Caveolin Proteins Are Essential for Distinct Effects of Membrane Estrogen Receptors in Neurons
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Progesterone Receptor Coregulators As Factors Supporting the Function of the Corpus Luteum in Cows
G C A T T A C G G C A T genes Article Progesterone Receptor Coregulators as Factors Supporting the Function of the Corpus Luteum in Cows Robert Rekawiecki * , Karolina Dobrzyn, Jan Kotwica and Magdalena K. Kowalik Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10, 10–747 Olsztyn, Poland; [email protected] (K.D.); [email protected] (J.K.); [email protected] (M.K.K.) * Correspondence: [email protected]; Tel.: +48-89-539-31-17 Received: 5 July 2020; Accepted: 7 August 2020; Published: 12 August 2020 Abstract: Progesterone receptor (PGR) for its action required connection of the coregulatory proteins, including coactivators and corepressors. The former group exhibits a histone acetyltransferase (HAT) activity, while the latter cooperates with histone deacetylase (HDAC). Regulations of the coregulators mRNA and protein and HAT and HDAC activity can have an indirect effect on the PGR function and thus progesterone (P4) action on target cells. The highest mRNA expression levels for the coactivators—histone acetyltransferase p300 (P300), cAMP response element-binding protein (CREB), and steroid receptor coactivator-1 (SRC-1)—and nuclear receptor corepressor-2 (NCOR-2) were found in the corpus luteum (CL) on days 6 to 16 of the estrous cycle. The CREB protein level was higher on days 2–10, whereas SRC-1 and NCOR-2 were higher on days 2–5. The activity of HAT and HDAC was higher on days 6–10 of the estrous cycle. All of the coregulators were localized in the nuclei of small and large luteal cells. -
The Title of the Dissertation
UNIVERSITY OF CALIFORNIA SAN DIEGO Novel network-based integrated analyses of multi-omics data reveal new insights into CD8+ T cell differentiation and mouse embryogenesis A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biology by Kai Zhang Committee in charge: Professor Wei Wang, Chair Professor Pavel Arkadjevich Pevzner, Co-Chair Professor Vineet Bafna Professor Cornelis Murre Professor Bing Ren 2018 Copyright Kai Zhang, 2018 All rights reserved. The dissertation of Kai Zhang is approved, and it is accept- able in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California San Diego 2018 iii EPIGRAPH The only true wisdom is in knowing you know nothing. —Socrates iv TABLE OF CONTENTS Signature Page ....................................... iii Epigraph ........................................... iv Table of Contents ...................................... v List of Figures ........................................ viii List of Tables ........................................ ix Acknowledgements ..................................... x Vita ............................................. xi Abstract of the Dissertation ................................. xii Chapter 1 General introduction ............................ 1 1.1 The applications of graph theory in bioinformatics ......... 1 1.2 Leveraging graphs to conduct integrated analyses .......... 4 1.3 References .............................. 6 Chapter 2 Systematic -
Functions of Vertebrate Ferlins
cells Review Functions of Vertebrate Ferlins Anna V. Bulankina 1 and Sven Thoms 2,* 1 Department of Internal Medicine 1, Goethe University Hospital Frankfurt, 60590 Frankfurt, Germany; [email protected] 2 Department of Child and Adolescent Health, University Medical Center Göttingen, 37075 Göttingen, Germany * Correspondence: [email protected] Received: 27 January 2020; Accepted: 20 February 2020; Published: 25 February 2020 Abstract: Ferlins are multiple-C2-domain proteins involved in Ca2+-triggered membrane dynamics within the secretory, endocytic and lysosomal pathways. In bony vertebrates there are six ferlin genes encoding, in humans, dysferlin, otoferlin, myoferlin, Fer1L5 and 6 and the long noncoding RNA Fer1L4. Mutations in DYSF (dysferlin) can cause a range of muscle diseases with various clinical manifestations collectively known as dysferlinopathies, including limb-girdle muscular dystrophy type 2B (LGMD2B) and Miyoshi myopathy. A mutation in MYOF (myoferlin) was linked to a muscular dystrophy accompanied by cardiomyopathy. Mutations in OTOF (otoferlin) can be the cause of nonsyndromic deafness DFNB9. Dysregulated expression of any human ferlin may be associated with development of cancer. This review provides a detailed description of functions of the vertebrate ferlins with a focus on muscle ferlins and discusses the mechanisms leading to disease development. Keywords: dysferlin; myoferlin; otoferlin; C2 domain; calcium-sensor; muscular dystrophy; dysferlinopathy; limb girdle muscular dystrophy type 2B (LGMD2B), membrane repair; T-tubule system; DFNB9 1. Introduction Ferlins belong to the superfamily of proteins with multiple C2 domains (MC2D) that share common functions in tethering membrane-bound organelles or recruiting proteins to cellular membranes. Ferlins are described as calcium ions (Ca2+)-sensors for vesicular trafficking capable of sculpturing membranes [1–3]. -
Engineering Zinc-Finger Protein and CRISPR/Cas9 Constructs to Model the Epigenetic and Transcriptional Phenomena That Underlie Cocaine-Related Behaviors
Engineering zinc-finger protein and CRISPR/Cas9 constructs to model the epigenetic and transcriptional phenomena that underlie cocaine-related behaviors Hamilton PJ, Heller EA, Ortiz Torres I, Burek DD, Lombroso SI, Pirpinias ST, Neve RL, Nestler EJ Multiple studies have implicated genome-wide epigenetic remodeling events in brain reward regions following drug exposure. However, only recently has it become possible to target a given type of epigenetic remodeling to a single gene of interest, in order to probe the causal relationship between such regulation and neuropsychiatric disease (Heller et al., Nat Neurosci, 2014). Our group has successfully utilized synthetic zinc- finger proteins (ZFPs), fused to either the transcriptional repressor, G9a, that promotes histone methylation or the transcriptional activator, p65, that promotes histone acetylation, to determine the behavioral effects of targeted in vivo epigenetic reprogramming in a locus-specific and cell-type specific manner. Given the success of our ZFP approaches, we have broadened our technical repertoire to include the more novel and flexible CRISPR/Cas9 technology. We designed guide RNAs to target nuclease-dead Cas9 (dCas9) fused to effector domains to the fosB gene locus, a locus heavily implicated in the pathogenesis of drug abuse. We observe that dCas9 fused to the transcriptional activator, VP64, or the transcriptional repressor, KRAB, and targeted to specific sites in the fosB promoter is sufficient to regulate FosB and ΔFosB mRNA levels, in both cultured cells and in the nucleus accumbens (NAc) of mice receiving viral delivery of CRISPR constructs. Next, we designed a fusion construct linking the dCas9 moiety to a pseudo-phosphorylated isoform of the transcription factor CREB (dCas9 CREB(S133D)). -
Caveolin-1 Is Down-Regulated in Alveolar Rhabdomyosarcomas and Negatively Regulates Tumor Growth
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 5, No. 20 Caveolin-1 is down-regulated in alveolar rhabdomyosarcomas and negatively regulates tumor growth Juan Huertas-Martínez1, Santiago Rello-Varona1, David Herrero-Martín1, Ignasi Barrau1, Silvia García-Monclús1, Miguel Sáinz-Jaspeado1, Laura Lagares-Tena1, Yaiza Núñez-Álvarez5, Silvia Mateo-Lozano2, Jaume Mora2, Josep Roma3, Nuria Toran3, Sebastian Moran4, Roser López-Alemany1, Soledad Gallego3, Manel Esteller4, Miguel A. Peinado5, Xavier García del Muro1 and Oscar M. Tirado1 1 Sarcoma research group, Molecular Oncology Lab, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain 2 Developmental Tumor Biology Laboratory, Hospital Sant Joan de Deu, Barcelona, Spain 3 Biomedical Research Unit, Hospital Universitari Vall d’Hebron, Barcelona, Spain 4 Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L’ Hospitalet de Llobregat, Barcelona, Spain 5 Institut de Medicina Predictiva i Personalitzada del Càncer, Badalona, Barcelona, Spain Correspondence to: Oscar M. Tirado, email: [email protected] Keywords: alveolar rhabdomyosarcoma, Caveolin-1, muscular differentiation, 5-AZA-2’-deoxycytidine, epigenetics, cell death Received: June 26, 2014 Accepted: August 26, 2014 Published: August 27, 2014 This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Rhabdomyosarcoma is the most common soft tissue sarcoma of childhood and adolescence. Despite advances in therapy, patients with histological variant of rhabdomyosarcoma known as alveolar rhabdomyosarcoma (ARMS) have a 5-year survival of less than 30%. Caveolin-1 (CAV1), encoding the structural component of cellular caveolae, is a suggested tumor suppressor gene involved in cell signaling. -
Estrogen Receptor-Α Interaction with the CREB Binding Protein
307 Estrogen receptor- interaction with the CREB binding protein coactivator is regulated by the cellular environment B M Jaber, R Mukopadhyay and C L Smith Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA (Requests for offprints should be addressed to C L Smith; Email: [email protected]) Abstract The p160 coactivators, steroid receptor coactivator-1 (SRC-1), transcriptional intermediary factor-2 (TIF2) and receptor-associated coactivator-3 (RAC3), as well as the coactivator/integrator CBP, mediate estrogen receptor- (ER)-dependent gene expression. Although these coactivators are widely expressed, ER transcriptional activity is cell-type dependent. In this study, we investigated ER interaction with p160 coactivators and CBP in HeLa and HepG2 cell lines. Basal and estradiol (E2)-dependent interactions between the ER ligand-binding domain (LBD) and SRC-1, TIF2 or RAC3 were observed in HeLa and HepG2 cells. The extents of hormone-dependent interactions were similar and interactions between each of the p160 coactivators and the ER LBD were not enhanced by 4-hydroxytamoxifen in either cell type. In contrast to the situation for p160 coactivators, E2-dependent interaction of the ER LBD with CBP or p300 was detected in HeLa but not HepG2 cells by mammalian two-hybrid and coimmunoprecipitation assays, indicating that the cellular environment modulates ER-CBP/p300 interaction. Furthermore, interactions between CBP and p160 coactivators are much more robust in HeLa than HepG2 cells suggesting that poor CBP-p160 interactions are insufficient to support ER–CBP–p160 ternary complexes important for nuclear receptor–CBP interactions. Alterations in p160 coactivators or CBP expression between these two cell types did not account for differences in ER–p160–CBP interactions. -
Circadian- and Sex-Dependent Increases in Intravenous Cocaine Self-Administration in Npas2 Mutant Mice
bioRxiv preprint doi: https://doi.org/10.1101/788786; this version posted October 1, 2019. 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. Circadian- and sex-dependent increases in intravenous cocaine self-administration in Npas2 mutant mice Lauren M. DePoy1,2, Darius D. Becker-Krail1,2, Neha M. Shah1, Ryan W. Logan1,2,3, Colleen A. McClung1,2,3 1Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine 2Center for Neuroscience, University of Pittsburgh 3Center for Systems Neurogenetics of Addiction, The Jackson Laboratory Contact: Lauren DePoy, PhD 450 Technology Dr. Ste 223 Pittsburgh, PA 15219 412-624-5547 [email protected] Running Title: Increased self-administration in female Npas2 mutant mice Key words: circadian, sex-differences, cocaine, self-administration, addiction, Npas2 Abstract: 250 Body: 3996 Figures: 6 Tables: 1 Supplement: 3 Figures Acknowledgements: We Would like to thank Mariah Hildebrand and Laura Holesh for animal care and genotyping. We thank Drs. Steven McKnight and David Weaver for providing the Npas2 mutant mice. This work was funded by the National Institutes of Health: DA039865 (PI: Colleen McClung, PhD) and DA046117 (PI: Lauren DePoy). Disclosures: All authors have no financial disclosures or conflicts of interest to report. 1 bioRxiv preprint doi: https://doi.org/10.1101/788786; this version posted October 1, 2019. 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 Background: Addiction is associated With disruptions in circadian rhythms. -
Novel Missense Mutation in the Caveolin-3 Gene in a Belgian Family
1349 J Neurol Neurosurg Psychiatry: first published as 10.1136/jnnp.2003.028217 on 16 August 2004. Downloaded from SHORT REPORT Novel missense mutation in the caveolin-3 gene in a Belgian family with rippling muscle disease P Y K Van den Bergh, J M Ge´rard, J A Elosegi, M U Manto, C Kubisch, B G H Schoser ............................................................................................................................... J Neurol Neurosurg Psychiatry 2004;75:1349–1351. doi: 10.1136/jnnp.2003.028217 too small’’). The patient was diagnosed as having fibromyal- Rippling muscle disease (RMD) is a rare muscle disorder gia, which led to secondary depression and loss of her job. characterised by muscle stiffness, exercise induced myalgia, Muscle weakness and pigmenturia were absent. The medical and cramp-like sensations. It is genetically heterogeneous history was remarkable for mild hypothyroidism, peptic and can be acquired, but most cases show autosomal oesophagitis, and tobacco related asthmatiform bronchitis dominant inheritance due to mutations in the caveolin-3 with emphysema. At age 38, she had a neurological work-up. (CAV3) gene. We report a novel heterozygous missense The cranial nerves, muscle bulk, muscle strength, and deep mutation in CAV3 in a Belgian family with autosomal tendon reflexes were normal, and plantar responses were dominant RMD. flexor. Tapping with the reflex hammer or with the finger on A 40 year old woman complained of fatigue, exercise the muscles provoked an immediate, short lasting, forceful induced muscle pain, and muscle cramps since the age of 35. contraction and/or painful local mounding lasting for several Neurological examination revealed percussion induced seconds. PIRCs were most pronounced in the sternocleido- rapid muscle contractions (PIRCs) and localised muscle mastoid, deltoid, biceps, brachioradialis, finger and wrist mounding on percussion; muscle rippling was not observed. -
The Role of Gata2 in Hematopoietic and Vascular Development By
The Role of Gata2 in Hematopoietic and Vascular Development by William D Brandt A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Cellular and Molecular Biology) in The University of Michigan 2009 Doctoral Committee: Professor James Douglas Engel, Chair Professor Eric R Fearon Professor Deborah L Gumucio Associate Professor Thomas M Glaser William D Brandt 2009 Dedication To my family, without whom this PhD would never have been possible. ii Acknowledgements The Engel lab and the University of Michigan will always have my deepest gratitude, particularly the lab’s proprietor and my thesis advisor Doug Engel, whose love of science and good nature has always been a source of inspiration. Doug has been instrumental in my growth as a nascent scientist and I will forever be indebted to him. My gratitude also goes to Kim-Chew Lim and Tomo Hosoya, whose wealth of knowledge and support were relied upon regularly. To Deb Gumucio, Tom Glaser, and Eric Fearon, whose advice and support facilitated my maturation from a naïve student to a proficient scientist – thank you. And to Lori Longeway and Kristin Hug, whose capabilities as department representatives I repeatedly put to the test; you came through for me every time. Thank you. Finally, no amount of words can express how truly grateful and indebted I am to my parents and sister – Cary, Kim, and Jenelle. I would not be in this position today without their unerring love and support. iii Table of Contents Dedication ii Acknowledgements iii List of Figures v List of Tables vi Abstract vii Chapter 1. -
Resetting the Biological Clock: Mediation of Nocturnal CREB Phosphorylation Via Light, Glutamate, and Nitric Oxide
The Journal of Neuroscience, January 15, 1997, 17(2):667–675 Resetting the Biological Clock: Mediation of Nocturnal CREB Phosphorylation via Light, Glutamate, and Nitric Oxide Jian M. Ding,1,3 Lia E. Faiman,1 William J. Hurst,1 Liana R. Kuriashkina,2 and Martha U. Gillette1,2,3 1Department of Cell and Structural Biology, 2Molecular and Integrative Physiology, and 3The Neuroscience Program, University of Illinois, Urbana, Illinois 61801 Synchronization between the environmental lighting cycle and neurons in which P-CREB-lir was induced by light were the biological clock in the suprachiasmatic nucleus (SCN) is NADPH-diaphorase-positive neurons of the SCN’s retinorecipi- correlated with phosphorylation of the Ca21/cAMP response ent area. Glu treatment increased the intensity of a 43 kDa band element binding protein (CREB) at the transcriptional activating recognized by anti-P-CREB antibodies in subjective night but site Ser133. Mechanisms mediating the formation of phospho- not day, whereas anti-aCREB-lir of this band remained con- CREB (P-CREB) and their relation to clock resetting are un- stant between night and day. Inhibition of NOS during Glu known. To address these issues, we probed the signaling stimulation diminished the anti-P-CREB-lir of this 43 kDa band. pathway between light and P-CREB. Nocturnal light rapidly and Together, these data couple nocturnal light, Glu, NMDA recep- transiently induced P-CREB-like immunoreactivity (P-CREB-lir) tor activation and NO signaling to CREB phosphorylation in the in the rat SCN. Glutamate (Glu) or nitric oxide (NO) donor transduction of brief environmental light stimulation of the ret- administration in vitro also induced P-CREB-lir in SCN neurons ina into molecular changes in the SCN resulting in phase re- only during subjective night. -
Review Function and Regulation of CREB Family Transcription Factors
Neuron, Vol. 35, 605–623, August 15, 2002, Copyright 2002 by Cell Press Function and Regulation Review of CREB Family Transcription Factors in the Nervous System Bonnie E. Lonze and David D. Ginty1 domain, which is consistent with the findings that these Department of Neuroscience factors can form both homo- and heterodimers, and Howard Hughes Medical Institute that each can bind to the same cis-regulatory element The Johns Hopkins University School of Medicine (reviewed in De Cesare et al., 1999; Mayr and Montminy, Baltimore, Maryland 21205 2001; Shaywitz and Greenberg, 1999). This element, the cAMP response element (CRE), consists of the palin- dromic consensus sequence TGACGTCA. While many CREB and its close relatives are now widely accepted CREB binding sites are comprised of variations of this as prototypical stimulus-inducible transcription fac- consensus motif, almost all harbor the core sequence tors. In many cell types, these factors function as ef- CGTCA. fector molecules that bring about cellular changes in While the bZIP domain mediates DNA binding and response to discrete sets of instructions. In neurons, dimerization, the remaining domains of CREB family a wide range of extracellular stimuli are capable of members serve to facilitate interactions with coactiva- activating CREB family members, and CREB-depen- tors and components of the transcriptional machinery dent gene expression has been implicated in complex that ultimately carry out RNA synthesis. The functional and diverse processes ranging from development to domains of CREB and its relatives (Foulkes et al., 1991; plasticity to disease. In this review, we focus on the Gonzalez et al., 1989; Hai et al., 1989; Hoeffler et al., current level of understanding of where, when, and 1988) are schematically represented in Figure 1. -
The Popeye Domain Containing Genes and Their Function in Striated Muscle
Journal of Cardiovascular Development and Disease Review The Popeye Domain Containing Genes and Their Function in Striated Muscle Roland F. R. Schindler 1, Chiara Scotton 2, Vanessa French 1, Alessandra Ferlini 2 and Thomas Brand 1,* 1 Developmental Dynamics, Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College London, Hill End Road, Harefield UB9 6JH, UK; [email protected] (R.F.R.S.); [email protected] (V.F.) 2 Department of Medical Sciences, Medical Genetics Unit, University of Ferrara, Ferrara 44121, Italy; [email protected] (C.S.); fl[email protected] (A.F.) * Correspondence: [email protected]; Tel.: +44-189-582-8900 Academic Editors: Robert E. Poelmann and Monique R.M. Jongbloed Received: 26 April 2016; Accepted: 13 June 2016; Published: 15 June 2016 Abstract: The Popeye domain containing (POPDC) genes encode a novel class of cAMP effector proteins, which are abundantly expressed in heart and skeletal muscle. Here, we will review their role in striated muscle as deduced from work in cell and animal models and the recent analysis of patients carrying a missense mutation in POPDC1. Evidence suggests that POPDC proteins control membrane trafficking of interacting proteins. Furthermore, we will discuss the current catalogue of established protein-protein interactions. In recent years, the number of POPDC-interacting proteins has been rising and currently includes ion channels (TREK-1), sarcolemma-associated proteins serving functions in mechanical stability (dystrophin), compartmentalization (caveolin 3), scaffolding (ZO-1), trafficking (NDRG4, VAMP2/3) and repair (dysferlin) or acting as a guanine nucleotide exchange factor for Rho-family GTPases (GEFT).