Interaction Proteomics Identifies Estrogen Receptor Beta
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Asian Zika Virus Isolate Significantly Changes the Transcriptional Profile
viruses Article Asian Zika Virus Isolate Significantly Changes the Transcriptional Profile and Alternative RNA Splicing Events in a Neuroblastoma Cell Line Gaston Bonenfant 1,2, Ryan Meng 2, Carl Shotwell 2,3 , Pheonah Badu 1,2, Anne F. Payne 4, Alexander T. Ciota 4,5, Morgan A. Sammons 1, J. Andrew Berglund 1,2 and Cara T. Pager 1,2,* 1 Department of Biological Sciences, University at Albany-SUNY, Albany, NY 12222, USA; [email protected] (G.B.); [email protected] (P.B.); [email protected] (M.A.S.); [email protected] (J.A.B.) 2 The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA; [email protected] (R.M.); [email protected] (C.S.) 3 Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA 4 Wadsworth Center, New York State Department of Health (NYSDOH), Slingerlands, NY 12159, USA; [email protected] (A.F.P.); [email protected] (A.T.C.) 5 Department of Biomedical Sciences, University at Albany-SUNY, School of Public Health, Rensselaer, NY 12144, USA * Correspondence: [email protected]; Tel.: +1-518-591-8841 Received: 9 April 2020; Accepted: 27 April 2020; Published: 5 May 2020 Abstract: The alternative splicing of pre-mRNAs expands a single genetic blueprint to encode multiple, functionally diverse protein isoforms. Viruses have previously been shown to interact with, depend on, and alter host splicing machinery. The consequences, however, incited by viral infection on the global alternative slicing (AS) landscape are under-appreciated. Here, we investigated the transcriptional and alternative splicing profile of neuronal cells infected with a contemporary Puerto Rican Zika virus (ZIKVPR) isolate, an isolate of the prototypical Ugandan ZIKV (ZIKVMR), and dengue virus 2 (DENV2). -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
RING1 Antibody (N-Term) Affinity Purified Rabbit Polyclonal Antibody (Pab) Catalog # AP14560A
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 RING1 Antibody (N-term) Affinity Purified Rabbit Polyclonal Antibody (Pab) Catalog # AP14560A Specification RING1 Antibody (N-term) - Product Information Application WB,E Primary Accession Q06587 Other Accession Q6MGB6, O35730, NP_002922.2 Reactivity Human Predicted Mouse, Rat Host Rabbit Clonality Polyclonal Isotype Rabbit Ig Antigen Region 95-123 RING1 Antibody (N-term) - Additional Information RING1 Antibody (N-term) (Cat. #AP14560a) Gene ID 6015 western blot analysis in MDA-MB453 cell line lysates (35ug/lane).This demonstrates the Other Names RING1 antibody detected the RING1 protein E3 ubiquitin-protein ligase RING1, 632-, (arrow). Polycomb complex protein RING1, RING finger protein 1, Really interesting new gene 1 protein, RING1, RNF1 RING1 Antibody (N-term) - Background Target/Specificity This gene belongs to the RING finger family, This RING1 antibody is generated from members of rabbits immunized with a KLH conjugated synthetic peptide between 95-123 amino which encode proteins characterized by a RING acids from the N-terminal region of human domain, a RING1. zinc-binding motif related to the zinc finger domain. The gene Dilution product can bind DNA and can act as a WB~~1:1000 transcriptional repressor. It is associated with the multimeric polycomb Format group protein complex. Purified polyclonal antibody supplied in PBS The gene product interacts with the polycomb with 0.09% (W/V) sodium azide. This group proteins BMI1, antibody is purified through a protein A EDR1, and CBX4, and colocalizes with these column, followed by peptide affinity proteins in large purification. -
Genome-Wide DNA Methylation Analysis of KRAS Mutant Cell Lines Ben Yi Tew1,5, Joel K
www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1. -
RING1 Proteins Contribute to Early Proximal-Distal Specification of The
© 2016. Published by The Company of Biologists Ltd | Development (2016) 143, 276-285 doi:10.1242/dev.127506 RESEARCH ARTICLE RING1 proteins contribute to early proximal-distal specification of the forelimb bud by restricting Meis2 expression Nayuta Yakushiji-Kaminatsui1,*,‡, Takashi Kondo1,2,3, Takaho A. Endo4, Yoko Koseki1,2, Kaori Kondo1,2,3, Osamu Ohara4, Miguel Vidal5 and Haruhiko Koseki1,2,‡ ABSTRACT subunits to catalyze histone H2A monoubiquitylation at lysine 119 Polycomb group (PcG) proteins play a pivotal role in silencing (H2AK119ub1). PRC1 also targets chromatin compaction by SAM developmental genes and help to maintain various stem and domain polymerization of PHC1 and PHC2, a mammalian PH precursor cells and regulate their differentiation. PcG factors also ortholog, via H3K27me3 recognition by chromodomain proteins regulate dynamic and complex regional specification, particularly in such as CBX7 and CBX2 (Cao et al., 2002; Endoh et al., 2012; mammals, but this activity is mechanistically not well understood. In Isono et al., 2013; Kuzmichev et al., 2002). Recent studies identified this study, we focused on proximal-distal (PD) patterning of the a variant PRC1 complex containing RYBP (Ring1 and YY1 mouse forelimb bud to elucidate how PcG factors contribute to a binding protein)/YAF (YY1-associated factor), RING1A/B and a regional specification process that depends on developmental distinct PCGF subunit (Gao et al., 2012; Tavares et al., 2012), and signals. Depletion of the RING1 proteins RING1A (RING1) and demonstrated that H2AK119ub1 mediated by this variant PRC1 RING1B (RNF2), which are essential components of Polycomb leads to the recruitment of PRC2 and placement of H3K27me3 to repressive complex 1 (PRC1), led to severe defects in forelimb initiate Polycomb repression (Blackledge et al., 2014). -
The Structure-Function Relationship of Angular Estrogens and Estrogen Receptor Alpha to Initiate Estrogen-Induced Apoptosis in Breast Cancer Cells S
Supplemental material to this article can be found at: http://molpharm.aspetjournals.org/content/suppl/2020/05/03/mol.120.119776.DC1 1521-0111/98/1/24–37$35.00 https://doi.org/10.1124/mol.120.119776 MOLECULAR PHARMACOLOGY Mol Pharmacol 98:24–37, July 2020 Copyright ª 2020 The Author(s) This is an open access article distributed under the CC BY Attribution 4.0 International license. The Structure-Function Relationship of Angular Estrogens and Estrogen Receptor Alpha to Initiate Estrogen-Induced Apoptosis in Breast Cancer Cells s Philipp Y. Maximov, Balkees Abderrahman, Yousef M. Hawsawi, Yue Chen, Charles E. Foulds, Antrix Jain, Anna Malovannaya, Ping Fan, Ramona F. Curpan, Ross Han, Sean W. Fanning, Bradley M. Broom, Daniela M. Quintana Rincon, Jeffery A. Greenland, Geoffrey L. Greene, and V. Craig Jordan Downloaded from Departments of Breast Medical Oncology (P.Y.M., B.A., P.F., D.M.Q.R., J.A.G., V.C.J.) and Computational Biology and Bioinformatics (B.M.B.), University of Texas, MD Anderson Cancer Center, Houston, Texas; King Faisal Specialist Hospital and Research (Gen.Org.), Research Center, Jeddah, Kingdom of Saudi Arabia (Y.M.H.); The Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois (R.H., S.W.F., G.L.G.); Center for Precision Environmental Health and Department of Molecular and Cellular Biology (C.E.F.), Mass Spectrometry Proteomics Core (A.J., A.M.), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Mass Spectrometry Proteomics Core (A.M.), and Dan L. Duncan molpharm.aspetjournals.org -
Vitamin D Genes & Exposure in Relation to Kidney Cancer by Sara
Vitamin D Genes & Exposure in Relation to Kidney Cancer by Sara Karami B.S., Biology, James Madison University, 2002 M.P.H, Epidemiology, The George Washington University, 2004 A Dissertation submitted to The Faculty of The Columbian College of Arts and Science of The George Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy August 31, 2009 Dissertation directed by Katherine L. Hunting Professor of Environmental and Occupational Health and of Epidemiology and Biostatistics and Lee E. Moore Epidemiological Investigator, NIH, NCI The Columbian College of Arts and Science of The George Washington University certifies that Sara Karami has passed the Final Examination for the degree of Doctor of Philosophy as of August 12, 2009. This is the final and approved form of the dissertation. Vitamin D Genes & Exposure in Relation to Kidney Cancer Sara Karami Dissertation Research Committee: Katherine L. Hunting, Professor of Environmental and Occupational Health and of Epidemiology and Biostatistics, Dissertation Director Lee E. Moore, Epidemiological Investigator, NIH, NCI, Co-Director Paul H. Levine, Professor of Epidemiology and Biostatistics, Committee Member Yinglei Lai, Assistant Professor of Statistics, Committee Member ii © Copyright 2009 by Sara Karami All rights reserved iii Dedication The author wishes to thank everyone involved in the dissertation process for their guidance and support. Special thanks to Dr. Lee Moore, Dr. Katherine Hunting, Dr. Paul Levine, Dr. Yinglei Lai, Dr. Sean Cleary, and Dr. Donte Verme. iv Acknowledgement The author wishes to acknowledge the National Cancer Institute, the International Agency for Research on Cancer, and the School of Public Health and Health Services of The George Washington University for their assistance. -
Structural and Spatial Chromatin Features at Developmental Gene Loci in Human Pluripotent Stem Cells
ARTICLE DOI: 10.1038/s41467-017-01679-x OPEN Structural and spatial chromatin features at developmental gene loci in human pluripotent stem cells Hiroki Ikeda1, Masamitsu Sone1,2, Shinya Yamanaka1,3 & Takuya Yamamoto 1,2,4 Higher-order chromatin organization controls transcriptional programs that govern cell properties and functions. In order for pluripotent stem cells (PSCs) to appropriately respond 1234567890 to differentiation signals, developmental gene loci should be structurally and spatially regu- lated to be readily available for immediate transcription, even though these genes are hardly expressed in PSCs. Here, we show that both chromatin interaction profiles and nuclear positions at developmental gene loci differ between human somatic cells and hPSCs, and that changes in the chromatin interactions are closely related to the nuclear repositioning. Moreover, we also demonstrate that developmental gene loci, which have bivalent histone modifications, tend to colocalize in PSCs. Furthermore, this colocalization requires PRC1, PRC2, and TrxG complexes, which are essential regulatory factors for the maintenance of transcriptionally poised developmental genes. Our results indicate that higher-order chro- matin regulation may be an integral part of the differentiation capacity that defines pluripotency. 1 Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan. 2 Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan. 3 Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA. 4 AMED-CREST, AMED 1-7-1 Otemach, Chiyodaku, Tokyo 100-0004, Japan. Correspondence and requests for materials should be addressed to T.Y. -
Table S1. Identified Proteins with Exclusive Expression in Cerebellum of Rats of Control, 10Mg F/L and 50Mg F/L Groups
Table S1. Identified proteins with exclusive expression in cerebellum of rats of control, 10mg F/L and 50mg F/L groups. Accession PLGS Protein Name Group IDa Score Q3TXS7 26S proteasome non-ATPase regulatory subunit 1 435 Control Q9CQX8 28S ribosomal protein S36_ mitochondrial 197 Control P52760 2-iminobutanoate/2-iminopropanoate deaminase 315 Control Q60597 2-oxoglutarate dehydrogenase_ mitochondrial 67 Control P24815 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 1 84 Control Q99L13 3-hydroxyisobutyrate dehydrogenase_ mitochondrial 114 Control P61922 4-aminobutyrate aminotransferase_ mitochondrial 470 Control P10852 4F2 cell-surface antigen heavy chain 220 Control Q8K010 5-oxoprolinase 197 Control P47955 60S acidic ribosomal protein P1 190 Control P70266 6-phosphofructo-2-kinase/fructose-2_6-bisphosphatase 1 113 Control Q8QZT1 Acetyl-CoA acetyltransferase_ mitochondrial 402 Control Q9R0Y5 Adenylate kinase isoenzyme 1 623 Control Q80TS3 Adhesion G protein-coupled receptor L3 59 Control B7ZCC9 Adhesion G-protein coupled receptor G4 139 Control Q6P5E6 ADP-ribosylation factor-binding protein GGA2 45 Control E9Q394 A-kinase anchor protein 13 60 Control Q80Y20 Alkylated DNA repair protein alkB homolog 8 111 Control P07758 Alpha-1-antitrypsin 1-1 78 Control P22599 Alpha-1-antitrypsin 1-2 78 Control Q00896 Alpha-1-antitrypsin 1-3 78 Control Q00897 Alpha-1-antitrypsin 1-4 78 Control P57780 Alpha-actinin-4 58 Control Q9QYC0 Alpha-adducin 270 Control Q9DB05 Alpha-soluble NSF attachment protein 156 Control Q6PAM1 Alpha-taxilin 161 -
The Arabidopsis PRC1-Like Ring-Finger Proteins Are Necessary for Repression of Embryonic Traits During Vegetative Growth
npg AtRING1/AtBMI1 are crucial for embryonic trait repression Cell Research (2010) 20:1332-1344. 1332 © 2010 IBCB, SIBS, CAS All rights reserved 1001-0602/10 $ 32.00 npg ORIGINAL ARTICLE www.nature.com/cr The Arabidopsis PRC1-like ring-finger proteins are necessary for repression of embryonic traits during vegetative growth Donghong Chen1, Anne Molitor1, Chunlin Liu2, Wen-Hui Shen1 1Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France; 2Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China Polycomb group genes play crucial roles in the maintenance of the transcriptionally silenced state of genes for proper cell differentiation in animals and plants. While components of the polycomb repressive complex2 (PRC2) are evolutionarily conserved and their functions are extensively studied in plants, PRC1 differs considerably between animals and plants, and its functions in plants are as yet not well described. Previous studies have identified the Arabidopsis AtRING1a and AtRING1b as homologues of the animal PRC1 subunit RING1. Here, we show that the Atring1a Atring1b double mutant exhibits derepression of embryonic traits during vegetative growth. Accordingly, several key regulatory genes involved in embryogenesis and stem cell activity are ectopically expressed in the mutant. Furthermore, we show that the mutant phenotypes and increased expression of regulatory genes are enhanced by the PRC2 mutant clf. Finally, we show that three homologues of the animal PRC1-subunit ring-finger protein BMI1, AtBMI1a, AtBMI1b and AtBMI1c, can bind with AtRING1a or AtRING1b, and in addition, AtBMI1c can bind with LHP1. -
Figure S1. HAEC ROS Production and ML090 NOX5-Inhibition
Figure S1. HAEC ROS production and ML090 NOX5-inhibition. (a) Extracellular H2O2 production in HAEC treated with ML090 at different concentrations and 24 h after being infected with GFP and NOX5-β adenoviruses (MOI 100). **p< 0.01, and ****p< 0.0001 vs control NOX5-β-infected cells (ML090, 0 nM). Results expressed as mean ± SEM. Fold increase vs GFP-infected cells with 0 nM of ML090. n= 6. (b) NOX5-β overexpression and DHE oxidation in HAEC. Representative images from three experiments are shown. Intracellular superoxide anion production of HAEC 24 h after infection with GFP and NOX5-β adenoviruses at different MOIs treated or not with ML090 (10 nM). MOI: Multiplicity of infection. Figure S2. Ontology analysis of HAEC infected with NOX5-β. Ontology analysis shows that the response to unfolded protein is the most relevant. Figure S3. UPR mRNA expression in heart of infarcted transgenic mice. n= 12-13. Results expressed as mean ± SEM. Table S1: Altered gene expression due to NOX5-β expression at 12 h (bold, highlighted in yellow). N12hvsG12h N18hvsG18h N24hvsG24h GeneName GeneDescription TranscriptID logFC p-value logFC p-value logFC p-value family with sequence similarity NM_052966 1.45 1.20E-17 2.44 3.27E-19 2.96 6.24E-21 FAM129A 129. member A DnaJ (Hsp40) homolog. NM_001130182 2.19 9.83E-20 2.94 2.90E-19 3.01 1.68E-19 DNAJA4 subfamily A. member 4 phorbol-12-myristate-13-acetate- NM_021127 0.93 1.84E-12 2.41 1.32E-17 2.69 1.43E-18 PMAIP1 induced protein 1 E2F7 E2F transcription factor 7 NM_203394 0.71 8.35E-11 2.20 2.21E-17 2.48 1.84E-18 DnaJ (Hsp40) homolog. -
Chapter 6 CSE1L, DIDO1 and RBM39 in Colorectal
VU Research Portal Chromosome 20q genes in the pathogenesis of colorectal cancer Sillars-Hardebol, A.H. 2012 document version Publisher's PDF, also known as Version of record Link to publication in VU Research Portal citation for published version (APA) Sillars-Hardebol, A. H. (2012). Chromosome 20q genes in the pathogenesis of colorectal cancer. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. E-mail address: [email protected] Download date: 29. Sep. 2021 CHAPTER 6 CSE1L, DIDO1 and RBM39 in colorectal adenoma to carcinoma progression Submitted for publication Anke H Sillars-Hardebol Beatriz Carvalho Jeroen A M Beliën Meike de Wit Pien M Delis-van Diemen Marianne Tijssen Mark A van de Wiel Fredrik Pontén Remond J A Fijneman Gerrit A Meijer Chapter 6 Abstract Background: Gain of chromosome 20q is an important factor in the progression from colorectal adenomas to carcinomas.