Flexible, Unbiased Analysis of Biological Characteristics Associated with Genomic Regions
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SRC Antibody - N-Terminal Region (ARP32476 P050) Data Sheet
SRC antibody - N-terminal region (ARP32476_P050) Data Sheet Product Number ARP32476_P050 Product Name SRC antibody - N-terminal region (ARP32476_P050) Size 50ug Gene Symbol SRC Alias Symbols ASV; SRC1; c-SRC; p60-Src Nucleotide Accession# NM_005417 Protein Size (# AA) 536 amino acids Molecular Weight 60kDa Product Format Lyophilized powder NCBI Gene Id 6714 Host Rabbit Clonality Polyclonal Official Gene Full Name V-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) Gene Family SH2D This is a rabbit polyclonal antibody against SRC. It was validated on Western Blot by Aviva Systems Biology. At Aviva Systems Biology we manufacture rabbit polyclonal antibodies on a large scale (200-1000 Description products/month) of high throughput manner. Our antibodies are peptide based and protein family oriented. We usually provide antibodies covering each member of a whole protein family of your interest. We also use our best efforts to provide you antibodies recognize various epitopes of a target protein. For availability of antibody needed for your experiment, please inquire (). Peptide Sequence Synthetic peptide located within the following region: QTPSKPASADGHRGPSAAFAPAAAEPKLFGGFNSSDTVTSPQRAGPLAGG This gene is highly similar to the v-src gene of Rous sarcoma virus. This proto-oncogene may play a role in the Description of Target regulation of embryonic development and cell growth. SRC protein is a tyrosine-protein kinase whose activity can be inhibited by phosphorylation by c-SRC kinase. Mutations in this gene could be involved in the -
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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. -
Integrative Analysis Reveals RNA G-Quadruplexes in Utrs Are Selectively Constrained and Enriched for Functional Associations
ARTICLE https://doi.org/10.1038/s41467-020-14404-y OPEN Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations David S.M. Lee 1, Louis R. Ghanem 2* & Yoseph Barash 1,3* G-quadruplex (G4) sequences are abundant in untranslated regions (UTRs) of human messenger RNAs, but their functional importance remains unclear. By integrating multiple 1234567890():,; sources of genetic and genomic data, we show that putative G-quadruplex forming sequences (pG4) in 5’ and 3’ UTRs are selectively constrained, and enriched for cis-eQTLs and RNA-binding protein (RBP) interactions. Using over 15,000 whole-genome sequences, we find that negative selection acting on central guanines of UTR pG4s is comparable to that of missense variation in protein-coding sequences. At multiple GWAS-implicated SNPs within pG4 UTR sequences, we find robust allelic imbalance in gene expression across diverse tissue contexts in GTEx, suggesting that variants affecting G-quadruplex formation within UTRs may also contribute to phenotypic variation. Our results establish UTR G4s as important cis-regulatory elements and point to a link between disruption of UTR pG4 and disease. 1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. 2 Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children’s Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA. 3 Department -
Splicing Regulatory Factors in Breast Cancer Hallmarks and Disease Progression
www.oncotarget.com Oncotarget, 2019, Vol. 10, (No. 57), pp: 6021-6037 Review Splicing regulatory factors in breast cancer hallmarks and disease progression Esmee Koedoot1, Liesanne Wolters1, Bob van de Water1 and Sylvia E. Le Dévédec1 1Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, The Netherlands Correspondence to: Sylvia E. Le Dévédec, email: [email protected] Keywords: hallmarks of cancer; breast cancer; alternative splicing; splice factors; RNA sequencing Received: April 23, 2019 Accepted: August 29, 2019 Published: October 15, 2019 Copyright: Koedoot et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT By regulating transcript isoform expression levels, alternative splicing provides an additional layer of protein control. Recent studies show evidence that cancer cells use different splicing events to fulfill their requirements in order to develop, progress and metastasize. However, there has been less attention for the role of the complex catalyzing the complicated multistep splicing reaction: the spliceosome. The spliceosome consists of multiple sub-complexes in total comprising 244 proteins or splice factors and 5 associated RNA molecules. Here we discuss the role of splice factors in the oncogenic processes tumors cells need to fulfill their oncogenic properties (the so-called the hallmarks of cancer). Despite the fact that splice factors have been investigated only recently, they seem to play a prominent role in already five hallmarks of cancer: angiogenesis, resisting cell death, sustaining proliferation, deregulating cellular energetics and invasion and metastasis formation by affecting major signaling pathways such as epithelial-to-mesenchymal transition, the Warburg effect, DNA damage response and hormone receptor dependent proliferation. -
University of Groningen BRCA2 Deficiency Instigates Cgas
University of Groningen BRCA2 deficiency instigates cGAS-mediated inflammatory signaling and confers sensitivity to tumor necrosis factor-alpha-mediated cytotoxicity Heijink, Anne Margriet; Talens, Francien; Jae, Lucas T; van Gijn, Stephanie E; Fehrmann, Rudolf S N; Brummelkamp, Thijn R; van Vugt, Marcel A T M Published in: Nature Communications DOI: 10.1038/s41467-018-07927-y IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2019 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Heijink, A. M., Talens, F., Jae, L. T., van Gijn, S. E., Fehrmann, R. S. N., Brummelkamp, T. R., & van Vugt, M. A. T. M. (2019). BRCA2 deficiency instigates cGAS-mediated inflammatory signaling and confers sensitivity to tumor necrosis factor-alpha-mediated cytotoxicity. Nature Communications, 10(1), [100]. https://doi.org/10.1038/s41467-018-07927-y Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. -
Progesterone Receptor Membrane Component 1 Promotes Survival of Human Breast Cancer Cells and the Growth of Xenograft Tumors
Cancer Biology & Therapy ISSN: 1538-4047 (Print) 1555-8576 (Online) Journal homepage: http://www.tandfonline.com/loi/kcbt20 Progesterone receptor membrane component 1 promotes survival of human breast cancer cells and the growth of xenograft tumors Nicole C. Clark, Anne M. Friel, Cindy A. Pru, Ling Zhang, Toshi Shioda, Bo R. Rueda, John J. Peluso & James K. Pru To cite this article: Nicole C. Clark, Anne M. Friel, Cindy A. Pru, Ling Zhang, Toshi Shioda, Bo R. Rueda, John J. Peluso & James K. Pru (2016) Progesterone receptor membrane component 1 promotes survival of human breast cancer cells and the growth of xenograft tumors, Cancer Biology & Therapy, 17:3, 262-271, DOI: 10.1080/15384047.2016.1139240 To link to this article: http://dx.doi.org/10.1080/15384047.2016.1139240 Accepted author version posted online: 19 Jan 2016. Published online: 19 Jan 2016. Submit your article to this journal Article views: 49 View related articles View Crossmark data Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=kcbt20 Download by: [University of Connecticut] Date: 26 May 2016, At: 11:28 CANCER BIOLOGY & THERAPY 2016, VOL. 17, NO. 3, 262–271 http://dx.doi.org/10.1080/15384047.2016.1139240 RESEARCH PAPER Progesterone receptor membrane component 1 promotes survival of human breast cancer cells and the growth of xenograft tumors Nicole C. Clarka,*, Anne M. Frielb,*, Cindy A. Prua, Ling Zhangb, Toshi Shiodac, Bo R. Ruedab, John J. Pelusod, and James K. Prua aDepartment of Animal Sciences, -
Effect of Chromosomal Copy Number Variations on Congenital Birth Defects and Human Developmental Disorders
EFFECT OF CHROMOSOMAL COPY NUMBER VARIATIONS ON CONGENITAL BIRTH DEFECTS AND HUMAN DEVELOPMENTAL DISORDERS APPROVED BY SUPERVISORY COMMITTEE Andrew R. Zinn, M.D., Ph.D Christine K. Garcia, M.D., Ph.D Orson Moe, M.D., Ph.D Ralph DeBerardinis, M.D., Ph.D DEDICATION Many many people have given me love, support, advice, and caffeine over the course of my graduate research to which I am eternally grateful. To Andrew, my mentor for many years and scientific guide- if someday I become half the researcher you are, I will have turned out. There aren’t enough words- thank you, thank you, thank you. To my thesis committee- thank for your insightful comments, direction and criticism and most for your genuine desire to see me succeed. To my collaborators, Vidu Garg and Linda Baker- thank you for sharing your research with a lowly grad student. I would literally have nothing to research without your generosity. To the lab-thanks for listening to boring mitochondrial results each week. I will miss you terribly. To Miguel- No puedo poner a las palabras la profundidad de mi amor para usted. Usted es mi amigo, mi amor, mi corazón, mi amante, mi ayuda y mi ancla. Con usted por mi lado puedo lograr las cosas magníficas que no podría solamente. Te amo. To Justin- the talk of complex four late at night was worth it. Love you. To Kim, Kristen and Adriane- my absolute favorite people- thank you for believing even when I did not. Thank you for listening to me when I needed it most. -
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) -
Supplementary Table S1. Upregulated Genes Differentially
Supplementary Table S1. Upregulated genes differentially expressed in athletes (p < 0.05 and 1.3-fold change) Gene Symbol p Value Fold Change 221051_s_at NMRK2 0.01 2.38 236518_at CCDC183 0.00 2.05 218804_at ANO1 0.00 2.05 234675_x_at 0.01 2.02 207076_s_at ASS1 0.00 1.85 209135_at ASPH 0.02 1.81 228434_at BTNL9 0.03 1.81 229985_at BTNL9 0.01 1.79 215795_at MYH7B 0.01 1.78 217979_at TSPAN13 0.01 1.77 230992_at BTNL9 0.01 1.75 226884_at LRRN1 0.03 1.74 220039_s_at CDKAL1 0.01 1.73 236520_at 0.02 1.72 219895_at TMEM255A 0.04 1.72 201030_x_at LDHB 0.00 1.69 233824_at 0.00 1.69 232257_s_at 0.05 1.67 236359_at SCN4B 0.04 1.64 242868_at 0.00 1.63 1557286_at 0.01 1.63 202780_at OXCT1 0.01 1.63 1556542_a_at 0.04 1.63 209992_at PFKFB2 0.04 1.63 205247_at NOTCH4 0.01 1.62 1554182_at TRIM73///TRIM74 0.00 1.61 232892_at MIR1-1HG 0.02 1.61 204726_at CDH13 0.01 1.6 1561167_at 0.01 1.6 1565821_at 0.01 1.6 210169_at SEC14L5 0.01 1.6 236963_at 0.02 1.6 1552880_at SEC16B 0.02 1.6 235228_at CCDC85A 0.02 1.6 1568623_a_at SLC35E4 0.00 1.59 204844_at ENPEP 0.00 1.59 1552256_a_at SCARB1 0.02 1.59 1557283_a_at ZNF519 0.02 1.59 1557293_at LINC00969 0.03 1.59 231644_at 0.01 1.58 228115_at GAREM1 0.01 1.58 223687_s_at LY6K 0.02 1.58 231779_at IRAK2 0.03 1.58 243332_at LOC105379610 0.04 1.58 232118_at 0.01 1.57 203423_at RBP1 0.02 1.57 AMY1A///AMY1B///AMY1C///AMY2A///AMY2B// 208498_s_at 0.03 1.57 /AMYP1 237154_at LOC101930114 0.00 1.56 1559691_at 0.01 1.56 243481_at RHOJ 0.03 1.56 238834_at MYLK3 0.01 1.55 213438_at NFASC 0.02 1.55 242290_at TACC1 0.04 1.55 ANKRD20A1///ANKRD20A12P///ANKRD20A2/// -
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.