DOCSLIB.ORG

Role of Senataxin in RNA: DNA Hybrids Resolution at DNA Double

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Role of Senataxin in RNA: DNA Hybrids Resolution at DNA Double Role of senataxin in RNA : DNA hybrids resolution at DNA double strand breaks Sarah Cohen To cite this version: Sarah Cohen. Role of senataxin in RNA : DNA hybrids resolution at DNA double strand breaks. Cellular Biology. Université Paul Sabatier - Toulouse III, 2019. English. NNT : 2019TOU30125. tel-02930730 HAL Id: tel-02930730 https://tel.archives-ouvertes.fr/tel-02930730 Submitted on 4 Sep 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. ����� ���� ������������������ ������������������������������������ ��������� ���!������"������ �� "��#�$�% ��� � ���� %��"���������"� ��� ��� � � � &������ ������������ ������� ����'������"�� � (����� �"�� ���"�� �������"�&)�����"����*���� (�+ "" ��"��� ��������"�����!��� ������������������,�,�$�,����-��.�� ���.�,����+&����-��" �������������,����/�������������� �������������������� �,�0�%�$�� ��� ���������,����-������� � �������0���+ � ����� ������'������� ������'������������ %����1�� ����� ����������������� /��������/�,�� ��� ���������� ������������������� ������������������������������ �� ����������������� ���������� ����������������� !���� ����������� ����"�� �� �"#����������������������� 1 Summaries 2 Actively transcribed genes can be the source of genome instability through numerous mechanisms. Those genes are characterized by the formation of secondary structures such as RNA- DNA hybrids. They are formed when nascent RNA exiting RNA polymerase II hybridizes single stranded DNA. Numerous studies have shown that RNA-DNA hybrids accumulation can lead to DNA damages. Among those damages, DNA double strand breaks (DSB) are the most deleterious for cells since they can generate mutations and chromosomal rearrangements. Two major repair mechanisms exist in the cell: Non-Homologous End-Joining (NHEJ) and Homologous recombination (HR). My lab showed recently that DSB occurring in transcribed genes are preferentially repaired by HR. Moreover, multiple studies have shown a cross talk between transcription and DSB repair. Those results led us to propose that actively transcribed genes could be repaired by a specific mechanism implicating proteins associated with transcription: “Transcription-coupled DSB repair”. During my PhD, using the DIvA (DSB Induction via AsiSI) cell line allowing the induction of annotated DSB through the genome, I worked on 2 projects focusing on DSB repair in transcribed genes. First, we showed that DSB repair in transcribed loci requires a known RNA: DNA helicase: senataxin (SETX). After DSB induction in an active gene, SETX is recruited which allows RNA-DNA hybrid resolution (mapped by DRIP-seq). We also showed that SETX activity allows RAD51 loading and limits DSB illegitimate rejoining and consequently promotes cell survival after DSB induction. This study shows that DSB in transcribed loci require specific RNA-DNA hybrids removal by SETX for accurate repair. Second, we showed an interplay between SETX and Bloom (BLM) a G4 DNA helicase in DSB repair induced in transcribed loci. We showed that BLM is also recruited at DSB in transcribed loci where it promotes resection and repair fidelity. Strikingly, we showed that BLM depletion rescued the survival defects observed in SETX depleted cells following DSB induction. Knock down of other G4-helicases (RTEL1, FANCJ) also promoted cell survival in SETX depleted cells upon damage. Those data suggest an interplay between G4 helicases and RNA: DNA resolution for DSB repair in active genes. Altogether, these studies promote a better understanding of the specificity of DSB repair in transcriptionally active genes, and notably identification of proteins involved in “Transcription-coupled DSB repair”. 3 Les gènes transcriptionellement actifs peuvent être la source de l'instabilité du génome via de nombreux mécanismes. Ces gènes sont caractérisés par la formation de structures secondaires telles que les hybrides ADN : ARN. Ils se forment lorsque l'ARN sortant l'ARN polymérase II s'hybride au simple brin d'ADN. De nombreuses études ont montrées que l’accumulation de ces hybrides peut mener à la création de dommages à l'ADN. Parmi ces dommages, les Cassures Double Brins (CDB) sont les plus dangereuses pour la cellule puisqu'elles peuvent produire des mutations et des réarrangements chromosomiques. Il existe deux mécanismes de réparation majeurs dans la cellule : la Jonction Non-Homologue des Extrémités (NHEJ) et la Recombinaison Homologue (HR). Mon équipe a récemment montré que les CDB localisées dans les gènes transcrits sont préférentiellement réparés par HR. De plus, de nombreuses études ont montrées une interaction entre transcription et réparation des CDB. Au vue de ces résultats, nous avons donc émis l'hypothèse que les gènes transcriptionellement actifs pourraient être réparés par un mécanisme spécifique nécessitant l'activité de protéines associées à la transcription : "Réparation couplée à la transcription". Durant ma thèse, je me suis intéressée au rôle de deux protéines dans la réparation des régions transcrites en utilisant la lignée cellulaire DIvA (DSB Induction via AsiSI) qui permet l'induction de cassures annotées sur tout le génome. Premièrement, nous avons montré que la réparation des CDB dans des loci transcrits nécessitent une hélicase ADN : ARN connue : sénataxine (SETX). Après induction d'une cassure dans un gène, SETX est recrutée ce qui permet la résolution d'hybride ADN : ARN (cartographié par DRIP- seq). Nous avons aussi montré que SETX permet le recrutement de RAD51 et limite les jonctions illégitimes des CDB et par conséquent promeut la survie des cellules après induction des cassures. Cette étude montre que les CDB dans les loci transcrits requièrent la résolution spécifique des hybrides ADN : ARN par SETX pour permettre une réparation précise et est absolument indispensable pour la survie cellulaire. Deuxièmement, nous avons montré une interaction entre SETX et Bloom (BLM) une G4 DNA hélicase dans la réparation des CDB dans les régions transcrites. Nous avons montré que BLM est aussi recrutée au CDB dans les loci transcrits où elle est nécessaire à la résection et à la fidélité de réparation. De façon importante, nous avons montré que la déplétion de BLM restaure le défaut de survie cellulaire observé dans les cellules déplétées pour SETX après induction des CDB. La déplétion d'autres hélicases G4 (RTEL1, FANCJ) promeut aussi la survie des cellules déplétées pour SETX après dommages. Ces résultats suggèrent une interaction entre les hélicases G4 et la résolution des hybrides ADN : ARN dans la réparation des gènes actifs. En conclusion, ces études permettent une meilleure compréhension de la spécificité de la réparation des régions transcrites du génome, et notamment l'identification de protéines impliquées dans la "Réparation couplée à la Transcription". 4 Table of contents 5 Table of contents Summaries............................................................................................................................ 2 Table of contents................................................................................................................... 5 Introduction ........................................................................................................................... 9 I. Transcription ...................................................................................................10 A. Steps of transcription................................................................................10 Initiation ...................................................................................................10 Elongation/Splicing ..................................................................................11 Termination..............................................................................................12 B. Non coding RNAs processing...................................................................12 Small RNA ...............................................................................................12 Long non-coding RNA..............................................................................13 C. Secondary structure: R-loops ...................................................................13 Formation.................................................................................................14 Processing ...............................................................................................15 Detection techniques................................................................................16 D. Transcription induces genome instability..................................................17 Common fragile site and replication collapse ...........................................17 Topoisomerase II activity .........................................................................18 R-loops ....................................................................................................19 R-loops in human diseases......................................................................22 II. DNA double strand breaks repair.................................................................25
Load more

Recommended publications
  • By Submitted in Partial Satisfaction of the Requirements for Degree of in In
    Developments of Two Imaging based Technologies for Cell Biology Researches by Xiaowei Yan DISSERTATION Submitted in partial satisfaction of the requirements for degree of DOCTOR OF PHILOSOPHY in Biochemistry and Molecular Biology in the GRADUATE DIVISION of the UNIVERSITY OF CALIFORNIA, SAN FRANCISCO Approved: ______________________________________________________________________________Ronald Vale Chair ______________________________________________________________________________Jonathan Weissman ______________________________________________________________________________Orion Weiner ______________________________________________________________________________ ______________________________________________________________________________ Committee Members Copyright 2021 By Xiaowei Yan ii DEDICATION Everything happens for the best. To my family, who supported me with all their love. iii ACKNOWLEDGEMENTS The greatest joy of my PhD has been joining UCSF, working and learning with such a fantastic group of scientists. I am extremely grateful for all the support and mentorship I received and would like to thank: My mentor, Ron Vale, who is such a great and generous person. Thank you for showing me that science is so much fun and thank you for always giving me the freedom in pursuing my interest. I am grateful for all the guidance from you and thank you for always supporting me whenever I needed. You are a person full of wisdom, and I have been learning so much from you and your attitude to science, science community and even life will continue inspire me. Thank you for being my mentor and thank you for being such a great mentor. Everyone else in Vale lab, past and present, for making our lab a sweet home. I would like to give my special thank to Marvin (Marvin Tanenbaum) and Nico (Nico Stuurman), two other mentors for me in the lab. I would like to thank them for helping me adapt to our lab, for all the valuable advice and for all the happiness during the time that we work together.
    [Show full text]
  • 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.
    [Show full text]
  • USP16 Counteracts Mono-Ubiquitination of Rps27a And
    RESEARCH ARTICLE USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit Christian Montellese1†, Jasmin van den Heuvel1,2, Caroline Ashiono1, Kerstin Do¨ rner1,2, Andre´ Melnik3‡, Stefanie Jonas1§, Ivo Zemp1, Paola Picotti3, Ludovic C Gillet1, Ulrike Kutay1* 1Institute of Biochemistry, ETH Zurich, Zurich, Switzerland; 2Molecular Life Sciences Ph.D. Program, Zurich, Switzerland; 3Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland Abstract Establishment of translational competence represents a decisive cytoplasmic step in the biogenesis of 40S ribosomal subunits. This involves final 18S rRNA processing and release of residual biogenesis factors, including the protein kinase RIOK1. To identify novel proteins promoting the final maturation of human 40S subunits, we characterized pre-ribosomal subunits trapped on RIOK1 by mass spectrometry, and identified the deubiquitinase USP16 among the captured factors. We demonstrate that USP16 constitutes a component of late cytoplasmic pre-40S subunits that promotes the removal of ubiquitin from an internal lysine of ribosomal protein *For correspondence: RPS27a/eS31. USP16 deletion leads to late 40S subunit maturation defects, manifesting in [email protected] incomplete processing of 18S rRNA and retarded recycling of late-acting ribosome biogenesis Present address: †CSL Behring, factors, revealing an unexpected contribution of USP16 to the ultimate step of 40S synthesis. CSL Biologics Research Center, Finally, ubiquitination of RPS27a appears to depend on active translation, pointing at a potential ‡ Bern, Switzerland; MSD Merck connection between 40S maturation and protein synthesis. Sharp & Dohme AG, Lucerne, Switzerland; §Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland Introduction Ribosomes stand at the center of translation in all kingdoms of life, catalyzing the synthesis of pro- Competing interests: The teins by reading a messenger RNA (mRNA) template.
    [Show full text]
  • Burden of Rare Variants in ALS and Axonal Hereditary Neuropathy Genes Influence Survival In
    International Journal of Molecular Sciences Article Burden of Rare Variants in ALS and Axonal Hereditary Neuropathy Genes Influence Survival in ALS: Insights from a Next Generation Sequencing Study of an Italian ALS Cohort Stefania Scarlino 1, Teuta Domi 1, Laura Pozzi 1 , Alessandro Romano 1, Giovanni Battista Pipitone 2, Yuri Matteo Falzone 1,3, Lorena Mosca 4, Silvana Penco 4, Christian Lunetta 5, Valeria Sansone 5,6, Lucio Tremolizzo 7, Raffaella Fazio 3, Federica Agosta 8, 3,8,9,10 2 1,3, , 1, Massimo Filippi , Paola Carrera , Nilo Riva * y and Angelo Quattrini y 1 Experimental Neuropathology Unit, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy; [email protected] (S.S.); [email protected] (T.D.); [email protected] (L.P.); [email protected] (A.R.); [email protected] (Y.M.F.); [email protected] (A.Q.) 2 Laboratory of Clinical Molecular Biology, Unit of Genomics for Human Disease Diagnosis, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, 20132 Milan, Italy; [email protected] (G.B.P.); [email protected] (P.C.) 3 Neurology Unit, San Raffaele Scientific Institute, 20132 Milan, Italy; fazio.raff[email protected] (R.F.); fi[email protected] (M.F.) 4 Medical Genetic Unit, Department of Laboratory Medicine, Niguarda Hospital, 20132 Milan, Italy; [email protected] (L.M.); [email protected] (S.P.) 5 NEuroMuscular Omnicentre (NEMO), Fondazione Serena Onlus, Milan 20132, Italy; [email protected]
    [Show full text]
  • Aberrant Gene Expression: Diagnostic Markers and Therapeutic Targets for Pancreatic Cancer
    ABERRANT GENE EXPRESSION: DIAGNOSTIC MARKERS AND THERAPEUTIC TARGETS FOR PANCREATIC CANCER Jeran Kent Stratford A dissertation submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Pharmacology. Chapel Hill 2014 Approved by: Jen Jen Yeh Channing J. Der Gary L. Johnson Adrienne D. Cox Timothy C. Elston © 2014 Jeran Kent Stratford ALL RIGHTS RESERVED ii ABSTRACT Jeran Kent Stratford: Aberrant gene expression: diagnostic markers and therapeutic targets for pancreatic cancer (Under the direction of Jen Jen Yeh and Channing J. Der) Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer and the fourth leading cause of cancer-related death in the United States. The overall median survival for patients diagnosed with PDAC is five to eight months. The poor outcome is due, in part, to a lack of disease-specific symptoms that can be used for early detection, and as such, most patients present with locally advanced or metastatic disease at the time of diagnosis. Therefore, the need for diagnostic tools is both great and urgent. Furthermore, current chemotherapies have low response rates and high toxicity, limiting their use, and there are currently no effective targeted therapies for PDAC. Therefore, a greater understanding of the underlying biology of pancreatic cancer is needed to identify tumor-specific vulnerabilities that can be therapeutically exploited. Pancreatic cancer development is driven by genomic changes that alter gene expression. Aberrant gene expression produces changes in protein expression, which in turn may confer growth advantages to the tumor; often the tumor then develops a dependency on continued aberrant gene and protein expression.
    [Show full text]
  • Nº Ref Uniprot Proteína Péptidos Identificados Por MS/MS 1 P01024
    Document downloaded from http://www.elsevier.es, day 26/09/2021. This copy is for personal use. Any transmission of this document by any media or format is strictly prohibited. Nº Ref Uniprot Proteína Péptidos identificados 1 P01024 CO3_HUMAN Complement C3 OS=Homo sapiens GN=C3 PE=1 SV=2 por 162MS/MS 2 P02751 FINC_HUMAN Fibronectin OS=Homo sapiens GN=FN1 PE=1 SV=4 131 3 P01023 A2MG_HUMAN Alpha-2-macroglobulin OS=Homo sapiens GN=A2M PE=1 SV=3 128 4 P0C0L4 CO4A_HUMAN Complement C4-A OS=Homo sapiens GN=C4A PE=1 SV=1 95 5 P04275 VWF_HUMAN von Willebrand factor OS=Homo sapiens GN=VWF PE=1 SV=4 81 6 P02675 FIBB_HUMAN Fibrinogen beta chain OS=Homo sapiens GN=FGB PE=1 SV=2 78 7 P01031 CO5_HUMAN Complement C5 OS=Homo sapiens GN=C5 PE=1 SV=4 66 8 P02768 ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2 66 9 P00450 CERU_HUMAN Ceruloplasmin OS=Homo sapiens GN=CP PE=1 SV=1 64 10 P02671 FIBA_HUMAN Fibrinogen alpha chain OS=Homo sapiens GN=FGA PE=1 SV=2 58 11 P08603 CFAH_HUMAN Complement factor H OS=Homo sapiens GN=CFH PE=1 SV=4 56 12 P02787 TRFE_HUMAN Serotransferrin OS=Homo sapiens GN=TF PE=1 SV=3 54 13 P00747 PLMN_HUMAN Plasminogen OS=Homo sapiens GN=PLG PE=1 SV=2 48 14 P02679 FIBG_HUMAN Fibrinogen gamma chain OS=Homo sapiens GN=FGG PE=1 SV=3 47 15 P01871 IGHM_HUMAN Ig mu chain C region OS=Homo sapiens GN=IGHM PE=1 SV=3 41 16 P04003 C4BPA_HUMAN C4b-binding protein alpha chain OS=Homo sapiens GN=C4BPA PE=1 SV=2 37 17 Q9Y6R7 FCGBP_HUMAN IgGFc-binding protein OS=Homo sapiens GN=FCGBP PE=1 SV=3 30 18 O43866 CD5L_HUMAN CD5 antigen-like OS=Homo
    [Show full text]
  • Ohnologs in the Human Genome Are Dosage Balanced and Frequently Associated with Disease
    Ohnologs in the human genome are dosage balanced and frequently associated with disease Takashi Makino1 and Aoife McLysaght2 Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland Edited by Michael Freeling, University of California, Berkeley, CA, and approved April 9, 2010 (received for review December 21, 2009) About 30% of protein-coding genes in the human genome are been duplicated by WGD, subsequent loss of individual genes related through two whole genome duplication (WGD) events. would result in a dosage imbalance due to insufficient gene Although WGD is often credited with great evolutionary impor- product, thus leading to biased retention of dosage-balanced tance, the processes governing the retention of these genes and ohnologs. In fact, evidence for preferential retention of dosage- their biological significance remain unclear. One increasingly pop- balanced genes after WGD is accumulating (4, 7, 11–20). Copy ular hypothesis is that dosage balance constraints are a major number variation [copy number polymorphism (CNV)] describes determinant of duplicate gene retention. We test this hypothesis population level polymorphism of small segmental duplications and show that WGD-duplicated genes (ohnologs) have rarely and is known to directly correlate with gene expression levels (21– experienced subsequent small-scale duplication (SSD) and are also 24). Thus, CNV of dosage-balanced genes is also expected to be refractory to copy number variation (CNV) in human populations deleterious. This model predicts that retained ohnologs should be and are thus likely to be sensitive to relative quantities (i.e., they are enriched for dosage-balanced genes that are resistant to sub- dosage-balanced).
    [Show full text]
  • Inhibiting USP16 Rescues Stem Cell Aging and Memory in An
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.383059; this version posted December 22, 2020. 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. Title: Inhibiting USP16 rescues stem cell aging and memory in an Alzheimer’s model Authors: Felicia Reinitz1†, Elizabeth Chen1†, Benedetta Nicolis di Robilant1†, Bayarsaikhan Chuluun2, Jane Antony1, Robert C. Jones3, Neha Gubbi1, Sai Saroja Kolluru3, Dalong Qian1, Katja Piltti4, Aileen Anderson4, Michelle Monje1, H. Craig Heller2, Stephen Quake3, Michael F. Clarke1* Affiliations: 1Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA. 2Department of Biology, Stanford University School of Medicine, Stanford, California 94305, USA. 3Bioengineering, Stanford University School of Engineering and Medicine, Stanford, California, 94305, USA. 4Sue and Bill Gross Stem Cell Research Center, University of California, Irvine *Lead contact and all other correspondence to: [email protected] †These authors contributed equally. 1 Summary: Alzheimer’s disease (AD) is a progressive neurodegenerative disease observed with 2 aging that represents the most common form of dementia. To date, therapies targeting end-stage 3 disease plaques, tangles, or inflammation have limited efficacy. Therefore, we set out to identify 4 an earlier targetable phenotype. Utilizing a mouse model of AD and human fetal cells harboring 5 mutant amyloid precursor protein, we show cell intrinsic neural precursor cell (NPC) dysfunction 6 precedes widespread inflammation and amyloid plaque pathology, making it the earliest defect in 7 the evolution of disease.
    [Show full text]
  • Genomic Portrait of a Sporadic Amyotrophic Lateral Sclerosis Case in a Large Spinocerebellar Ataxia Type 1 Family
    Journal of Personalized Medicine Article Genomic Portrait of a Sporadic Amyotrophic Lateral Sclerosis Case in a Large Spinocerebellar Ataxia Type 1 Family Giovanna Morello 1,2, Giulia Gentile 1 , Rossella Spataro 3, Antonio Gianmaria Spampinato 1,4, 1 2 3 5, , Maria Guarnaccia , Salvatore Salomone , Vincenzo La Bella , Francesca Luisa Conforti * y 1, , and Sebastiano Cavallaro * y 1 Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; [email protected] (G.M.); [email protected] (G.G.); [email protected] (A.G.S.); [email protected] (M.G.) 2 Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, 95123 Catania, Italy; [email protected] 3 ALS Clinical Research Center and Neurochemistry Laboratory, BioNeC, University of Palermo, 90127 Palermo, Italy; [email protected] (R.S.); [email protected] (V.L.B.) 4 Department of Mathematics and Computer Science, University of Catania, 95123 Catania, Italy 5 Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, 87036 Rende, Italy * Correspondence: [email protected] (F.L.C.); [email protected] (S.C.); Tel.: +39-0984-496204 (F.L.C.); +39-095-7338111 (S.C.); Fax: +39-0984-496203 (F.L.C.); +39-095-7338110 (S.C.) F.L.C. and S.C. are co-last authors on this work. y Received: 6 November 2020; Accepted: 30 November 2020; Published: 2 December 2020 Abstract: Background: Repeat expansions in the spinocerebellar ataxia type 1 (SCA1) gene ATXN1 increases the risk for amyotrophic lateral sclerosis (ALS), supporting a relationship between these disorders.
    [Show full text]
  • Morphology, Behavior, and the Sonic Hedgehog Pathway in Mouse Models of Down Syndrome
    MORPHOLOGY, BEHAVIOR, AND THE SONIC HEDGEHOG PATHWAY IN MOUSE MODELS OF DOWN SYNDROME by Tara Dutka A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2014 © 2014 Tara Dutka All Rights Reserved Abstract Down Syndrome (DS) is caused by a triplication of human chromosome 21 (Hsa21). Ts65Dn, a mouse model of DS, contains a freely segregating extra chromosome consisting of the distal portion of mouse chromosome 16 (Mmu16), a region orthologous to part of Hsa21, and a non-Hsa21 orthologous region of mouse chromosome 17. All individuals with DS display some level of craniofacial dysmorphology, brain structural and functional changes, and cognitive impairment. Ts65Dn recapitulates these features of DS and aspects of each of these traits have been linked in Ts65Dn to a reduced response to Sonic Hedgehog (SHH) in trisomic cells. Dp(16)1Yey is a new mouse model of DS which has a direct duplication of the entire Hsa21 orthologous region of Mmu16. Dp(16)1Yey’s creators found similar behavioral deficits to those seen in Ts65Dn. We performed a quantitative investigation of the skull and brain of Dp(16)1Yey as compared to Ts65Dn and found that DS-like changes to brain and craniofacial morphology were similar in both models. Our results validate examination of the genetic basis for these phenotypes in Dp(16)1Yey mice and the genetic links for these phenotypes previously found in Ts65Dn , i.e., reduced response to SHH. Further, we hypothesized that if all trisomic cells show a reduced response to SHH, then up-regulation of the SHH pathway might ameliorate multiple phenotypes.
    [Show full text]
  • A Systematic Genome-Wide Association Analysis for Inflammatory Bowel Diseases (IBD)
    A systematic genome-wide association analysis for inflammatory bowel diseases (IBD) Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel vorgelegt von Dipl.-Biol. ANDRE FRANKE Kiel, im September 2006 Referent: Prof. Dr. Dr. h.c. Thomas C.G. Bosch Koreferent: Prof. Dr. Stefan Schreiber Tag der mündlichen Prüfung: Zum Druck genehmigt: der Dekan “After great pain a formal feeling comes.” (Emily Dickinson) To my wife and family ii Table of contents Abbreviations, units, symbols, and acronyms . vi List of figures . xiii List of tables . .xv 1 Introduction . .1 1.1 Inflammatory bowel diseases, a complex disorder . 1 1.1.1 Pathogenesis and pathophysiology. .2 1.2 Genetics basis of inflammatory bowel diseases . 6 1.2.1 Genetic evidence from family and twin studies . .6 1.2.2 Single nucleotide polymorphisms (SNPs) . .7 1.2.3 Linkage studies . .8 1.2.4 Association studies . 10 1.2.5 Known susceptibility genes . 12 1.2.5.1 CARD15. .12 1.2.5.2 CARD4. .15 1.2.5.3 TNF-α . .15 1.2.5.4 5q31 haplotype . .16 1.2.5.5 DLG5 . .17 1.2.5.6 TNFSF15 . .18 1.2.5.7 HLA/MHC on chromosome 6 . .19 1.2.5.8 Other proposed IBD susceptibility genes . .20 1.2.6 Animal models. 21 1.3 Aims of this study . 23 2 Methods . .24 2.1 Laboratory information management system (LIMS) . 24 2.2 Recruitment. 25 2.3 Sample preparation. 27 2.3.1 DNA extraction from blood. 27 2.3.2 Plate design .
    [Show full text]
  • The Histone H2A Deubiquitinase Usp16 Regulates Hematopoiesis
    The histone H2A deubiquitinase Usp16 regulates PNAS PLUS hematopoiesis and hematopoietic stem cell function Yue Gua,1, Amanda E. Jonesa,1, Wei Yanga,1, Shanrun Liua, Qian Daib, Yudong Liuc, C. Scott Swindled, Dewang Zhoua, Zhuo Zhanga, Thomas M. Ryana, Tim M. Townesa, Christopher A. Klugd, Dongquan Chene, and Hengbin Wanga,2 aDepartment of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294; bDepartment of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294; cDepartment of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294; dDepartment of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294; and eDivision of Preventive Medicine, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294 Edited by Louise T. Chow, University of Alabama at Birmingham, Birmingham, AL, and approved November 23, 2015 (received for review August 26, 2015) Epigenetic mechanisms play important regulatory roles in hema- are also impaired in proliferative response to mitogens. The topoiesis and hematopoietic stem cell (HSC) function. Subunits of critical role of Bmi1 is largely attributed to dysregulation of polycomb repressive complex 1 (PRC1), the major histone H2A the Ink4A locus (19). Bmi1 also plays an indispensable role in the ubiquitin ligase, are critical for both normal and pathological maintenance of leukemic stem cells (19, 20). Furthermore, hematopoiesis; however, it is unclear which of the several counter- Ring1B knockout results in hypo-cellular BM but enlarged pools acting H2A deubiquitinases functions along with PRC1 to control of hyper-proliferating immature cells. Although HSCs and pro- H2A ubiquitination (ubH2A) level and regulates hematopoiesis in genitor cells maintain differentiation potential, they exhibit high vivo.
    [Show full text]