SF3B2-Mediated RNA Splicing Drives Human Prostate
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Mutated SF3B1 Is Associated with Transcript Isoform Changes of The
bioRxiv preprint doi: https://doi.org/10.1101/000992; this version posted July 13, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Reyes et al. RESEARCH Mutated SF3B1 is associated with transcript isoform changes of the genes UQCC and RPL31 both in CLLs and uveal melanomas Alejandro Reyes1, Carolin Blume2, Vincent Pelechano1, Petra Jakob1, Lars M Steinmetz1,3, Thorsten Zenz2,4 and Wolfgang Huber1* *Correspondence: [email protected] 1European Molecular Biology Abstract Laboratory, Genome Biology Unit, 69117, Heidelberg Germany Background: Genome sequencing studies of chronic lympoid leukemia (CLL) Full list of author information is have provided a comprehensive overview of recurrent somatic mutations in coding available at the end of the article genes. One of the most intriguing discoveries has been the prevalence of mutations in the HEAT-repeat domain of the splicing factor SF3B1. A frequently observed variant is predicted to cause the substitution of a lysine with a glutamic acid at position 700 of the protein (K700E). However, the molecular consequences of the mutations are largely unknown. Results: To start exploring this question, we sequenced the transcriptomes of six samples: four samples of CLL tumour cells, of which two contained the K700E mutation in SF3B1, and CD19 positive cells from two healthy donors. We identified 41 genes that showed differential usage of exons statistically associated with the mutated status of SF3B1 (false discovery rate of 10%). -
Urabe VK, Et Al. Influences on U2 Snrna Structure U2
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.05.451154; this version posted July 6, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Urabe VK, et al. Influences on U2 snRNA structure U2 snRNA structure is influenced by SF3A and SF3B proteins but not by SF3B inhibitors Veronica K. Urabe1, Meredith Stevers1, Arun K. Ghosh3 and Melissa S. Jurica1,2 * 1Department of Molecular Cell and Developmental Biology and 2Center for Molecular Biology of RNA, University of California, Santa Cruz, California, United States of America 3Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana United States of America *Corresponding author E-mail: [email protected] (MSJ) bioRxiv preprint doi: https://doi.org/10.1101/2021.07.05.451154; this version posted July 6, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Urabe VK, et al. Influences on U2 snRNA structure Abstract U2 snRNP is an essential component of the spliceosome. It is responsible for branch point recognition in the spliceosome A-complex via base-pairing of U2 snRNA with an intron to form the branch helix. Small molecule inhibitors target the SF3B component of the U2 snRNP and interfere with A-complex formation during spliceosome assembly. -
SF3B2 Monoclonal Antibody (M01J), Clone 5D2
SF3B2 monoclonal antibody (M01J), clone 5D2 Catalog # : H00010992-M01J 規格 : [ 100 ug ] List All Specification Application Image Product Mouse monoclonal antibody raised against a partial recombinant Western Blot (Cell lysate) Description: SF3B2. Immunogen: SF3B2 (NP_006833, 592 a.a. ~ 645 a.a) partial recombinant protein with GST tag. MW of the GST tag alone is 26 KDa. Sequence: YEGKEFETRLKEKKPGDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYG PPPSY enlarge Western Blot (Cell lysate) Host: Mouse Reactivity: Human, Mouse, Rat Preparation Cell Culture Production Method: (CX Grade Antibody List) enlarge Isotype: IgG2a Kappa Western Blot (Recombinant protein) Quality Control Antibody Reactive Against Recombinant Protein. Immunofluorescence Testing: enlarge Immunohistochemistry (Formalin/PFA-fixed paraffin- embedded sections) Western Blot detection against Immunogen (31.68 KDa) . Storage Buffer: In 1x PBS, pH 7.4 Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. enlarge Instruction: Sandwich ELISA (Recombinant protein) MSDS: Download Interspecies Mouse (98); Rat (98) Antigen Sequence: Datasheet: Download enlarge ELISA Applications Western Blot (Cell lysate) Page 1 of 3 2021/6/15 SF3B2 monoclonal antibody (M01J), clone 5D2. Western Blot analysis of SF3B2 expression in Hela S3 NE. Protocol Download Western Blot (Cell lysate) SF3B2 monoclonal antibody (M01J), clone 5D2. Western Blot analysis of SF3B2 expression in Jurkat. Protocol Download Western Blot (Recombinant protein) Protocol Download Immunofluorescence enlarge this image Immunofluorescence of monoclonal antibody to SF3B2 on HeLa cell . [antibody concentration 10 ug/ml] Immunohistochemistry (Formalin/PFA-fixed paraffin-embedded sections) enlarge this image Page 2 of 3 2021/6/15 Immunoperoxidase of monoclonal antibody to SF3B2 on formalin-fixed paraffin-embedded human kidney. [antibody concentration 6 ug/ml] Protocol Download Sandwich ELISA (Recombinant protein) Detection limit for recombinant GST tagged SF3B2 is 0.1 ng/ml as a capture antibody. -
Anti-Phospho-SF3B1 (Sap155) (Ser129) Pab
PD043 Page 1 For Research Use Only. Not for use in diagnostic procedures. Anti-Phospho-SF3B1 (Sap155) (Ser129) pAb CODE No. PD043 CLONALITY Polyclonal ISOTYPE Rabbit Ig, affinity purified QUANTITY 100 L SOURCE Purified IgG from rabbit serum IMMUNOGEN KLH conjugated synthetic peptide, RTMII(pS)PERL (corresponding to amino acid residues 124-133 of human SF3B1) FORMURATION PBS containing 50% Glycerol (pH 7.2). No preservative is contained. STORAGE This antibody solution is stable for one year from the date of purchase when stored at -20°C. APPLICATION-CONFIRMED Western blotting 1:1000 for chemiluminescence detection system SPECIES CROSS REACTIVITY on WB Species Human Mouse Rat Hamster Cell HeLa, Raji NIH/3T3, WR19L Not tested Not tested Reactivity Entrez Gene ID 23451 (Human), 81898 (Mouse) REFERENCES 1) Wang, C., et al., Genes Dev. 12, 1409-1414 (1998) 2) Shi, Y., et al., Mol Cell 23, 819-829 (2006) 3) Tanuma, N., et al., J. Biol. Chem., 283, 35805-35814 (2008) 4) Yoshida, K., et al., Nature 478, 64-69 (2011) 5) Rossi, D., et al., Blood 118, 6904-6908 (2011) 6) Quesada, V., et al., Nat Genet 44, 47-52 (2011) 7) Wang, L., et al., N Engl J Med. 365, 2497-2506 (2011) 8) Biankin, A. V., et al., Nature 491, 399-405 (2012) For more information, please visit our web site http://ruo.mbl.co.jp/ MEDICAL & BIOLOGICAL LABORATORIES CO., LTD. URL http://ruo.mbl.co.jp/ e-mail [email protected], TEL 052-238-1904 PD043 Page 2 P a g RELATED PRODUCTS e PD043 Anti-Phospho-SF3B1 (Sap155) (Ser129) pAb D138-3 Anti-Sap155 (SF3B12) mAb D221-3 Anti-Sap155 (SF3B1) -
Monoclonal B-Cell Lymphocytosis Is Characterized by Mutations in CLL Putative Driver Genes and Clonal Heterogeneity Many Years Before Disease Progression
Leukemia (2014) 28, 2395–2424 © 2014 Macmillan Publishers Limited All rights reserved 0887-6924/14 www.nature.com/leu LETTERS TO THE EDITOR Monoclonal B-cell lymphocytosis is characterized by mutations in CLL putative driver genes and clonal heterogeneity many years before disease progression Leukemia (2014) 28, 2395–2398; doi:10.1038/leu.2014.226 (Beckton Dickinson) and data analyzed using Cell Quest software. On the basis of FACS (fluorescence-activated cell sorting) analysis, we observed after enrichment an average of 91% of CD19+ cells Monoclonal B-cell lymphocytosis (MBL) is defined as an asympto- (range 76–99%) and 91% of the CD19+ fraction were CD19+/CD5+ matic expansion of clonal B cells with less than 5 × 109/L cells in the cells (range 66–99%). We used the values of the CD19+/CD5+ peripheral blood and without other manifestations of chronic fraction to calculate the leukemic B-cell fraction and reduce any lymphocytic leukemia (CLL; for example, lymphadenopathy, cyto- significant contamination of non-clonal B cells in each biopsy. DNA penias, constitutional symptoms).1 Approximately 1% of the MBL was extracted from the clonal B cells and non-clonal (that is, T cells) cohort develops CLL per year. Evidence suggests that nearly all CLL cells using the Gentra Puregene Cell Kit (Qiagen, Hilden, Germany). 2 fi fi cases are preceded by an MBL state. Our understanding of the Extracted DNAs were ngerprinted to con rm the relationship genetic basis, clonal architecture and evolution in CLL pathogenesis between samples of the same MBL individual and to rule out sample has undergone significant improvements in the last few years.3–8 In cross-contamination between individuals. -
SF3B2-Mediated RNA Splicing Drives Human Prostate Cancer Progression
Published OnlineFirst August 20, 2019; DOI: 10.1158/0008-5472.CAN-18-3965 Cancer Molecular Cell Biology Research SF3B2-Mediated RNA Splicing Drives Human Prostate Cancer Progression Norihiko Kawamura1,2, Keisuke Nimura1, Kotaro Saga1, Airi Ishibashi1, Koji Kitamura1,3, Hiromichi Nagano1, Yusuke Yoshikawa4, Kyoso Ishida1,5, Norio Nonomura2, Mitsuhiro Arisawa4, Jun Luo6, and Yasufumi Kaneda1 Abstract Androgen receptor splice variant-7 (AR-V7) is a General RNA splicing SF3B2 complex-mediated alternative RNA splicing constitutively active AR variant implicated in U2 castration-resistant prostate cancers. Here, we show U2 snRNA that the RNA splicing factor SF3B2, identified by 3’ 3’ in silico and CRISPR/Cas9 analyses, is a critical 5’ 3’ splice site 5’ SF3B7 AR-V7 5’ A U2AF2 AGA Exon ? determinant of expression and is correlated SF3B6(p14) SF3B4 SF3B1 SF3B4 SF3B1 with aggressive cancer phenotypes. Transcriptome SF3B5 SF3B2 SF3B3 SF3B2 SF3B3 and PAR-CLIP analyses revealed that SF3B2 con- SF3A3 SF3B2 complex SF3A3 SF3A1 SF3A1 SF3b complex trols the splicing of target genes, including AR, to AR pre-mRNA drive aggressive phenotypes. SF3B2-mediated CE3 aggressive phenotypes in vivo were reversed by AR-V7 mRNA AR mRNA AR-V7 knockout. Pladienolide B, an inhibitor of CE3 a splicing modulator of the SF3b complex, sup- Drive malignancy pressed the growth of tumors addicted to high While the SF3b complex is critical for general RNA splicing, SF3B2 promotes inclusion of the target exon through recognizing a specific RNA motif. SF3B2 expression. These findings support the idea © 2019 American Association for Cancer Research that alteration of the splicing pattern by high SF3B2 expression is one mechanism underlying prostate cancer progression and therapeutic resistance. -
Essential Genes and Their Role in Autism Spectrum Disorder
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2017 Essential Genes And Their Role In Autism Spectrum Disorder Xiao Ji University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, and the Genetics Commons Recommended Citation Ji, Xiao, "Essential Genes And Their Role In Autism Spectrum Disorder" (2017). Publicly Accessible Penn Dissertations. 2369. https://repository.upenn.edu/edissertations/2369 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2369 For more information, please contact [email protected]. Essential Genes And Their Role In Autism Spectrum Disorder Abstract Essential genes (EGs) play central roles in fundamental cellular processes and are required for the survival of an organism. EGs are enriched for human disease genes and are under strong purifying selection. This intolerance to deleterious mutations, commonly observed haploinsufficiency and the importance of EGs in pre- and postnatal development suggests a possible cumulative effect of deleterious variants in EGs on complex neurodevelopmental disorders. Autism spectrum disorder (ASD) is a heterogeneous, highly heritable neurodevelopmental syndrome characterized by impaired social interaction, communication and repetitive behavior. More and more genetic evidence points to a polygenic model of ASD and it is estimated that hundreds of genes contribute to ASD. The central question addressed in this dissertation is whether genes with a strong effect on survival and fitness (i.e. EGs) play a specific oler in ASD risk. I compiled a comprehensive catalog of 3,915 mammalian EGs by combining human orthologs of lethal genes in knockout mice and genes responsible for cell-based essentiality. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Flexible, Unbiased Analysis of Biological Characteristics Associated with Genomic Regions
bioRxiv preprint doi: https://doi.org/10.1101/279612; this version posted March 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. BioFeatureFinder: Flexible, unbiased analysis of biological characteristics associated with genomic regions Felipe E. Ciamponi 1,2,3; Michael T. Lovci 2; Pedro R. S. Cruz 1,2; Katlin B. Massirer *,1,2 1. Structural Genomics Consortium - SGC, University of Campinas, SP, Brazil. 2. Center for Molecular Biology and Genetic Engineering - CBMEG, University of Campinas, Campinas, SP, Brazil. 3. Graduate program in Genetics and Molecular Biology, PGGBM, University of Campinas, Campinas, SP, Brazil. *Corresponding author: [email protected] Mailing address: Center for Molecular Biology and Genetic Engineering - CBMEG, University of Campinas, Campinas, SP, Brazil. Av Candido Rondo, 400 Cidade Universitária CEP 13083-875, Campinas, SP Phone: 55-19-98121-937 bioRxiv preprint doi: https://doi.org/10.1101/279612; this version posted March 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Abstract BioFeatureFinder is a novel algorithm which allows analyses of many biological genomic landmarks (including alternatively spliced exons, DNA/RNA- binding protein binding sites, and gene/transcript functional elements, nucleotide content, conservation, k-mers, secondary structure) to identify distinguishing features. -
Full-Length Transcript Characterization of SF3B1 Mutation in Chronic Lymphocytic Leukemia Reveals Downregulation of Retained Introns
ARTICLE https://doi.org/10.1038/s41467-020-15171-6 OPEN Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns Alison D. Tang 1, Cameron M. Soulette 2, Marijke J. van Baren1, Kevyn Hart1, Eva Hrabeta-Robinson1, ✉ Catherine J. Wu 3,4,5 & Angela N. Brooks 1 SF3B1 1234567890():,; While splicing changes caused by somatic mutations in are known, identifying full- length isoform changes may better elucidate the functional consequences of these mutations. We report nanopore sequencing of full-length cDNA from CLL samples with and without SF3B1 mutation, as well as normal B cell samples, giving a total of 149 million pass reads. We present FLAIR (Full-Length Alternative Isoform analysis of RNA), a computational workflow to identify high-confidence transcripts, perform differential splicing event analysis, and dif- ferential isoform analysis. Using nanopore reads, we demonstrate differential 3’ splice site changes associated with SF3B1 mutation, agreeing with previous studies. We also observe a strong downregulation of intron retention events associated with SF3B1 mutation. Full-length transcript analysis links multiple alternative splicing events together and allows for better estimates of the abundance of productive versus unproductive isoforms. Our work demon- strates the potential utility of nanopore sequencing for cancer and splicing research. 1 Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95062, USA. 2 Department of Molecular Cell & Developmental Biology, University of California, Santa Cruz, CA 95062, USA. 3 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. 4 Broad Institiute of Harvard and MIT, Cambridge, MA, USA. -
Structural Insights Into How Prp5 Proofreads the Pre-Mrna Branch Site
Article Structural insights into how Prp5 proofreads the pre-mRNA branch site https://doi.org/10.1038/s41586-021-03789-5 Zhenwei Zhang1, Norbert Rigo2, Olexandr Dybkov2, Jean-Baptiste Fourmann2, Cindy L. Will2, Vinay Kumar2, Henning Urlaub3,4, Holger Stark1 ✉ & Reinhard Lührmann2 ✉ Received: 10 December 2020 Accepted: 30 June 2021 During the splicing of introns from precursor messenger RNAs (pre-mRNAs), the U2 Published online: 4 August 2021 small nuclear ribonucleoprotein (snRNP) must undergo stable integration into the Open access spliceosomal A complex—a poorly understood, multistep process that is facilitated by Check for updates the DEAD-box helicase Prp5 (refs. 1–4). During this process, the U2 small nuclear RNA (snRNA) forms an RNA duplex with the pre-mRNA branch site (the U2–BS helix), which is proofread by Prp5 at this stage through an unclear mechanism5. Here, by deleting the branch-site adenosine (BS-A) or mutating the branch-site sequence of an actin pre-mRNA, we stall the assembly of spliceosomes in extracts from the yeast Saccharomyces cerevisiae directly before the A complex is formed. We then determine the three-dimensional structure of this newly identifed assembly intermediate by cryo-electron microscopy. Our structure indicates that the U2–BS helix has formed in this pre-A complex, but is not yet clamped by the HEAT domain of the Hsh155 protein (Hsh155HEAT), which exhibits an open conformation. The structure further reveals a large-scale remodelling/repositioning of the U1 and U2 snRNPs during the formation of the A complex that is required to allow subsequent binding of the U4/U6.U5 tri-snRNP, but that this repositioning is blocked in the pre-A complex by the presence of Prp5. -
Report Summary 4 Clinically Significant Variants & Combinations 0 Relevant Therapies 0 Other Biomarkers
Inov Klinisches Labor Schützengraben 42, 4051 Basel, Switzerland Tel: +41 61 123 4567 Case ID Patient sex Diagnosis Tumor purity Ordering physician XB-1064 Female Chronic lymphocytic leukemia not specified Dr. Niklaus Marti Patient MRN Patient DOB Sample type Sample collection date Ordering institution MRN1234567 04/08/1957 Blood 10/01/2020 Universitätsklinik Liestal Patient name Patient ethnicity Sample site Sample receipt date Ordering institution ID not specified not specified Blood 10/03/2020 OID123 Report summary 4 clinically significant variants & combinations 0 relevant therapies 0 other biomarkers variant variant variant variant SF3B1 p.K700E NOTCH1 p.P2514fs NPM1 p.W288fs CTNNB1 p.D32Y variant SF3B1 p.K700E VAF 36% RD 67 Tier I-A SF3B1 mutations are associated with worse or intermediate prognosis in CLL (WHO, NCCN, ESMO). These mutations may be present in CHIP (WHO). no approved therapies variant NOTCH1 p.P2514fs VAF 28% RD 25 Tier I-B In a phase III trial, the addition of rituximab to FC chemotherapy showed no benefit in patients with CLL harboring NOTCH1 P2514Rfs*4. NOTCH1 P2514Rfs*4 was associated with poor overall survival, progression-free survival, and treatment risk in clinical studies of CLL patients. no approved therapies variant NPM1 p.W288fs VAF 27% RD 1,590 Tier II-C NPM1 mutations are associated with with a favorable prognosis in cytogenetically normal acute myeloid leukemia (AML), (NCCN), (ESMO), (ELN), (WHO, 2016). Multiple clinical studies have reported that NPM1 mutation is associated with favorable prognosis in AML lacking FLT3 internal tandem duplication or other FLT3 mutation. NPM1 mutation is an important diagnostic marker in AML (NCCN), (WHO), and testing is strongly recommended for certain patients with suspected or confirmed AML (CAP-ASH) to confirm molecular subtype.