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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 ...
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
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.
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 ...
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 ...
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 ...
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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.
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 ...
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…
Principal Investigator:MUTO Yutaka, Project Period (FY):1996 - 1998, Research Category:Grant-in-Aid for Scientific Research (C), Section:一般, Research Field:Structural biochemistry
5CXT: Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Unknown at 2.20 A resolution
Role of RNA binding Proteins (RBPs) in response to abiotic stress in plants. Proteins accompany RNA molecules from cradle to grave. In eukaryotes, RNA-binding proteins participate in synthesizing, processing, editing, modifying and exporting RNA molecules from the nucleus. They carry RNA molecules between cells and to their destinations within cells. They are involved in all aspects of translating mRNAs, as well as regulating the stability of mRNA and degrade it. Mechanistically, each of these events is regulated by the formation of different ribonucleoprotein (RNP) complexes with RNA-binding proteins (RBPs) at their core. Although relatively few plant RNA-binding proteins have been characterised genetically and biochemically, presence of more than 250 RBDs in Arabidopsis and rice suggest that they might serve specific plant function. Besides their role in normal cellular functions, RBPs are also emerging as an important class of proteins which provide plants the ability to respond rapidly ...
Rabbit recombinant monoclonal Elav-type RNA-binding protein ETR3 antibody [EPR13374-2]. Validated in WB, IP, IHC, Flow Cyt, ICC/IF and tested in Mouse, Rat, Human. Cited in 3 publication(s)…
Proper regulation of gene expression at a cellular level is required in all organisms for their successful adaptation and survival to physiological or environmental changes. In eukaryotes, a convenient way of regulating gene expression is achieved by post-transcriptionally adjusting the decay rates of different mRNAs. The Puf family of proteins in yeast belong to a widespread group of eukaryotic RNA-binding proteins that regulate the lifespans of target mRNAs by sequence specifically binding to 3 untranslated regions (UTRs) and modulating their decay rates. For example, the yeast Puf3 protein binds the COX17 3 UTR, stimulating its deadenylation and subsequent decay. However, the specific mechanism by which Puf3p regulates these decay processes was not known. In this research, insight was gained on Puf3 protein interactions and its mechanism of action for COX17 mRNA regulation. Through biochemical and genetic approaches, several decay factors involved in decapping and deadenylation events were
Complete information for RBM20 gene (Protein Coding), RNA Binding Motif Protein 20, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
Gene Information Encodes a Serine/arginine-rich (SR) protein RSZp22. SR proteins are splicing regulators that share a modular structure consisting of one or two N-terminal RNA recognition motif domains and a C-terminal RS-rich domain. RSZp22 is located in the nucleolus. It is a nucleocytoplasmic shuttling protein and an interacting partner to the Arabidopsis U1-70K.. ...
1KOH: The crystal structure and mutational analysis of a novel RNA-binding domain found in the human Tap nuclear mRNA export factor.
by Sarah Yang (510) 486-4575. Mistakes happen. This is the case in the process of transporting genetic information in cells. How our cells keep errors in this process in check is the subject of a new paper by researchers at the Department of Energys Lawrence Berkeley National Laboratory (Berkeley Lab).. They found that RNA-binding proteins are regulated such that gateway proteins can recognize and block aberrant strands of genetic code from exiting the nucleus. Unused messenger RNA (mRNA) strands that cannot exit the nucleus would eventually disintegrate.. Their findings, published today in the journal Scientific Reports, shed light on a complex system of cell regulation that acts as a form of quality control for the transport of genetic information out of the nucleus.. Getting a more complete picture of how genetic information gets expressed in cells is important in disease research, the researchers said.. "Some components of this machinery are dysregulated in various types of cancers," said ...
Complete information for DAZL gene (Protein Coding), Deleted In Azoospermia Like, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
RNA binding proteins: pathways to blastic transformation. RNA binding proteins play an essential role in RNA metabolism because they regulate the mRNA fate from the active site of transcription to that of translation (17). In fact, nuclear RNA binding proteins, involved in the regulation of transcription, interact with the nascent pre-mRNA when genes are actively transcribed by RNA polymerase II. Following synthesis, other RNA binding proteins prepare the pre-mRNA for cytoplasmic export, which requires the activity of ribonucleoprotein capable of nucleocytoplasmic shuttling. In this initial journey, the mRNA becomes 5′-capped and polyadenylated and undergoes splicing. Once exported into the cytoplasm, the mature mRNA is transported to the translational machinery where, on association with ribosomes, it is decoded and used several times as a template for protein synthesis. During the entire process, the mRNA is not naked but different RNA binding proteins take turn and bind to regulatory ...
Provided is a method for designing a protein capable of selectively binding RNA bases or specifically binding an RNA base sequence. This protein includes 1 or more (preferably 2-14) PPR motifs comprising a polypeptide represented by formula (1) and having a length of 30-38 amino acids (in formula (1): Helix A is a moiety which is represented by formula (2), has a length of 12 amino acids, and is capable of forming an alpha-helix structure (in formula (2), A1-A12 each independently represent an amino acid)X is a moiety which is either not present or which has a length of 1-9 amino acidsHelix B is a moiety that has a length of 11-13 amino acids, and is capable of forming an alpha-helix structureL is a moiety which is represented by formula (3) and has a length of 2-7 amino acids (in formula (3), each amino acid is numbered from the C-terminus in the following manner i(-1), ii(-2), on condition that in some cases Liii to Lvii are not present)). The protein corresponding to the RNA bases or base
Compared with nucleolar proteins, proteins concentrated in splicing speckles have a more complex architecture, with half of the proteins containing two or more recognizable conserved motifs or domains. The domain that occurs most commonly amongst proteins in the splicing speckles is the RNA recognition motif RRM (25/65 proteins) (Table II). This is an abundant motif in the human proteome (http://www.ensembl.org/IPtop500.html). Despite the fact that the nucleolus is also involved in (ribosomal) RNA processing, RRM domains are not that abundant amongst published nucleolar proteins (3/97), but instead a more diverse array of other RNA‐binding motifs (e.g. KH and RGG domains) appears to be utilized by these proteins. Half of the splicing proteins with RRM(s) also contain an RS domain. RS domain‐containing proteins are abundant amongst splicing proteins (21/65) (Mintz et al., 1999; Sutherland et al., 2001). Despite the functional relationship between Cajal bodies and splicing proteins, only one ...
The protein encoded by this gene is a member of the serine/arginine (SR)-rich family of pre-mRNA splicing factors, which constitute part of the spliceosome. Each of these factors contains an RNA recognition motif (RRM) for binding RNA and an RS domain for binding other proteins. The RS domain is rich in serine and arginine residues and facilitates interaction between different SR splicing factors. In addition to being critical for mRNA splicing, the SR proteins have also been shown to be involved in mRNA export from the nucleus and in translation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016 ...
Component of the spliceosome A complex. Regulates alternative splicing of a number of mRNAs. May modulate splice site pairing after recruitment of the U1 and U2 snRNPs to the 5 and 3 splice sites of the intron. May both positively and negatively regulate apoptosis by regulating the alternative splicing of several genes involved in this process, including FAS and CASP2/caspase-2. In the case of FAS, promotes exclusion of exon 6 thereby producing a soluble form of FAS that inhibits apoptosis. In the case of CASP2/caspase-2, promotes exclusion of exon 9 thereby producing a catalytically active form of CASP2/Caspase-2 that induces apoptosis ...
A main focus in the Sattler group is to understand the structural basis of regulatory protein-RNA interactions that are functionally important for various aspects of gene expression, such as the regulation of (alternative) pre-mRNA splicing and gene silencing by non-coding RNAs (siRNAs, miRNAs). More than 90% of human multi-exon genes are alternatively spliced and misregulation of splicing is linked to various human diseases. Early and critical steps in the regulation of alternative splicing involve the binding of trans-acting factors to the pre-mRNA to modulate the splicing decision. These are multi-domain RNA binding proteins that mediate dynamic molecular interactions, where specific and tight complexes are formed by the cooperative combination of multiple weak protein-protein and protein-RNA interactions. Current projects focus on protein-protein and protein-RNA interactions that play important roles in the recognition of the 3 splice site by U2AF and SF1 required for constitutive splicing ...
i did several EMSA recently, and I guess a RNA/Protein complex(es) is/are formed. I think its specific as i can compete it away using cold probe. But the problem is, no matter how long i run the gel, the band appears at the very top position. I am using 4% polyacryamide gel and run overnight already? will it be due to the large size of my probe, ~660 bp.... ...