Facioscapulohumeral Muscular Dystrophy and DUX4: Breaking the Silence
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Genome-Wide Analysis of Macrosatellite
Schaap et al. BMC Genomics 2013, 14:143 http://www.biomedcentral.com/1471-2164/14/143 RESEARCH ARTICLE Open Access Genome-wide analysis of macrosatellite repeat copy number variation in worldwide populations: evidence for differences and commonalities in size distributions and size restrictions Mireille Schaap1, Richard JLF Lemmers1, Roel Maassen1, Patrick J van der Vliet1, Lennart F Hoogerheide2, Herman K van Dijk3, Nalan Baştürk4,5, Peter de Knijff1 and Silvère M van der Maarel1* Abstract Background: Macrosatellite repeats (MSRs), usually spanning hundreds of kilobases of genomic DNA, comprise a significant proportion of the human genome. Because of their highly polymorphic nature, MSRs represent an extreme example of copy number variation, but their structure and function is largely understudied. Here, we describe a detailed study of six autosomal and two X chromosomal MSRs among 270 HapMap individuals from Central Europe, Asia and Africa. Copy number variation, stability and genetic heterogeneity of the autosomal macrosatellite repeats RS447 (chromosome 4p), MSR5p (5p), FLJ40296 (13q), RNU2 (17q) and D4Z4 (4q and 10q) and X chromosomal DXZ4 and CT47 were investigated. Results: Repeat array size distribution analysis shows that all of these MSRs are highly polymorphic with the most genetic variation among Africans and the least among Asians. A mitotic mutation rate of 0.4-2.2% was observed, exceeding meiotic mutation rates and possibly explaining the large size variability found for these MSRs. By means of a novel Bayesian approach, statistical support for a distinct multimodal rather than a uniform allele size distribution was detected in seven out of eight MSRs, with evidence for equidistant intervals between the modes. -
Utility of Subtelomeric Fluorescent DNA Probes for Detection of Chromosome Anomalies in 425 Patients Syed M
article January/February 2003 ⅐ Vol. 5 ⅐ No. 1 Utility of subtelomeric fluorescent DNA probes for detection of chromosome anomalies in 425 patients Syed M. Jalal, PhD1, Aaron R. Harwood1, Gurbax S. Sekhon, PhD3, Cindy Pham Lorentz, MS1, Rhett P. Ketterling, MD1, Dusica Babovic-Vuksanovic, MD2, Reid G. Meyer1, Regina Ensenauer, MD2, Marvin H. Anderson, Jr1, and Virginia V. Michels, MD2 Purpose: A complete set of subtelomeric fluorescent DNA probes, except the acrocentric p-arms, was developed in 1996, was optimized in 1998, and is commercially available. These and other fluorescence in situ hybridization (FISH) probes have been used to detect anomalies of the subtelomere regions among groups of patients with idiopathic mental retardation (MR), developmental delay (DD), and/or nonspecific dysmorphic features (NDF), and individuals with multiple miscarriages (MM) who were karyotypically normal by standard G-banding techniques. Methods: A total of 425 patients were analyzed, of whom 372 had idiopathic MR/DD/NDF and 53 were involved in MM. An effort was made to select individuals for this study who were either normal karyotypically or who had subtle chromosomal anomalies that were inconclusive by banded chromosome analysis, although this was not always possible. Results: Anomalies involving the subtelomere regions were detected at a frequency of 6.8% in the MR/DD/NDF group. The cryptic or subtle anomalies are estimated to be about 3.4%. It was necessary to use M-FISH, chromosome, and locus specific FISH probes to clarify some of the abnormalities. No abnormalities were detected in the MM group. Deletion variants were present for 2qter, 7pter, and Xpter/Ypter subtelomeric regions ranging from Ͻ1 to 9.6%. -
DUX4, a Zygotic Genome Activator, Is Involved in Oncogenesis and Genetic Diseases Anna Karpukhina, Yegor Vassetzky
DUX4, a Zygotic Genome Activator, Is Involved in Oncogenesis and Genetic Diseases Anna Karpukhina, Yegor Vassetzky To cite this version: Anna Karpukhina, Yegor Vassetzky. DUX4, a Zygotic Genome Activator, Is Involved in Onco- genesis and Genetic Diseases. Ontogenez / Russian Journal of Developmental Biology, MAIK Nauka/Interperiodica, 2020, 51 (3), pp.176-182. 10.1134/S1062360420030078. hal-02988675 HAL Id: hal-02988675 https://hal.archives-ouvertes.fr/hal-02988675 Submitted on 17 Nov 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. ISSN 1062-3604, Russian Journal of Developmental Biology, 2020, Vol. 51, No. 3, pp. 176–182. © Pleiades Publishing, Inc., 2020. Published in Russian in Ontogenez, 2020, Vol. 51, No. 3, pp. 210–217. REVIEWS DUX4, a Zygotic Genome Activator, Is Involved in Oncogenesis and Genetic Diseases Anna Karpukhinaa, b, c, d and Yegor Vassetzkya, b, * aCNRS UMR9018, Université Paris-Sud Paris-Saclay, Institut Gustave Roussy, Villejuif, F-94805 France bKoltzov Institute of Developmental Biology of the Russian Academy of Sciences, -
Harnessing Single-Molecule Sequencing to Characterize the Fast-Evolving Drosophila Subtelomere Xander M
Harnessing single-molecule sequencing to characterize the fast-evolving Drosophila subtelomere Xander M. Gottfried, COL 2021 Mia T. Levine, College of Arts and Sciences Department of Biology Abstract ORF polymorphism is concentrated closer to telomere The telomere and subtelomere are repetitive sequences at the ends of chromosomes Use genome BLAST to find subtelomeric genes required for chromosome length preservation. In Drosophila, telomere and subtelomere are highly plastic; each of them varies in copy number and sequence both within and across species. In addition, there is evidence of functional crosstalk between telomere and subtelomere, suggesting that the two regions may co-evolve to maintain system fidelity. However, without characterizing the sequence of the subtelomere, we cannot investigate whether subtelomere evolution affects telomere function. This characterization has recently been made possible due to the advent of single-molecule sequencing, which can be used to assemble repetitive regions using long, 100 kilobase reads. Here, we begin to characterize the composition and variability of subtelomeric genes, focusing on exon duplications, intergenic distance variability, and functional open reading frame polymorphism. The Drosophila Subtelomere • Highly variable in copy number and sequence within species • Rapidly evolving Exon fragment duplications are more common closer across species to the telomere • Pervasive terminal Chromosome 2L Average # Exon Fragment Duplications Across Genomes 12 deletions • Functional Experimental Validation: crosstalk with 8 • PCR: primers to absent genes, primers to unorthodox telomere has break points, primers across gaps implications for • Cell biology: DNA FISH to gene sequences, IF to 4 genome integrity proteins RNAseq to dysfunctional ORFs Average # ofExon FragmentDuplications # Average 0 References: Anderson, J.A., Song, Y.S., and Langley, C.H. -
Neuromuscular Disease Journal Article on IRC 2019
Available online at www.sciencedirect.com Neuromuscular Disorders 29 (2019) 811–817 www.elsevier.com/locate/nmd Research conference report 26th Annual Facioscapulohumeral Dystrophy International Research Congress Marseille, France, 19–20 June 2019 a b, ∗ c June Kinoshita , Frédérique Magdinier , George W. Padberg a FSHD Society, 450 Bedford Street, Lexington, MA, USA b Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics, Marseille, France c Radboud UMC, Nijmegen, The Netherlands Received 2 August 2019 1. Introduction In the welcome session, Mark Stone, CEO of the FSHD Society, summarized the international patient advocacy group Research in Facioscapulohumeral Muscular Dystrophy meeting that was held on the previous day (June 18), which (FSHD) has reached the stage where we are seeing the gathered representatives of patients associations from six first drug trials aiming at reduction of its pathological gene European countries as well as Brazil, China, Israel, Japan, product DUX4. Driven by this development and by increased and the United States. international collaboration on translational research and trial preparedness, the FSHD Society has decided to hold its 2. Plenary and keynote lectures annual International Research Conference (IRC) alternating between the USA and in Europe, beginning this year with the The meeting opened with a plenary session aimed at 26th IRC held in Marseille, France. The meeting occurred on presenting the condition from the point of view of affected 19–20 June, 2019, at the Palais du Pharo, a historical palace individuals. A 10-min video gave an intimate look into the built in the second half of the 19th century by Napoleon III life of Pierre Laurian. -
Epigenetic Characteristics of Human Subtelomeres Vary in Cells Utilizing the Alternative Lengthening of Telomeres (ALT) Pathway
life Article Epigenetic Characteristics of Human Subtelomeres Vary in Cells Utilizing the Alternative Lengthening of Telomeres (ALT) Pathway Shir Toubiana 1,† , Aya Tzur-Gilat 1,† and Sara Selig 1,2,* 1 Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel; [email protected] (S.T.); [email protected] (A.T.-G.) 2 Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa 31096, Israel * Correspondence: [email protected] † Both authors contributed equally. Abstract: Most human cancers circumvent senescence by activating a telomere length maintenance mechanism, most commonly involving telomerase activation. A minority of cancers utilize the recombination-based alternative lengthening of telomeres (ALT) pathway. The exact requirements for unleashing normally repressed recombination at telomeres are yet unclear. Epigenetic modifications at telomeric regions were suggested to be pivotal for activating ALT; however, conflicting data exist regarding their exact nature and necessity. To uncover common ALT-positive epigenetic characteristics, we performed a comprehensive analysis of subtelomeric DNA methylation, histone modifications, and TERRA expression in several ALT-positive and ALT-negative cell lines. We found that subtelomeric DNA methylation does not differentiate between the ALT-positive and ALT- negative groups, and most of the analyzed subtelomeres within each group do not share common Citation: Toubiana, S.; Tzur-Gilat, A.; DNA methylation patterns. Additionally, similar TERRA levels were measured in the ALT-positive Selig, S. Epigenetic Characteristics of and ALT-negative groups, and TERRA levels varied significantly among the members of the ALT- Human Subtelomeres Vary in Cells positive group. Subtelomeric H3K4 and H3K9 trimethylation also differed significantly between Utilizing the Alternative Lengthening samples in the ALT-positive group. -
A Novel Trna Variable Number Tandem Repeat at Human Chromosome 1Q23.3 Is Implicated As a Boundary Element Based on Conservation of a CTCF Motif in Mouse Emily M
Published online 21 April 2014 Nucleic Acids Research, 2014, Vol. 42, No. 10 6421–6435 doi: 10.1093/nar/gku280 A novel tRNA variable number tandem repeat at human chromosome 1q23.3 is implicated as a boundary element based on conservation of a CTCF motif in mouse Emily M. Darrow and Brian P. Chadwick* Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA Received February 14, 2014; Revised March 24, 2014; Accepted March 25, 2014 ABSTRACT dividuals making macrosatellites some of the largest vari- able number tandem repeats (VNTRs) in the genome The human genome contains numerous large tan- (3,5,6,7,8,9,10,11,12). dem repeats, many of which remain poorly charac- What role macrosatellites fulfill in our genome is un- terized. Here we report a novel transfer RNA (tRNA) clear. Some contain open reading frames (ORFs) that tandem repeat on human chromosome 1q23.3 that are predominantly expressed in the testis or certain can- shows extensive copy number variation with 9–43 cers (13,14,15), whereas the expression of others is more repeat units per allele and displays evidence of mei- widespread (16,17,18,19). However, reduced copy number otic and mitotic instability. Each repeat unit consists of some is associated with disease (5,20) due to inappro- of a 7.3 kb GC-rich sequence that binds the insulator priate reactivation of expression (21). Others contain no protein CTCF and bears the chromatin hallmarks of obvious ORF (6,11); further complicating what purpose a bivalent domain in human embryonic stem cells. -
2021 IRC Abstract Book
ABSTRACT BOOK THANK YOU TO OUR SPONSORS S = session; P = poster; author in bold = presenting author Page | 2 SPEAKER PRESENTATIONS DAY 1 – THURSDAY, JUNE 24, 2021 . Discovery Research S1.100 Transient DUX4 expression provokes long-lasting cellular and molecular muscle alterations Darko Bosnakovski, Ahmed Shams, Madison Douglas, Natalie Xu, Christian Palumbo, David Oyler, Elizabeth Ener, Daniel Chi, Erik Toso, Michael Kyba S1.101 Identification of the first endogenous inhibitor of DUX4 in FSHD muscular dystrophy Paola Ghezzi, Valeria Runfola, Maria Pannese, Claudia Caronni, Roberto Giambruno, Annapaola Andolfo, Davide Gabellini S1.102 Use of snRNA-seq to characterize the skeletal muscle microenvironment during pathogenesis in FSHD Anugraha Raman, Anthony Accorsi, Michelle Mellion, Bobby Riehle, Lucienne Ronco, L. Alejandro Rojas, Christopher Moxham . Genetics & Epigenetics S2.200 Identification of a druggable epigenetic target required for DUX4 expression and DUX4-mediated toxicity in FSHD muscular dystrophy Emanuele Mocciaro, Roberto Giambruno, Stefano Micheloni, Cristina Consonni, Maria Pannese, Valeria Runfola, Giulia Ferri, Davide Gabellini S2.201 Accessing D4Z4 (epi)genetics with long-read sequencing Quentin Gouil, Ayush Semwal, Frédérique Magdinier, Marnie Blewitt . Pathology & Disease Mechanisms S3.300 System biology approach links muscle weakening to alteration of the contractile apparatus in FSHD Camille Laberthonnière, Megane Delourme, Raphael Chevalier, Elva-Maria Novoa-del-Toro, Emmanuelle Salort Campana, Shahram Attarian, -
FSHD Region Gene 1 (FRG1) Is Crucial for Angiogenesis Linking FRG1 to Facioscapulohumeral Muscular Dystrophy-Associated Vasculopathy
University of Massachusetts Medical School eScholarship@UMMS Peter Jones Lab Publications Cell and Developmental Biology Laboratories 2009-05-01 FSHD region gene 1 (FRG1) is crucial for angiogenesis linking FRG1 to facioscapulohumeral muscular dystrophy-associated vasculopathy Ryan Wuebbles University of Illinois at Urbana-Champaign Et al. Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/peterjones Part of the Cell Biology Commons, Developmental Biology Commons, Molecular Biology Commons, Molecular Genetics Commons, Musculoskeletal Diseases Commons, and the Nervous System Diseases Commons Repository Citation Wuebbles R, Hanel ML, Jones PL. (2009). FSHD region gene 1 (FRG1) is crucial for angiogenesis linking FRG1 to facioscapulohumeral muscular dystrophy-associated vasculopathy. Peter Jones Lab Publications. https://doi.org/10.1242/dmm.002261. Retrieved from https://escholarship.umassmed.edu/ peterjones/11 Creative Commons License This work is licensed under a Creative Commons Attribution 3.0 License. This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in Peter Jones Lab Publications by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. Disease Models & Mechanisms 2, 267-274 (2009) doi:10.1242/dmm.002261 RESEARCH ARTICLE FSHD region gene 1 (FRG1) is crucial for angiogenesis linking FRG1 to facioscapulohumeral muscular dystrophy-associated vasculopathy Ryan D. Wuebbles1,*, Meredith L. Hanel1,* and Peter L. Jones1,‡ SUMMARY The genetic lesion that is diagnostic for facioscapulohumeral muscular dystrophy (FSHD) results in an epigenetic misregulation of gene expression, which ultimately leads to the disease pathology. FRG1 (FSHD region gene 1) is a leading candidate for a gene whose misexpression might lead to FSHD. -
Gene Expression During Normal and FSHD Myogenesis Tsumagari Et Al
Gene expression during normal and FSHD myogenesis Tsumagari et al. Tsumagari et al. BMC Medical Genomics 2011, 4:67 http://www.biomedcentral.com/1755-8794/4/67 (27 September 2011) Tsumagari et al. BMC Medical Genomics 2011, 4:67 http://www.biomedcentral.com/1755-8794/4/67 RESEARCHARTICLE Open Access Gene expression during normal and FSHD myogenesis Koji Tsumagari1, Shao-Chi Chang1, Michelle Lacey2,3, Carl Baribault2,3, Sridar V Chittur4, Janet Sowden5, Rabi Tawil5, Gregory E Crawford6 and Melanie Ehrlich1,3* Abstract Background: Facioscapulohumeral muscular dystrophy (FSHD) is a dominant disease linked to contraction of an array of tandem 3.3-kb repeats (D4Z4) at 4q35. Within each repeat unit is a gene, DUX4, that can encode a protein containing two homeodomains. A DUX4 transcript derived from the last repeat unit in a contracted array is associated with pathogenesis but it is unclear how. Methods: Using exon-based microarrays, the expression profiles of myogenic precursor cells were determined. Both undifferentiated myoblasts and myoblasts differentiated to myotubes derived from FSHD patients and controls were studied after immunocytochemical verification of the quality of the cultures. To further our understanding of FSHD and normal myogenesis, the expression profiles obtained were compared to those of 19 non-muscle cell types analyzed by identical methods. Results: Many of the ~17,000 examined genes were differentially expressed (> 2-fold, p < 0.01) in control myoblasts or myotubes vs. non-muscle cells (2185 and 3006, respectively) or in FSHD vs. control myoblasts or myotubes (295 and 797, respectively). Surprisingly, despite the morphologically normal differentiation of FSHD myoblasts to myotubes, most of the disease-related dysregulation was seen as dampening of normal myogenesis- specific expression changes, including in genes for muscle structure, mitochondrial function, stress responses, and signal transduction. -
The Cancer-Associated CTCFL/BORIS Protein Targets Multiple Classes of Genomic Repeats, with a Distinct Binding and Functional Pr
Pugacheva et al. Epigenetics & Chromatin (2016) 9:35 DOI 10.1186/s13072-016-0084-2 Epigenetics & Chromatin RESEARCH Open Access The cancer‑associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid‑specific SVA transposable elements Elena M. Pugacheva2, Evgeny Teplyakov1, Qiongfang Wu1, Jingjing Li1, Cheng Chen1, Chengcheng Meng1, Jian Liu1, Susan Robinson2, Dmitry Loukinov2, Abdelhalim Boukaba1, Andrew Paul Hutchins3, Victor Lobanenkov2 and Alexander Strunnikov1* Abstract Background: A common aberration in cancer is the activation of germline-specific proteins. The DNA-binding pro- teins among them could generate novel chromatin states, not found in normal cells. The germline-specific transcrip- tion factor BORIS/CTCFL, a paralog of chromatin architecture protein CTCF, is often erroneously activated in cancers and rewires the epigenome for the germline-like transcription program. Another common feature of malignancies is the changed expression and epigenetic states of genomic repeats, which could alter the transcription of neighboring genes and cause somatic mutations upon transposition. The role of BORIS in transposable elements and other repeats has never been assessed. Results: The investigation of BORIS and CTCF binding to DNA repeats in the K562 cancer cells dependent on BORIS for self-renewal by ChIP-chip and ChIP-seq revealed three classes of occupancy by these proteins: elements cohabited by BORIS and CTCF, CTCF-only bound, or BORIS-only bound. The CTCF-only enrichment is characteristic for evolu- tionary old and inactive repeat classes, while BORIS and CTCF co-binding predominately occurs at uncharacterized tandem repeats. These repeats form staggered cluster binding sites, which are a prerequisite for CTCF and BORIS co-binding. -
Estimation of the RNU2 Macrosatellite Mutation Rate by BRCA1 Mutation
Published online 17 July 2014 Nucleic Acids Research, 2014, Vol. 42, No. 14 9121–9130 doi: 10.1093/nar/gku639 Estimation of the RNU2 macrosatellite mutation rate by BRCA1 mutation tracing Chloe´ Tessereau1,2, Yann Lesecque3, Nastasia Monnet1, Monique Buisson1, Laure Barjhoux1,Melanie´ Leon´ e´ 4, Bingjian Feng5, David E. Goldgar5,Olga M. Sinilnikova1,4, Sylvain Mousset3, Laurent Duret3 and Sylvie Mazoyer1,* 1Genetics of Breast Cancer Team, Cancer Research Centre of Lyon, CNRS UMR5286, Inserm U1052, Universite´ Lyon 1, Centre Leon´ Berard,´ Lyon, France, 2Genomic Vision, Bagneux, Paris, France, 3Laboratoire de Biometrie´ et Biologie Evolutive, CNRS UMR5558, Universite´ Lyon 1, France, 4Unite´ Mixte de Gen´ etique´ Constitutionnelle des Cancers Frequents,´ Hospices Civils de Lyon/Centre Leon´ Berard,´ Lyon, France and 5Department of Dermatology and Huntsman Cancer Institute University of Utah School of Medicine, Salt Lake City, Utah, USA Received April 4, 2014; Revised June 26, 2014; Accepted July 1, 2014 ABSTRACT traits, including diseases. The most extensively studied tan- dem repeat DNA sequences so far have been microsatellites Large tandem repeat sequences have been poorly (composed of units from 1 to 10 bp), in particular those in- investigated as severe technical limitations and their volved in trinucleotide repeat disorders, and minisatellites frequent absence from the genome reference hinder (units from 10 to a few hundreds bp long). Comparatively, their analysis. Extensive allelotyping of this class of little is known about tandemly repeated sequences longer variation has not been possible until now and their than 1 kb, also known as multi-allelic tandem copy number mutational dynamics are still poorly known.