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Journal articles on the topic 'RNA-protein interactions. Protein binding. RNA splicing'

Author: Grafiati

Published: 4 June 2021

Last updated: 11 February 2022

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1

Sawicka, Kirsty, Martin Bushell, Keith A. Spriggs, and Anne E. Willis. "Polypyrimidine-tract-binding protein: a multifunctional RNA-binding protein." Biochemical Society Transactions 36, no. 4 (2008): 641–47. http://dx.doi.org/10.1042/bst0360641.

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PTB (polypyrimidine-tract-binding protein) is a ubiquitous RNA-binding protein. It was originally identified as a protein with a role in splicing but it is now known to function in a large number of diverse cellular processes including polyadenylation, mRNA stability and translation initiation. Specificity of PTB function is achieved by a combination of changes in the cellular localization of this protein (its ability to shuttle from the nucleus to the cytoplasm is tightly controlled) and its interaction with additional proteins. These differences in location and trans-acting factor requiremen

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2

Das, Arundhati, Tanvi Sinha, Sharmishtha Shyamal, and Amaresh Chandra Panda. "Emerging Role of Circular RNA–Protein Interactions." Non-Coding RNA 7, no. 3 (2021): 48. http://dx.doi.org/10.3390/ncrna7030048.

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Circular RNAs (circRNAs) are emerging as novel regulators of gene expression in various biological processes. CircRNAs regulate gene expression by interacting with cellular regulators such as microRNAs and RNA binding proteins (RBPs) to regulate downstream gene expression. The accumulation of high-throughput RNA–protein interaction data revealed the interaction of RBPs with the coding and noncoding RNAs, including recently discovered circRNAs. RBPs are a large family of proteins known to play a critical role in gene expression by modulating RNA splicing, nuclear export, mRNA stability, localiz

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3

Lang, Benjamin, Jae-Seong Yang, Mireia Garriga-Canut, et al. "Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins." Nucleic Acids Research 49, no. 12 (2021): 6702–21. http://dx.doi.org/10.1093/nar/gkab490.

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Abstract RNA-binding proteins (RBPs) are crucial factors of post-transcriptional gene regulation and their modes of action are intensely investigated. At the center of attention are RNA motifs that guide where RBPs bind. However, sequence motifs are often poor predictors of RBP-RNA interactions in vivo. It is hence believed that many RBPs recognize RNAs as complexes, to increase specificity and regulatory possibilities. To probe the potential for complex formation among RBPs, we assembled a library of 978 mammalian RBPs and used rec-Y2H matrix screening to detect direct interactions between RB

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4

Shi, H., B. E. Hoffman, and J. T. Lis. "A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52." Molecular and Cellular Biology 17, no. 5 (1997): 2649–57. http://dx.doi.org/10.1128/mcb.17.5.2649.

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B52, also known as SRp55, is a member of the Drosophila melanogaster SR protein family, a group of nuclear proteins that are both essential splicing factors and specific splicing regulators. Like most SR proteins, B52 contains two RNA recognition motifs in the N terminus and a C-terminal domain rich in serine-arginine dipeptide repeats. Since B52 is an essential protein and is expected to play a role in splicing a subset of Drosophila pre-mRNAs, its function is likely to be mediated by specific interactions with RNA. To investigate the RNA-binding specificity of B52, we isolated B52-binding RN

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Soucek, Sharon, Yi Zeng, Deepti L. Bellur, et al. "Evolutionarily Conserved Polyadenosine RNA Binding Protein Nab2 Cooperates with Splicing Machinery To Regulate the Fate of Pre-mRNA." Molecular and Cellular Biology 36, no. 21 (2016): 2697–714. http://dx.doi.org/10.1128/mcb.00402-16.

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Numerous RNA binding proteins are deposited onto an mRNA transcript to modulate posttranscriptional processing events ensuring proper mRNA maturation. Defining the interplay between RNA binding proteins that couple mRNA biogenesis events is crucial for understanding how gene expression is regulated. To explore how RNA binding proteins control mRNA processing, we investigated a role for the evolutionarily conserved polyadenosine RNA binding protein, Nab2, in mRNA maturation within the nucleus. This study reveals thatnab2mutant cells accumulate intron-containing pre-mRNAin vivo. We extend this a

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Delgado Blanco, Javier, Leandro G. Radusky, Damiano Cianferoni, and Luis Serrano. "Protein-assisted RNA fragment docking (RnaX) for modeling RNA–protein interactions using ModelX." Proceedings of the National Academy of Sciences 116, no. 49 (2019): 24568–73. http://dx.doi.org/10.1073/pnas.1910999116.

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RNA–protein interactions are crucial for such key biological processes as regulation of transcription, splicing, translation, and gene silencing, among many others. Knowing where an RNA molecule interacts with a target protein and/or engineering an RNA molecule to specifically bind to a protein could allow for rational interference with these cellular processes and the design of novel therapies. Here we present a robust RNA–protein fragment pair-based method, termed RnaX, to predict RNA-binding sites. This methodology, which is integrated into the ModelX tool suite (http://modelx.crg.es), take

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Markovtsov, Vadim, Julia M. Nikolic, Joseph A. Goldman, Christoph W. Turck, Min-Yuan Chou, and Douglas L. Black. "Cooperative Assembly of an hnRNP Complex Induced by a Tissue-Specific Homolog of Polypyrimidine Tract Binding Protein." Molecular and Cellular Biology 20, no. 20 (2000): 7463–79. http://dx.doi.org/10.1128/mcb.20.20.7463-7479.2000.

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ABSTRACT Splicing of the c-src N1 exon in neuronal cells depends in part on an intronic cluster of RNA regulatory elements called the downstream control sequence (DCS). Using site-specific cross-linking, RNA gel shift, and DCS RNA affinity chromatography assays, we characterized the binding of several proteins to specific sites along the DCS RNA. Heterogeneous nuclear ribonucleoprotein (hnRNP) H, polypyrimidine tract binding protein (PTB), and KH-type splicing-regulatory protein (KSRP) each bind to distinct elements within this sequence. We also identified a new 60-kDa tissue-specific protein

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Burgute, Bhagyashri D., Vivek S. Peche, Anna-Lena Steckelberg, et al. "NKAP is a novel RS-related protein that interacts with RNA and RNA binding proteins." Nucleic Acids Research 42, no. 5 (2013): 3177–93. http://dx.doi.org/10.1093/nar/gkt1311.

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Abstract NKAP is a highly conserved protein with roles in transcriptional repression, T-cell development, maturation and acquisition of functional competency and maintenance and survival of adult hematopoietic stem cells. Here we report the novel role of NKAP in splicing. With NKAP-specific antibodies we found that NKAP localizes to nuclear speckles. NKAP has an RS motif at the N-terminus followed by a highly basic domain and a DUF 926 domain at the C-terminal region. Deletion analysis showed that the basic domain is important for speckle localization. In pull-down experiments, we identified R

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Mattaj, Iain W. "A binding consensus: RNA-protein interactions in splicing, snRNPs, and sex." Cell 57, no. 1 (1989): 1–3. http://dx.doi.org/10.1016/0092-8674(89)90164-5.

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10

Kafasla, Panagiota, Ian Mickleburgh, Miriam Llorian, et al. "Defining the roles and interactions of PTB." Biochemical Society Transactions 40, no. 4 (2012): 815–20. http://dx.doi.org/10.1042/bst20120044.

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PTB (polypyrimidine tract-binding protein) is an abundant and widely expressed RNA-binding protein with four RRM (RNA recognition motif) domains. PTB is involved in numerous post-transcriptional steps in gene expression in both the nucleus and cytoplasm, but has been best characterized as a regulatory repressor of some ASEs (alternative splicing events), and as an activator of translation driven by IRESs (internal ribosome entry segments). We have used a variety of approaches to characterize the activities of PTB and its molecular interactions with RNA substrates and protein partners. Using sp

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Maji, Debanjana, Eliezra Glasser, Steven Henderson, et al. "Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing." Journal of Biological Chemistry 295, no. 50 (2020): 17148–57. http://dx.doi.org/10.1074/jbc.ra120.015339.

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High-throughput sequencing of hematologic malignancies and other cancers has revealed recurrent mis-sense mutations of genes encoding pre-mRNA splicing factors. The essential splicing factor U2AF2 recognizes a polypyrimidine-tract splice-site signal and initiates spliceosome assembly. Here, we investigate representative, acquired U2AF2 mutations, namely N196K or G301D amino acid substitutions associated with leukemia or solid tumors, respectively. We determined crystal structures of the wild-type (WT) compared with N196K- or G301D-substituted U2AF2 proteins, each bound to a prototypical AdML p

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Gontarek, R. R., and D. Derse. "Interactions among SR proteins, an exonic splicing enhancer, and a lentivirus Rev protein regulate alternative splicing." Molecular and Cellular Biology 16, no. 5 (1996): 2325–31. http://dx.doi.org/10.1128/mcb.16.5.2325.

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We examine here the roles of cellular splicing factors and virus regulatory proteins in coordinately regulating alternative splicing of the tat/rev mRNA of equine infectious anemia virus (EIAV). This bicistronic mRNA contains four exons; exons 1 and 2 encode Tat, and exons 3 and 4 encode Rev. In the absence of Rev expression, the four-exon mRNA is synthesized exclusively, but when Rev is expressed, exon 3 is skipped to produce an mRNA that contains only exons 1, 2, and 4. We identify a purine-rich exonic splicing enhancer (ESE) in exon 3 that promotes exon inclusion. Similar to other cellular

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Zheng, Shuailong, Xujia Zhang, Emmanuel Odame, et al. "CircRNA—Protein Interactions in Muscle Development and Diseases." International Journal of Molecular Sciences 22, no. 6 (2021): 3262. http://dx.doi.org/10.3390/ijms22063262.

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Circular RNA (circRNA) is a kind of novel endogenous noncoding RNA formed through back-splicing of mRNA precursor. The biogenesis, degradation, nucleus–cytoplasm transport, location, and even translation of circRNA are controlled by RNA-binding proteins (RBPs). Therefore, circRNAs and the chaperoned RBPs play critical roles in biological functions that significantly contribute to normal animal development and disease. In this review, we systematically characterize the possible molecular mechanism of circRNA–protein interactions, summarize the latest research on circRNA–protein interactions in

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Günzl, A., M. Cross, and A. Bindereif. "Domain structure of U2 and U4/U6 small nuclear ribonucleoprotein particles from Trypanosoma brucei: identification of trans-spliceosomal specific RNA-protein interactions." Molecular and Cellular Biology 12, no. 2 (1992): 468–79. http://dx.doi.org/10.1128/mcb.12.2.468.

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Maturation of mRNAs in trypanosomes involves trans splicing of the 5' end of the spliced leader RNA and the exons of polycistronic pre-mRNAs, requiring small nuclear ribonucleoproteins (snRNPs) as cofactors. We have mapped protein-binding sites in the U2 and U4/U6 snRNPs by a combination of RNase H protection analysis, native gel electrophoresis, and CsCl density gradient centrifugation. In the U2 snRNP, protein binding occurs primarily in the 3'-terminal domain; through U2 snRNP reconstitution and chemical modification-interference assays, we have identified discrete positions within stem-loo

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Günzl, A., M. Cross, and A. Bindereif. "Domain structure of U2 and U4/U6 small nuclear ribonucleoprotein particles from Trypanosoma brucei: identification of trans-spliceosomal specific RNA-protein interactions." Molecular and Cellular Biology 12, no. 2 (1992): 468–79. http://dx.doi.org/10.1128/mcb.12.2.468-479.1992.

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Maturation of mRNAs in trypanosomes involves trans splicing of the 5' end of the spliced leader RNA and the exons of polycistronic pre-mRNAs, requiring small nuclear ribonucleoproteins (snRNPs) as cofactors. We have mapped protein-binding sites in the U2 and U4/U6 snRNPs by a combination of RNase H protection analysis, native gel electrophoresis, and CsCl density gradient centrifugation. In the U2 snRNP, protein binding occurs primarily in the 3'-terminal domain; through U2 snRNP reconstitution and chemical modification-interference assays, we have identified discrete positions within stem-loo

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16

Gamberi, C., E. Izaurralde, C. Beisel, and I. W. Mattaj. "Interaction between the human nuclear cap-binding protein complex and hnRNP F." Molecular and Cellular Biology 17, no. 5 (1997): 2587–97. http://dx.doi.org/10.1128/mcb.17.5.2587.

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hnRNP F was identified in a screen for proteins that interact with human CBP80 and CBP20, the components of the nuclear cap-binding complex (CBC). In vitro interaction studies showed that hnRNP F can bind to both CBP20 and CBP80 individually. hnRNP F and CBC bind independently to RNA, but hnRNP F binds preferentially to CBC-RNA complexes rather than to naked RNA. The hnRNP H protein, which is 78% identical to hnRNP F and also interacts with both CBP80 and CBP20 in vitro, does not discriminate between naked RNA and CBC-RNA complexes, showing that this effect is specific. Depletion of hnRNP F fr

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17

Yang, Xiao-Juan, Hong Zhu, Shi-Rong Mu, et al. "Crystal structure of a Y-box binding protein 1 (YB-1)–RNA complex reveals key features and residues interacting with RNA." Journal of Biological Chemistry 294, no. 28 (2019): 10998–1010. http://dx.doi.org/10.1074/jbc.ra119.007545.

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The Y-box binding protein 1 (YB-1) is a member of the cold shock domain (CSD) protein family and is recognized as an oncogenic factor in several solid tumors. By binding to RNA, YB-1 participates in several steps of posttranscriptional regulation of gene expression, including mRNA splicing, stability, and translation; microRNA processing; and stress granule assembly. However, the mechanisms in YB-1–mediated regulation of RNAs are unclear. Previously, we used both systematic evolution of ligands by exponential enrichment (SELEX) and individual-nucleotide resolution UV cross-linking and immunopr

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Selvanathan, Saravana P., Garrett T. Graham, Hayriye V. Erkizan, et al. "Oncogenic fusion protein EWS-FLI1 is a network hub that regulates alternative splicing." Proceedings of the National Academy of Sciences 112, no. 11 (2015): E1307—E1316. http://dx.doi.org/10.1073/pnas.1500536112.

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The synthesis and processing of mRNA, from transcription to translation initiation, often requires splicing of intragenic material. The final mRNA composition varies based on proteins that modulate splice site selection. EWS-FLI1 is an Ewing sarcoma (ES) oncoprotein with an interactome that we demonstrate to have multiple partners in spliceosomal complexes. We evaluate the effect of EWS-FLI1 on posttranscriptional gene regulation using both exon array and RNA-seq. Genes that potentially regulate oncogenesis, including CLK1, CASP3, PPFIBP1, and TERT, validate as alternatively spliced by EWS-FLI

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Porto, Felipe Wendt, Swapna Vidhur Daulatabad, and Sarath Chandra Janga. "Long Non-Coding RNA Expression Levels Modulate Cell-Type-Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins." Genes 10, no. 8 (2019): 593. http://dx.doi.org/10.3390/genes10080593.

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Recent developments in our understanding of the interactions between long non-coding RNAs (lncRNAs) and cellular components have improved treatment approaches for various human diseases including cancer, vascular diseases, and neurological diseases. Although investigation of specific lncRNAs revealed their role in the metabolism of cellular RNA, our understanding of their contribution to post-transcriptional regulation is relatively limited. In this study, we explore the role of lncRNAs in modulating alternative splicing and their impact on downstream protein–RNA interaction networks. Analysis

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Bansal, Prashali, Johannes Madlung, Kristina Schaaf, Boris Macek, and Fulvia Bono. "An Interaction Network of RNA-Binding Proteins Involved in Drosophila Oogenesis." Molecular & Cellular Proteomics 19, no. 9 (2020): 1485–502. http://dx.doi.org/10.1074/mcp.ra119.001912.

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During Drosophila oogenesis, the localization and translational regulation of maternal transcripts relies on RNA-binding proteins (RBPs). Many of these RBPs localize several mRNAs and may have additional direct interaction partners to regulate their functions. Using immunoprecipitation from whole Drosophila ovaries coupled to mass spectrometry, we examined protein-protein associations of 6 GFP-tagged RBPs expressed at physiological levels. Analysis of the interaction network and further validation in human cells allowed us to identify 26 previously unknown associations, besides recovering seve

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Lee, Nara, Therese A. Yario, Jessica S. Gao, and Joan A. Steitz. "EBV noncoding RNA EBER2 interacts with host RNA-binding proteins to regulate viral gene expression." Proceedings of the National Academy of Sciences 113, no. 12 (2016): 3221–26. http://dx.doi.org/10.1073/pnas.1601773113.

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Epstein–Barr virus (EBV) produces a highly abundant noncoding RNA called EBV-encoded RNA 2 (EBER2) that interacts indirectly with the host transcription factor paired box protein 5 (PAX5) to regulate viral latent membrane protein 1/2 (LMP1/2) gene expression as well as EBV lytic replication. To identify intermediary proteins, we isolated EBER2–PAX5-containing complexes and analyzed the protein components by mass spectrometry. The top candidates include three host proteins splicing factor proline and glutamine rich (SFPQ), non-POU domain-containing octamer-binding protein (NONO), and RNA bindin

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Shipman, Kristy L., Phillip J. Robinson, Bruce R. King, Roger Smith, and Richard C. Nicholson. "Identification of a family of DNA-binding proteins with homology to RNA splicing factors." Biochemistry and Cell Biology 84, no. 1 (2006): 9–19. http://dx.doi.org/10.1139/o05-139.

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We describe a unique family of human proteins that are capable of binding to the cAMP regulatory element (CRE) and that are homologous to RNA splicing proteins. A human cDNA was isolated that encodes a protein with a distinctive combination of modular domain structures: 2 leucine-zipper-like domains, a DNA-binding zinc-finger-like domain, an RNA-binding zinc-finger-like domain, and 2 coiled-coil protein–protein interaction domains. It also has a serine–arginine - rich domain, commonly found in proteins involved in RNA splicing. The protein was discovered using the CRE as bait in a yeast 1-hybr

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Todorova, Roumiana. "Functional Interactions in Transcription and Splicing of Ewing’s Sarcoma." ISRN Genetics 2013 (July 22, 2013): 1–6. http://dx.doi.org/10.5402/2013/184063.

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Ewing’s sarcoma (EWS) protein is a member of the TET (TLS/EWS/TAF15) family of RNA and DNA-binding proteins with unknown cellular role. EWS protein is encoded by the EWS oncogene on chromosome 22q12, a target of chromosomal translocations in Ewing’s sarcoma tumors. The exact mechanism of EWS participation in gene expression and pathogenesis of the resulting cancers is not defined. The binding partners of native EWS and EWS fusion proteins (EFPs) are described schematically in a model, an attempt to link the transcription with the splicing. The experimental data about the partnerships of EWS an

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Ramchatesingh, J., A. M. Zahler, K. M. Neugebauer, M. B. Roth, and T. A. Cooper. "A subset of SR proteins activates splicing of the cardiac troponin T alternative exon by direct interactions with an exonic enhancer." Molecular and Cellular Biology 15, no. 9 (1995): 4898–907. http://dx.doi.org/10.1128/mcb.15.9.4898.

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The cardiac troponin T pre-mRNA contains an exonic splicing enhancer that is required for inclusion of the alternative exon 5. Here we show that enhancer activity is exquisitely sensitive to changes in the sequence of a 9-nucleotide motif (GAGGAAGAA) even when its purine content is preserved. A series of mutations that increased or decreased the level of exon inclusion in vivo were used to correlate enhancer strength with RNA-protein interactions in vitro. Analyses involving UV cross-linking and immunoprecipitation indicated that only four (SRp30a, SRp40, SRp55, and SRp75) of six essential spl

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Hönig, Arnd, Didier Auboeuf, Marjorie M. Parker, Bert W. O'Malley, and Susan M. Berget. "Regulation of Alternative Splicing by the ATP-Dependent DEAD-Box RNA Helicase p72." Molecular and Cellular Biology 22, no. 16 (2002): 5698–707. http://dx.doi.org/10.1128/mcb.22.16.5698-5707.2002.

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ABSTRACT Although a number of ATP-dependent RNA helicases are important for constitutive RNA splicing, no helicases have been implicated in alternative RNA splicing. Here, we show that the abundant DEAD-box RNA helicase p72, but not its close relative p68, affects the splicing of alternative exons containing AC-rich exon enhancer elements. The effect of p72 was tested by using mini-genes that undergo different types of alternative splicing. When the concentration of p72 was increased in transient transfections, the inclusion of enhancer-containing CD44 alternative exons v4 and v5 increased usi

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Zhang, Jian, Yen K. Lieu, Abdullah M. Ali, et al. "Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities." Proceedings of the National Academy of Sciences 112, no. 34 (2015): E4726—E4734. http://dx.doi.org/10.1073/pnas.1514105112.

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Serine/arginine-rich splicing factor 2 (SRSF2) is an RNA-binding protein that plays important roles in splicing of mRNA precursors. SRSF2 mutations are frequently found in patients with myelodysplastic syndromes and certain leukemias, but how these mutations affect SRSF2 function has only begun to be examined. We used clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease to introduce the P95H mutation to SRSF2 in K562 leukemia cells, generating an isogenic model so that splicing alterations can be attributed solely to mutant SRSF2. We found tha

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Paronetto, Maria Paola, Tilman Achsel, Autumn Massiello, Charles E. Chalfant, and Claudio Sette. "The RNA-binding protein Sam68 modulates the alternative splicing of Bcl-x." Journal of Cell Biology 176, no. 7 (2007): 929–39. http://dx.doi.org/10.1083/jcb.200701005.

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The RNA-binding protein Sam68 is involved in apoptosis, but its cellular mRNA targets and its mechanism of action remain unknown. We demonstrate that Sam68 binds the mRNA for Bcl-x and affects its alternative splicing. Depletion of Sam68 by RNA interference caused accumulation of antiapoptotic Bcl-x(L), whereas its up-regulation increased the levels of proapoptotic Bcl-x(s). Tyrosine phosphorylation of Sam68 by Fyn inverted this effect and favored the Bcl-x(L) splice site selection. A point mutation in the RNA-binding domain of Sam68 influenced its splicing activity and subnuclear localization

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Rajiv, Caroline, S. RaElle Jackson, Simon Cocklin, Elan Z. Eisenmesser, and Tara L. Davis. "The spliceosomal proteins PPIH and PRPF4 exhibit bi-partite binding." Biochemical Journal 474, no. 21 (2017): 3689–704. http://dx.doi.org/10.1042/bcj20170366.

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Pre-mRNA splicing is a dynamic, multistep process that is catalyzed by the RNA (ribonucleic acid)–protein complex called the spliceosome. The spliceosome contains a core set of RNAs and proteins that are conserved in all organisms that perform splicing. In higher organisms, peptidyl-prolyl isomerase H (PPIH) directly interacts with the core protein pre-mRNA processing factor 4 (PRPF4) and both integrate into the pre-catalytic spliceosome as part of the tri-snRNP (small nuclear RNA–protein complex) subcomplex. As a first step to understand the protein interactions that dictate PPIH and PRPF4 fu

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Liu, Liangliang, Ning Xie, Paul Rennie, et al. "Consensus PP1 Binding Motifs Regulate Transcriptional Corepression and Alternative RNA Splicing Activities of the Steroid Receptor Coregulators, p54nrb and PSF." Molecular Endocrinology 25, no. 7 (2011): 1197–210. http://dx.doi.org/10.1210/me.2010-0517.

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Abstract Originally identified as essential pre-mRNA splicing factors, non-POU-domain-containing, octamer binding protein (p54nrb) and PTB-associated RNA splicing factor (PSF) are also steroid receptor corepressors. The mechanisms by which p54nrb and PSF regulate gene transcription remain unclear. Both p54nrb and PSF contain protein phosphatase 1 (PP1) consensus binding RVxF motifs, suggesting that PP1 may regulate phosphorylation status of p54nrb and PSF and thus their function in gene transcription. In this report, we demonstrated that PP1 forms a protein complex with both p54nrb and PSF. PP

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Patton, J. R., W. Habets, W. J. van Venrooij, and T. Pederson. "U1 small nuclear ribonucleoprotein particle-specific proteins interact with the first and second stem-loops of U1 RNA, with the A protein binding directly to the RNA independently of the 70K and Sm proteins." Molecular and Cellular Biology 9, no. 8 (1989): 3360–68. http://dx.doi.org/10.1128/mcb.9.8.3360.

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The U1 small nuclear ribonucleoprotein particle (U1 snRNP), a cofactor in pre-mRNA splicing, contains three proteins, termed 70K, A, and C, that are not present in the other spliceosome-associated snRNPs. We studied the binding of the A and C proteins to U1 RNA, using a U1 snRNP reconstitution system and an antibody-induced nuclease protection technique. Antibodies that reacted with the A and C proteins induced nuclease protection of the first two stem-loops of U1 RNA in reconstituted U1 snRNP. Detailed analysis of the antibody-induced nuclease protection patterns indicated the existence of re

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Patton, J. R., W. Habets, W. J. van Venrooij, and T. Pederson. "U1 small nuclear ribonucleoprotein particle-specific proteins interact with the first and second stem-loops of U1 RNA, with the A protein binding directly to the RNA independently of the 70K and Sm proteins." Molecular and Cellular Biology 9, no. 8 (1989): 3360–68. http://dx.doi.org/10.1128/mcb.9.8.3360-3368.1989.

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The U1 small nuclear ribonucleoprotein particle (U1 snRNP), a cofactor in pre-mRNA splicing, contains three proteins, termed 70K, A, and C, that are not present in the other spliceosome-associated snRNPs. We studied the binding of the A and C proteins to U1 RNA, using a U1 snRNP reconstitution system and an antibody-induced nuclease protection technique. Antibodies that reacted with the A and C proteins induced nuclease protection of the first two stem-loops of U1 RNA in reconstituted U1 snRNP. Detailed analysis of the antibody-induced nuclease protection patterns indicated the existence of re

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Chong, Geeng Loo, Mung Hsia Foo, Wen-Dar Lin, Min May Wong, and Paul E. Verslues. "Highly ABA-Induced 1 (HAI1)-Interacting protein HIN1 and drought acclimation-enhanced splicing efficiency at intron retention sites." Proceedings of the National Academy of Sciences 116, no. 44 (2019): 22376–85. http://dx.doi.org/10.1073/pnas.1906244116.

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The Highly ABA-Induced 1 (HAI1) protein phosphatase is a central component of drought-related signaling. A screen for HAI1-interacting proteins identified HAI1-Interactor 1 (HIN1), a nuclear protein of unknown function which could be dephosphorylated by HAI1 in vitro. HIN1 colocalization and interaction with serine-arginine rich (SR) splicing factors and appearance of nuclear speckle-localized HIN1 during low water potential (ψw) stress suggested a pre-mRNA splicing-related function. RNA sequencing of Arabidopsis Col-0 wild type identified more than 500 introns where moderate severity low ψw a

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Suzuki, Masataka G., Shigeo Imanishi, Naoshi Dohmae, Miwako Asanuma, and Shogo Matsumoto. "Identification of a Male-Specific RNA Binding Protein That Regulates Sex-Specific Splicing of Bmdsx by Increasing RNA Binding Activity of BmPSI." Molecular and Cellular Biology 30, no. 24 (2010): 5776–86. http://dx.doi.org/10.1128/mcb.00444-10.

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ABSTRACT Bmdsx is a sex-determining gene in the silkworm and is alternatively spliced in males and females. CE1 is a splicing silencer element responsible for the sex-specific splicing of Bmdsx. To identify sex-specific factors implicated in the sex-specific splicing of Bmdsx, we performed RNA affinity chromatography using CE1 RNA as a ligand. We have identified BmIMP, a Bombyx homolog of IGF-II mRNA binding protein (IMP), as a male-specific factor that specifically binds to CE1. The gene encoding BmIMP is localized on the Z chromosome and is male-specifically expressed in various tissues. Ant

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Belshan, Michael, Gregory S. Park, Patricia Bilodeau, C. Martin Stoltzfus, and Susan Carpenter. "Binding of Equine Infectious Anemia Virus Rev to an Exon Splicing Enhancer Mediates Alternative Splicing and Nuclear Export of Viral mRNAs." Molecular and Cellular Biology 20, no. 10 (2000): 3550–57. http://dx.doi.org/10.1128/mcb.20.10.3550-3557.2000.

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ABSTRACT In addition to facilitating the nuclear export of incompletely spliced viral mRNAs, equine infectious anemia virus (EIAV) Rev regulates alternative splicing of the third exon of thetat/rev mRNA. In the presence of Rev, this exon of the bicistronic RNA is skipped in a fraction of the spliced mRNAs. In this report, the cis-acting requirements for exon 3 usage were correlated with sequences necessary for Rev binding and transport of incompletely spliced RNA. The presence of a purine-rich exon splicing enhancer (ESE) was required for exon 3 recognition, and the addition of Rev inhibited e

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Rejeski, Kai, Yang Liang, Toma Tebaldi, et al. "Integrative Genome-Wide Analysis of RNA Binding and Splicing Reveals Complex Loss and Gain of Function Alterations By SRSF2 P95 Mutations in Myelodysplasia." Blood 126, no. 23 (2015): 141. http://dx.doi.org/10.1182/blood.v126.23.141.141.

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Abstract Specific splicing Factor (SF) mutations are recurrent and mutually exclusive in hematopoietic diseases.Mutations in the splicing factor SRSF2 occur in nearly 40% of patients with CMML, 14% of MDS, and 19% of secondary AML, and portend a poor prognosis. SRSF2 binds to exonic splicing enhancers (ESEs), thereby affecting exon inclusion or exclusion. We have recently shown that SRSF2 mutations result in altered RNA binding affinity and specificity via in vitro structure-function studies, specifically isothermal titration calorimetry and nuclear magnetic resonance (NMR) modeling. While wil

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Samuels, M. E., D. Bopp, R. A. Colvin, R. F. Roscigno, M. A. Garcia-Blanco, and P. Schedl. "RNA binding by Sxl proteins in vitro and in vivo." Molecular and Cellular Biology 14, no. 7 (1994): 4975–90. http://dx.doi.org/10.1128/mcb.14.7.4975.

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Sxl has been proposed to regulate splicing of specific target genes by directly interacting with their pre-mRNAs. We have therefore examined the RNA-binding properties of Sxl protein in vitro and in vivo. Gel shift and UV cross-linking assays with a purified recombinant MBP-Sxl fusion protein demonstrated preferential binding to RNAs containing poly(U) tracts, and the protein footprinted over the poly(U) region. The protein did not appear to recognize either branch point or AG dinucleotide sequences, but an adenosine residue at the 5' end of the poly(U) tract enhanced binding severalfold. MBP-

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Samuels, M. E., D. Bopp, R. A. Colvin, R. F. Roscigno, M. A. Garcia-Blanco, and P. Schedl. "RNA binding by Sxl proteins in vitro and in vivo." Molecular and Cellular Biology 14, no. 7 (1994): 4975–90. http://dx.doi.org/10.1128/mcb.14.7.4975-4990.1994.

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Sxl has been proposed to regulate splicing of specific target genes by directly interacting with their pre-mRNAs. We have therefore examined the RNA-binding properties of Sxl protein in vitro and in vivo. Gel shift and UV cross-linking assays with a purified recombinant MBP-Sxl fusion protein demonstrated preferential binding to RNAs containing poly(U) tracts, and the protein footprinted over the poly(U) region. The protein did not appear to recognize either branch point or AG dinucleotide sequences, but an adenosine residue at the 5' end of the poly(U) tract enhanced binding severalfold. MBP-

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Brown, J. W. S., C. G. Simpson, G. Thow, et al. "Splicing signals and factors in plant intron removal." Biochemical Society Transactions 30, no. 2 (2002): 146–49. http://dx.doi.org/10.1042/bst0300146.

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Constitutive splicing of the potato invertase miniexon 2 (9 nt long) requires a branchpoint sequence positioned around 50 nt upstream of the 5′ splice site of the adjacent intron and a U11 element found just downstream of the branchpoint in the upstream intron [Simpson, Hedley, Watters, Clark, McQuade, Machray and Brown (2000) RNA 6, 422–433]. The sensitivity of this in vivo plant splicing system has been used to demonstrate exon scanning in plants, and to characterize plant intronic elements, such as branchpoint and poly-pyrimidine tract sequences. Plant introns differ from their vertebrate a

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Gampel, A., M. Nishikimi, and A. Tzagoloff. "CBP2 protein promotes in vitro excision of a yeast mitochondrial group I intron." Molecular and Cellular Biology 9, no. 12 (1989): 5424–33. http://dx.doi.org/10.1128/mcb.9.12.5424.

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The terminal intron (bI2) of the yeast mitochondrial cytochrome b gene is a group I intron capable of self-splicing in vitro at high concentrations of Mg2+. Excision of bI2 in vivo, however, requires a protein encoded by the nuclear gene CBP2. The CBP2 protein has been partially purified from wild-type yeast mitochondria and shown to promote splicing at physiological concentrations of Mg2+. The self-splicing and protein-dependent splicing reactions utilized a guanosine nucleoside cofactor, the hallmark of group I intron self-splicing reactions. Furthermore, mutations that abolished the autocat

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40

Gampel, A., M. Nishikimi, and A. Tzagoloff. "CBP2 protein promotes in vitro excision of a yeast mitochondrial group I intron." Molecular and Cellular Biology 9, no. 12 (1989): 5424–33. http://dx.doi.org/10.1128/mcb.9.12.5424-5433.1989.

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The terminal intron (bI2) of the yeast mitochondrial cytochrome b gene is a group I intron capable of self-splicing in vitro at high concentrations of Mg2+. Excision of bI2 in vivo, however, requires a protein encoded by the nuclear gene CBP2. The CBP2 protein has been partially purified from wild-type yeast mitochondria and shown to promote splicing at physiological concentrations of Mg2+. The self-splicing and protein-dependent splicing reactions utilized a guanosine nucleoside cofactor, the hallmark of group I intron self-splicing reactions. Furthermore, mutations that abolished the autocat

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41

Dedow, Lauren K., and Julia Bailey-Serres. "Searching for a Match: Structure, Function and Application of Sequence-Specific RNA-Binding Proteins." Plant and Cell Physiology 60, no. 9 (2019): 1927–38. http://dx.doi.org/10.1093/pcp/pcz072.

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Abstract Plants encode over 1800 RNA-binding proteins (RBPs) that modulate a myriad of steps in gene regulation from chromatin organization to translation, yet only a small number of these proteins and their target transcripts have been functionally characterized. Two classes of eukaryotic RBPs, pentatricopeptide repeat (PPR) and pumilio/fem-3 binding factors (PUF), recognize and bind to specific sequential RNA sequences through protein–RNA interactions. These modular proteins possess helical structural units containing key residues with high affinity for specific nucleotides, whose sequential

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Buratti, Emanuele, Andrés F. Muro, Maurizio Giombi, Daniel Gherbassi, Alessandra Iaconcig, and Francisco E. Baralle. "RNA Folding Affects the Recruitment of SR Proteins by Mouse and Human Polypurinic Enhancer Elements in the Fibronectin EDA Exon." Molecular and Cellular Biology 24, no. 3 (2004): 1387–400. http://dx.doi.org/10.1128/mcb.24.3.1387-1400.2004.

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ABSTRACT In humans, inclusion or exclusion of the fibronectin EDA exon is mainly regulated by a polypurinic enhancer element (exonic splicing enhancer [ESE]) and a nearby silencer element (exonic splicing silencer [ESS]). While human and mouse ESEs behave identically, mutations introduced into the homologous mouse ESS sequence result either in no change in splicing efficiency or in complete exclusion of the exon. Here, we show that this apparently contradictory behavior cannot be simply accounted for by a localized sequence variation between the two species. Rather, the nucleotide differences

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Aubol, Brandon E., Pedro Serrano, Laurent Fattet, Kurt Wüthrich, and Joseph A. Adams. "Molecular interactions connecting the function of the serine-arginine–rich protein SRSF1 to protein phosphatase 1." Journal of Biological Chemistry 293, no. 43 (2018): 16751–60. http://dx.doi.org/10.1074/jbc.ra118.004587.

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Splicing generates many mRNA strands from a single precursor mRNA, expanding the proteome and enhancing intracellular diversity. Both initial assembly and activation of the spliceosome require an essential family of splicing factors called serine-arginine (SR) proteins. Protein phosphatase 1 (PP1) regulates the SR proteins by controlling phosphorylation of a C-terminal arginine-serine–rich (RS) domain. These modifications are vital for the subcellular localization and mRNA splicing function of the SR protein. Although PP1 has been shown to dephosphorylate the prototype SR protein splicing fact

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Heinemann, Udo, and Yvette Roske. "Cold-Shock Domains—Abundance, Structure, Properties, and Nucleic-Acid Binding." Cancers 13, no. 2 (2021): 190. http://dx.doi.org/10.3390/cancers13020190.

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The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predomin

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Heinemann, Udo, and Yvette Roske. "Cold-Shock Domains—Abundance, Structure, Properties, and Nucleic-Acid Binding." Cancers 13, no. 2 (2021): 190. http://dx.doi.org/10.3390/cancers13020190.

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The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predomin

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Wersig, C., and A. Bindereif. "Reconstitution of functional mammalian U4 small nuclear ribonucleoprotein: Sm protein binding is not essential for splicing in vitro." Molecular and Cellular Biology 12, no. 4 (1992): 1460–68. http://dx.doi.org/10.1128/mcb.12.4.1460.

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We have developed an in vitro splicing complementation assay to investigate the domain structure of the mammalian U4 small nuclear RNA (snRNA) through mutational analysis. The addition of affinity-purified U4 snRNP or U4 RNA to U4-depleted nuclear extract efficiently restores splicing activity. In the U4-U6 interaction domain of U4 RNA, only stem II was found to be essential for splicing activity; the 5' loop is important for spliceosome stability. In the central domain, we have identified a U4 RNA sequence element that is important for splicing and spliceosome assembly. Surprisingly, an intac

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47

Wersig, C., and A. Bindereif. "Reconstitution of functional mammalian U4 small nuclear ribonucleoprotein: Sm protein binding is not essential for splicing in vitro." Molecular and Cellular Biology 12, no. 4 (1992): 1460–68. http://dx.doi.org/10.1128/mcb.12.4.1460-1468.1992.

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We have developed an in vitro splicing complementation assay to investigate the domain structure of the mammalian U4 small nuclear RNA (snRNA) through mutational analysis. The addition of affinity-purified U4 snRNP or U4 RNA to U4-depleted nuclear extract efficiently restores splicing activity. In the U4-U6 interaction domain of U4 RNA, only stem II was found to be essential for splicing activity; the 5' loop is important for spliceosome stability. In the central domain, we have identified a U4 RNA sequence element that is important for splicing and spliceosome assembly. Surprisingly, an intac

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48

Medenbach, Jan, Silke Schreiner, Sunbin Liu, Reinhard Lührmann, and Albrecht Bindereif. "Human U4/U6 snRNP Recycling Factor p110: Mutational Analysis Reveals the Function of the Tetratricopeptide Repeat Domain in Recycling." Molecular and Cellular Biology 24, no. 17 (2004): 7392–401. http://dx.doi.org/10.1128/mcb.24.17.7392-7401.2004.

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ABSTRACT After each spliceosome cycle, the U4 and U6 snRNAs are released separately and are recycled to the functional U4/U6 snRNP, requiring in the mammalian system the U6-specific RNA binding protein p110 (SART3). Its domain structure is made up of an extensive N-terminal domain with at least seven tetratricopeptide repeat (TPR) motifs, followed by two RNA recognition motifs (RRMs) and a highly conserved C-terminal sequence of 10 amino acids. Here we demonstrate under in vitro recycling conditions that U6-p110 is an essential splicing factor. Recycling activity requires both the RRMs and the

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Borchardt, Erin K., Nicole M. Martinez, and Wendy V. Gilbert. "Regulation and Function of RNA Pseudouridylation in Human Cells." Annual Review of Genetics 54, no. 1 (2020): 309–36. http://dx.doi.org/10.1146/annurev-genet-112618-043830.

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Recent advances in pseudouridine detection reveal a complex pseudouridine landscape that includes messenger RNA and diverse classes of noncoding RNA in human cells. The known molecular functions of pseudouridine, which include stabilizing RNA conformations and destabilizing interactions with varied RNA-binding proteins, suggest that RNA pseudouridylation could have widespread effects on RNA metabolism and gene expression. Here, we emphasize how much remains to be learned about the RNA targets of human pseudouridine synthases, their basis for recognizing distinct RNA sequences, and the mechanis

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Schluepen, Christina, Robert Lersch, Sherry L. Gee, and John G. Conboy. "Protein 4.1R Exon 16 Splicing Regulation by Antagonistic Activities of Fox-2 and hnRNP A1 Splicing Factors." Blood 106, no. 11 (2005): 804. http://dx.doi.org/10.1182/blood.v106.11.804.804.

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Abstract An erythroid differentiation stage-specific alternative splicing switch involving activation of protein 4.1R exon 16 splicing is critical for the mechanical stability of the erythrocyte plasma membrane. We have previously shown that inclusion of E16 can be negatively regulated by binding of hnRNP A/B proteins to splicing silencer element(s) in E16 and that strongly decreased expression of hnRNP A/B proteins is temporally correlated with exon 16 activation. Moreover, our earlier unpublished data showed that Fox-2 is a candidate activator protein for this splicing switch, based on obser

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