Mutational Landscape of EGFR-, MYC-, and Kras-Driven Genetically
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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/// -
RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases
G C A T T A C G G C A T genes Review RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases Amber Willbanks, Shaun Wood and Jason X. Cheng * Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL 60637, USA; [email protected] (A.W.); [email protected] (S.W.) * Correspondence: [email protected] Abstract: Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases. Keywords: 5’ cap (5’ cap); 7-methylguanosine (m7G); R-loops; N6-methyladenosine (m6A); RNA editing; A-to-I; C-to-U; 2’-O-methylation (Nm); 5-methylcytosine (m5C); NOL1/NOP2/sun domain Citation: Willbanks, A.; Wood, S.; (NSUN); MYC Cheng, J.X. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes 2021, 12, 627. -
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. -
Noelia Díaz Blanco
Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr. -
SMYD4 Antibody
Efficient Professional Protein and Antibody Platforms SMYD4 Antibody Basic information: Catalog No.: UPA06235 Source: Rabbit Size: 50ul/100ul Clonality: Polyclonal Concentration: 1mg/ml Isotype: IgG Purification: The antibody was purified by immunogen affinity chromatography. Useful Information: WB: 1:500 - 1:2000 Applications: IHC: 1:50-1:200 IF/IC: 1:50-1:100 Reactivity: Human, Mouse Specificity: Recognizes endogenous levels of SMYD4 protein. Immunogen: Recombinant full length protein of human SMYD4 Description: Rabbit polyclonal antibody to SMYD4 Uniprot: Q8IYR2(Human), Q8BTK5(Mouse) BiowMW: Refer to Figures Liquid in 0.42% Potassium phosphate, 0.87% Sodium chloride, pH 7.3, 30% Buffer: glycerol, and 0.01% sodium azide. Storage: Store at 4°C short term and -20°C long term. Avoid freeze-thaw cycles. Note: For research use only, not for use in diagnostic procedure. Data: Western blot analysis of SMYD4 expression in mouse brain (A), mouse ovary (B), rat kidney (C) whole cell lysates. Gene Universal Technology Co. Ltd www.universalbiol.com Tel: 0550-3121009 E-mail: [email protected] Efficient Professional Protein and Antibody Platforms Immunohistochemical analysis of SMYD4 staining in human stomach cancer formalin fixed paraffin embedded tissue section. The section was pre-treated using heat mediated antigen retrieval with sodium citrate buffer (pH 6.0). The section was then incubated with the antibody at room temperature and detected using an HRP conju- gated compact polymer system. DAB was used as the chromogen. The section was then counter- stained with haematoxylin and mounted with DPX. Immunofluorescent analysis of SMYD4 staining in MCF7 cells. Formalin-fixed cells were permea- bilized with 0.1% Triton X-100 in TBS for 5-10 minutes and blocked with 3% BSA-PBS for 30 minutes at room temperature. -
Genetic Regulation of Pigment Epithelium-Derived Factor (PEDF): an Exome-Chip Association Analysis in Chinese Subjects with Type 2 Diabetes
198 Diabetes Volume 68, January 2019 Genetic Regulation of Pigment Epithelium-Derived Factor (PEDF): An Exome-Chip Association Analysis in Chinese Subjects With Type 2 Diabetes Chloe Y.Y. Cheung,1,2 Chi-Ho Lee,1 Clara S. Tang,3 Aimin Xu,1,2,4,5 Ka-Wing Au,1 Carol H.Y. Fong,1 Kelvin K.K. Ng,1 Kelvin H.M. Kwok,1 Wing-Sun Chow,1 Yu-Cho Woo,1 Michele M.A. Yuen,1 JoJo Hai,1 Kathryn C.B. Tan,1 Tai-Hing Lam,6 Hung-Fat Tse,1,7 Pak-Chung Sham,8,9,10 and Karen S.L. Lam1,2,4 Diabetes 2019;68:198–206 | https://doi.org/10.2337/db18-0500 Elevated circulating levels of pigment epithelium-derived (P = 0.085). Our study provided new insights into the factor (PEDF) have been reported in patients with type genetic regulation of PEDF and further support for its po- 2 diabetes (T2D) and its associated microvascular com- tential application as a biomarker for diabetic nephrop- plications. This study aimed to 1) identify the genetic athy and sight-threatening diabetic retinopathy. Further determinants influencing circulating PEDF levels in a studies to explore the causal relationship of PEDF with clinical setting of T2D, 2) examine the relationship be- diabetes complications are warranted. tween circulating PEDF and diabetes complications, and 3) explore the causal relationship between PEDF and di- abetes complications. An exome-chip association study Pigment epithelium-derived factor (PEDF) is a multifunc- on circulating PEDF levels was conducted in 5,385 Chi- tional glycoprotein that belongs to the serine protease nese subjects with T2D. -
Expression, Purification and Characterization of Lysine Methyltransferase Smyd5 Wen Xue Wayne State University
Wayne State University Wayne State University Theses 1-1-2017 Expression, Purification And Characterization Of Lysine Methyltransferase Smyd5 Wen Xue Wayne State University, Follow this and additional works at: https://digitalcommons.wayne.edu/oa_theses Part of the Biochemistry Commons, and the Molecular Biology Commons Recommended Citation Xue, Wen, "Expression, Purification And Characterization Of Lysine Methyltransferase Smyd5" (2017). Wayne State University Theses. 596. https://digitalcommons.wayne.edu/oa_theses/596 This Open Access Thesis is brought to you for free and open access by DigitalCommons@WayneState. It has been accepted for inclusion in Wayne State University Theses by an authorized administrator of DigitalCommons@WayneState. Expression, Purification and Characterization of Lysine Methyltransferase SMYD5 by Wen Xue THESIS Submitted to the Graduate School Of Wayne State University, Detroit, Michigan In partial fulfillment of the requirements for the degree of MASTERS OF SCIENCE 2017 MAJOR: BIOCHEMISTRY AND MOLECULAR BIOLOGY Approved by: Advisor Date © COPYRIGHT BY WEN XUE 2017 All Rights Reserved DEDICATION To everyone who contributed to the better version of myself ii ACKNOWLEDGEMENTS I would like to thank all of my committee members, Dr. Zhe Yang, Dr. Ladislau Kovari, Dr. David Evans, for the academic support and advice they have provided to me throughout the last two years. I am very grateful to have met such an inspirational and kind group of individuals. All of you truly make the Wayne State University feel like a community for me. I would also like to say a very special thanks to my mentor Dr. Zhe Yang, who has taught me how to learn things and solve problems. -
Pharmacological Targeting of the Mitochondrial Phosphatase PTPMT1 by Dahlia Doughty Shenton Department of Biochemistry Duke
Pharmacological Targeting of the Mitochondrial Phosphatase PTPMT1 by Dahlia Doughty Shenton Department of Biochemistry Duke University Date: May 1 st 2009 Approved: ___________________________ Dr. Patrick J. Casey, Supervisor ___________________________ Dr. Perry J. Blackshear ___________________________ Dr. Anthony R. Means ___________________________ Dr. Christopher B. Newgard ___________________________ Dr. John D. York Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biochemistry in the Graduate School of Duke University 2009 ABSTRACT Pharmacological Targeting of the Mitochondrial Phosphatase PTPMT1 by Dahlia Doughty Shenton Department of Biochemistry Duke University Date: May 1 st 2009 Approved: ___________________________ Dr. Patrick J. Casey, Supervisor ___________________________ Dr. Perry J. Blackshear ___________________________ Dr. Anthony R. Means ___________________________ Dr. Christopher B. Newgard ___________________________ Dr. John D. York An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biochemistry in the Graduate School of Duke University 2009 Copyright by Dahlia Doughty Shenton 2009 Abstract The dual specificity protein tyrosine phosphatases comprise the largest and most diverse group of protein tyrosine phosphatases and play integral roles in the regulation of cell signaling events. The dual specificity protein tyrosine phosphatases impact multiple -
Structural and Functional Analysis of PTPMT1, a Phosphatase Required for Cardiolipin Synthesis
Structural and functional analysis of PTPMT1, a phosphatase required for cardiolipin synthesis Junyu Xiaoa,1, James L. Engela,1, Ji Zhanga, Mark J. Chenb, Gerard Manningb, and Jack E. Dixona,c,d,e,2 aDepartment of Pharmacology, University of California, La Jolla, CA 92093; bRazavi Newman Center for Bioinformatics, Salk Institute, La Jolla, CA 92037; cDepartment of Cellular and Molecular Medicine, University of California, La Jolla, CA 92093; dDepartment of Chemistry and Biochemistry, University of California, La Jolla, CA 92093; and eHoward Hughes Medical Institute, Chevy Chase, MD 20815 Contributed by Jack E. Dixon, June 9, 2011 (sent for review December 29, 2010) PTPMT1 (PTP localized to the Mitochondrion 1) is a member of the chondria, and its level is not affected by the loss of PTPMT1, sug- protein tyrosine phosphatase superfamily that is localized exclu- gesting that PI(5)P is not its endogenous substrate (10). We sively to the mitochondrion. We recently reported that PTPMT1 recently demonstrated that the physiological target of PTPMT1 dephosphorylates phosphatidylglycerol phosphate, an essential is phosphatidylglycerol phosphate (PGP) (11), which is structu- intermediate of cardiolipin biosynthesis. To gain further insights rally remarkably similar to PI(5)P (Fig. 1C). into the molecular basis of PTPMT1 function, we determined the Phosphatidylglycerol (PG), the product of PTPMT1’s activity, crystal structures of the phosphatase domain of PTPMT1. PTPMT1 is an essential component of pulmonary surfactant, and a precur- exhibits a canonical protein tyrosine phosphatase domain fold, sor for cardiolipin biosynthesis (Fig. 1D and Fig. S2). Cardiolipin resembling many dual-specificity phosphatases such as phospha- is a glycerophospholipid found predominantly in the mitochon- tase and tensin homolog and vaccinia H1-related phosphatase. -
Insertional Mutagenesis in Mice Deficient for P15ink4b, P16ink4a, P21cip1, P27kip1 Reveals Cancer Gene Interactions and Correlations with Tumor Phenotypes
Published in final edited form as: Cancer Res. 2010 January 15; 70(2): 520–531. doi:10.1158/0008-5472.CAN-09-2736. Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes Jaap Kool1, Anthony G. Uren1, Carla P. Martins1,7, Daoud Sie2, Jeroen de Ridder3,4, Geoffrey Turner5,8, Miranda van Uitert3, Konstantin Matentzoglu1,9, Wendy Lagcher1, Paul Krimpenfort1, Jules Gadiot1, Colin Pritchard1, Jack Lenz5, Anders H. Lund1,10, Jos Jonkers3, Jane Rogers6,11, David J. Adams6, Lodewyk Wessels3,4, Anton Berns1, and Maarten van Lohuizen1 1Division of Molecular Genetics, The Centre of Biomedical Genetics, Academic Medical Center and Cancer Genomics Centre, Netherlands Cancer Institute, Amsterdam, The Netherlands 2Central Microarray Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands 3Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands 4Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, The Netherlands 5Albert Einstein College of Medicine, Bronx, NY, U.S.A. 6Wellcome Trust Sanger Institute, Hinxton, UK Abstract The cyclin dependent kinase (CDK) inhibitors p15, p16, p21 and p27 are frequently deleted, silenced or downregulated in many malignancies. Inactivation of CDK inhibitors predisposes mice to tumor development demonstrating that these genes can act as tumor suppressors. Here we describe high-throughput murine leukemia virus (MuLV) insertional mutagenesis screens in mice deficient for one or a combination of two CDK inhibitors. We retrieved 9117 retroviral insertions from 476 lymphomas and find hundreds of loci that are mutated significantly more frequently than expected by chance. Many of these are skewed toward a specific genetic context of predisposing germline and somatic mutations. -
The Lysine Methylase SMYD3 Modulates Mesendodermal Commitment During Development
cells Article The Lysine Methylase SMYD3 Modulates Mesendodermal Commitment during Development Raffaella Fittipaldi 1,†, Pamela Floris 1,† , Valentina Proserpio 1,2 , Franco Cotelli 1, Monica Beltrame 1 and Giuseppina Caretti 1,* 1 Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy; raffaella.fi[email protected] (R.F.); pamela.fl[email protected] (P.F.); [email protected] (V.P.); [email protected] (F.C.); [email protected] (M.B.) 2 Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy * Correspondence: [email protected]; Tel.: +39-025-031-5002 † These authors contributed equally. Abstract: SMYD3 (SET and MYND domain containing protein 3) is a methylase over-expressed in cancer cells and involved in oncogenesis. While several studies uncovered key functions for SMYD3 in cancer models, the SMYD3 role in physiological conditions has not been fully elucidated yet. Here, we dissect the role of SMYD3 at early stages of development, employing mouse embryonic stem cells (ESCs) and zebrafish as model systems. We report that SMYD3 depletion promotes the induction of the mesodermal pattern during in vitro differentiation of ESCs and is linked to an upregulation of cardiovascular lineage markers at later stages. In vivo, smyd3 knockdown in zebrafish favors the upregulation of mesendodermal markers during zebrafish gastrulation. Overall, our study reveals that SMYD3 modulates levels of mesendodermal markers, both in development and in embryonic stem cell differentiation. Citation: Fittipaldi, R.; Floris, P.; Proserpio, V.; Cotelli, F.; Beltrame, M.; Keywords: embryonic stem cells; SMYD3; zebrafish; development Caretti, G. The Lysine Methylase SMYD3 Modulates Mesendodermal Commitment during Development. Cells 2021, 10, 1233. -
UC San Diego UC San Diego Electronic Theses and Dissertations
UC San Diego UC San Diego Electronic Theses and Dissertations Title Astrocyte activity modulated by S1P-signaling in a multiple sclerosis model Permalink https://escholarship.org/uc/item/2bn557vr Author Groves, Aran Publication Date 2015 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Astrocyte activity modulated by S1P-signaling in a multiple sclerosis model A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Neurosciences by Aran Groves Committee in charge: Professor Jerold Chun, Chair Professor JoAnn Trejo, Co-Chair Professor Jody Corey-Bloom Professor Mark Mayford Professor William Mobley 2015 The Dissertation of Aran Groves is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California, San Diego 2015 iii TABLE OF CONTENTS Signature Page ..................................................................................................... iii Table of Contents ................................................................................................. iv List of Figures ....................................................................................................... vi List of Tables ....................................................................................................... viii Acknowledgments ................................................................................................