A CRISPR Knockout Screen Identifies SETDB1-Target Retroelement Silencing Factors in Embryonic Stem Cells
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Structure of the Tripartite Motif of KAP1/TRIM28 Identifies Molecular Interfaces Required for Transcriptional Silencing of Retrotransposons
bioRxiv preprint doi: https://doi.org/10.1101/505677; this version posted December 25, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Structure of the tripartite motif of KAP1/TRIM28 identifies molecular interfaces required for transcriptional silencing of retrotransposons Guido A. Stoll1, Shun-ichiro Oda1, Zheng-Shan Chong1, Minmin Yu2, Stephen H. McLaughlin2 and Yorgo Modis1,* 1 Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK 2 MRC Laboratory oF Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK * Correspondence: [email protected] (Y.M.) Abstract Transcription oF transposable elements is tightly regulated to prevent damage to the genome. The family of KRAB domain-containing zinc Finger proteins (KRAB-ZFPs) and KRAB-associated protein 1 (KAP1/TRIM28) play a key role in regulating retrotransposons. KRAB-ZFPs recognize speciFic retrotransposon sequences and recruit KAP1, which controls the assembly of an epigenetic silencing complex including histone H3K9 methyltransferase SETDB1. The chromatin remodeling activities of this complex repress transcription of the targeted transposable element and any adjacent genes. Here, we use biophysical and structural approaches to show that the tripartite motif (TRIM) of KAP1 Forms antiparallel dimers, which Further assemble into tetramers and higher-order oligomers in a concentration-dependent manner. Structure-based mutations in the B-box 1 domain prevented higher-order oligomerization without a signiFicant loss oF retrotransposon silencing activity in a cell-based assay, indicating that, in contrast to other TRIM family members, selF-assembly is not essential For the function of KAP1. -
Entrez Symbols Name Termid Termdesc 117553 Uba3,Ube1c
Entrez Symbols Name TermID TermDesc 117553 Uba3,Ube1c ubiquitin-like modifier activating enzyme 3 GO:0016881 acid-amino acid ligase activity 299002 G2e3,RGD1310263 G2/M-phase specific E3 ubiquitin ligase GO:0016881 acid-amino acid ligase activity 303614 RGD1310067,Smurf2 SMAD specific E3 ubiquitin protein ligase 2 GO:0016881 acid-amino acid ligase activity 308669 Herc2 hect domain and RLD 2 GO:0016881 acid-amino acid ligase activity 309331 Uhrf2 ubiquitin-like with PHD and ring finger domains 2 GO:0016881 acid-amino acid ligase activity 316395 Hecw2 HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 GO:0016881 acid-amino acid ligase activity 361866 Hace1 HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1 GO:0016881 acid-amino acid ligase activity 117029 Ccr5,Ckr5,Cmkbr5 chemokine (C-C motif) receptor 5 GO:0003779 actin binding 117538 Waspip,Wip,Wipf1 WAS/WASL interacting protein family, member 1 GO:0003779 actin binding 117557 TM30nm,Tpm3,Tpm5 tropomyosin 3, gamma GO:0003779 actin binding 24779 MGC93554,Slc4a1 solute carrier family 4 (anion exchanger), member 1 GO:0003779 actin binding 24851 Alpha-tm,Tma2,Tmsa,Tpm1 tropomyosin 1, alpha GO:0003779 actin binding 25132 Myo5b,Myr6 myosin Vb GO:0003779 actin binding 25152 Map1a,Mtap1a microtubule-associated protein 1A GO:0003779 actin binding 25230 Add3 adducin 3 (gamma) GO:0003779 actin binding 25386 AQP-2,Aqp2,MGC156502,aquaporin-2aquaporin 2 (collecting duct) GO:0003779 actin binding 25484 MYR5,Myo1e,Myr3 myosin IE GO:0003779 actin binding 25576 14-3-3e1,MGC93547,Ywhah -
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. -
(Ser739) Antibody-SL10016R
SunLong Biotech Co.,LTD Tel: 0086-571- 56623320 Fax:0086-571- 56623318 E-mail:[email protected] www.sunlongbiotech.com Rabbit Anti-phospho-ZCWCC1 (Ser739) antibody SL10016R Product Name: phospho-ZCWCC1 (Ser739) Chinese Name: 磷酸化ZCWCC1抗体 AC004542.C22.1.; p-MORC2(Ser739); phospho-ZCWCC1(Ser739); CW type with coiled coil domain 1; KIAA0852; ZCW3; ZCWCC1; Zinc finger; Zinc finger CW type Alias: coiled coil domain protein 1; Zinc finger CW type with coiled coil domain 1; Zing finger CW type 3 zinc finger CW-type coiled-coil domain protein 1; MORC family CW-type zine finger 2; MORC2. Organism Species: Rabbit Clonality: Polyclonal React Species: Human,Mouse,Rat, WB=1:500-2000ELISA=1:500-1000IHC-P=1:400-800IHC-F=1:400-800ICC=1:100- 500IF=1:100-500(Paraffin sections need antigen repair) Applications: not yet tested in other applications. optimal dilutions/concentrations should be determined by the end user. Molecular weight: 114kDa Cellular localization: The nucleuscytoplasmic Form: Lyophilizedwww.sunlongbiotech.com or Liquid Concentration: 1mg/ml KLH conjugated synthesised phosphopeptide derived from human MORC2 around the immunogen: phosphorylation site of Ser739:KR(p-S)VA Lsotype: IgG Purification: affinity purified by Protein A Storage Buffer: 0.01M TBS(pH7.4) with 1% BSA, 0.03% Proclin300 and 50% Glycerol. Store at -20 °C for one year. Avoid repeated freeze/thaw cycles. The lyophilized antibody is stable at room temperature for at least one month and for greater than a year Storage: when kept at -20°C. When reconstituted in sterile pH 7.4 0.01M PBS or diluent of antibody the antibody is stable for at least two weeks at 2-4 °C. -
Transcriptome Analyses of Tumor-Adjacent Somatic Tissues Reveal Genes Co-Expressed with Transposable Elements Nicky Chung1†, G
Chung et al. Mobile DNA (2019) 10:39 https://doi.org/10.1186/s13100-019-0180-5 RESEARCH Open Access Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements Nicky Chung1†, G. M. Jonaid1†, Sophia Quinton1†, Austin Ross1†, Corinne E. Sexton1, Adrian Alberto2, Cody Clymer2, Daphnie Churchill2, Omar Navarro Leija 2 and Mira V. Han1,3* Abstract Background: Despite the long-held assumption that transposons are normally only expressed in the germ-line, recent evidence shows that transcripts of transposable element (TE) sequences are frequently found in the somatic cells. However, the extent of variation in TE transcript levels across different tissues and different individuals are unknown, and the co-expression between TEs and host gene mRNAs have not been examined. Results: Here we report the variation in TE derived transcript levels across tissues and between individuals observed in the non-tumorous tissues collected for The Cancer Genome Atlas. We found core TE co-expression modules consisting mainly of transposons, showing correlated expression across broad classes of TEs. Despite this co-expression within tissues, there are individual TE loci that exhibit tissue-specific expression patterns, when compared across tissues. The core TE modules were negatively correlated with other gene modules that consisted of immune response genes in interferon signaling. KRAB Zinc Finger Proteins (KZFPs) were over-represented gene members of the TE modules, showing positive correlation across multiple tissues. But we did not find overlap between TE-KZFP pairs that are co-expressed and TE-KZFP pairs that are bound in published ChIP-seq studies. -
Molecular Mechanism of the MORC4 Atpase Activation
ARTICLE https://doi.org/10.1038/s41467-020-19278-8 OPEN Molecular mechanism of the MORC4 ATPase activation Adam H. Tencer1, Khan L. Cox2, Gregory M. Wright1, Yi Zhang 1, Christopher J. Petell3, Brianna J. Klein1, ✉ Brian D. Strahl 3, Joshua C. Black1, Michael G. Poirier2 & Tatiana G. Kutateladze 1 Human Microrchidia 4 (MORC4) is associated with acute and chronic pancreatitis, inflam- matory disorders and cancer but it remains largely uncharacterized. Here, we describe the 1234567890():,; structure–function relationship of MORC4 and define the molecular mechanism for MORC4 activation. Enzymatic and binding assays reveal that MORC4 has ATPase activity, which is dependent on DNA-binding functions of both the ATPase domain and CW domain of MORC4. The crystal structure of the ATPaseCW cassette of MORC4 and mutagenesis studies show that the DNA-binding site and the histone/ATPase binding site of CW are located on the opposite sides of the domain. The ATPase and CW domains cooperate in binding of MORC4 to the nucleosome core particle (NCP), enhancing the DNA wrapping around the histone core and impeding binding of DNA-associated proteins, such as tran- scription factors, to the NCP. In cells, MORC4 mediates formation of nuclear bodies in the nucleus and has a role in the progression of S-phase of the cell cycle, and both these functions require CW and catalytic activity of MORC4. Our findings highlight the mechanism for MORC4 activation, which is distinctly different from the mechanisms of action observed in other MORC family members. 1 Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA. -
Genome-Wide DNA Methylation Analysis on C-Reactive Protein Among Ghanaians Suggests Molecular Links to the Emerging Risk of Cardiovascular Diseases ✉ Felix P
www.nature.com/npjgenmed ARTICLE OPEN Genome-wide DNA methylation analysis on C-reactive protein among Ghanaians suggests molecular links to the emerging risk of cardiovascular diseases ✉ Felix P. Chilunga 1 , Peter Henneman2, Andrea Venema2, Karlijn A. C. Meeks 3, Ana Requena-Méndez4,5, Erik Beune1, Frank P. Mockenhaupt6, Liam Smeeth7, Silver Bahendeka8, Ina Danquah9, Kerstin Klipstein-Grobusch10,11, Adebowale Adeyemo 3, Marcel M.A.M Mannens2 and Charles Agyemang1 Molecular mechanisms at the intersection of inflammation and cardiovascular diseases (CVD) among Africans are still unknown. We performed an epigenome-wide association study to identify loci associated with serum C-reactive protein (marker of inflammation) among Ghanaians and further assessed whether differentially methylated positions (DMPs) were linked to CVD in previous reports, or to estimated CVD risk in the same population. We used the Illumina Infinium® HumanMethylation450 BeadChip to obtain DNAm profiles of blood samples in 589 Ghanaians from the RODAM study (without acute infections, not taking anti-inflammatory medications, CRP levels < 40 mg/L). We then used linear models to identify DMPs associated with CRP concentrations. Post-hoc, we evaluated associations of identified DMPs with elevated CVD risk estimated via ASCVD risk score. We also performed subset analyses at CRP levels ≤10 mg/L and replication analyses on candidate probes. Finally, we assessed for biological relevance of our findings in public databases. We subsequently identified 14 novel DMPs associated with CRP. In post-hoc evaluations, we found 1234567890():,; that DMPs in PC, BTG4 and PADI1 showed trends of associations with estimated CVD risk, we identified a separate DMP in MORC2 that was associated with CRP levels ≤10 mg/L, and we successfully replicated 65 (24%) of previously reported DMPs. -
EVALUATION of BMP2/Mirna CO-EXPRESSION SYSTEMS for POTENT THERAPEUTIC EFFICACY in BONE-TISSUE REGENERATION
EuropeanTK Brenner Cells et al. and Materials Vol. 41 2021 (pages 245-268) DOI: Non-viral 10.22203/eCM.v041a18 BMP2/miRNA co-expression ISSN 1473-2262 systems EVALUATION OF BMP2/miRNA CO-EXPRESSION SYSTEMS FOR POTENT THERAPEUTIC EFFICACY IN BONE-TISSUE REGENERATION T.K. Brenner1,§, K. Posa-Markaryan1,§, D. Hercher1,4, S. Sperger1,4, P. Heimel1,4, C. Keibl1, S. Nürnberger1,2,3,4, J. Grillari1,4,5, H. Redl1,4 and A. Hacobian1,4,* 1 Ludwig Boltzmann Institute for Experimental and Clinical Traumatology/AUVA Research Centre, The Austrian Cluster for Tissue Regeneration, European Institute of Excellence on Tissue Engineering and Regenerative Medicine Research (Expertissues EEIG), Donaueschingenstrasse 13, 1200 Vienna, Austria 2 Department of Orthopaedics and Trauma-Surgery, Division of Trauma-Surgery, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria 3 University Clinic of Dentistry, Medical University of Vienna, Sensengasse 2a, 1090 Vienna, Austria 4 Austrian Cluster for Tissue Engineering 5 Institute for Molecular Biotechnology, Department of Biotechnology, BOKU – University of Natural Resources and Life Sciences, Vienna, Austria § These authors contributed equally to this work Abstract Reconstruction of bone defects and compensation of deficient repair mechanisms represent important goals within the field of regenerative medicine and require novel safe strategies for translation into the clinic. A non-viral osteogenic gene therapeutic vector system (‘hybrid vectors’) was generated, combining an improved bone morphogenetic protein 2 (BMP2) gene cassette and single pro-osteogenic microRNAs (miR-148b-3p, miR-20-5p, miR-590b-5p), driven by the U6 promoter. The vectors were tested in vitro for their osteogenic differentiation potential in C2C12 and C3H/10T1/2 cell lines, usingBMP2 alone as a control. -
ARTICLE Classification of Human Chromosome 21 Gene-Expression Variations in Down Syndrome: Impact on Disease Phenotypes
ARTICLE Classification of Human Chromosome 21 Gene-Expression Variations in Down Syndrome: Impact on Disease Phenotypes E. Aı¨t Yahya-Graison, J. Aubert, L. Dauphinot, I. Rivals, M. Prieur, G. Golfier, J. Rossier, L. Personnaz, N. Cre´au, H. Ble´haut, S. Robin, J. M. Delabar, and M.-C. Potier Down syndrome caused by chromosome 21 trisomy is the most common genetic cause of mental retardation in humans. Disruption of the phenotype is thought to be the result of gene-dosage imbalance. Variations in chromosome 21 gene expression in Down syndrome were analyzed in lymphoblastoid cells derived from patients and control individuals. Of the 359 genes and predictions displayed on a specifically designed high-content chromosome 21 microarray, one-third were expressed in lymphoblastoid cells. We performed a mixed-model analysis of variance to find genes that are differ- entially expressed in Down syndrome independent of sex and interindividual variations. In addition, we identified genes with variations between Down syndrome and control samples that were significantly different from the gene-dosage effect (1.5). Microarray data were validated by quantitative polymerase chain reaction. We found that 29% of the expressed chromosome 21 transcripts are overexpressed in Down syndrome and correspond to either genes or open reading frames. Among these, 22% are increased proportional to the gene-dosage effect, and 7% are amplified. The other 71% of expressed sequences are either compensated (56%, with a large proportion of predicted genes and antisense transcripts) or highly variable among individuals (15%). Thus, most of the chromosome 21 transcripts are compensated for the gene-dosage effect. -
A KAP1 Phosphorylation Switch Controls Myod Function During Skeletal Muscle Differentiation
Downloaded from genesdev.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation Kulwant Singh,1,5 Marco Cassano,2,5 Evarist Planet,2 Soji Sebastian,1 Suk Min Jang,2 Gurjeev Sohi,1 Herve Faralli,1 Jinmi Choi,3 Hong-Duk Youn,3 F. Jeffrey Dilworth,1,4 and Didier Trono2 1Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada; 2School of Life Sciences, Ecole Polytechnique Fed erale de Lausanne (EPFL), 1015 Lausanne, Switzerland; 3Department of Biomedical Sciences and Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 110-799, Korea; 4Department of Cellular and Molecular Medicine, University of Ottawa, Ontario K1H 8L6, Canada The transcriptional activator MyoD serves as a master controller of myogenesis. Often in partnership with Mef2 (myocyte enhancer factor 2), MyoD binds to the promoters of hundreds of muscle genes in proliferating myoblasts yet activates these targets only upon receiving cues that launch differentiation. What regulates this off/on switch of MyoD function has been incompletely understood, although it is known to reflect the action of chromatin modifiers. Here, we identify KAP1 (KRAB [Kruppel-like€ associated box]-associated protein 1)/TRIM28 (tripartite motif protein 28) as a key regulator of MyoD function. In myoblasts, KAP1 is present with MyoD and Mef2 at many muscle genes, where it acts as a scaffold to recruit not only coactivators such as p300 and LSD1 but also corepressors such as G9a and HDAC1 (histone deacetylase 1), with promoter silencing as the net outcome. -
Hippocampal Dysfunction in the Euchromatin Histone Methyltransferase 1 Heterozygous Knockout Mouse Model for Kleefstra Syndrome
Human Molecular Genetics, 2013, Vol. 22, No. 5 852–866 doi:10.1093/hmg/dds490 Advance Access published on November 21, 2012 Hippocampal dysfunction in the Euchromatin histone methyltransferase 1 heterozygous knockout mouse model for Kleefstra syndrome Monique C.M. Balemans1,2, Nael Nadif Kasri3, Maksym V. Kopanitsa5, Nurudeen O. Afinowi5, Ger Ramakers6, Theo A. Peters4, Andy J. Beynon4, Sanne M. Janssen1, Rik C.J. van Summeren1,2, Jorine M. Eeftens1, Nathalie Eikelenboom1, Marco Benevento3, Makoto Tachibana7, Yoichi Shinkai7, Tjitske Kleefstra1, Hans van Bokhoven1,3,∗,{ and Catharina E.E.M. Van der Zee2,∗,{ 1Department of Human Genetics, 2Department of Cell Biology, Nijmegen Centre for Molecular Life Sciences, 3Department of Cognitive Neurosciences, and 4Department of Otorhinolaryngology, Donders Institute for Brain, Downloaded from Cognition and Behavior, Radboud University, Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands 5Synome Ltd, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, UK, 6Department of Developmental Psychology, University of Amsterdam, Roetersstraat 15, 1018 WB Amsterdam, the Netherlands and 7Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto, University, 53 Shogoin, http://hmg.oxfordjournals.org/ Kawara-cho, Sakyo-ku, Kyoto, Japan Received October 21, 2012; Revised October 21, 2012; Accepted November 15, 2012 Euchromatin histone methyltransferase 1 (EHMT1) is a highly conserved protein that catalyzes mono- and dimethylation of histone H3 lysine 9, thereby epigenetically regulating transcription. Kleefstra syndrome (KS), is caused by haploinsufficiency of the EHMT1 gene, and is an example of an emerging group of intel- lectual disability (ID) disorders caused by genes encoding epigenetic regulators of neuronal gene activity. by guest on March 24, 2016 Little is known about the mechanisms underlying this disorder, prompting us to study the Euchromatin his- tone methyltransferase 1 heterozygous knockout (Ehmt11/2) mice as a model for KS. -
The Histone Methyltransferase SETDB1 Represses Endogenous and Exogenous Retroviruses in B Lymphocytes
The histone methyltransferase SETDB1 represses endogenous and exogenous retroviruses in B lymphocytes Patrick L. Collinsa, Katherine E. Kylea, Takeshi Egawaa, Yoichi Shinkaib, and Eugene M. Oltza,1 aDepartment of Pathology, Washington University School of Medicine, St. Louis, MO 63110; and bCellular Memory Laboratory, RIKEN, Saitama 351-0198, Japan Edited by John V. Moran, University of Michigan, Ann Arbor, MI, and accepted by the Editorial Board May 21, 2015 (received for review November 19, 2014) Genome stability relies on epigenetic mechanisms that enforce tumor viruses (MMTVs). Reintegration of these expressed viruses repression of endogenous retroviruses (ERVs). Current evidence can generate mutations with potential oncogenic consequences suggests that distinct chromatin-based mechanisms repress ERVs (7). Thus, suppression of ERVs via epigenetic mechanisms is es- in cells of embryonic origin (histone methylation dominant) vs. pecially important in adult tissues that harbor cells with a high more differentiated cells (DNA methylation dominant). However, proliferative capacity. the latter aspect of this model has not been tested. Remarkably, Recent studies suggest that the mechanisms of ERV re- and in contrast to the prevailing model, we find that repressive pression in differentiated adult tissues are distinct from those histone methylation catalyzed by the enzyme SETDB1 is critical for in embryonic stem cells (ESCs) or early lineage progenitors (3). In fully differentiated cells, such as fibroblasts, DNA methylation suppression of specific ERV families and exogenous retroviruses in appears to be particularly important for ERV suppression, committed B-lineage cells from adult mice. The profile of ERV whereas HMTs responsible for H3K9me3 are largely dispens- activation in SETDB1-deficient B cells is distinct from that observed able (3, 4).