DOCSLIB.ORG

Mouse Rab21 Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Rab21 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Rab21 Knockout Project (CRISPR/Cas9) Objective: To create a Rab21 knockout Mouse model (C57BL/6N) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Rab21 gene (NCBI Reference Sequence: NM_024454 ; Ensembl: ENSMUSG00000020132 ) is located on Mouse chromosome 10. 7 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 7 (Transcript: ENSMUST00000020343). Exon 2~6 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 2 starts from about 23.12% of the coding region. Exon 2~6 covers 56.46% of the coding region. The size of effective KO region: ~7921 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 6 7 Legends Exon of mouse Rab21 Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of Exon 2 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of Exon 6 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Page 3 of 8 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(24.3% 486) | C(20.15% 403) | T(31.1% 622) | G(24.45% 489) Note: The 2000 bp section upstream of Exon 2 is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Overview of the GC Content Distribution (down) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(26.7% 534) | C(20.65% 413) | T(28.7% 574) | G(23.95% 479) Note: The 2000 bp section downstream of Exon 6 is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Page 4 of 8 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 2000 1 2000 2000 100.0% chr10 - 115302792 115304791 2000 browser details YourSeq 113 411 1313 2000 90.0% chr18 + 34693095 34899577 206483 browser details YourSeq 105 375 604 2000 79.9% chr11 + 115127300 115148627 21328 browser details YourSeq 84 411 614 2000 71.3% chr6 + 52848736 52848941 206 browser details YourSeq 77 1274 1381 2000 89.0% chr1 - 160913456 160913566 111 browser details YourSeq 76 411 616 2000 79.9% chr12 - 108828510 108828717 208 browser details YourSeq 75 406 594 2000 88.0% chr2 + 7891063 7891254 192 browser details YourSeq 73 498 614 2000 85.0% chr11 + 120217739 120525291 307553 browser details YourSeq 72 392 570 2000 70.5% chr19 - 3594816 3594997 182 browser details YourSeq 70 1276 1381 2000 86.5% chr14 + 26509987 26510093 107 browser details YourSeq 69 1276 1381 2000 88.9% chr15 - 98981579 98981685 107 browser details YourSeq 69 411 613 2000 87.1% chr11 - 8543241 8543445 205 browser details YourSeq 68 1285 1377 2000 89.6% chr2 + 155108266 155108359 94 browser details YourSeq 68 1276 1378 2000 87.0% chr11 + 85177556 85494099 316544 browser details YourSeq 67 1275 1381 2000 94.7% chr7 - 73504748 73504857 110 browser details YourSeq 67 1276 1377 2000 85.3% chr11 - 96869070 96869172 103 browser details YourSeq 66 1276 1378 2000 85.9% chr2 + 157136044 157136147 104 browser details YourSeq 65 1285 1380 2000 86.6% chr4 - 139163811 139163907 97 browser details YourSeq 65 398 570 2000 69.7% chr4 - 136017650 136017829 180 browser details YourSeq 65 511 618 2000 82.7% chr9 + 21126735 21126843 109 Note: The 2000 bp section upstream of Exon 2 is BLAT searched against the genome. No significant similarity is found. BLAT Search Results (down) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 2000 1 2000 2000 100.0% chr10 - 115292871 115294870 2000 browser details YourSeq 57 71 160 2000 82.3% chr19 + 43501517 43501607 91 browser details YourSeq 50 71 157 2000 79.4% chr3 + 98191849 98191936 88 browser details YourSeq 49 71 160 2000 77.8% chr6 - 114872512 114872602 91 browser details YourSeq 47 71 154 2000 78.6% chr1 - 9812762 9812846 85 browser details YourSeq 46 71 154 2000 91.1% chr12 + 87442707 87442793 87 browser details YourSeq 43 135 180 2000 97.9% chr8 + 50545206 50545274 69 browser details YourSeq 41 72 159 2000 93.8% chr14 - 122242363 122242453 91 browser details YourSeq 38 122 173 2000 93.2% chr4 - 128750380 128750456 77 browser details YourSeq 38 71 160 2000 95.3% chr2 + 56727355 56727445 91 browser details YourSeq 38 119 160 2000 95.3% chr16 + 57639123 57639164 42 browser details YourSeq 36 119 160 2000 92.9% chr6 - 120449576 120449617 42 browser details YourSeq 35 119 161 2000 90.7% chr9 - 63072740 63072782 43 browser details YourSeq 35 71 132 2000 79.1% chr14 + 101725121 101725183 63 browser details YourSeq 35 120 160 2000 92.7% chr1 + 59338370 59338410 41 browser details YourSeq 34 119 154 2000 97.3% chr7 + 140355498 140355533 36 browser details YourSeq 34 119 160 2000 90.5% chr5 + 100662838 100662879 42 browser details YourSeq 34 123 160 2000 94.8% chr2 + 164503511 164503548 38 browser details YourSeq 34 119 160 2000 90.5% chr19 + 7639895 7639936 42 browser details YourSeq 34 107 150 2000 88.7% chr16 + 97893216 97893259 44 Note: The 2000 bp section downstream of Exon 6 is BLAT searched against the genome. No significant similarity is found. Page 5 of 8 https://www.alphaknockout.com Gene and protein information: Rab21 RAB21, member RAS oncogene family [ Mus musculus (house mouse) ] Gene ID: 216344, updated on 12-Aug-2019 Gene summary Official Symbol Rab21 provided by MGI Official Full Name RAB21, member RAS oncogene family provided by MGI Primary source MGI:MGI:894308 See related Ensembl:ENSMUSG00000020132 Gene type protein coding RefSeq status PROVISIONAL Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as 9630024B22 Expression Ubiquitous expression in heart adult (RPKM 17.5), bladder adult (RPKM 15.7) and 28 other tissues See more Orthologs human all Genomic context Location: 10; 10 D2 See Rab21 in Genome Data Viewer Exon count: 7 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (115289862..115317419, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (114726918..114752647, complement) Chromosome 10 - NC_000076.6 Page 6 of 8 https://www.alphaknockout.com Transcript information: This gene has 2 transcripts Gene: Rab21 ENSMUSG00000020132 Description RAB21, member RAS oncogene family [Source:MGI Symbol;Acc:MGI:894308] Location Chromosome 10: 115,287,084-115,315,594 reverse strand. GRCm38:CM001003.2 About this gene This gene has 2 transcripts (splice variants), 194 orthologues, 62 paralogues, is a member of 1 Ensembl protein family and is associated with 2 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Rab21-201 ENSMUST00000020343.8 4602 222aa ENSMUSP00000020343.7 Protein coding CCDS24177 P35282 Q0PD35 TSL:1 GENCODE basic APPRIS P1 Rab21-202 ENSMUST00000218831.1 843 94aa ENSMUSP00000151464.1 Protein coding - A0A1W2P6Z4 TSL:NA GENCODE basic 48.51 kb Forward strand 115.28Mb 115.29Mb 115.30Mb 115.31Mb 115.32Mb Genes Gm10752-201 >TEC (Comprehensive set... Contigs AC153497.8 > Genes (Comprehensive set... < Rab21-201protein coding < Rab21-202protein coding Regulatory Build 115.28Mb 115.29Mb 115.30Mb 115.31Mb 115.32Mb Reverse strand 48.51 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding processed transcript Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000020343 < Rab21-201protein coding Reverse strand 28.51 kb ENSMUSP00000020... Low complexity (Seg) TIGRFAM Small GTP-binding protein domain Superfamily P-loop containing nucleoside triphosphate hydrolase SMART SM00173 SM00174 SM00176 SM00175 Prints PR00449 Pfam Small GTPase PROSITE profiles PS51419 PANTHER Small GTPase superfamily, Ras-type PTHR24070:SF385 Gene3D 3.40.50.300 CDD Rab21 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend inframe insertion synonymous variant Scale bar 0 20 40 60 80 100 120 140 160 180 200 222 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
Load more

Recommended publications
  • Small RAB Gtpases Regulate Multiple Steps of Mitosis
    CORE Metadata, citation and similar papers at core.ac.uk Provided by CONICET Digital REVIEW published: 17 February 2016 doi: 10.3389/fcell.2016.00002 Small RAB GTPases Regulate Multiple Steps of Mitosis Stéphanie Miserey-Lenkei 1* and María I. Colombo 2 1 Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport Group, CNRS UMR 144, Paris, France, 2 Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología-CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina GTPases of the RAB family are key regulators of multiple steps of membrane trafficking. Several members of the RAB GTPase family have been implicated in mitotic progression. In this review, we will first focus on the function of endosome-associated RAB GTPases reported in early steps of mitosis, spindle pole maturation, and during cytokinesis. Second, we will discuss the role of Golgi-associated RAB GTPases at the metaphase/anaphase transition and during cytokinesis. Keywords: RABs GTPases, mitosis, endosomes, golgi complex, trafficking INTRODUCTION Edited by: In mammalian cells, GTPases of the RAB family are key regulators of multiple steps of membrane Letizia Lanzetti, traffic. RAB GTPases play a central role in the formation of transport carriers from a donor University of Turin, Italy membrane, movement of these carriers along cytoskeletal tracks and finally anchoring/fusion Reviewed by: to the correct acceptor membrane (Stenmark, 2009). RAB GTPases represent a large family Andrew Alexander Peden, of small guanosine triphosphate (GTP)-binding proteins that comprise more than 60 known University of Sheffield, UK Anna Akhmanova, members. RAB GTPases are localized on distinct membrane-bound compartments and cycle Utrecht University, Netherlands between an active GTP-bound form and an inactive guanosine diphosphate (GDP)-bound *Correspondence: form.
    [Show full text]
  • Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
    Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing
    [Show full text]
  • Structure of the APPL1 BAR-PH Domain and EMBO Characterization of Its Interaction with Rab5 Open
    The EMBO Journal (2007) 26, 3484–3493 | & 2007 European Molecular Biology Organization | Some Rights Reserved 0261-4189/07 www.embojournal.org TTHEH E EEMBOMBO JJOURNALOURN AL Structure of the APPL1 BAR-PH domain and EMBO characterization of its interaction with Rab5 open This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits distribution, and reproductioninany medium, provided the original authorand source are credited. This license does not permit commercial exploitation or the creation of derivative works without specific permission. Guangyu Zhu1, Jia Chen2, Jay Liu3, Introduction Joseph S Brunzelle4, Bo Huang2, Endocytosis induced by ligandÀreceptor interaction has been Nancy Wakeham1, Simon Terzyan1, 2 2 3 directly linked to signal transduction mediated by Rab5 and Xuemei Li , Zihe Rao , Guangpu Li its effector APPL1 (Adaptor protein containing PH domain 1,2, and Xuejun C Zhang * PTB domain and Leucine zipper motif; Miaczynska et al, 1Crystallography Research Program, Oklahoma Medical Research 2004; Mao et al, 2006). The small GTPase Rab5 is a generally Foundation, Oklahoma City, OK, USA, 2National Laboratory of acknowledged prominent regulator of vesicle trafficking en- Biomacromolecules, Institute of Biophysics, Chinese Academy of route from the plasma membrane to early endosomes (Li, 3 Sciences, Beijing, China, Department of Biochemistry and Molecular 1996), whereas APPL1 (also called DIP13a) is identified with Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA and 4Department of Molecular Pharmacology and signaling pathways of adiponectin, insulin, EGF, follicle Biological Chemistry, Feinberg Medical School, Northwestern stimulating hormone receptor, neurotrophin receptor University, Chicago, IL, USA (TrkA), oxidative stress, and DCC-mediated apoptosis (Liu et al, 2002; Miaczynska et al, 2004; Lin et al, 2006; Mao et al, APPL1 is an effector of the small GTPase Rab5.
    [Show full text]
  • Datasheet: MCA5197Z Product Details
    Datasheet: MCA5197Z Description: MOUSE ANTI HUMAN RAB21:Preservative Free Specificity: RAB21 Format: Preservative Free Product Type: Monoclonal Antibody Clone: 1F6 Isotype: IgG1 Quantity: 0.1 mg Product Details Applications This product has been reported to work in the following applications. This information is derived from testing within our laboratories, peer-reviewed publications or personal communications from the originators. Please refer to references indicated for further information. For general protocol recommendations, please visit www.bio-rad-antibodies.com/protocols. Yes No Not Determined Suggested Dilution Immunohistology - Paraffin 0.1 - 10 ug/ml Western Blotting 0.1 - 10 ug/ml Immunofluorescence 0.1 - 10 ug/ml Where this product has not been tested for use in a particular technique this does not necessarily exclude its use in such procedures. Suggested working dilutions are given as a guide only. It is recommended that the user titrates the product for use in their own system using appropriate negative/positive controls. Target Species Human Product Form Purified IgG - liquid Preparation Purified IgG prepared by affinity chromatography on Protein A Buffer Solution Phosphate buffered saline Preservative None present Stabilisers Approx. Protein Ig concentration 0.5 mg/ml Concentrations Immunogen Recombinant protein corresponding to aa 116-226 of human RAB21. External Database Links UniProt: Q9UL25 Related reagents Entrez Gene: 23011 RAB21 Related reagents Page 1 of 2 Synonyms KIAA0118 Fusion Partners Spleen cells from BALB/c mice were fused with cells from the Sp2/0 myeloma cell line. Specificity Mouse anti Human RAB21 antibody, clone 1F6 recognizes human Ras-related protein Rab-21, also known as RAB21.
    [Show full text]
  • Original Article Identification of Prognostic Genes in Paediatric Medulloblastoma from Mrna Expression Profiles
    Int J Clin Exp Med 2016;9(10):19925-19929 www.ijcem.com /ISSN:1940-5901/IJCEM0017954 Original Article Identification of prognostic genes in paediatric medulloblastoma from mRNA expression profiles Changjun Cao, Wei Wang, Pucha Jiang Department of Neurosurgery, Zhongnan Hospital of Wuhan University, China Received October 15, 2015; Accepted March 1, 2016; Epub October 15, 2016; Published October 30, 2016 Abstract: Medulloblastoma is the most common malignant brain tumour of childhood. The identification of prognos- tic biomarkers correlated with overall survival remains a crucial step towards the refinement of medulloblastoma treatment. A total of 100 medulloblastoma samples from two independent cohorts were included in this study. The statistical modelling approach, Bayesian Model Averaging algorithm, was used to discover the prognostic biomark- ers. Six genes including BICD2, CD300LG, RAB21, RAD18, SYNRG and TNFSF13 were identified to be related to medulloblastoma overall survival. We demonstrated this six-gene signature could successfully discriminate low-risk group from high-risk groups in two independent medulloblastoma cohorts. We have successfully identified a six- gene medulloblastoma prognostic signature. We anticipate that these genes could serve as biomarkers or drug targets in personalised therapy of medulloblastoma. Keywords: Prognosis, medulloblastoma, mRNA expression, bayesian model averaging Introduction [9]. The ability of measuring mRNA expression levels of thousands of genes at one time has Medulloblastoma is the most common malig- made the microarray technology a promising nant brain tumour of childhood and accounts direction in cancer research. Based on microar- for 15%-20% of all paediatric primary brain ray data, many gene signatures have also been tumours [1]. Although there is approximately identified for the prediction of medulloblastoma 70% improvement in 5-year survival rates of prognosis [10, 11].
    [Show full text]
  • Activity in Primary Mammary Tumors Role for Wnt-Signaling in Mediating
    Downloaded from http://www.jimmunol.org/ by guest on October 2, 2021 is online at: average * The Journal of Immunology , 25 of which you can access for free at: 2010; 184:702-712; Prepublished online 16 from submission to initial decision 4 weeks from acceptance to publication December 2009; doi: 10.4049/jimmunol.0902360 http://www.jimmunol.org/content/184/2/702 Gene Expression Analysis of Macrophages That Facilitate Tumor Invasion Supports a Role for Wnt-Signaling in Mediating Their Activity in Primary Mammary Tumors Laureen S. Ojalvo, Charles A. Whittaker, John S. Condeelis and Jeffrey W. Pollard J Immunol cites 69 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription http://www.jimmunol.org/content/suppl/2009/12/15/jimmunol.090236 0.DC1 This article http://www.jimmunol.org/content/184/2/702.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2010 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of October 2, 2021. The Journal of Immunology Gene Expression Analysis of Macrophages That Facilitate Tumor Invasion Supports a Role for Wnt-Signaling in Mediating Their Activity in Primary Mammary Tumors Laureen S.
    [Show full text]
  • Utilizing Pacbio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza Sativa L
    International Journal of Molecular Sciences Article Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. Stephanie Schaarschmidt 1,* , Axel Fischer 1, Lovely Mae F. Lawas 1,2 , Rejbana Alam 3, Endang M. Septiningsih 4 , Julia Bailey-Serres 3, S. V. Krishna Jagadish 5,6 , Bruno Huettel 7, 1, 1, Dirk K. Hincha y and Ellen Zuther * 1 Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; afi[email protected] (A.F.); lfl[email protected] (L.M.F.L.); [email protected] (D.K.H.) 2 Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA 3 Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; [email protected] (R.A.); [email protected] (J.B.-S.) 4 Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; [email protected] 5 International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines; [email protected] 6 Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA 7 Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne, Germany; [email protected] * Correspondence: [email protected] (S.S.); [email protected] (E.Z.) We dedicate this paper to the memory of our colleague Dirk K. Hincha who passed away during the y preparation of this manuscript. Received: 28 September 2020; Accepted: 30 October 2020; Published: 31 October 2020 Abstract: The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding.
    [Show full text]
  • Pituitary Cell Translation and Secretory Capacities Are Enhanced Cell Autonomously by the Transcription Factor Creb3l2
    ARTICLE https://doi.org/10.1038/s41467-019-11894-3 OPEN Pituitary cell translation and secretory capacities are enhanced cell autonomously by the transcription factor Creb3l2 Konstantin Khetchoumian1, Aurélio Balsalobre1, Alexandre Mayran1, Helen Christian2, Valérie Chénard3, Julie St-Pierre3 & Jacques Drouin1,3 1234567890():,; Translation is a basic cellular process and its capacity is adapted to cell function. In particular, secretory cells achieve high protein synthesis levels without triggering the protein stress response. It is unknown how and when translation capacity is increased during differentiation. Here, we show that the transcription factor Creb3l2 is a scaling factor for translation capacity in pituitary secretory cells and that it directly binds ~75% of regulatory and effector genes for translation. In parallel with this cell-autonomous mechanism, implementation of the phy- siological UPR pathway prevents triggering the protein stress response. Knockout mice for Tpit, a pituitary differentiation factor, show that Creb3l2 expression and its downstream regulatory network are dependent on Tpit. Further, Creb3l2 acts by direct targeting of translation effector genes in parallel with signaling pathways that otherwise regulate protein synthesis. Expression of Creb3l2 may be a useful means to enhance production of therapeutic proteins. 1 Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada. 2 Departments of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX2 6HS, UK. 3 Department of Biochemistry, McGill University, Rosalind and Morris Goodman Research Centre, Montréal, QC H3A 1A3, Canada. Correspondence and requests for materials should be addressed to K.K. (email: [email protected]) or to J.D.
    [Show full text]
  • Rab Gtpases: Switching to Human Diseases
    cells Review Rab GTPases: Switching to Human Diseases Noemi Antonella Guadagno and Cinzia Progida * Department of Biosciences, University of Oslo, 0316 Oslo, Norway * Correspondence: [email protected]; Tel.: +47-22-85-44-41 Received: 30 June 2019; Accepted: 14 August 2019; Published: 16 August 2019 Abstract: Rab proteins compose the largest family of small GTPases and control the different steps of intracellular membrane traffic. More recently, they have been shown to also regulate cell signaling, division, survival, and migration. The regulation of these processes generally occurs through recruitment of effectors and regulatory proteins, which control the association of Rab proteins to membranes and their activation state. Alterations in Rab proteins and their effectors are associated with multiple human diseases, including neurodegeneration, cancer, and infections. This review provides an overview of how the dysregulation of Rab-mediated functions and membrane trafficking contributes to these disorders. Understanding the altered dynamics of Rabs and intracellular transport defects might thus shed new light on potential therapeutic strategies. Keywords: GTPases; Rab proteins; membrane trafficking; neurodegeneration; cancer; intracellular pathogens 1. Introduction Intracellular membrane trafficking is essential for the transport of membranes and cargoes between the different compartments in eukaryotic cells. It uses vesicular or tubular carriers that travel along the endocytic and exocytic pathways and it is regulated by complex protein machineries [1]. Rab GTPases are evolutionarily conserved regulators of vesicular transport, with more than 60 members described in humans [2,3]. They are localized to different membrane compartments in order to control both the specificity and the directionality of membrane trafficking.
    [Show full text]
  • APPL1 Regulates Basal NF-Kb Activity by Stabilizing
    4090 Research Article APPL1 regulates basal NF-kB activity by stabilizing NIK Anna Hupalowska, Beata Pyrzynska and Marta Miaczynska* International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland *Author for correspondence ([email protected]) Accepted 3 May 2012 Journal of Cell Science 125, 4090–4102 ß 2012. Published by The Company of Biologists Ltd doi: 10.1242/jcs.105171 Summary APPL1 is a multifunctional adaptor protein that binds membrane receptors, signaling proteins and nuclear factors, thereby acting in endosomal trafficking and in different signaling pathways. Here, we uncover a novel role of APPL1 as a positive regulator of transcriptional activity of NF-kB under basal but not TNFa-stimulated conditions. APPL1 was found to directly interact with TRAF2, an adaptor protein known to activate canonical NF-kB signaling. APPL1 synergized with TRAF2 to induce NF-kB activation, and both proteins were necessary for this process and function upstream of the IKK complex. Although TRAF2 was not detectable on APPL endosomes, endosomal recruitment of APPL1 was required for its function in the NF-kB pathway. Importantly, in the canonical pathway, APPL1 appeared to regulate the proper spatial distribution of the p65 subunit of NF-kB in the absence of cytokine stimulation, since its overexpression enhanced and its depletion reduced the nuclear accumulation of p65. By analyzing the patterns of gene transcription upon APPL1 overproduction or depletion we found altered expression of NF-kB target genes that encode cytokines. At the molecular level, overexpressed APPL1 markedly increased the level of NIK, the key component of the noncanonical NF-kB pathway, by reducing its association with the degradative complex containing TRAF2, TRAF3 and cIAP1.
    [Show full text]
  • Chromosome 12, Frequently Deleted in Human Pancreatic Cancer, May Encode a Tumor-Suppressor Gene That Suppresses Angiogenesis
    Laboratory Investigation (2004) 84, 1339–1351 & 2004 USCAP, Inc All rights reserved 0023-6837/04 $30.00 www.laboratoryinvestigation.org Chromosome 12, frequently deleted in human pancreatic cancer, may encode a tumor-suppressor gene that suppresses angiogenesis Sumitaka Yamanaka1,2,*, Makoto Sunamura3,*, Toru Furukawa1, Libo Sun3, Liviu P Lefter1,3, Tadayoshi Abe1,3, Toshimasa Yatsuoka1,3, Hiroko Fujimura3, Emiko Shibuya3, Noriko Kotobuki4, Mitsuo Oshimura4, Akira Sakurada2, Masami Sato2, Takashi Kondo2, Seiki Matsuno3 and Akira Horii1 1Department of Molecular Pathology, Tohoku University School of Medicine, Sendai, Japan; 2Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan; 3Department of Gastroenterological Surgery, Tohoku University School of Medicine, Sendai, Japan and 4Department of Cell Technology, Tottori University School of Medicine, Yonago, Japan Several lines of evidence have suggested that the long arm of chromosome 12 may carry a tumor-suppressor gene(s) that plays a role in pancreatic ductal carcinogenesis. We have previously found a significant association between loss of heterozygosity of the 12q arm and a poor prognosis in pancreatic cancer patients. In this study, we introduced a normal copy of chromosome 12 into some pancreatic ductal carcinoma cells. Both anchorage-dependent and -independent proliferations as well as invasiveness were similar throughout the hybrid clones when compared with their corresponding parental cells. In sharp contrast, significant suppression of tumorigenesis was observed after inoculation of the hybrid clones into nude mice. Measurements made up to 1 month later showed that there was a significant delay in the growth of tumors into which the introduced normal copy of chromosome 12 had been restored.
    [Show full text]
  • Methylome-Wide Change Associated with Response to Electroconvulsive Therapy in Depressed Patients Lea Sirignano 1,Joseffrank 1, Laura Kranaster 2, Stephanie H
    Sirignano et al. Translational Psychiatry (2021) 11:347 https://doi.org/10.1038/s41398-021-01474-9 Translational Psychiatry ARTICLE Open Access Methylome-wide change associated with response to electroconvulsive therapy in depressed patients Lea Sirignano 1,JosefFrank 1, Laura Kranaster 2, Stephanie H. Witt 1,FabianStreit 1, Lea Zillich1, Alexander Sartorius2, Marcella Rietschel 1 and Jerome C. Foo 1 Abstract Electroconvulsive therapy (ECT) is a quick-acting and powerful antidepressant treatment considered to be effective in treating severe and pharmacotherapy-resistant forms of depression. Recent studies have suggested that epigenetic mechanisms can mediate treatment response and investigations about the relationship between the effects of ECT and DNA methylation have so far largely taken candidate approaches. In the present study, we examined the effects of ECT on the methylome associated with response in depressed patients (n = 34), testing for differentially methylated CpG sites before the first and after the last ECT treatment. We identified one differentially methylated CpG site associated with the effect of ECT response (defined as >50% decrease in Hamilton Depression Rating Scale score, HDRS), TNKS (q < 0.05; p = 7.15 × 10−8). When defining response continuously (ΔHDRS), the top suggestive differentially methylated CpG site was in FKBP5 (p = 3.94 × 10−7). Regional analyses identified two differentially methylated regions on chromosomes 8 (Šídák’s p = 0.0031) and 20 (Šídák’s p = 4.2 × 10−5) associated with ΔHDRS. Functional pathway analysis did not identify any significant pathways. A confirmatory look at candidates previously proposed to be involved in ECT mechanisms found CpG sites associated with response only at the nominally significant level (p < 0.05).
    [Show full text]