Subcellular Distribution of HDAC1 in Neurotoxic Conditions Is Dependent on Serine Phosphorylation
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Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. -
Mapping Influenza-Induced Posttranslational Modifications On
viruses Article Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells Svetlana Rezinciuc 1, Zhixin Tian 2, Si Wu 2, Shawna Hengel 2, Ljiljana Pasa-Tolic 2 and Heather S. Smallwood 1,3,* 1 Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; [email protected] 2 Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; [email protected] (Z.T.); [email protected] (S.W.); [email protected] (S.H.); [email protected] (L.P.-T.) 3 Children’s Foundation Research Institute, Memphis, TN 38105, USA * Correspondence: [email protected]; Tel.: +1-(901)-448–3068 Academic Editor: Italo Tempera Received: 10 October 2020; Accepted: 2 December 2020; Published: 8 December 2020 Abstract: T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) to histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis by MS can detect species missed by bottom-up approaches. We used a novel approach of online two-dimensional liquid chromatography-tandem MS with high-resolution reversed-phase liquid chromatography (RPLC), alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. The first online RPLC separation sorted histone families, then RPLC or weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative identifications were assigned by matching proteoform masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for histone-intact protein PTM mapping (HiPTMap) to identify and quantify proteoforms purified from CD8 T cells after in vivo influenza infection. -
Exogenous Hydrogen Sulfide Plays an Important Role by Regulating
International Journal of Molecular Sciences Review Exogenous Hydrogen Sulfide Plays an Important Role by Regulating Autophagy in Diabetic-Related Diseases Shuangyu Lv , Huiyang Liu and Honggang Wang * Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng 475000, China; [email protected] (S.L.); [email protected] (H.L.) * Correspondence: [email protected] Abstract: Autophagy is a vital cell mechanism which plays an important role in many physiological processes including clearing long-lived, accumulated and misfolded proteins, removing damaged organelles and regulating growth and aging. Autophagy also participates in a variety of biological functions, such as development, cell differentiation, resistance to pathogens and nutritional hunger. Recently, autophagy has been reported to be involved in diabetes, but the mechanism is not fully understood. Hydrogen sulfide (H2S) is a colorless, water-soluble, flammable gas with the typical odor of rotten eggs, which has been known as a highly toxic gas for many years. However, it has been reported recently that H2S, together with nitric oxide and carbon monoxide, is an important gas signal transduction molecule. H2S has been reported to play a protective role in many diabetes- related diseases, but the mechanism is not fully clear. Recent studies indicate that H2S plays an important role by regulating autophagy in many diseases including cancer, tissue fibrosis diseases and glycometabolic diseases; however, the related mechanism has not been fully studied. In this review, we summarize recent research on the role of H2S in regulating autophagy in diabetic-related diseases to provide references for future related research. -
Determining HDAC8 Substrate Specificity by Noah Ariel Wolfson A
Determining HDAC8 substrate specificity by Noah Ariel Wolfson A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biological Chemistry) in the University of Michigan 2014 Doctoral Committee: Professor Carol A. Fierke, Chair Professor Robert S. Fuller Professor Anna K. Mapp Associate Professor Patrick J. O’Brien Associate Professor Raymond C. Trievel Dedication My thesis is dedicated to all my family, mentors, and friends who made getting to this point possible. ii Table of Contents Dedication ....................................................................................................................................... ii List of Figures .............................................................................................................................. viii List of Tables .................................................................................................................................. x List of Appendices ......................................................................................................................... xi Abstract ......................................................................................................................................... xii Chapter 1 HDAC8 substrates: Histones and beyond ...................................................................... 1 Overview ..................................................................................................................................... 1 HDAC introduction -
Up-Regulation of UVRAG by HDAC1 Inhibition Attenuates 5FU-Induced
ANTICANCER RESEARCH 38 : 271-277 (2018) doi:10.21873/anticanres.12218 Up-regulation of UVRAG by HDAC1 Inhibition Attenuates 5FU-induced Cell Death in HCT116 Colorectal Cancer Cells YOON KYUNG JO 1* , NA YEON PARK 1* , JI HYUN SHIN 1, DOO SIN JO 1, JI-EUN BAE 1, EUN SUN CHOI 1, SUNGHO MAENG 1, HONG BAE JEON 2, SEON AE ROH 3, JONG WOOK CHANG 4, JIN CHEON KIM 3,5 and DONG-HYUNG CHO 1 1Department of Gerontology, Graduate School of East-West Medical Science, Kyung Hee University, Seoul, Republic of Korea; 2Biomedical Research Institute, MEDIPOST Corporation, Seongnam, Republic of Korea; 3Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea; 4Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul, Republic of Korea; 5Department of Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea Abstract. The ultraviolent irradiation resistance-associated Autophagy has important roles in cellular homeostasis gene (UVRAG), a component of the Beclin 1/autophagy- through the degradation of useless or damaged proteins and related 6 complex, regulates the autophagy initiation step organelles via lysosomes (1, 2). The primordial function of and functions in the DNA-damage response. UVRAG is autophagy is a response to stress, such as starvation, frequently mutated in various cancer types, and mutations of oxidative stress, and ion stress (1, 2). Given that multiple UVRAG increase sensitivity to chemotherapy by impairing signaling pathways are involved in the regulation of DNA-damage repair. In this study, we addressed the autophagy progress, various autophagy-related (ATG) epigenetic regulation of UVRAG in colorectal cancer cells. -
Small-Molecule Suppressors of Cytokine-Induced Beta-Cell Apoptosis
Small-Molecule Suppressors of Cytokine-Induced Beta-Cell Apoptosis The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Chou, Danny Hung-Chieh. 2011. Small-Molecule Suppressors of Cytokine-Induced Beta-Cell Apoptosis. Doctoral dissertation, Harvard University. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:10121978 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA © 2011- Hung-Chieh Chou All rights reserved. Professor Stuart Schreiber Danny Hung-Chieh Chou Small-molecule suppressors of cytokine-induced beta-cell apoptosis Abstract Type-1 diabetes is caused by the autoimmune destruction of insulin-producing beta cells in the pancreas. Beta-cell apoptosis involves a complex set of signaling cascades initiated by interleukin-1 (IL-1), interferon- (IFN-), and tumor necrosis factor- (TNF- ). IL-1 and TNF- induce NFB expression, while IFN- induces STAT1 activation. These cytokines lead to a decrease of beta-cell function. The goal of this thesis is to identify small-molecule suppressors of cytokine-induced beta-cell apoptosis using high- throughput screening approach. Using the rat INS-1E beta-cell line, I developed an assay to measure cellular viability after 48 hours of cytokine treatment. I screened 29,760 compounds for their ability to suppress the negative effects of the cytokines. I identified several compounds to be suppressors of beta-cell apoptosis. -
Biotin Rescues Mitochondrial Dysfunction and Neurotoxicity in a Tauopathy Model
Biotin rescues mitochondrial dysfunction and neurotoxicity in a tauopathy model Kelly M. Lohra,b, Bess Frostc, Clemens Scherzerd, and Mel B. Feanya,1 aDepartment of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115; bDepartment of Biology, Washington & Jefferson College, Washington, PA 15301; cDepartment of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229; and dNeurogenomics Laboratory, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 Edited by Solomon H. Snyder, Johns Hopkins University School of Medicine, Baltimore, MD, and approved September 17, 2020 (received for review December 21, 2019) Mitochondrial and metabolic dysfunction are often implicated in We combined Drosophila genetics with a variety of molecular neurological disease, but effective mechanism-based therapies re- and cellular approaches to explore the role of mitochondrial and main elusive. We performed a genome-scale forward genetic metabolic pathways in tauopathy and neuronal survival. We screen in a Drosophila model of tauopathy, a class of neurodegen- identified dysfunction within the biotin pathway in tauopathy and erative disorders characterized by the accumulation of the protein showed that biotin supplementation both rescues mitochondrial tau, and identified manipulation of the B-vitamin biotin as a po- deficits and improves neuronal health in vivo. Furthermore, we tential therapeutic approach in tauopathy. We show that tau demonstrate parallel mechanisms in human Alzheimer’s disease transgenic flies have an innate biotin deficiency due to tau-medi- brain. Together, these findings emphasize the importance of ated relaxation of chromatin and consequent aberrant expression biotin handling in mitochondrial and metabolic processes in of multiple biotin-related genes, disrupting both carboxylase and neurons, suggesting a key role for biotin in both the healthy and mitochondrial function. -
Histone Deacetylases 1 and 2 Regulate the Transcriptional Programs Of
© 2018. Published by The Company of Biologists Ltd | Development (2018) 145, dev153619. doi:10.1242/dev.153619 STEM CELLS AND REGENERATION RESEARCH ARTICLE Histone deacetylases 1 and 2 regulate the transcriptional programs of nephron progenitors and renal vesicles Hongbing Liu*, Shaowei Chen, Xiao Yao, Yuwen Li, Chao-Hui Chen, Jiao Liu, Zubaida Saifudeen and Samir S. El-Dahr ABSTRACT Six2, a homeodomain transcription factor, is a key factor within Nephron progenitor cells (NPCs) are Six2-positive metanephric the kidney metanephric mesenchyme that maintains the NPC pool mesenchyme cells, which undergo self-renewal and differentiation (Kobayashi et al., 2008; Self et al., 2006). In Six2 null mice, ectopic to give rise to nephrons until the end of nephrogenesis. Histone renal vesicles (the earliest epithelialized forms of nascent nephrons) deacetylases (HDACs) are a group of epigenetic regulators that develop at the onset of nephrogenesis and the progenitor pool is – control cell fate, but their role in balancing NPC renewal and rapidly lost (Self et al., 2006). Many transcriptional regulators differentiation is unknown. Here, we report that NPC-specific such as Osr1, WT1 and Sall1/Mi-2b (Chd4)/nucleosome deletion of Hdac1 and Hdac2 genes in mice results in early remodeling and deacetylase (NuRD), which function to maintain – postnatal lethality owing to renal hypodysplasia and loss of NPCs. the NPC pool display genetic interactions with Six2 (Basta et al., HDAC1/2 interact with the NPC renewal regulators Six2, Osr1 and 2014; Denner and Rauchman, 2013; Hartwig et al., 2010; Kanda Sall1, and are co-bound along with Six2 on the Six2 enhancer. et al., 2014; Xu et al., 2014). -
Oligodendroglial Energy Metabolism and (Re)Myelination
life Review Oligodendroglial Energy Metabolism and (re)Myelination Vanja Tepavˇcevi´c Achucarro Basque Center for Neuroscience, University of the Basque Country, Parque Cientifico de la UPV/EHU, Barrio Sarriena s/n, Edificio Sede, Planta 3, 48940 Leioa, Spain; [email protected] Abstract: Central nervous system (CNS) myelin has a crucial role in accelerating the propagation of action potentials and providing trophic support to the axons. Defective myelination and lack of myelin regeneration following demyelination can both lead to axonal pathology and neurode- generation. Energy deficit has been evoked as an important contributor to various CNS disorders, including multiple sclerosis (MS). Thus, dysregulation of energy homeostasis in oligodendroglia may be an important contributor to myelin dysfunction and lack of repair observed in the disease. This article will focus on energy metabolism pathways in oligodendroglial cells and highlight differences dependent on the maturation stage of the cell. In addition, it will emphasize that the use of alternative energy sources by oligodendroglia may be required to save glucose for functions that cannot be fulfilled by other metabolites, thus ensuring sufficient energy input for both myelin synthesis and trophic support to the axons. Finally, it will point out that neuropathological findings in a subtype of MS lesions likely reflect defective oligodendroglial energy homeostasis in the disease. Keywords: energy metabolism; oligodendrocyte; oligodendrocyte progenitor cell; myelin; remyeli- nation; multiple sclerosis; glucose; ketone bodies; lactate; N-acetyl aspartate Citation: Tepavˇcevi´c,V. Oligodendroglial Energy Metabolism 1. Introduction and (re)Myelination. Life 2021, 11, Myelination is the key evolutionary event in the development of higher vertebrates. 238. -
A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase. -
Grimme, Acadia.Pdf
MECHANISM OF ACTION OF HISTONE DEACETYLASE INHIBITORS ON SURVIVAL MOTOR NEURON 2 PROMOTER by Acadia L. Grimme A thesis submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Bachelors of Science in Biological Sciences with Distinction Spring 2018 © 2018 Acadia Grimme All Rights Reserved MECHANISM OF ACTION OF HISTONE DEACETYLASE INHIBITORS ON SURVIVAL MOTOR NEURON 2 PROMOTER by Acadia L. Grimme Approved: __________________________________________________________ Matthew E. R. Butchbach, Ph.D. Professor in charge of thesis on behalf of the Advisory Committee Approved: __________________________________________________________ Deni S. Galileo, Ph.D. Professor in charge of thesis on behalf of the Advisory Committee Approved: __________________________________________________________ Carlton R. Cooper, Ph.D. Committee member from the Department of Biological Sciences Approved: __________________________________________________________ Gary H. Laverty, Ph.D. Committee member from the Board of Senior Thesis Readers Approved: __________________________________________________________ Michael Chajes, Ph.D. Chair of the University Committee on Student and Faculty Honors ACKNOWLEDGMENTS I would like to acknowledge my thesis director Dr. Butchbach for his wonderful guidance and patience as I worked through my project. He has been an excellent research mentor over the last two years and I am forever thankful that he welcomed me into his lab. His dedication to his work inspires me as an aspiring research scientist. His lessons will carry on with me as I pursue future research in graduate school and beyond. I would like to thank both current and former members of the Motor Neuron Disease Laboratory: Sambee Kanda, Kyle Hinkle, and Andrew Connell. Sambee and Andrew patiently taught me many of the techniques I utilized in my project, and without them it would not be what it is today. -
Structure and Function of Metallohydrolases in the Arginase- Deacetylase Family
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2016 Structure and Function of Metallohydrolases in the Arginase- Deacetylase Family Yang Hai University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biochemistry Commons Recommended Citation Hai, Yang, "Structure and Function of Metallohydrolases in the Arginase-Deacetylase Family" (2016). Publicly Accessible Penn Dissertations. 1753. https://repository.upenn.edu/edissertations/1753 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1753 For more information, please contact [email protected]. Structure and Function of Metallohydrolases in the Arginase-Deacetylase Family Abstract Arginases and deacetylases are metallohydrolases that catalyze two distinct chemical transformations. The arginases catalyze the hydrolysis of the guanidinium group of arginine by using a hydroxide ion 2+ 2+ bridging the binuclear manganese cluster (Mn A-Mn B) for nucleophilic attack. The deacetylases catalyze the hydrolysis of amide bonds by using a mononuclear Zn2+-ion activated water molecule as the nucleophile. Despite the diverse functions, metallohydrolases of the arginase-deacetylase superfamily 2+ share the same characteristic α/β hydrolase core fold and a conserved metal binding site (the Mn B site in arginase corresponds to the catalytic Zn2+ site in deacetylase) which is essential for catalysis in both enzymes. We report crystal structure of formiminoglutamase from the parasitic protozoan Trypanosoma cruzi and confirm that formiminoglutamase is a Mn2+-requiring hydrolase that belongs to the arginase- deacetylase superfamily. We also report the crystal structure of an arginase-like protein from Trypanosoma brucei (TbARG) with unknown function. Although its biological role remains enigmatic, the 2+ evolutionarily more conserved Mn B site can be readily restored in TbARG through side-directed mutagenesis.