to be associated with poor prognosis in several cancer forms e.g. breast, ovarian, colorectal, prostate cancer and malignant melanoma. The aim of this study was to examine the prognostic impact of RBM3 expression in urinary bladder cancer.. METHODS: Immunohistochemical RBM3 expression was examined in tumours from 343 patients with urothelial bladder cancer. Chi-square and Spearmans correlation tests were applied to explore associations between RBM3 expression and clinicopathological characteristics. The impact of RBM3 expression on disease-specific survival (DSS), 5-year overall survival (OS) and progression-free survival (PFS) was assessed by Kaplan-Meier analysis and Cox proportional hazards modelling.. RESULTS: Reduced nuclear RBM3 expression was significantly associated with more advanced tumour (T) stage (p ,0.001) and high grade tumours (p=0.004). Negative RBM3 expression was associated ...
p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.,/p> ,p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.,/p> ,p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).,/p> ,p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x,sup>64,/sup> + x,sup>4,/sup> + x,sup>3,/sup> + x + 1. The algorithm is described in the ISO 3309 standard. ,/p> ,p class=publication>Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.,br /> ,strong>Cyclic redundancy and other checksums,/strong>,br /> ,a href=http://www.nrbook.com/b/bookcpdf.php>Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993),/a>),/p> Checksum:i ...
In eukaryotic cells, a multitude of RNA-binding proteins play key roles in the posttranscriptional regulation of gene expression. Characterization of these proteins has led to the identification of several RNA-binding motifs, and recent experiments have begun to illustrate how several of them bind RNA. The significance of these interactions is reflected in the recent discoveries that several human and other vertebrate genetic disorders are caused by aberrant expression of RNA-binding proteins. The major RNA-binding motifs are described and examples of how they may function are given. ...
TY - JOUR. T1 - She2p is a novel RNA binding protein with a basic helical hairpin motif. AU - Niessing, Dierk. AU - Hüttelmaier, Stefan. AU - Zenklusen, Daniel. AU - Singer, Robert H.. AU - Burley, Stephen K.. PY - 2004/11/12. Y1 - 2004/11/12. N2 - Selective transport of mRNAs in ribonucleoprotein particles (mRNP) ensures asymmetric distribution of information within and among eukaryotic cells. Actin-dependent transport of ASH1 mRNA in yeast represents one of the best-characterized examples of mRNP translocation. Formation of the ASH1 mRNP requires recognition of zip code elements by the RNA binding protein She2p. We determined the X-ray structure of She2p at 1.95 Å resolution. She2p is a member of a previously unknown class of nucleic acid binding proteins, composed of a single globular domain with a five α helix bundle that forms a symmetric homodimer. After demonstrating potent, dimer-dependent RNA binding in vitro, we mapped the RNA binding surface of She2p to a basic helical hairpin in ...
Expression of the RNA-binding protein RBM3 is associated with a favourable prognosis and cisplatin sensitivity in epithelial ovarian cancer. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Author: Maatz, H. et al.; Genre: Journal Article; Published in Print: 2014-08; Open Access; Title: RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing
The protamine mRNAs are stored for up to 8 days as translationally repressed ribonucleoprotein particles during murine spermatogenesis. Translational repression of the protamine 1, Prm1, mRNA is controlled by sequences in its 3-untranslated region (UTR). In this study we used the yeast three-hybrid system to clone Msy4, which encodes a novel member of the Y box family of nucleic acid binding proteins. MSY4 specifically binds to a site within the 5 most 37 nucleotides in the Prm1 3 UTR. Msy4 is highly expressed in the testis, and the protein is detected in the cytoplasm of germ cells in both the testis and the ovary, where repressed messages are stored. Analysis of a previously described 48/50-kDa binding activity in testis extracts by electrophoretic mobility shift assays and immunoprecipitation indicates the activity is composed of MSY4 and MSY2, another mouse Y box protein. Polysome analysis demonstrates MSY4 is associated with mRNPs, consistent with MSY4 having a role in storing
Algorithms designed to identify canonical yeast prions predict that around 250 human proteins, including several RNA-binding proteins associated with neurodegenerative disease, harbour a distinctive prion-like domain (PrLD) enriched in uncharged polar amino acids and glycine. PrLDs in RNA-binding proteins are essential for the assembly of ribonucleoprotein granules. However, the interplay between human PrLD function and disease is not understood. Here we define pathogenic mutations in PrLDs of heterogeneous nuclear ribonucleoproteins (hnRNPs) A2B1 and A1 in families with inherited degeneration affecting muscle, brain, motor neuron and bone, and in one case of familial amyotrophic lateral sclerosis. Wild-type hnRNPA2 (the most abundant isoform of hnRNPA2B1) and hnRNPA1 show an intrinsic tendency to assemble into self-seeding fibrils, which is exacerbated by the disease mutations. Indeed, the pathogenic mutations strengthen a steric zipper motif in the PrLD, which accelerates the formation of self
ZBP1 (zipcode binding proteins 1) is an RNA-binding protein involved in many posttranscriptional processes such as RNA localization RNA stability and translational control. both cell adhesion and transcription specifically binds to the ZBP1 promoter via a conserved β-catenin/TCF4 response element and activates its gene expression. ZBP1 activation is also closely correlated with nuclear translocation of β-catenin in human breast tumors. We further demonstrate feedback regulation by finding that ZBP1 physically associates with β-catenin mRNA in vivo and increases its stability. These experiments suggest that in breast Pomalidomide cancer cells the expression of ZBP1 and the expression of β-catenin are coordinately regulated. β-Catenin mediates the transcription of the ZBP1 gene while ZBP1 promotes the stability of β-catenin mRNA. ZBP1 (zipcode binding protein 1) belongs to a conserved family of RNA-binding proteins that contain four hnRNP K (KH) domains and Pomalidomide two RNA recognition ...
Understanding how biomolecules interact is a major task of systems biology. To model protein-nucleic acid interactions, it is important to identify the DNA or RNA-binding residues in proteins. Protein sequence features, including the biochemical property of amino acids and evolutionary information in terms of position-specific scoring matrix (PSSM), have been used for DNA or RNA-binding site prediction. However, PSSM is rather designed for PSI-BLAST searches, and it may not contain all the evolutionary information for modelling DNA or RNA-binding sites in protein sequences. In the present study, several new descriptors of evolutionary information have been developed and evaluated for sequence-based prediction of DNA and RNA-binding residues using support vector machines (SVMs). The new descriptors were shown to improve classifier performance. Interestingly, the best classifiers were obtained by combining the new descriptors and PSSM, suggesting that they captured different aspects of evolutionary
RNA-protein interactions are pivotal in fundamental cellular processes such as translation, mRNA processing, early development, and infection by RNA viruses. However, in spite of the central importance of these interactions, few approaches are available to analyze them rapidly in vivo. We describe a yeast genetic method to detect and analyze RNA-protein interactions in which the binding of a bifunctional RNA to each of two hybrid proteins activates transcription of a reporter gene in vivo. We demonstrate that this three-hybrid system enables the rapid, phenotypic detection of specific RNA-protein interactions. As examples, we use the binding of the iron regulatory protein 1 (IRP1) to the iron response element (IRE), and of HIV trans-activator protein (Tat) to the HIV trans-activation response element (TAR) RNA sequence. The three-hybrid assay we describe relies only on the physical properties of the RNA and protein, and not on their natural biological activities; as a result, it may have broad ...
RNA-binding proteins regulate a number of cellular processes, including synthesis, folding, translocation, assembly and clearance of RNAs. Recent studies have reported that an unexpectedly large number of proteins are able to interact with RNA, but partners of many RNA-binding proteins are still uncharacterized.
Understanding interactions between proteins and RNA is key to deciphering the mechanisms of many important biological processes. Here we describe RNABindR, a web-based server that identifies and displays RNA-binding residues in known protein-RNA complexes and predicts RNA-binding residues in proteins of unknown structure. RNABindR uses a distance cutoff to identify which amino acids contact RNA in solved complex structures (from the Protein Data Bank) and provides a labeled amino acid sequence and a Jmol graphical viewer in which RNA-binding residues are displayed in the context of the three-dimensional structure. Alternatively, RNABindR can use a Naive Bayes classifier trained on a non-redundant set of protein-RNA complexes from the PDB to predict which amino acids in a protein sequence of unknown structure are most likely to bind RNA. RNABindR automatically displays high specificity and high sensitivity predictions of RNA-binding residues. RNABindR is freely available at http://bindr.gdcb.iastate
Sepsis represents uncontrolled inflammation due to an infection. Cold-inducible RNA-binding protein (CIRP) is a stress-induced damage-associated molecular pattern (DAMP). A subset of neutrophils expressing ICAM-1+ neutrophils was previously shown to produce high levels of reactive oxygen species. The role of CIRP for the development and function of ICAM-1+ neutrophils during sepsis is unknown. We hypothesize that CIRP induces ICAM-1 expression in neutrophils causing injury to the lungs during sepsis. Using a mouse model of cecal ligation and puncture (CLP)-induced sepsis, we found increased expression of CIRP and higher frequencies and numbers of ICAM-1+ neutrophils in the lungs ...
RNA-binding protein which may be involved in spermatogenesis. Required for sperm development, possibly by participating in pre-mRNA splicing in the testis.
Pentatricopeptide repeat (PPR) proteins are characterized by tandem repeats of a degenerate 35 amino acid motif [1]. Most of PPR proteins have roles in mitochondria or plastid. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [1,2]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [3,4,5]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see ,PDOC50005,) [1]. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organization [6,7]: ...
As published in the January 15th issue of G&D, Dr. Joel Richter s laboratory at UMASS Medical School has identified a critical role for the RINGO/Spy protein in the control of cytoplasmic polyadenylation. CPEB is a highly conserved, sequence-specific RNA-binding protein that modulates polyadenylation, and thereby mRNA translation. Dr. Richter and his graduate student, Kiran Padmanabhan, now show that CPEB phosphorylation (and subsequent activation) is regulated by RINGO/Spy in Xenopus oocytes. ...
The double-stranded RNA binding protein Staufen is required for the microtubule-dependent localization of bicoid and oskar mRNAs to opposite poles of the Drosophila oocyte and also mediates the actin-dependent localization of prospero mRNA during the asymmetric neuroblast divisions. The posterior localization of oskar mRNA requires Staufen RNA binding domain 2, whereas prospero mRNA localization mediated the binding of Miranda to RNA binding domain 5, suggesting that different Staufen domains couple mRNAs to distinct localization pathways. This study shows that the expression of Miranda during mid-oogenesis targets Staufen/oskar mRNA complexes to the anterior of the oocyte, resulting in bicaudal embryos that develop an abdomen and pole cells instead of the head and thorax. Anterior Miranda localization requires microtubules, rather than actin, and depends on the function of Exuperantia and Swallow, indicating that Miranda links Staufen/oskar mRNA complexes to the bicoid mRNA localization ...
We have characterized two RNA-binding proteins, of apparent molecular masses of approximately 40 and 35 kDa, which possess a single N-terminal RNA-recognition motif (RRM) followed by a C-terminal domain rich in serine-arginine dipeptides. Their primary structures resemble the single-RRM serine-arginine (SR) protein, SC35; however their functional effects are quite distinctive. The 40-kDa protein cannot complement SR protein-deficient HeLa cell S100 extract and showed a dominant negative effect in vitro against the authentic SR proteins, SF2/ASF and SC35. Interestingly, the 40- and 35-kDa proteins antagonize SR proteins and activate the most distal alternative 5 splice site of adenovirus E1A pre-mRNA in vivo, an activity that is similar to that characterized previously for the heterogeneous nuclear ribonucleoprotein particles A/B group of proteins. A series of recombinant chimeric proteins consisting of domains from these proteins and SC35 in various combinations showed that the RRM, but not the C
Fingerprint Dive into the research topics of RNA-binding protein RBM24 regulates p63 expression via mRNA stability. Together they form a unique fingerprint. ...
Alternative pre-mRNA splicing is a powerful mechanism that is exploited by higher eukaryotes to diversify their proteomes, and to differentially regulate the expression, function, and localization of mRNA and proteins. Pre-mRNA splicing is typically regulated by RNA-binding proteins that recognize cis-acting RNA elements, and either activate or repress splicing of adjacent exons in a temporal, and tissue specific, manner. Understanding how RNA-binding proteins control the splicing code is fundamental to understanding organismal development and disease. The SR proteins are a well-conserved class of RNA-binding proteins that have an essential role in the regulation of splice site selection, and have also been implicated as key regulators during other stages of RNA metabolism. The complexity of the RNA targets, and specificity of RNA binding location remains poorly understood for many members of the SR protein family. Here, we present a comprehensive study to elucidate how the SR proteins ...
RNA-binding proteins have been suggested to move in association with RNA as it leaves the nucleus. The NPL3 gene of the yeast Saccharomyces cerevisiae encodes in nuclear protein with consensus RNA-binding motifs and similarity to heterogeneous nuclear ribonucleoproteins and members of the S/R protein family. We show that although Npl3 is located in the nucleus, it can shuttle between nuclei in yeast heterokaryons. In contrast, other nucleus-targeted proteins do not leave the nucleus under similar conditions. Mutants missing the RNA-binding motifs or the N terminus are still capable of shuttling in and out of the nucleus. Npl3 mutants missing the C terminus fail to localize to the nucleus. Overproduction of Npl3 in wild-type cells shows cell growth. This toxicity depends on the presence of series of unique repeats in the N terminus and localization to the nucleus. We suggest that the properties of Npl3 are consistent with it being involved in export of RNAs from the nucleus. ...
The myeloid translocation gene (MTG) proteins are non-DNA-binding transcriptional regulators capable of interacting with chromatin modifying proteins. As a consequence of leukemia-associated chromosomal translocations, two of the MTG proteins, MTG8 and MTG16, are fused to the DNA-binding domain of AML1, a transcriptional activator crucial for hematopoiesis. The AML1-MTG fusion proteins, as the wild type MTGs, display four conserved homology regions (NHR1-4) related to the Drosophila nervy protein. Structural protein analyses led us to test the hypothesis that specific MTG domains may mediate RNA binding. By using an RNA-binding assay based on synthetic RNA homopolymers and a panel of MTG deletion mutants, here we show that all the MTG proteins can bind RNA. The RNA-binding properties can be traced to two regions: the Zinc finger domains in the NHR4, which mediate Zinc-dependent RNA binding, and a novel short basic region (SBR) upstream of the NHR2, which mediates Zinc-independent RNA binding. The two
RNA-binding proteins (RBPs) allow cells to carry out pre-RNA processing and post-transcriptional regulation of gene expression, and aberrations in RBP functions have been linked to many diseases, including neurological disorders and cancer. Human cells encode thousands of RNA-binding proteins with u …
TY - JOUR. T1 - Nuclear-Import Receptors Reverse Aberrant Phase Transitions of RNA-Binding Proteins with Prion-like Domains. AU - Guo, Lin. AU - Kim, Hong Joo. AU - Wang, Hejia. AU - Monaghan, John. AU - Freyermuth, Fernande. AU - Sung, Julie C.. AU - ODonovan, Kevin. AU - Fare, Charlotte M.. AU - Diaz, Zamia. AU - Singh, Nikita. AU - Zhang, Zi Chao. AU - Coughlin, Maura. AU - Sweeny, Elizabeth A.. AU - DeSantis, Morgan E.. AU - Jackrel, Meredith E.. AU - Rodell, Christopher B.. AU - Burdick, Jason A.. AU - King, Oliver D.. AU - Gitler, Aaron D.. AU - Lagier-Tourenne, Clotilde. AU - Pandey, Udai Bhan. AU - Chook, Yuh Min. AU - Taylor, J. Paul. AU - Shorter, James. PY - 2018/4/19. Y1 - 2018/4/19. N2 - RNA-binding proteins (RBPs) with prion-like domains (PrLDs) phase transition to functional liquids, which can mature into aberrant hydrogels composed of pathological fibrils that underpin fatal neurodegenerative disorders. Several nuclear RBPs with PrLDs, including TDP-43, FUS, hnRNPA1, and ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Signaling-protein mRNAs tend to have long untranslated regions (UTRs) containing binding sites for RNA-binding proteins regulating gene expression. Here we show that a PUF-family RNA-binding protein, Mpt5, represses the yeast MAP-kinase pathway controlling differentiation to the filamentous form. Mpt5 represses the protein levels of two pathway components, the Ste7 MAP-kinase kinase and the Tec1 transcriptional activator, and negatively regulates the kinase activity of the Kss1 MAP kinase. Moreover, Mpt5 specifically inhibits the output of the pathway in the absence of stimuli, and thereby prevents inappropriate cell differentiation. The results provide an example of what may be a genome-scale level of regulation at the interface of signaling networks and protein-RNA binding networks.
Shop Nuclear polyadenylated RNA-binding protein ELISA Kit, Recombinant Protein and Nuclear polyadenylated RNA-binding protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
Allows to analyse binding sites of RNA-binding proteins. CLIPZ is a database and an analysis environment which supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins to identify the binding sites of these proteins. The software allows users to upload their own sequence data sets while being able to limit the access to these data to specific users.
Fingerprint Dive into the research topics of Splicing of the Drosophila Sex-lethal early transcripts involves exon skipping that is independent of Sex-lethal protein. Together they form a unique fingerprint. ...
Sigma-Aldrich offers abstracts and full-text articles by [Philip J Uren, Dat T Vo, Patricia Rosa de Araujo, Rebecca Pötschke, Suzanne C Burns, Emad Bahrami-Samani, Mei Qiao, Raquel de Sousa Abreu, Helder I Nakaya, Bruna R Correa, Caspar Kühnöl, Jernej Ule, Jennifer L Martindale, Kotb Abdelmohsen, Myriam Gorospe, Andrew D Smith, Luiz O F Penalva].
Mai S, et al. Global regulation of alternative RNA splicing by the SR-rich protein RBM39. Biochim Biophys Acta. 2016 Aug;1859(8):1014-24. (IF=5.373). ...
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 ...
Fingerprint Dive into the research topics of Regulation of tau RNA maturation by thyroid hormone is mediated by the neural RNA-binding protein musashi-1. Together they form a unique fingerprint. ...
Transcription factors (TFs) are well-established key factors orchestrating gene transcription, and RNA-binding proteins (RBPs) are mainly thought to participate in post-transcriptional control of gene. In fact, these two steps are functionally coupled, offering a possibility for reciprocal communications between transcription and regulatory RNAs and RBPs. Recently, a series of exploratory studies, utilizing functional genomic strategies, have revealed that RBPs are prevalently involved in transcription control genome-wide through their interactions with chromatin. Here, we present a refined census of RBPs to grope for such an emerging role and discuss the global view of RBP-chromatin interactions and their functional diversities in transcription regulation. ...
Sigma-Aldrich offers abstracts and full-text articles by [Meghdad Yeganeh, Ehsan Seyedjafari, Farnaz Akbari Kamrani, Nasser Ghaemi].
The expression profile of a panel of RNA-binding proteins (heterogeneous ribonucleoprotein (hnRNP) A1, hnRNP C1/C2, hnRNP H, hnRNP I, ASF/SF2, SR proteins, HuR and U2AF(65)) and markers of differentiation, proliferation and neoplasia (cytokeratin (CK) 13, CK-14, proliferating cell nuclear antigen (PCNA), Syndecan-1 and p16INK4a) were analyzed in 50 formalin fixed paraffin embedded cervical tissues using immunohistochemistry. The samples included histologically normal cervical epithelium, human papillomavirus (HPV) induced low-grade and high-grade pre-malignant lesions and cervical cancers. All samples were tested for HPV DNA using nested PCR. Forty-nine of the 50 tissue samples tested positive for HPV, 27 tissue samples (54%) were HPV-16 positive and 4 samples (8%) were HPV-18 positive. The immunohistochemistry results detected different expression levels of the various proteins in basal epithelial cells in histologically normal epithelium followed by an increase in expression in the ...
RNA-binding proteins (RBPs) are effectors and regulators of posttranscriptional gene regulation (PTGR). RBPs regulate stability, maturation, and turnover of all RNAs, often binding thousands of target
RNA in cells is always associated with RNA-binding proteins that regulate all aspects of RNA metabolism including RNA splicing, export from the nucleus, RNA localization, mRNA turn-over as well as translation. Given their diverse functions, cells express a variety of RNA-binding proteins, which play important roles in the pathologies of a number of diseases. In this review we focus on the effect of alcohol on different RNA-binding proteins and their possible contribution to alcohol-related disorders, and discuss the role of these proteins in the development of neurological diseases and cancer. We further discuss the conventional methods and newer techniques that are employed to identify RNA-binding proteins.
Regulation of gene expression, protein synthesis, replication and assembly of many viruses involve RNA-protein interactions. Although some successful computational tools have been reported to recognize RNA binding sites in proteins, the problem of specificity remains poorly investigated. After the nucleotide base composition, the dinucleotide is the smallest unit of RNA sequence information and many RNA-binding proteins simply bind to regions enriched in one dinucleotide. Interaction preferences of protein subsequences and dinucleotides can be inferred from protein-RNA complex structures, enabling a training-based prediction approach. We analyzed basic statistics of amino acid-dinucleotide contacts in protein-RNA complexes and found their pairing preferences could be identified. Using a standard approach to represent protein subsequences by their evolutionary profile, we trained neural networks to predict multiclass target vectors corresponding to 16 possible contacting dinucleotide subsequences. In the
In addition to DNA, gametes contribute epigenetic information in the form of histones and non-coding RNA. Epigenetic programs often respond to stressful environmental conditions and provide a heritable history of ancestral stress that allows for adaptation and propagation of the species. In the nematode C. elegans, defective epigenetic transmission often manifests as progressive germline mortality. We previously isolated sup-46 in a screen for suppressors of the hexosamine pathway gene mutant, gna-2(qa705). In this study, we examine the role of SUP-46 in stress resistance and progressive germline mortality. We identified SUP-46 as an HNRNPM family RNA-binding protein, and uncovered a highly novel role for SUP-46 in preventing paternally-mediated progressive germline mortality following mating. Proximity biotinylation profiling of human homologs (HNRNPM, MYEF2) identified proteins of ribonucleoprotein complexes previously shown to contain non-coding RNA. Like HNRNPM and MYEF2, SUP-46 was associated with
Small RNAs, 5 UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence. FEMS Microbiol Rev. 2015 May;39(3):331-349 Authors: Oliva G, Sahr T, Buchrieser C Abstract Sequencing-based studies have illuminated increased transcriptional complexity within the genome structure of bacteria and have resulted in the identification of many small regulatory RNAs (sRNA) and…
Looking for online definition of RNA-binding motif protein 30 in the Medical Dictionary? RNA-binding motif protein 30 explanation free. What is RNA-binding motif protein 30? Meaning of RNA-binding motif protein 30 medical term. What does RNA-binding motif protein 30 mean?
Looking for online definition of putative RNA-binding protein 11 in the Medical Dictionary? putative RNA-binding protein 11 explanation free. What is putative RNA-binding protein 11? Meaning of putative RNA-binding protein 11 medical term. What does putative RNA-binding protein 11 mean?
TY - JOUR. T1 - Mammalian ELAV-like neuronal RNA-binding proteins HuB and HuC promote neuronal development in both the central and the peripheral nervous systems. AU - Akamatsu, Wado. AU - Okano, Hirotaka J.. AU - Osumi, Noriko. AU - Inoue, Takayoshi. AU - Nakamura, Shun. AU - Sakakibara, Shin Ichi. AU - Miura, Masayuki. AU - Matsuo, Nobutake. AU - Darnell, Robert B.. AU - Okano, Hideyuki. PY - 1999/8/17. Y1 - 1999/8/17. N2 - Hu proteins are mammalian embryonic lethal abnormal visual system (ELAV)-like neuronal RNA-binding proteins that contain three RNA recognition motifs. Although Drosophila ELAV is required for the correct differentiation and survival of neurons, the roles played by the Hu genes in the mammalian nervous system remain largely unknown. To explore the in vivo functions of mouse Hu proteins, we overexpressed them in rat pheochromocytoma PC12 cells, where they induced neuronal phenotype in the absence of nerve growth factor. We have characterized the functions of various forms of ...
Nuclear RNA processing is a critical stage in eukaryotic gene expression, and is controlled in part by the expression and concentration of nuclear RNA-binding proteins. Different nuclear RNA-binding proteins are differentially expressed in different cells, helping the spliceosome to decode pre-mRNAs into alternatively spliced mRNAs. Recent post-genomic technology has exposed the complexity of nuclear RNA processing, and is starting to reveal the mechanisms and rules through which networks of RNA-binding proteins can regulate multiple parallel pathways. Identification of multiple parallel processing pathways regulated by nuclear RNA-binding proteins is leading to a systems-wide understanding of the rules and consequences of alternative nuclear RNA processing.. ...
TY - JOUR. T1 - Interaction of RNA-binding proteins HuR and AUF1 with the human ATF3 mRNA 3′-untranslated region regulates its amino acid limitation-induced stabilization. AU - Pan, Yuan Xiang. AU - Chen, Hong. AU - Kilberg, Michael S.. PY - 2005/10/14. Y1 - 2005/10/14. N2 - ATF3 expression is induced in cells exposed to a variety of stress conditions, including nutrient limitation. Here we demonstrated that the mechanism by which the ATF3 mRNA content is increased following amino acid limitation of human HepG2 hepatoma cells is mRNA stabilization. Analysis of ATF3 mRNA turnover revealed that the half-life was increased from about 1 h in control cells to greater than 8 h in the histidine-deprived state, demonstrating mRNA stabilization in response to nutrient deprivation. Treatment of HepG2 cells with thapsigargin, which causes endoplasmic reticulum stress, also increased the half-life of ATF3 mRNA. HuR is an RNA-binding protein that regulates both the stability and cytoplasmic/nuclear ...
TY - JOUR. T1 - Antitumor effects of EMAP II against pancreatic cancer through inhibition of fibronectin-dependent proliferation. AU - Schwarz, Roderich E.. AU - Awasthi, Niranjan. AU - Konduri, Srivani. AU - Caldwell, Lauren. AU - Cafasso, Danielle. AU - Schwarz, Margaret A.. N1 - Copyright: Copyright 2017 Elsevier B.V., All rights reserved.. PY - 2010/4/15. Y1 - 2010/4/15. N2 - Pancreatic ductal adenocarcinoma (PDAC) is highly resistant to conventional chemotherapy. The presence of both cellular and stromal fibronectin (FN) and its interaction with integrins is necessary for PDAC progression. We tested the efficacy of endothelial monocyte-activating polypeptide II (EMAP II) to inhibit PDAC progression and its ability to interfere with FN-integrin angiogenesis signaling. In heterotopic PDAC tumors EMAP II caused a significant reduction (,65%) in tumor growth, accompanied by a ,50% and 44% decrease in microvessel density and proliferative activity, respectively. EMAP II therapy caused a 62% and ...
Elucidation of the interaction of proteins with different molecules is of significance in the understanding of cellular processes. Computational methods have been developed for the prediction of protein-protein interactions. But insufficient attention has been paid to the prediction of protein-RNA interactions, which play central roles in regulating gene expression and certain RNA-mediated enzymatic processes. This work explored the use of a machine learning method, support vector machines (SVM), for the prediction of RNA-binding proteins directly from their primary sequence. Based on the knowledge of known RNA-binding and non-RNA-binding proteins, an SVM system was trained to recognize RNA-binding proteins. A total of 4011 RNA-binding and 9781 non-RNA-binding proteins was used to train and test the SVM classification system, and an independent set of 447 RNA-binding and 4881 non-RNA-binding proteins was used to evaluate the classification accuracy. Testing results using this independent ...
Mammalian gene expression patterns change profoundly in response to low oxygen levels. These changes in gene expression programs are strongly influenced by post-transcriptional mechanisms mediated by mRNA-binding factors: RNA-binding proteins (RBPs) and microRNAs (miRNAs). Here, we review the RBPs and miRNAs that modulate mRNA turnover and translation in response to hypoxic challenge. RBPs such as HuR (human antigen R), PTB (polypyrimidine tract-binding protein), heterogeneous nuclear ribonucleoproteins (hnRNPs), tristetraprolin, nucleolin, iron-response element binding proteins (IRPs), and cytoplasmic polyadenylation-element-binding proteins (CPEBs), selectively bind to numerous hypoxia-regulated transcripts and play a major role in establishing hypoxic gene expression patterns. MiRNAs including miR-210, miR-373, and miR-21 associate with hypoxia-regulated transcripts and further modulate the levels of the encoded proteins to implement the hypoxic gene expression profile. We discuss the potent
Methionyl-tRNA synthetase (MetRS) belongs to the family of 20 enzymes essential for protein biosynthesis. It links covalently methionine with its cognate tRNA. Crystal structures solved for bacterial MetRSs have given a number of interesting insights into enzyme architecture and methionylation catalysis. A comparison of sequences of MetRSs belonging to all kingdoms of life, as well as numerous biochemical and genetic studies have revealed the presence of various additional domains appended to the catalytic core of synthetase. They are responsible for interactions with tRNA and proteins. Tertiary structure of C-terminal tRNA-binding appendices can be deduced from those determined for their homologues: tRNA binding protein 111 and endothelial monocyte-activating polypeptide II. Contacts between MetRS and other proteins could be mediated not only by noncatalytic peptides but also by structural elements present in the catalytic core, e.g. Arg-Gly-Asp (RGD) motifs. Additional activities involve MetRS ...
TY - JOUR. T1 - Hrb27C, Sqd and Otu cooperatively regulate gurken RNA localization and mediate nurse cell chromosome dispersion in Drosophila oogenesis. AU - Goodrich, Jennifer S.. AU - Clouse, K. Nicole. AU - Schüpbach, Trudi. PY - 2004/5. Y1 - 2004/5. N2 - Heterogeneous nuclear ribonucleoproteins, hnRNPs, are RNA-binding proteins that play crucial roles in controlling gene expression. In Drosophila oogenesis, the hnRNP Squid (Sqd) functions in the localization and translational regulation of gurken (grk) mRNA. We show that Sqd interacts with Hrb27C, an hnRNP previously implicated in splicing. Like sqd, hrb27C mutants lay eggs with dorsoventral defects and Hrb27C can directly bind to grk RNA. Our data demonstrate a novel role for Hrb27C in promoting grk localization. We also observe a direct physical interaction between Hrb27C and Ovarian tumor (Otu), a cytoplasmic protein implicated in RNA localization. We find that some otu alleles produce dorsalized eggs and it appears that Otu cooperates ...
TY - JOUR. T1 - Conserved RNA-binding specificity of polycomb repressive complex 2 is achieved by dispersed amino acid patches in EZH2. AU - Long, Yicheng. AU - Bolanos, Ben. AU - Gong, Lihu. AU - Liu, Wei. AU - Goodrich, Karen J.. AU - Yang, Xin. AU - Chen, Siming. AU - Gooding, Anne R.. AU - Maegley, Karen A.. AU - Gajiwala, Ketan S.. AU - Brooun, Alexei. AU - Cech, Thomas R.. AU - Liu, Xin. N1 - Funding Information: We thank members of the Cech lab, Oncology Structural Biology and Protein Science group, and the Liu lab for useful conversations. We also thank Daniel T Youmans for technical advice and reagents for the RNA immunoprecipitation experiments. TRC is an investigator of the HHMI, which supported this research. This research was supported by Welch Foundation research grant I-1790, CPRIT research grant R1119, Rita Allen Foundation research grant, UT Southwestern Medical Center Endowed Scholar fund, and NIH grants GM114576 and GM121662 to XL XL is a W W Caruth, Jr. Scholar in Biomedical ...
TY - JOUR. T1 - Xenopus Staufen is a component of a ribonucleoprotein complex containing Vg1 RNA and kinesin. AU - Yoon, Young J.. AU - Mowry, Kimberly L.. PY - 2004/7. Y1 - 2004/7. N2 - RNA localization is a key mechanism for generating cell and developmental polarity in a wide variety of organisms. We have performed studies to investigate a role for the Xenopus homolog of the double-stranded RNA-binding protein, Staufen, in RNA localization during oogenesis. We have found that Xenopus Staufen (XStau) is present in a ribonucleoprotein complex, and associates with both a kinesin motor protein and vegetally localized RNAs Vg1 and VegT. A functional role for XStau was revealed through expression of a dominant-negative version that blocks localization of Vg1 RNA in vivo. Our results suggest a central role for XStau in RNA localization in Xenopus oocytes, and provide evidence that Staufen is a conserved link between specific mRNAs and the RNA localization machinery.. AB - RNA localization is a key ...
The mouse cytoplasmic polyadenylation element-binding protein 3 (CPEB3) is a translational regulator implicated in long-term memory maintenance. Invertebrate orthologs of CPEB3 in Aplysia and Drosophila are functional prions that are physiologically active in the aggregated state. To determine if this principle applies to the mammalian CPEB3, we expressed it in yeast and found that it forms heritable aggregates that are the hallmark of known prions. In addition, we confirm in the mouse the importance of CPEB3s prion formation for CPEB3 function. Interestingly, deletion analysis of the CPEB3 prion domain uncovered a tripartite organization: two aggregation-promoting domains surround a regulatory module that affects interaction with the actin cytoskeleton. In all, our data provide direct evidence that CPEB3 is a functional prion in the mammalian brain and underline the potential importance of an actin/CPEB3 feedback loop for the synaptic plasticity underlying the persistence of long-term memory ...
Co-Coordinator , Professor, Dept. of Molecular Genetics & Microbiology , [email protected] Maurice Swanson is the co-coordinator of the Genetics & genomics doctoral program, and a professor in the department of molecular genetics & microbiology in the College of Medicine. Swanson works with incoming and current students, guiding them from the application process and through the doctoral program.. Swanson received his PhD from the University of California at Berkeley, followed by a postdoctoral fellowship at Northwestern University, where he studied the functions of nuclear and cytoplasmic RNA-binding proteins in RNA processing and mRNA translation. His current research is focused on the functions of repetitive DNA, particularly the roles of unstable microsatellites in RNA-mediated neurological and neuromuscular diseases.. ...
Mitochondrial RNA-binding proteins, molecular model. This complex consists of two mitochondrial RNA-binding proteins MRP1 and MRP2. These act together to bind to RNA (ribonucleic acid). Here, they here form a heteromeric complex, specifically a heterotetramer, with fourfold symmetry. These two proteins are from the protozoan Trypanosoma brucei. - Stock Image C015/4586
Mitochondrial RNA-binding proteins, molecular model. This complex consists of two mitochondrial RNA-binding proteins MRP1 and MRP2. These act together to bind to RNA (ribonucleic acid). Here, they here form a heteromeric complex, specifically a heterotetramer, with fourfold symmetry. These two proteins are from the protozoan Trypanosoma brucei. - Stock Image C015/4007
Project C1: The role of selected RNA-binding proteins and small RNAs in bacterial pathogenicity Monika Helm studied biochemistry at the Martin-Luther-University Halle-Wittenberg (2009-2014). As a PhD student Monika investigates potential roles of selected small RNAs (sRNAs) and putative RNA-binding proteins in the virulence of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv). Although a number of small RNAs were recently discovered in Xcv and virulence functions have been demonstrated for two of them, the targets of the other sRNAs are not known. Furthermore, the involvement of RNA-binding proteins in regulation of small RNA activity in Xcv is not well studied yet. Therefore, Monika aims at the identification and characterization of novel small RNA-binding proteins.. Supervisor: Prof. Ulla Bonas. Contact:. phone: 0345-5526296. eMail: monika.arnold(at)genetik.uni-halle.de. ...
PUFs are RNA binding proteins that promote mRNA deadenylation and decay and inhibit translation. Yeast Puf5 is the prototype for studying PUF-dependent gene repression. Puf5 binds to the Pop2 subunit of the Ccr4-Pop2-NOT mRNA deadenylase, recruiting the deadenylase and associated translational repressors to mRNAs. Here we used yeast genetics to show that Puf5 has additional roles in vivo that do not require Pop2. Deletion of PUF5 caused increased sensitivity to DNA replication stress in cells lacking Pop2, as well as in cells mutated for two activities recruited to mRNAs by the Puf5-Pop2 interaction, the deadenylase Ccr4 and the translational repressor Dhh1. A functional Puf5 RNA binding domain was required, and Puf5 cytoplasmic localisation was sufficient for resistance to replication stress, indicating posttranscriptional gene expression control is involved. In contrast to DNA replication stress, in response to the cell wall integrity pathway activator caffeine, PUF5 and POP2 acted in the same genetic
Polypyrimidine Tract Binding Protein (PTB) is an intensely studied RNA binding protein involved in several post-transcriptional regulatory events of gene expression. Initially described as a pre-mRNA splicing regulator, PTB is now widely accepted as a multifunctional protein shuttling between nucleus and cytoplasm. Accordingly, PTB can interact with selected RNA targets, structural elements and proteins. There is increasing evidence that PTB and its paralog PTBP2 play a major role as repressors of alternatively spliced exons, whose transcription is tissue-regulated. In addition to alternative splicing, PTB is involved in almost all steps of mRNA metabolism, including polyadenylation, mRNA stability and initiation of protein translation. Furthermore, it is well established that PTB recruitment in internal ribosome entry site (IRES) activates the translation of picornaviral and cellular proteins. Detailed studies of the structural properties of PTB have contributed to our understanding of the mechanism of
Human RNA-binding protein (HuR), a ubiquitously expressed member of the Hu protein family, plays an important role in mRNA degradation and has been implicated as a key post-transcriptional regulator. HuR contains three RNA-recognition motif (RRM) domains. The two N-terminal tandem RRM domains can se …
The discovery that repeat expansions in C9orf72 gene has led to many exciting discoveries in the past few years. This expansion causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) and is responsible for the majority of ALS and FTD cases of European ancestry. Three, not mutually exclusive pathological mechanisms have been proposed: i) Formation of RNA foci sequestering specific RNA-binding proteins and impairing their normal function; ii) Repeat-associated non-AUG-initiated (RAN) translation of RNA repeats into toxic dipeptide repeat proteins (DPRs) and iii) haploinsufficiency resulting in reduced levels of the C9orf72 protein contributing to pathogenesis.The pathological mechanisms of C9orf72-linked disease are a very active and timely research field and many original papers and reviews are regularly published on this subject. Therefore, the goal of this Research Topic is to address the most recent progress in unraveling molecular mechanisms of C9orf72 neurodegeneration.
Heme oxygenase-1 (HO-1) is an inducible rate-controlling enzyme of heme catabolism. The cytoprotective function of HO-1 activity has been verified in multiple studies, and together with its by-products is considered a key component of the cellular stress response. The transcriptional induction of HO-1 has been largely studied in response to multiple forms of stressful stimuli but our understanding of HO-1 post-transcriptional control mechanisms in neuronal cells is currently lacking. In the present report we show the involvement of the RNA-binding proteins ELAV in the regulation of HO-1 gene expression. Our study demonstrates a specific binding between HO-1 mRNA and ELAV proteins, accompanied by an increased expression of HO-1 at protein level, in a human neuroblastoma cell line treated with hemin. Clarifying the induction of HO-1 expression at post-transcriptional level may open therapeutic perspectives for treatments associated with the modulation of HO-1 expression.. ...
An RNA-binding protein that is overproduced in ovarian cancer may pres...Researchers in the UIC College of Pharmacy found that interfering with... In a previous study we observed that human ovarian tumors overexpres...In the new study Beck and research assistant professor Xiaolong He sh...The research has been published in the online version of the journal O...,RNA,splicing,factor,implicated,in,ovarian,tumor,cell,growth,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
J.C. Schöning, et al., Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis, Nucleic Acids Research, vol. 36, 2008, pp. 6977-6987 ...
RNA-binding proteins interact with specific RNA molecules to regulate important cellular processes. It is therefore necessary to identify the RNA interaction partners in order to understand the precise functions of such proteins. Protein-RNA interactions are typically characterized using in vivo and in vitro experiments but these may not detect all binding partners. Therefore, computational methods that capture the protein-dependent nature of such binding interactions could help to predict potential binding partners in silico. We have developed three methods to predict whether an RNA can interact with a particular RNA-binding protein using support vector machines and different features based on the sequence (the Oli method), the motif score (the OliMo method) and the secondary structure (the OliMoSS method). We applied these approaches to different experimentally-derived datasets and compared the predictions with RNAcontext and RPISeq. Oli outperformed OliMoSS and RPISeq, confirming our protein-specific
Sense and antisense transcripts of the repeat accumulate in ubiquitous small nuclear, and occasionally cytoplasmic, RNA foci. Many (G4C2) n -binding proteins have been identified that are partially sequestered by the repeat RNA. Several of the trapped RNA-binding proteins are involved in alternative splicing and splicing abnormalities have been reported in C9orf72 patients [22, 25]. However, a sophisticated study on 63 C9orf72 cases shows no correlation of sense and antisense foci with neurodegeneration or clinical parameters [6], although antisense foci have been linked to TDP-43 pathology by others [5].. Repeat-associated non-ATG (RAN) translation of both sense and antisense repeat transcripts in all reading frames generates five co-aggregating dipeptide repeat (DPR) proteins: poly-GA/GP/GR from the sense transcript and poly-GP/PA/PR from the antisense transcript. The sense-strand derived DPRs are abundant throughout the neocortex, hippocampus, thalamus and cerebellum, but scarce in brain stem ...
The selective expression of Musashi1 in stem cells or immature cells of these tissues led us to speculate that it plays a role in keeping these cells in an undifferentiated state during post-transcriptional gene regulation. We sought to identify its target RNA by using a strategy similar to that used in the study of Drosophila Musashi. By in vitro selection, we determined that the consensus ligand RNA sequence for mammalian Musashi1 is G/AU2-3(AGU). We then explored candidates for the in vivo Musashi1 target gene on the basis of the results of in vitro selection experiments as well as expression patterns and functions. We speculated that mRNAs of genes regulating neural differentiation (either positively or negatively) would be downstream targets of Musashi1 since Musashi1 is preferentially expressed in undifferentiated neuronal progenitor cells.. One of the in vivo targets of Musashi1 is m-Numb mRNA, the 3′ UTR of which has a Musashi1-binding site ( Imai et al., 2001). The m-Numb and Musashi1 ...
RNA-Binding Motif Protein 17 or Splicing factor 45 is encoded by the gene RBM17. RBM17 is a component of the spliceosome complex and displays catalytic activity during mRNA splicing. RBM17 is involved in alternative splicing, resulting in different isoforms of a gene. RBM is also thought to play a role in DNA repair (Red: Chaouki et al 2006) RBM17 is widely expressed in the nucleus and important for development. Diseases associated with this gene include sickle cell anemia and forms of Ataxia 1 ...
File:OlivasLab-Pufaction.tiff Cells respond to environmental signals and stresses by transcriptional regulation of response genes, as well as activation of more rapid post-transcriptional regulatory pathways. Modulation of mRNA degradation and translation rates is an efficient method to rapidly alter protein production in response to cellular changes. The Puf family of eukaryotic RNA-binding proteins control critical decisions in cell development and differentiation by regulating the degradation and translation of target mRNAs through interactions with 3 untranslated regions (UTRs). Pufs are also involved in cellular stress responses. Research in our lab utilizes the yeast model system Saccharomyces cerevisiae to determine how Puf proteins integrate environmental signals to alter their regulation of mRNA metabolism. For example, we have demonstrated that Puf3p responds to environmental carbon source signals to regulate the decay of nuclear-encoded transcripts that code for mitochondrial ...
This enzyme is activated during Fas-mediated apoptosis. Following Fas ligation, the enzyme, which is constitutively phosphorylated, is dephosphorylated, and it is the dephosphorylated form that causes phosphorylation of TIA-1, a nuclear RNA-binding protein. Phosphorylation of TIA-1 precedes the onset of DNA fragmentation ...
RBMY2EP (RNA binding motif protein Y-linked family 2 member E, pseudogene), Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.
All of the work and power in the methodology is on the sample prep side, so hopefully you have someone great who does that for you! They validate the assay by using a human cancer cell line and identify about 1,000 RNA binding sites -- many previously characterized, and a bunch of new ones ...
Disruption of a mitochondrial RNA-binding protein gene results in decreased cytochrome b expression and a marked reduction in ubiquinol-cytochrome c reductase activity in mouse heart mitochondria ...
PMID: 14559993. SRrp86 is a unique member of the SR protein superfamily containing one RNA recognition motif and two serine-arginine (SR)-rich domains separated by an unusual glutamic acid-lysine (EK)-rich region. Previously, we showed that SRrp86 could regulate alternative splicing by both positively and negatively modulating the activity of other SR proteins and that the unique EK domain could inhibit both constitutive and alternative splicing. These functions were most consistent with the model in which SRrp86 functions by interacting with and thereby modulating the activity of target proteins. To identify the specific proteins that interact with SRrp86, we used a yeast two-hybrid library screen and immunoprecipitation coupled to mass spectrometry. We show that SRrp86 interacts with all of the core SR proteins, as well as a subset of other splicing regulatory proteins, including SAF-B, hnRNP G, YB-1, and p72. In contrast to previous results that showed activation of SRp20 by SRrp86, we now ...
We describe a novel RNA binding protein, Y14, a predominantly nuclear nucleocytoplasmic shuttling protein. Interestingly, Y14 associates preferentially with mRNAs produced by splicing but not with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Y14 associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs. Splicing of a single intron is sufficient for Y14 association. Y14-containing nuclear complexes are different from general hnRNP complexes. They contain hnRNP proteins and several unique proteins including the mRNA export factor TAP. Thus, Y14 defines novel intermediates in the pathway of gene expression, postsplicing nuclear preexport mRNPs, and newly exported cytoplasmic mRNPs, whose composition is established by splicing. These findings suggest that pre-mRNA splicing imprints mRNA with a unique set of proteins that persists in the cytoplasm and thereby communicates the history of the transcript ...
FMR1 is an RNA-binding protein that is either absent or mutated in patients affected by the fragile X syndrome, the most common inherited cause of mental retardation in humans. Sequence analysis of the FMR1 protein has suggested that RNA binding is related to the presence of two K-homologous (KH) modules and an RGG box. However, no attempt has been so far made to map the RNA-binding sites along the protein sequence and to identify possible differential RNA-sequence specificity. In the present article, we describe work done to dissect FMR1 into regions with structurally and functionally distinct properties. A semirational approach was followed to identify four regions: an N-terminal stretch of 200 amino acids, the two KH regions, and a C-terminal stretch. Each region was produced as a recombinant protein, purified, and probed for its state of folding by spectroscopical techniques. Circular dichroism and NMR spectra of the N-terminus show formation of secondary structure with a strong tendency to ...
1L3K: Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1.
The central dogma of biology describes the flow of genetic information from DNA to RNA to proteins. While RNA was originally believed to be a carrier of genetic information, subsequent work has shown something completely different: RNA is now known to have function independent of proteins, with a rich layer of regulatory networks. In fact, a large amount of the RNA present in a cell does not actually make proteins. This increased appreciation and understanding has led to many fascinating mechanistic insights into RNA and its role as a central player in cellular regulation and human disease.. Helping to facilitate RNA function are a large number of proteins that can bind to and regulate RNA. These RNA-binding proteins, or RBPs, number in the thousands and are made up of many different independent modular segments similar to a childs set of building blocks. In much a similar fashion, these blocks or domains provide nature with a way of mixing and matching different domains to generate new ...
Musashi Protein Powders and Supplements are well known for their Musashi Bulk, SLM, Creatine and Musashi protein bars. The Musashi brand produces supplements according to TGA standards of therapeutic goods which enables Musashi Supplements to meet world class nutrition standards. Musashi, Australias Trusted Performance Nutrition company was established in 1987. The business is named after Miyamoto Musashi, a Japanese swordsman famed for his duels and distinctive style as well as authoring The Book of Five Rings- a book on strategy, tactics, and philosophy.
TY - JOUR. T1 - Cyclin A2 is an RNA binding protein that controls Mre11 mRNA translation. AU - Kanakkanthara, Arun. AU - Jeganathan, Karthik B.. AU - Limzerwala, Jazeel F.. AU - Baker, Darren J.. AU - Hamada, Masakazu. AU - Nam, Hyun Ja. AU - Van Deursen, Willemijn H.. AU - Hamada, Naomi. AU - Naylor, Ryan M.. AU - Becker, Nicole A.. AU - Davies, Brian A.. AU - Van Ree, Janine H.. AU - Mer, Georges. AU - Shapiro, Virginia S.. AU - Maher, L. James. AU - Katzmann, David J.. AU - Van Deursen, Jan M.. N1 - Funding Information: We thank W. Zhou, M. Li, F. Jin, and X. Wang for assistance and D. Compton for providing photoactivatable GFP-tagged ?-tubulin. Supported by NIH grants CA126828 and CA168709 (J.M.v.D.) and CA166025 (L.J.M.). Publisher Copyright: © 2016, American Association for the Advancement of Science. All rights reserved.. PY - 2016/9/30. Y1 - 2016/9/30. N2 - Cyclin A2 activates the cyclin-dependent kinases Cdk1 and Cdk2 and is expressed at elevated levels from S phase until early ...
In a screen for RNA-binding proteins expressed during murine spermatogenesis, we have identified a cDNA that encodes a protein of 911 amino acids that contains two copies of the double-stranded RNA-binding ...
In a screen for RNA-binding proteins expressed during murine spermatogenesis, we have identified a cDNA that encodes a protein of 911 amino acids that contains two copies of the double-stranded RNA-binding ...