• We show that PEs in serine-arginine-rich (SR) proteins, a family of 14 essential SFs, are differentially spliced during induced pluripotent stem cell (iPSC) differentiation and in tumors versus normal tissues. (mendeley.com)
  • One such important family of regulatory RBPs is the Serine-Arginine (SR) family of proteins. (molcells.org)
  • Importantly, the alternative splicing of the LMNA gene was highly sensitive to the levels of specific Serine-Arginine rich (SR) proteins (5) , and produced several splicing isoforms that affect adipose tissue metabolism and aging in opposite manners, with Lamin A and Progerin promoting energy expenditure and aging, while Lamin C favors slower metabolism and moderately slows the aging process in mice (4) . (unil.ch)
  • To examine the involvement of interchromatin granule clusters (IGCs) in transcription and pre-mRNA splicing in mammalian cell nuclei, the serine-arginine (SR) protein kinase cdc2-like kinase (Clk)/STY was used as a tool to manipulate IGC integrity in vivo. (rupress.org)
  • SR proteins (serine/arginine-rich proteins) are a family of highly conserved splicing regulators that are also involved in other steps in RNA biogenesis and expression. (silverchair.com)
  • From NMR, the RRM domain of SRSF1, an SR protein, has a RNA binding fold structure. (wikipedia.org)
  • Most SR proteins are located exclusively in the nucleus, but some SR proteins (mainly SRSF1, SRSF3, and SRSF7) can shuttle between the nucleus and the cytoplasm. (molcells.org)
  • Our preliminary results suggest that SRSF1 (serine and arginine-rich splicing factor 1) and presumably other SR-proteins associate with non-coding (nc) RNAs, the highly structured 4.5SH RNA and Y RNAs. (forschung-sachsen-anhalt.de)
  • This suggests that ncRNAs counteract the oncogenic functions of SR-proteins especially those of SRSF1. (forschung-sachsen-anhalt.de)
  • Our research focuses on the roles of two particular RNA binding proteins of the SR protein family, SRSF1 and SRSF2, in metabolism and adipose tissue biology. (unil.ch)
  • Tissue-specific and SRSF1-dependent splicing of fibronectin, a matrix protein that controls host cell invasion. (unil.ch)
  • Here we critically evaluate members of the SR protein family (SRSF1-7) for their potential to act as NXF1 adaptors that couple pre-mRNA processing to mRNA export. (uni-frankfurt.de)
  • The following is a list of 14 human genes encoding SR proteins involved in splicing: SR proteins are characterized by an RS domain and at least one RNA recognition motif (RRM). (wikipedia.org)
  • Alternative splicing is the primary mechanism by which a limited number of protein-coding genes can generate proteome diversity. (biologists.com)
  • As the genomes of different organisms are sequenced and annotated it is becoming apparent that the complexity of an organism does not depend on the total number of protein-coding genes. (biologists.com)
  • The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways focused on the plant hormone signal transduction and mitogen-activated protein kinase signaling pathway. (researchsquare.com)
  • The valuable source of large-scale genomic information initiated attempts to identify the origin(s) of G protein-coupled receptors (GPCR), count and categorize those genes, and follow their evolutionary history. (springer.com)
  • The genes encoding CaaX protein prenyltransferases are considerably longer than those encoding non-CaaX subunits, as a result of longer introns. (biomedcentral.com)
  • The genomic organization of the human genes that encode protein prenyltransferases is shown in Figure 1 . (biomedcentral.com)
  • Gene structures and chromosomal locations of human protein prenyltransferase subunit genes. (biomedcentral.com)
  • (b) genes encoding non-CaaX protein prenyltransferases are much shorter. (biomedcentral.com)
  • Automatic comparisons of data from expressed sequence tags (ESTs) with genes (for example using the program Acembly, for which the results are available from the NCBI AceView server [ 2 ]) shows that all the human protein prenyltransferase genes have multiple alternative splice variants. (biomedcentral.com)
  • The chromosomal locations and number of exons from protein prenyltransferase genes in the major eukaryotic model organisms are shown in Table 2 . (biomedcentral.com)
  • Extended gene families, including novel genes involved in saccharification and proteolysis, were identified. (biomedcentral.com)
  • Perichromatin fibrils are areas of gene transcription and where SR proteins associate with RNA polymerase II for co-transcriptional splicing. (wikipedia.org)
  • This gene encodes the skeletal muscle specific member of the calsequestrin protein family. (nih.gov)
  • A mutation in the CASQ1 gene causes a vacuolar myopathy with accumulation of sarcoplasmic reticulum protein aggregates. (nih.gov)
  • Alternative splicing (AS) is the mechanism by which exons of a single gene can be spliced in various combinations to encode a diverse set of proteins. (biologists.com)
  • As splicing is linked to transcriptional and post-transcriptional steps, SR proteins are implicated in the regulation of multiple aspects of the gene expression program. (molcells.org)
  • Recent global analyses of SR-RNA interaction maps have advanced our understanding of SR-regulated gene expression. (molcells.org)
  • Small Ankyrins (sAnk1) are muscle-specific isoforms generated by the Ank1 gene that participate in the organization of the sarcoplasmic reticulum (SR) of striated muscles. (mdpi.com)
  • The CFHR5 gene provides instructions for making a protein called complement factor H-related 5. (medlineplus.gov)
  • However, its structure is similar to that of a protein called complement factor H (which is produced from the CFH gene). (medlineplus.gov)
  • We also evaluated the gene expression profile of representative USP family members using qRT-PCR. (biomedcentral.com)
  • Independent transcriptomic and proteomic datasets of ccRCC tumors were used for the analysis of gene and protein expression as well as the level of the immune infiltration. (bvsalud.org)
  • One of such pro-apoptotic gene families is the Secreted Frizzled-Related protein (sFRPs) family, an antagonist of the Wnt signalling pathway. (biomedcentral.com)
  • Unexpected complexity of the Aquaporin gene family in the moss Physcomitrella patens. (lu.se)
  • Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis. (cdc.gov)
  • Through the mTOR pathway and interactions with polyribosomes, SR proteins can increase translation of mRNA. (wikipedia.org)
  • RS domains regulate protein-protein interactions of SR proteins. (wikipedia.org)
  • The RRM domain mediates the RNA interactions of the SR proteins by binding to exon splicing enhancer sequences. (wikipedia.org)
  • In general, RRM domains recognize RNA, whereas RS domains participate in diverse protein-protein and protein-RNA interactions. (molcells.org)
  • Combining individual-resolution cross-linking and immunoprecipitation (iCLIP) and mass spectrometry, we show that elevated arginine methylation of SRSF5 and lower phosphorylation levels of cobound SRSF2 enhance shuttling of SRSF5 in P19 cells by modulating protein-protein and protein-RNA interactions. (uni-frankfurt.de)
  • Our data suggest that the protein-protein interactions responsible for the clustering of interchromatin granules are disrupted when SR proteins are hyperphosphorylated and stabilized when SR proteins are hypophosphorylated. (rupress.org)
  • The covalent modification of proteins by the addition or removal of ubiquitin, a highly conserved protein comprising of 76 amino acids, changes the molecular function of the target protein and can therefore influence its interactions with other proteins. (biomedcentral.com)
  • Splice site selection will reflect the relative occupation of these sequences and LY404039 interactions among different proteins on a pre-mRNA (Witten and Ule, 2011). (biomedigs.org)
  • Whereas the recombinant HIV-1 IN protein is sufficient to catalyze the 3' processing and strand transfer activities for in vitro integration, functional interactions between IN and host cell factors are required during the early events of HIV-1 replication in vivo [ 10 - 12 ]. (biomedcentral.com)
  • In this role, the Senior Scientist will develop and implement various mass spectrometry-based methods to characterize protein structures, study protein-substrate interactions, and understand cell biology to facilitate process development. (veteranjobcenter.com)
  • Three different protein prenyltransferases (farnesyltransferase and geranylgeranyltransferases I and II) catalyze the attachment of prenyl lipid anchors 15 or 20 carbons long to the carboxyl termini of a variety of eukaryotic proteins. (biomedcentral.com)
  • Many eukaryotic proteins that are known or supposed to bind single-stranded RNA contain one or more copies of a putative RNA-binding domain of about 90 amino acids. (embl.de)
  • In this mini-review, the essential functions of SR proteins in splicing regulation, with a focus on their roles as RNA binders in the ribonucleoprotein complex (RNP) will be summarized. (molcells.org)
  • In addition, shuttling SR proteins act as adaptors for mRNA export and as regulators for translation in the cytoplasm. (molcells.org)
  • SR proteins function in nuclear pre-mRNA processing, mRNA export, and translation. (uni-frankfurt.de)
  • Our findings indicate that posttranslational modification of SR proteins underlies the regulation of their mRNA export activities and distinguishes pluripotent from differentiated cells. (uni-frankfurt.de)
  • Click on the protein counts, or double click on taxonomic names to display all proteins containing SR domain in the selected taxonomic class. (embl.de)
  • To display all proteins with a RRM domain in a specific node, click on it. (embl.de)
  • In general, SR proteins bind ESE and enhance the splicing by recruiting the spliceosome. (molcells.org)
  • May bind bacterial antigens in the protein MARCO. (embl.de)
  • Macrophage scavenger receptors are integral membrane proteins whose ability to bind and degrade modified LDL has implicated them in the process of atherosclerotic foam cell formation. (embl.de)
  • Quantitative comparisons of RNA-binding sites showed that NXF1 and SR proteins bind mRNA targets at adjacent sites, indicative of cobinding. (uni-frankfurt.de)
  • These proteins bind specific sequences in the pre-mRNA called intronic or exonic splicing enhancer or LY404039 suppressor sequences. (biomedigs.org)
  • Maximizing our understanding of function over the universe of proteins in toto requires not only robust computational methods of inference but also a judicious allocation of experimental resources, focusing on proteins whose experimental characterization will maximize the number and accuracy of follow-on predictions. (plos.org)
  • In-depth structural characterization of biopharmaceuticals, such as recombinant proteins, bispecific antibodies, antibody drug conjugates. (veteranjobcenter.com)
  • Experience in biophysical characterization, proteomics MS, hydrogen-deuterium exchange (HDX) MS, nanoLC-MS, host cell protein (HCP) analysis by LC-MS, on-line Interfacing SEC-MS, IEC-MS, CE-MS (e.g. (veteranjobcenter.com)
  • Purification and characterization of two protein kinases acting on the aquaporin SoPIP2;1. (lu.se)
  • The first antibody, mAb104 found SR proteins in the nucleus of amphibian oocytes. (wikipedia.org)
  • The mAb104 antibody binds to a phosphoepitope on the C-terminal domain of SR proteins. (wikipedia.org)
  • This antibody allowed identification of four SR proteins (SRp20, SRp40, SRp55 and SRp75) and demonstrated their conservation among vertebrates and invertebrates. (wikipedia.org)
  • Simple Western: SR-BI Antibody [NB400-104] - Image shows a specific band for SR-BI in 0.5 mg/mL of HeLa lysate. (novusbio.com)
  • Western Blot: SR-BI Antibody [NB400-104] - SR-BI antibody was tested in human adrenal cell lysate. (novusbio.com)
  • Immunocytochemistry/ Immunofluorescence: SR-BI Antibody [NB400-104] - SR-BI antibody was tested in human fibroblast samples fixed in 4% PFA and permeabilized in PBS (0.2% Tween). (novusbio.com)
  • Flow Cytometry: SR-BI Antibody [NB400-104] - An intracellular stain was performed on HeLa cells with SR-BI antibody NB400-104AF488 (blue) and a matched isotype control NBP2-24893AF488 (orange). (novusbio.com)
  • Western Blot: SR-BI Antibody [NB400-104] - Detection of SR-BI in rat H4IIE total cell lysates and plasma membrane proteins. (novusbio.com)
  • Immunohistochemistry: SR-BI Antibody [NB400-104] - Immunolocalization of SR-BI in adult mink testis using NB400-104. (novusbio.com)
  • Immunohistochemistry-Paraffin: SR-BI Antibody [NB400-104] - FFPE tissue section of mouse liver using SR-BI antibody (Lot 8310) at 1:300 dilution with HRP-DAB detection and hematoxylin counterstaining. (novusbio.com)
  • Knockdown Validated: SR-BI Antibody [NB400-104] - HCV replication was increased by CD36. (novusbio.com)
  • Immunohistochemistry-Paraffin: SR-BI Antibody [NB400-104] - Staining of human adrenal cortex. (novusbio.com)
  • Immunocytochemistry/ Immunofluorescence: SR-BI Antibody [NB400-104] - HeLa cells were fixed and permeabilized for 10 minutes using -20C MeOH. (novusbio.com)
  • Flow Cytometry: SR-BI Antibody [NB400-104] - Analysis of Huh7 and HepG2 cells using SR-B1 antibody NB400-104. (novusbio.com)
  • We define sequences that regulate PE inclusion and protein expression of the oncogenic SF TRA2β using an RNA-targeting CRISPR screen. (mendeley.com)
  • Since biochemistry and genetics have not, by and large, enjoyed the same improvement of scale, public sequence repositories now predominantly contain putative protein sequences for which there is no direct experimental evidence of function. (plos.org)
  • Using profile analysis we constructed a database enriched in protein sequences containing one or more presumptive copies of the RNA-recognition motif (RRM). (embl.de)
  • We present a comprehensive table of 125 sequences containing 252 RRMs, including 22 previously unreported RRMs in 17 proteins. (embl.de)
  • For example, in both animals and plants, many SFs/RNA binding proteins (RBPs) and some core spliceosomal components themselves undergo AS in response to signals and even control their own levels and those of other SFs via AS (Kalyna et al. (biomedigs.org)
  • However, the mode of SR protein up-regulation in tumours is different to the E2-directed transcriptional regulation in normal transient HPV infection. (silverchair.com)
  • Computational approaches attempt to leverage evidence associated with the ever-smaller fraction of experimentally analyzed proteins to predict function for these putative proteins. (plos.org)
  • The presence of a putative RRM in these proteins, which are implicated in a variety of cellular processes, strongly suggests that their function involves binding to RNA. (embl.de)
  • By integrating multiple RNA-Seq datasets from siRNA-mediated perturbations of core components of the spliceosome, we have defined groups of spliceosomal proteins implicated in specific changes in alternative splice site choice. (fu-berlin.de)
  • The decision on which splice sites are selected under particular cellular conditions is determined by the interaction of additional proteins, globally designated as splicing factors (SFs), that guide spliceosomal components and thereby the spliceosome to the respective splice sites (Matlin et al. (biomedigs.org)
  • The HPV transcription/replication factor E2 (early 2) specifically up-regulates expression of the SR proteins SF2/ASF (splicing factor 2/alternative splicing factor), SRp20 and SC35 in infected epithelial cells. (silverchair.com)
  • Hüttelmaier S.: Analysis of the oncogenic potential of SR-proteins by e.g. migration, invasion and proliferation assays. (forschung-sachsen-anhalt.de)
  • We have investigated the role of the alternative-splicing factor Sfrs1, an arginine/serine-rich (SR)protein family member, during mouse retinal development. (biologists.com)
  • Oesterhelt D (1998) The structure and mechanism of the family of retinal proteins from halophilic archaea. (springer.com)
  • Sequence comparison does not support an evolutionary link between halobacterial retinal proteins including bacteriorhodopsin and eukaryotic G-protein-coupled receptors. (springer.com)
  • Diverse SR proteins play partially overlapping but distinct roles in transcription-coupled splicing and mRNA processing in the nucleus. (molcells.org)
  • The α subunits of protein prenyltransferases consist of tetratricopeptide repeats and are part of the tetratricopeptide repeat superfamily [ 5 ], which also includes functionally diverse proteins involved in transcription, co-chaperoning, protein transport, cell-cycle control and phosphorylation. (biomedcentral.com)
  • Tandem repeats of SRCR domains are common in the membrane bound proteins. (embl.de)
  • A novel murine plasma membrane protein has been identified in subpopulations of macrophages. (embl.de)
  • Transfected COS cells synthesized a native trimeric plasma membrane protein that bound labeled bacteria and acetylated LDL, but not yeast or Ficoll. (embl.de)
  • The results suggest that the novel protein is a macrophage-specific membrane receptor with a role in host defense, as it shows postnatal expression in macrophages, which are considered responsible for the binding of bacterial antigens and phagocytosis. (embl.de)
  • The predicted CD6 sequence is 468 amino acids long, with the typical features of a type I integral membrane protein. (embl.de)
  • Affinity tags can reduce merohedral twinning of membrane protein crystals. (lu.se)
  • Hartzell HC, Qu Z, Yu K, Xiao Q, Chien LT. Molecular physiology of bestrophins: multifunctional membrane proteins linked to best disease and other retinopathies. (medscape.com)
  • Miller SA, Bresnick GH, Chandra SR. Choroidal neovascular membrane in Best's vitelliform macular dystrophy. (medscape.com)
  • Alternatively, spliced mRNAs typically encode distinct proteins or harbor modified cis-regulatory elements, thereby altering the level of protein expression. (unil.ch)
  • 1000 endogenous mRNAs required individual SR proteins for nuclear export in vivo. (uni-frankfurt.de)
  • SR proteins are located in two different types of nuclear speckles, interchromatin granule clusters and perichromatin fibrils. (wikipedia.org)
  • The recommendation system is a proof of concept based on active learning principles and includes, for a given protein, criteria including phylogenetic distribution of its protein family, biological and clinical phenotypes associated with it, the availability of protein structure data, and its sequence distance from experimentally determined proteins or from the other proteins in its family. (plos.org)
  • This set of known sequence-function relationships will ultimately serve as the basis for making predictions for similar proteins whose functions have not been experimentally determined and can be used to train other types of prediction-generating algorithms. (plos.org)
  • It consists of five small nuclear ribonucleoprotein particles (snRNPs) and over 200 additional proteins (Wahl et al. (biomedigs.org)
  • The extracellular domain of CD6 is significantly related to the extracellular domain of the human and mouse T cell antigen CD5, the cysteine-rich domain of the bovine and mouse type I macrophage scavenger receptor, the extracellular domain of the sea urchin spermatozoa protein that crosslinks the egg peptide speract, the mammalian complement factor 1, and the human lung tumor antigen L3. (embl.de)
  • The molecules (proteins, metabolites) secreted by tumors affect their extracellular milieu to support cancer progression. (bvsalud.org)
  • Unreported homologies in the RRM-enriched database to the metazoan SR family of splicing factors are described for an Arg-rich human nuclear protein and two yeast proteins (S. pombe mei2 and S. cerevisiae Npl3). (embl.de)
  • Identification of bioluminescent proteins is more challenging due to their poor similarity in sequence. (biomedcentral.com)
  • So far, no specific method has been reported to identify bioluminescent proteins from primary sequence. (biomedcentral.com)
  • High prediction accuracy and successful prediction of hypothetical proteins suggests that BLProt can be a useful approach to identify bioluminescent proteins from sequence information, irrespective of their sequence similarity. (biomedcentral.com)
  • The core particles of the U1, U2, U4, and U5 snRNPs are formed by Sm proteins, whereas the LY404039 U6 snRNP contains the related Lsm2 (Like Sm2) to Lsm8 proteins (Tharun, 2009). (biomedigs.org)
  • Clearly, differences in the abundance, localization, and activity of proteins in different cells or in cells experiencing different internal or external cues will affect the splicing outcomes. (biomedigs.org)
  • Partial dephosphorylation of the RS domain causes the SR proteins to leave the nucleus and SR proteins with unphosphorylated RS domains are found in the cytosol. (wikipedia.org)
  • We now use classical biochemical experiments to gain mechanistic insights into protein-specific changes in splice site selection. (fu-berlin.de)
  • Published by Portland Press Limited on behalf of the Biochemical Society 2021 HIV microtubule microtubule-associated proteins post-translational modifications tubulin The eukaryotic cell is structured in different membranous and non-membranous organelles that compartmentalize. (silverchair.com)
  • Protein prenylation is the posttranslational attachment of either a farnesyl group or a geranylgeranyl group via a thioether linkage (-C-S-C-) to a cysteine at or near the carboxyl terminus of the protein. (biomedcentral.com)
  • Chad M. Swanson Human immunodeficiency virus type 1 ( HIV -1) mRNA translation is a complex process that uses the host translation machinery to synthesise viral proteins. (silverchair.com)
  • These SR proteins are essential for viral RNA processing. (silverchair.com)
  • Once splicing is complete the SR protein may or may not remain attached to help shuttle the mRNA strand out of the nucleus. (wikipedia.org)
  • SR proteins can be found in both the cytosol and in nuclear speckles in the nucleus. (wikipedia.org)
  • SR proteins are mostly found in the nucleus. (wikipedia.org)
  • In contrast to Y RNAs the 4.5SH RNA is enriched in splicing speckles, suggesting that these ncRNAs modulate the association of SR-proteins within splicing speckles as well as other nuclear functions. (forschung-sachsen-anhalt.de)
  • We hypothesize that ncRNAs tether SR-proteins in splicing speckles, competing with their role in mRNA splicing. (forschung-sachsen-anhalt.de)
  • Conversely, overexpression of a catalytically inactive mutant, Clk/STY(K190R), causes retention of hypophosphorylated SR proteins in nuclear speckles. (rupress.org)
  • SR proteins are ~200-600 amino acids in length and composed of two domains, the RNA recognition motif (RRM) region and the RS domain. (wikipedia.org)
  • All recognized mutations for AD are associated with increased deposition of amyloid-beta (Abeta), a peptide fragment comprising 39-43 amino acids that derive from the catabolism of the amyloid precursor protein (APP) molecule. (medscape.com)
  • This allowed us to revise and unify the fungal CHS classification and to study the evolutionary history of the CHS multigenic family. (biomedcentral.com)
  • Schioth HB, Fredriksson R (2005) The GRAFS classification system of G-protein coupled receptors in comparative perspective. (springer.com)
  • Bone morphogenetic proteins (BMPs) are osteoinductive substances and have been used in bone regeneration. (bvsalud.org)
  • SR proteins were discovered independently through the use of two different monoclonal antibodies. (wikipedia.org)
  • COS cells transfected with the CD6 clone express a 90-kD protein that reacts with all available anti-CD6 monoclonal antibodies. (embl.de)
  • Small angle neutron scattering (SANS) provides unique insight into biomacromolecular complexes by combining solvent contrast variation (H2O:D2O exchange) with either natural contrast between different classes of biomolecules (proteins, RNA/DNA, lipids/detergents) and/or by applying artificial contrast, i.e. deuteration of specific biomolecules. (lu.se)
  • In a first couple of examples, I will show how distance and shape restraints from SANS have helped to improve the uniqueness of structural models for two multi-protein-RNA complexes, in combination with NMR restraints and building blocks from crystallography [1, 2]. (lu.se)
  • Deltas C, Gale D, Cook T, Voskarides K, Athanasiou Y, Pierides A. C3 glomerulonephritis/CFHR5 nephropathy is an endemic disease in Cyprus: clinical and molecular findings in 21 families. (medlineplus.gov)
  • The main aim of our research is to understand the molecular details and physiological roles of the multitude of water channel-like proteins present in plants and animals. (lu.se)
  • The lymphocyte glycoprotein CD6 contains a repeated domain structure characteristic of a new family of cell surface and secreted proteins. (embl.de)
  • In line with a more complex picture, multiple isoforms of the protein likely exist and non-centrosomal sites of localisation have been reported. (springer.com)
  • Ataxia telangiectasia, neurofibromatosis type 1, several cancers, HIV-1, and spinal muscular atrophy have all been linked to alternative splicing by SR proteins. (wikipedia.org)
  • Alternative splicing multiplies the number of possible proteins generated from a single pre-mRNA and therefore is one of the most abundant mechanisms to control protein expression and function posttranscriptionally. (fu-berlin.de)
  • Ebola virus HIV lipid-protein interaction Marburg virus virus assembly virus budding. (silverchair.com)
  • This protein, also known as calmitine, functions as a calcium regulator in the mitochondria of skeletal muscle. (nih.gov)