The Results of an X-Chromosome Exome Sequencing Study
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The HECT Domain Ubiquitin Ligase HUWE1 Targets Unassembled Soluble Proteins for Degradation
OPEN Citation: Cell Discovery (2016) 2, 16040; doi:10.1038/celldisc.2016.40 ARTICLE www.nature.com/celldisc The HECT domain ubiquitin ligase HUWE1 targets unassembled soluble proteins for degradation Yue Xu1, D Eric Anderson2, Yihong Ye1 1Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA; 2Advanced Mass Spectrometry Core Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA In eukaryotes, many proteins function in multi-subunit complexes that require proper assembly. To maintain complex stoichiometry, cells use the endoplasmic reticulum-associated degradation system to degrade unassembled membrane subunits, but how unassembled soluble proteins are eliminated is undefined. Here we show that degradation of unassembled soluble proteins (referred to as unassembled soluble protein degradation, USPD) requires the ubiquitin selective chaperone p97, its co-factor nuclear protein localization protein 4 (Npl4), and the proteasome. At the ubiquitin ligase level, the previously identified protein quality control ligase UBR1 (ubiquitin protein ligase E3 component n-recognin 1) and the related enzymes only process a subset of unassembled soluble proteins. We identify the homologous to the E6-AP carboxyl terminus (homologous to the E6-AP carboxyl terminus) domain-containing protein HUWE1 as a ubiquitin ligase for substrates bearing unshielded, hydrophobic segments. We used a stable isotope labeling with amino acids-based proteomic approach to identify endogenous HUWE1 substrates. Interestingly, many HUWE1 substrates form multi-protein com- plexes that function in the nucleus although HUWE1 itself is cytoplasmically localized. Inhibition of nuclear entry enhances HUWE1-mediated ubiquitination and degradation, suggesting that USPD occurs primarily in the cytoplasm. -
The Inactive X Chromosome Is Epigenetically Unstable and Transcriptionally Labile in Breast Cancer
Supplemental Information The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer Ronan Chaligné1,2,3,8, Tatiana Popova1,4, Marco-Antonio Mendoza-Parra5, Mohamed-Ashick M. Saleem5 , David Gentien1,6, Kristen Ban1,2,3,8, Tristan Piolot1,7, Olivier Leroy1,7, Odette Mariani6, Hinrich Gronemeyer*5, Anne Vincent-Salomon*1,4,6,8, Marc-Henri Stern*1,4,6 and Edith Heard*1,2,3,8 Extended Experimental Procedures Cell Culture Human Mammary Epithelial Cells (HMEC, Invitrogen) were grown in serum-free medium (HuMEC, Invitrogen). WI- 38, ZR-75-1, SK-BR-3 and MDA-MB-436 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen) containing 10% fetal bovine serum (FBS). DNA Methylation analysis. We bisulfite-treated 2 µg of genomic DNA using Epitect bisulfite kit (Qiagen). Bisulfite converted DNA was amplified with bisulfite primers listed in Table S3. All primers incorporated a T7 promoter tag, and PCR conditions are available upon request. We analyzed PCR products by MALDI-TOF mass spectrometry after in vitro transcription and specific cleavage (EpiTYPER by Sequenom®). For each amplicon, we analyzed two independent DNA samples and several CG sites in the CpG Island. Design of primers and selection of best promoter region to assess (approx. 500 bp) were done by a combination of UCSC Genome Browser (http://genome.ucsc.edu) and MethPrimer (http://www.urogene.org). All the primers used are listed (Table S3). NB: MAGEC2 CpG analysis have been done with a combination of two CpG island identified in the gene core. Analysis of RNA allelic expression profiles (based on Human SNP Array 6.0) DNA and RNA hybridizations were normalized by Genotyping console. -
DNA Damage-Induced Histone H1 Ubiquitylation Is Mediated by HUWE1 and Stimulates the RNF8-RNF168 Pathway
www.nature.com/scientificreports OPEN DNA damage-induced histone H1 ubiquitylation is mediated by HUWE1 and stimulates the RNF8- Received: 27 April 2017 Accepted: 16 October 2017 RNF168 pathway Published: xx xx xxxx I. K. Mandemaker1, L. van Cuijk1, R. C. Janssens1, H. Lans 1, K. Bezstarosti2, J. H. Hoeijmakers1, J. A. Demmers2, W. Vermeulen1 & J. A. Marteijn1 The DNA damage response (DDR), comprising distinct repair and signalling pathways, safeguards genomic integrity. Protein ubiquitylation is an important regulatory mechanism of the DDR. To study its role in the UV-induced DDR, we characterized changes in protein ubiquitylation following DNA damage using quantitative di-Gly proteomics. Interestingly, we identifed multiple sites of histone H1 that are ubiquitylated upon UV-damage. We show that UV-dependent histone H1 ubiquitylation at multiple lysines is mediated by the E3-ligase HUWE1. Recently, it was shown that poly-ubiquitylated histone H1 is an important signalling intermediate in the double strand break response. This poly-ubiquitylation is dependent on RNF8 and Ubc13 which extend pre-existing ubiquitin modifcations to K63-linked chains. Here we demonstrate that HUWE1 depleted cells showed reduced recruitment of RNF168 and 53BP1 to sites of DNA damage, two factors downstream of RNF8 mediated histone H1 poly-ubiquitylation, while recruitment of MDC1, which act upstream of histone H1 ubiquitylation, was not afected. Our data show that histone H1 is a prominent target for ubiquitylation after UV-induced DNA damage. Our data are in line with a model in which HUWE1 primes histone H1 with ubiquitin to allow ubiquitin chain elongation by RNF8, thereby stimulating the RNF8-RNF168 mediated DDR. -
Roles of the HUWE1 Ubiquitin Ligase in Nervous System Development, Function and Disease Andrew C
Giles and Grill Neural Development (2020) 15:6 https://doi.org/10.1186/s13064-020-00143-9 REVIEW Open Access Roles of the HUWE1 ubiquitin ligase in nervous system development, function and disease Andrew C. Giles and Brock Grill* Abstract Huwe1 is a highly conserved member of the HECT E3 ubiquitin ligase family. Here, we explore the growing importance of Huwe1 in nervous system development, function and disease. We discuss extensive progress made in deciphering how Huwe1 regulates neural progenitor proliferation and differentiation, cell migration, and axon development. We highlight recent evidence indicating that Huwe1 regulates inhibitory neurotransmission. In covering these topics, we focus on findings made using both vertebrate and invertebrate in vivo model systems. Finally, we discuss extensive human genetic studies that strongly implicate HUWE1 in intellectual disability, and heighten the importance of continuing to unravel how Huwe1 affects the nervous system. Keywords: Huwe1, EEL-1, Ubiquitin ligase, HECT, Neuron, Neural progenitor, Neurotransmission, Axon, Transcription factor, Intellectual disability Introduction evidence implicating Huwe1 in multiple neurodevelop- HECT, UBA and WWE domain containing protein 1 mental disorders, including both non-syndromic and syn- (Huwe1) is an E3 ubiquitin ligase that is highly conserved dromic forms of X-linked intellectual disability (ID). In across the animal kingdom [1–4](Fig.1a). While rodent, this review, we discuss how Huwe1 contributes to nervous zebrafish and fly orthologs are also generally referred to as system development, function and disease. We hope that Huwe1, the C. elegans ortholog is called Enhancer of EFL- exploring this literature encourages further studies on 1 (EEL-1) based on its discovery in genetic screens. -
Assessment of Copy Number Variations in 120 Patients with Poland
Vaccari et al. BMC Medical Genetics (2016) 17:89 DOI 10.1186/s12881-016-0351-x RESEARCHARTICLE Open Access Assessment of copy number variations in 120 patients with Poland syndrome Carlotta Maria Vaccari1, Elisa Tassano2, Michele Torre3, Stefania Gimelli4, Maria Teresa Divizia2, Maria Victoria Romanini5, Simone Bossi1, Ilaria Musante1, Maura Valle6, Filippo Senes7, Nunzio Catena7, Maria Francesca Bedeschi8, Anwar Baban2,10, Maria Grazia Calevo9, Massimo Acquaviva1, Margherita Lerone2, Roberto Ravazzolo1,2 and Aldamaria Puliti1,2* Abstract Background: Poland Syndrome (PS) is a rare congenital disorder presenting with agenesis/hypoplasia of the pectoralis major muscle variably associated with thoracic and/or upper limb anomalies. Most cases are sporadic, but familial recurrence, with different inheritance patterns, has been observed. The genetic etiology of PS remains unknown. Karyotyping and array-comparative genomic hybridization (CGH) analyses can identify genomic imbalances that can clarify the genetic etiology of congenital and neurodevelopmental disorders. We previously reported a chromosome 11 deletion in twin girls with pectoralis muscle hypoplasia and skeletal anomalies, and a chromosome six deletion in a patient presenting a complex phenotype that included pectoralis muscle hypoplasia. However, the contribution of genomic imbalances to PS remains largely unknown. Methods: To investigate the prevalence of chromosomal imbalances in PS, standard cytogenetic and array-CGH analyses were performed in 120 PS patients. Results: Following the application of stringent filter criteria, 14 rare copy number variations (CNVs) were identified in 14 PS patients in different regions outside known common copy number variations: seven genomic duplications and seven genomic deletions, enclosing the two previously reported PS associated chromosomal deletions. These CNVs ranged from 0.04 to 4.71 Mb in size. -
Shinydepmap, a Tool to Identify Targetable Cancer Genes and Their Functional Connections from Cancer Dependency Map Data
TOOLS AND RESOURCES shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data Kenichi Shimada*, John A Bachman, Jeremy L Muhlich, Timothy J Mitchison Laboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, United States Abstract Individual cancers rely on distinct essential genes for their survival. The Cancer Dependency Map (DepMap) is an ongoing project to uncover these gene dependencies in hundreds of cancer cell lines. To make this drug discovery resource more accessible to the scientific community, we built an easy-to-use browser, shinyDepMap (https://labsyspharm.shinyapps.io/ depmap). shinyDepMap combines CRISPR and shRNA data to determine, for each gene, the growth reduction caused by knockout/knockdown and the selectivity of this effect across cell lines. The tool also clusters genes with similar dependencies, revealing functional relationships. shinyDepMap can be used to (1) predict the efficacy and selectivity of drugs targeting particular genes; (2) identify maximally sensitive cell lines for testing a drug; (3) target hop, that is, navigate from an undruggable protein with the desired selectivity profile, such as an activated oncogene, to more druggable targets with a similar profile; and (4) identify novel pathways driving cancer cell growth and survival. *For correspondence: [email protected]. Introduction edu Cancer is a disease of the genome. Hundreds, if not thousands, of driver mutations cause cancer in different patients (MC3 Working Group et al., 2018), and extensive collaborative efforts such as Competing interest: See the Cancer Genome Atlas Program (TCGA) have helped discover them (The Cancer Genome Atlas page 17 Research Network, 2019). -
Dynamic Changes in Paternal X-Chromosome Activity During Imprinted X-Chromosome Inactivation in Mice
Dynamic changes in paternal X-chromosome activity during imprinted X-chromosome inactivation in mice Catherine Patrata,b, Ikuhiro Okamotoa, Patricia Diabangouayaa, Vivian Vialonc, Patricia Le Baccond, Jennifer Chowa, and Edith Hearda,1 aMammalian Developmental Epigenetics Group, Institut Curie, Centre National Research Scientifique Unité Mixte de Recherche 3215, Institut Nationaldela Santé et de la Recherche Médicale U934, 75248 Paris, France; bLaboratoire de Biologie de la Reproduction and cMedical Informatics Unit, Université Paris Descartes, Assistance Publique-Hoˆpitaux de Paris, 75014 Paris, France; and dChromatin Dynamics Group, Institut Curie Centre National de la Recherche Scientifique Unite´Mixte de Recherche 218–Nuclear Dynamics and Genome Plasticity, 75248 Paris, France Edited by Mary F. Lyon, Medical Research Council, Didcot, Oxon, United Kingdom, and approved January 22, 2009 (received for review October 23, 2008) In mammals, X-chromosome dosage compensation is achieved by inactivate, the early activity of the paternal genome would result in inactivating one of the two X chromosomes in females. In mice, X paternal Xist activity and trigger subsequent Xp inactivation (12). inactivation is initially imprinted, with inactivation of the paternal Another hypothesis is that the Xp is transmitted to the zygote in a X (Xp) chromosome occurring during preimplantation develop- preinactivated state because of its passage through the male germ ment. One theory is that the Xp is preinactivated in female line (13). Here, the X and Y undergo meiotic sex chromosome embryos, because of its previous silence during meiosis in the male inactivation (MSCI) followed by postmeiotic sex chromatin forma- germ line. The extent to which the Xp is active after fertilization tion (PMSC) (14, 15). -
Modular HUWE1 Architecture Serves As Hub for Degradation of Cell-Fate Decision Factors
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.19.257352; this version posted August 19, 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. Modular HUWE1 architecture serves as hub for degradation of cell-fate decision factors Authors: Moritz Hunkeler1,2, Cyrus Y. Jin1,2, Michelle W. Ma1,2, Daan Overwijn1,2, Julie K. Monda3, Eric J. Bennett3, Eric S. Fischer1,2,4,* Affiliations: 1 Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA. 2 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA. 3Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA. 4 Lead contact. *Correspondence to: [email protected] Summary: HECT ubiquitin ligases play essential roles in metazoan development and physiology. The HECT ligase HUWE1 is central to the cellular stress response by mediating degradation of key death or survival factors including Mcl1, p53, DDIT4, and Myc. As a step toward understanding regulation of HUWE1 engagement with its diverse substrates, we present here the cryo-EM structure of HUWE1, offering a first complete molecular picture of a HECT ubiquitin ligase. The ~4400 amino acid residue polypeptide forms an alpha solenoid- shaped assembly with a central pore decorated with protein interaction modules. This modularity enables HUWE1 to target a wide range of substrates for destruction. The locations of human mutations associated with severe neurodevelopmental disorders link functions of this essential enzyme with its three-dimensional organization. -
Pathway Entry Into the T Lymphocyte Developmental Molecular Dissection of Prethymic Progenitor
The Journal of Immunology Molecular Dissection of Prethymic Progenitor Entry into the T Lymphocyte Developmental Pathway1 C. Chace Tydell,2 Elizabeth-Sharon David-Fung,2,3 Jonathan E. Moore, Lee Rowen,4 Tom Taghon,5 and Ellen V. Rothenberg6 Notch signaling activates T lineage differentiation from hemopoietic progenitors, but relatively few regulators that initiate this program have been identified, e.g., GATA3 and T cell factor-1 (TCF-1) (gene name Tcf7). To identify additional regulators of T cell specification, a cDNA library from mouse Pro-T cells was screened for genes that are specifically up-regulated in intrathymic T cell precursors as compared with myeloid progenitors. Over 90 genes of interest were iden- tified, and 35 of 44 tested were confirmed to be more highly expressed in T lineage precursors relative to precursors of B and/or myeloid lineage. To a remarkable extent, however, expression of these T lineage-enriched genes, including zinc finger transcription factor, helicase, and signaling adaptor genes, was also shared by stem cells (Lin؊Sca-1؉Kit؉CD27؊) and multipotent progenitors (Lin؊Sca-1؉Kit؉CD27؉), although down-regulated in other lineages. Thus, a major fraction of these early T lineage genes are a regulatory legacy from stem cells. The few genes sharply up-regulated between multipotent progenitors and Pro-T cell stages included those encoding transcription factors Bcl11b, TCF-1 (Tcf7), and HEBalt, Notch target Deltex1, Deltex3L, Fkbp5, Eva1, and Tmem131. Like GATA3 and Deltex1, Bcl11b, Fkbp5, and Eva1 were dependent on Notch/Delta signaling for induction in fetal liver precursors, but only Bcl11b and HEBalt were up-regulated between the first two stages of intrathymic T cell development (double negative 1 and double negative 2) corresponding to T lineage specification. -
HUWE1 Mutation Explains Phenotypic Severity in a Case of Familial Idiopathic Intellectual Disability
European Journal of Medical Genetics 56 (2013) 379e382 Contents lists available at SciVerse ScienceDirect European Journal of Medical Genetics journal homepage: http://www.elsevier.com/locate/ejmg Short clinical report HUWE1 mutation explains phenotypic severity in a case of familial idiopathic intellectual disability Mala Isrie a, Vera M. Kalscheuer b, Maureen Holvoet a, Nathalie Fieremans c, Hilde Van Esch a, Koenraad Devriendt a,* a Center for Human Genetics, University Hospitals Leuven, KU Leuven, Herestraat 49, 3000 Leuven, Belgium b Max Planck Institute for Molecular Genetics, Ihnestraße 63e73, 14195 Berlin, Germany c Human Genome Laboratory, VIB, Center for Human Genetics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium article info abstract Article history: The advent of next-generation sequencing has proven to be a key force in the identification of new genes Received 2 March 2013 associated with intellectual disability. In this study, high-throughput sequencing of the coding regions of Accepted 8 May 2013 the X-chromosome led to the identification of a missense variant in the HUWE1 gene. The same variant Available online 27 May 2013 has been reported before by Froyen et al. (2008). We compare the phenotypes and demonstrate that, in the present family, the HUWE1 mutation segregates with the more severe ID phenotypes of two out of Keywords: three brothers. The third brother has a milder form of ID and does not carry the mutation. HUWE1 Ó 2013 Elsevier Masson SAS. All rights reserved. Missense mutation Intellectual disability Chromosome X exome sequencing 1. Introduction family e is an important step toward correct genotypeephenotype correlations. In 1991, the FMR1 gene was discovered to be responsible for the Fragile X syndrome, the most common form of X-linked intellectual 2. -
Targeted Next-Generation Sequencing in Patients with Suggestive X-Linked Intellectual Disability
G C A T T A C G G C A T genes Article Targeted Next-Generation Sequencing in Patients with Suggestive X-Linked Intellectual Disability Nekane Ibarluzea 1,2 , Ana Belén de la Hoz 1,2, Olatz Villate 1,2,3, Isabel Llano 1,2,3 , Intzane Ocio 4, Itxaso Martí 5, Miriam Guitart 6, Elisabeth Gabau 6, Fernando Andrade 1,2, Blanca Gener 1,2,3 and María-Isabel Tejada 1,2,3,* 1 Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; [email protected] (N.I.); [email protected] (A.B.d.l.H.); [email protected] (O.V.); [email protected] (I.L.); [email protected] (F.A.); [email protected] (B.G.) 2 Spanish Consortium for Research on Rare Diseases (CIBERER), 28029 Madrid, Spain 3 Genetics Service, Cruces University Hospital, Osakidetza Basque Health Service, 48903 Barakaldo, Spain 4 Department of Paediatric Neurology, Araba University Hospital, Osakidetza Basque Health Service, 01009 Gasteiz, Spain; [email protected] 5 Department of Paediatric Neurology, Donostia University Hospital, Osakidetza Basque Health Service, 20014 Donostia, Spain; [email protected] 6 Genetics Laboratory, Paediatric Unit, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, 08208 Sabadell, Spain; [email protected] (M.G.); [email protected] (E.G.) * Correspondence: [email protected] Received: 3 December 2019; Accepted: 30 December 2019; Published: 2 January 2020 Abstract: X-linked intellectual disability (XLID) is known to contribute up to 10% of intellectual disability (ID) in males and could explain the increased ratio of affected males observed in patients with ID. -
Impaired Oxidative Stress Response Characterizes HUWE1-Promoted X-Linked Intellectual Disability
www.nature.com/scientificreports OPEN Impaired oxidative stress response characterizes HUWE1-promoted X-linked intellectual disability Received: 4 September 2017 Matthias Bosshard1, Rossana Aprigliano1,2, Cristina Gattiker1, Vuk Palibrk2, Enni Markkanen1, Accepted: 25 October 2017 Paul Hof Backe3, Stefania Pellegrino1, F. Lucy Raymond4, Guy Froyen5, Matthias Altmeyer1, Published: xx xx xxxx Magnar Bjørås2,3,6, Grigory L. Dianov7,8 & Barbara van Loon1,2,6 Mutations in the HECT, UBA and WWE domain-containing 1 (HUWE1) E3 ubiquitin ligase cause neurodevelopmental disorder X-linked intellectual disability (XLID). HUWE1 regulates essential processes such as genome integrity maintenance. Alterations in the genome integrity and accumulation of mutations have been tightly associated with the onset of neurodevelopmental disorders. Though HUWE1 mutations are clearly implicated in XLID and HUWE1 regulatory functions well explored, currently much is unknown about the molecular basis of HUWE1-promoted XLID. Here we showed that the HUWE1 expression is altered and mutation frequency increased in three diferent XLID individual (HUWE1 p.R2981H, p.R4187C and HUWE1 duplication) cell lines. The efect was most prominent in HUWE1 p.R4187C XLID cells and was accompanied with decreased DNA repair capacity and hypersensitivity to oxidative stress. Analysis of HUWE1 substrates revealed XLID-specifc down- regulation of oxidative stress response DNA polymerase (Pol) λ caused by hyperactive HUWE1 p.R4187C. The subsequent restoration of Polλ levels counteracted the oxidative hypersensitivity. The observed alterations in the genome integrity maintenance may be particularly relevant in the cortical progenitor zones of human brain, as suggested by HUWE1 immunofuorescence analysis of cerebral organoids. These results provide evidence that impairments of the fundamental cellular processes, like genome integrity maintenance, characterize HUWE1-promoted XLID.