Mouse Ppp2r5c Conditional Knockout Project (CRISPR/Cas9)

Total Page:16

File Type:pdf, Size:1020Kb

Mouse Ppp2r5c Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Ppp2r5c Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Ppp2r5c conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Ppp2r5c gene (NCBI Reference Sequence: NM_012023 ; Ensembl: ENSMUSG00000017843 ) is located on Mouse chromosome 12. 14 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 14 (Transcript: ENSMUST00000084985). Exon 3~5 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Ppp2r5c gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-143L24 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Mice homozygous for a gene-trapped allele show partial neonatal lethality, hypoactivity, and abnormal ventricular septum formation associated with increased fetal cardiomyocyte apoptosis. Surviving homozygotes develop obesity and show an abnormal gait, decreased grip strength, and impaired balance. Exon 3 starts from about 18.77% of the coding region. The knockout of Exon 3~5 will result in frameshift of the gene. The size of intron 2 for 5'-loxP site insertion: 21384 bp, and the size of intron 5 for 3'-loxP site insertion: 5160 bp. The size of effective cKO region: ~2327 bp. The cKO 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 3 4 5 14 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Ppp2r5c Homology arm cKO region loxP site Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region 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 GC Content Distribution Window size: 300 bp Sequence 12 Summary: Full Length(8827bp) | A(23.25% 2052) | C(25.48% 2249) | T(27.26% 2406) | G(24.02% 2120) Note: The sequence of homologous arms and cKO region 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 3 of 8 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr12 + 110540826 110543825 3000 browser details YourSeq 164 1989 2466 3000 95.1% chr9 - 73060108 73218591 158484 browser details YourSeq 152 1990 2466 3000 94.3% chr17 - 57009123 57155424 146302 browser details YourSeq 148 2015 2466 3000 94.2% chr10 + 62949868 62950628 761 browser details YourSeq 147 2012 2462 3000 96.3% chr14 + 67003031 67003662 632 browser details YourSeq 146 2307 2484 3000 92.4% chr6 - 113973376 113973559 184 browser details YourSeq 141 2321 2474 3000 96.2% chr9 - 105063014 105063174 161 browser details YourSeq 140 2321 2476 3000 95.5% chr4 + 48649658 48650193 536 browser details YourSeq 138 2323 2471 3000 96.7% chr17 - 83618988 83619143 156 browser details YourSeq 137 2320 2474 3000 94.9% chr8 - 86822856 86823396 541 browser details YourSeq 137 2317 2471 3000 96.7% chr7 - 114183128 114183296 169 browser details YourSeq 137 2323 2466 3000 98.0% chr12 - 7585506 7585656 151 browser details YourSeq 137 2321 2466 3000 97.3% chr11 - 80427072 80427224 153 browser details YourSeq 137 2321 2464 3000 98.0% chr9 + 58566218 58566368 151 browser details YourSeq 137 2321 2474 3000 94.9% chr13 + 117349327 117349487 161 browser details YourSeq 134 2325 2471 3000 96.0% chr16 - 13790948 13791101 154 browser details YourSeq 134 2321 2466 3000 96.6% chr2 + 181791058 181791213 156 browser details YourSeq 133 2321 2471 3000 94.8% chr14 - 19838424 19838582 159 browser details YourSeq 132 2321 2471 3000 94.1% chr17 - 84208148 84208305 158 browser details YourSeq 132 2323 2466 3000 96.6% chr11 - 104325797 104325949 153 Note: The 3000 bp section upstream of Exon 3 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 3000 1 3000 3000 100.0% chr12 + 110546153 110549152 3000 browser details YourSeq 160 2688 2905 3000 91.8% chr4 + 99129407 99129629 223 browser details YourSeq 145 2634 2906 3000 91.5% chr17 - 32961736 32962151 416 browser details YourSeq 139 2743 2957 3000 86.1% chr15 + 86212705 86212896 192 browser details YourSeq 137 2735 2900 3000 90.3% chr8 - 46553200 46553358 159 browser details YourSeq 137 2688 2902 3000 91.1% chr12 - 80349395 80349733 339 browser details YourSeq 137 2746 2906 3000 94.9% chr12 + 103087878 103088106 229 browser details YourSeq 136 2740 2899 3000 91.5% chr11 - 100350459 100350613 155 browser details YourSeq 135 2745 2901 3000 93.7% chr11 - 106497658 106637139 139482 browser details YourSeq 135 2734 2907 3000 91.0% chr9 + 44172991 44173164 174 browser details YourSeq 135 2688 2903 3000 85.5% chr7 + 102142653 102142846 194 browser details YourSeq 135 2688 2900 3000 85.3% chr2 + 34801149 34801329 181 browser details YourSeq 135 2742 2914 3000 90.0% chr11 + 55385874 55386044 171 browser details YourSeq 134 2740 2901 3000 90.2% chr9 - 108543608 108543763 156 browser details YourSeq 134 2688 2901 3000 90.4% chr7 - 30545088 30545340 253 browser details YourSeq 134 2740 2903 3000 89.3% chr5 - 111319376 111319534 159 browser details YourSeq 134 2740 2908 3000 93.0% chr11 + 45704885 45705054 170 browser details YourSeq 134 2679 2901 3000 93.0% chr10 + 99192104 99192483 380 browser details YourSeq 133 2743 2901 3000 90.2% chr19 - 5886319 5886472 154 browser details YourSeq 133 2742 2900 3000 90.8% chr18 - 34560013 34560166 154 Note: The 3000 bp section downstream of Exon 5 is BLAT searched against the genome. No significant similarity is found. Page 4 of 8 https://www.alphaknockout.com Gene and protein information: Ppp2r5c protein phosphatase 2, regulatory subunit B', gamma [ Mus musculus (house mouse) ] Gene ID: 26931, updated on 24-Oct-2019 Gene summary Official Symbol Ppp2r5c provided by MGI Official Full Name protein phosphatase 2, regulatory subunit B', gamma provided by MGI Primary source MGI:MGI:1349475 See related Ensembl:ENSMUSG00000017843 Gene type protein coding RefSeq status VALIDATED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as C85228; AI060890; AW545884; D12Bwg0916e; 2610043M05Rik; 2700063L20Rik Expression Ubiquitous expression in testis adult (RPKM 41.8), cortex adult (RPKM 18.2) and 27 other tissues See more Orthologs human all Genomic context Location: 12 F1; 12 60.56 cM See Ppp2r5c in Genome Data Viewer Exon count: 18 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (110447144..110583075) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 12 NC_000078.5 (111685389..111821271) Chromosome 12 - NC_000078.6 Page 5 of 8 https://www.alphaknockout.com Transcript information: This gene has 7 transcripts Gene: Ppp2r5c ENSMUSG00000017843 Description protein phosphatase 2, regulatory subunit B', gamma [Source:MGI Symbol;Acc:MGI:1349475] Gene Synonyms 2610043M05Rik, 2700063L20Rik, B56/PP2A gamma, Band 8A, D12Bwg0916e Location Chromosome 12: 110,447,120-110,583,062 forward strand. GRCm38:CM001005.2 About this gene This gene has 7 transcripts (splice variants), 220 orthologues, 4 paralogues, is a member of 1 Ensembl protein family and is associated with 19 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Ppp2r5c- ENSMUST00000109832.2 4108 485aa ENSMUSP00000105458.1 Protein coding CCDS36558 Q60996 TSL:2 202 GENCODE basic APPRIS ALT1 Ppp2r5c- ENSMUST00000084985.10 1847 524aa ENSMUSP00000082053.3 Protein coding CCDS36557 Q60996 TSL:2 201 GENCODE basic APPRIS P4 Ppp2r5c- ENSMUST00000221715.1 2367 452aa ENSMUSP00000152865.1 Protein coding - Q60996 TSL:1 205 GENCODE basic Ppp2r5c- ENSMUST00000221074.1 1971 496aa ENSMUSP00000152282.1 Protein coding - Q60996 TSL:5 204 GENCODE basic Ppp2r5c- ENSMUST00000222276.1 1802 49aa ENSMUSP00000152369.1 Protein coding - A0A1Y7VJC8 TSL:2 206 GENCODE basic Ppp2r5c- ENSMUST00000220509.1 956 283aa ENSMUSP00000152095.1 Protein coding - A0A1Y7VIR0 CDS 3' incomplete 203 TSL:5 Ppp2r5c- ENSMUST00000223168.1 2790 No - Retained intron - - TSL:2 207 protein Page 6 of 8 https://www.alphaknockout.com 155.94 kb Forward strand 110.44Mb 110.46Mb 110.48Mb 110.50Mb 110.52Mb 110.54Mb 110.56Mb 110.58Mb Genes (Comprehensive set... Ppp2r5c-206 >protein coding Ppp2r5c-205 >protein coding Ppp2r5c-203 >protein coding B930059L03Rik-201 >lncRNA Ppp2r5c-207 >retained intron Ppp2r5c-202 >protein coding Ppp2r5c-204 >protein coding Ppp2r5c-201 >protein coding Contigs AL591582.32 > AC152827.4 > Genes < Gm19605-202lncRNA (Comprehensive set... < Gm19605-203lncRNA < Gm19605-205lncRNA
Recommended publications
  • PPP2R3C Gene Variants Cause Syndromic 46,XY Gonadal
    5 180 T Guran and others PPP2R3C in testis developmentQ1 180:5 291–309 Clinical Study and spermatogenesis PPP2R3C gene variants cause syndromic 46,XY gonadal dysgenesis and impaired spermatogenesis in humans Tulay Guran1, Gozde Yesil2, Serap Turan1, Zeynep Atay3, Emine Bozkurtlar4, AghaRza Aghayev5, Sinem Gul6, Ilker Tinay7, Basak Aru8, Sema Arslan9, M Kutay Koroglu10, Feriha Ercan10, Gulderen Y Demirel8, Funda S Eren4, Betul Karademir9 and Abdullah Bereket1 1Department of Paediatric Endocrinology and Diabetes, Marmara University, 2Department of Genetics, Bezm-i Alem University, 3Department of Paediatric Endocrinology and Diabetes, Medipol University, 4Department of Pathology, Marmara University, School of Medicine, Istanbul, Turkey, 5Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey, 6Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey, 7Department of Urology, Marmara University, School of Medicine, Istanbul, Turkey, 8Department of Immunology, Yeditepe Correspondence University, Faculty of Medicine, Istanbul, Turkey, 9Department of Biochemistry, Genetic and Metabolic Diseases should be addressed Research and Investigation Center, and 10Department of Histology and Embryology, Marmara University, School of to T Guran Medicine, Istanbul, Turkey Email [email protected] Abstract Context: Most of the knowledge on the factors involved in human sexual development stems from studies of rare cases with disorders of sex development. Here, we have described a novel 46, XY complete gonadal dysgenesis syndrome caused by homozygous variants in PPP2R3C gene. This gene encodes B″gamma regulatory subunit of the protein phosphatase 2A (PP2A), which is a serine/threonine phosphatase involved in the phospho-regulation processes of most mammalian cell types. PPP2R3C gene is most abundantly expressed in testis in humans, while its function was hitherto unknown.
    [Show full text]
  • Temporal Proteomic Analysis of HIV Infection Reveals Remodelling of The
    1 1 Temporal proteomic analysis of HIV infection reveals 2 remodelling of the host phosphoproteome 3 by lentiviral Vif variants 4 5 Edward JD Greenwood 1,2,*, Nicholas J Matheson1,2,*, Kim Wals1, Dick JH van den Boomen1, 6 Robin Antrobus1, James C Williamson1, Paul J Lehner1,* 7 1. Cambridge Institute for Medical Research, Department of Medicine, University of 8 Cambridge, Cambridge, CB2 0XY, UK. 9 2. These authors contributed equally to this work. 10 *Correspondence: [email protected]; [email protected]; [email protected] 11 12 Abstract 13 Viruses manipulate host factors to enhance their replication and evade cellular restriction. 14 We used multiplex tandem mass tag (TMT)-based whole cell proteomics to perform a 15 comprehensive time course analysis of >6,500 viral and cellular proteins during HIV 16 infection. To enable specific functional predictions, we categorized cellular proteins regulated 17 by HIV according to their patterns of temporal expression. We focussed on proteins depleted 18 with similar kinetics to APOBEC3C, and found the viral accessory protein Vif to be 19 necessary and sufficient for CUL5-dependent proteasomal degradation of all members of the 20 B56 family of regulatory subunits of the key cellular phosphatase PP2A (PPP2R5A-E). 21 Quantitative phosphoproteomic analysis of HIV-infected cells confirmed Vif-dependent 22 hyperphosphorylation of >200 cellular proteins, particularly substrates of the aurora kinases. 23 The ability of Vif to target PPP2R5 subunits is found in primate and non-primate lentiviral 2 24 lineages, and remodeling of the cellular phosphoproteome is therefore a second ancient and 25 conserved Vif function.
    [Show full text]
  • Loss of PPP2R2A Inhibits Homologous Recombination DNA Repair and Predicts
    Author Manuscript Published OnlineFirst on October 18, 2012; DOI: 10.1158/0008-5472.CAN-12-1667 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Loss of PPP2R2A inhibits homologous recombination DNA repair and predicts tumor sensitivity to PARP inhibition Peter Kalev1, Michal Simicek1, Iria Vazquez1, Sebastian Munck1, Liping Chen2, Thomas Soin1, Natasha Danda1, Wen Chen2 and Anna Sablina1,* 1VIB Center for the Biology of Disease; Center for Human Genetics, KULeuven, Leuven 3000 Belgium 2Department of Toxicology, Faculty of Preventive Medicine, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China *Corresponding author information: [email protected] Contact information: Anna A. Sablina, Ph.D. CME Department, KULeuven O&N I Herestraat 49, bus 602 Leuven, Belgium 3000 Tel: +3216330790 Fax: +3216330145 Running title: The role of PPP2R2A in DNA repair Keywords: PP2A, ATM, DNA repair, cancer, PARP inhibition Conflict of interests: The authors claim no conflict of interest. - 1 - Downloaded from cancerres.aacrjournals.org on September 27, 2021. © 2012 American Association for Cancer Research. Author Manuscript Published OnlineFirst on October 18, 2012; DOI: 10.1158/0008-5472.CAN-12-1667 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Abstract Reversible phosphorylation plays a critical role in DNA repair. Here we report the results of a loss-of-function screen that identifies the PP2A heterotrimeric serine/threonine phosphatases PPP2R2A, PPP2R2D, PPP2R5A and PPP2R3C in double-strand break (DSB) repair. In particular, we found that PPP2R2A-containing complexes directly dephosphorylated ATM at S367, S1893, and S1981 to regulate its retention at DSB sites.
    [Show full text]
  • Protein Family Members. the GENE.FAMILY
    Table 3: Protein family members. The GENE.FAMILY col- umn shows the gene family name defined either by HGNC (superscript `H', http://www.genenames.org/cgi-bin/family_ search) or curated manually by us from Entrez IDs in the NCBI database (superscript `C' for `Custom') that we have identified as corresonding for each ENTITY.ID. The members of each gene fam- ily that are in at least one of our synaptic proteome datasets are shown in IN.SYNAPSE, whereas those not found in any datasets are in the column OUT.SYNAPSE. In some cases the intersection of two HGNC gene families are needed to specify the membership of our protein family; this is indicated by concatenation of the names with an ampersand. ENTITY.ID GENE.FAMILY IN.SYNAPSE OUT.SYNAPSE AC Adenylate cyclasesH ADCY1, ADCY2, ADCY10, ADCY4, ADCY3, ADCY5, ADCY7 ADCY6, ADCY8, ADCY9 actin ActinsH ACTA1, ACTA2, ACTB, ACTC1, ACTG1, ACTG2 ACTN ActininsH ACTN1, ACTN2, ACTN3, ACTN4 AKAP A-kinase anchoring ACBD3, AKAP1, AKAP11, AKAP14, proteinsH AKAP10, AKAP12, AKAP17A, AKAP17BP, AKAP13, AKAP2, AKAP3, AKAP4, AKAP5, AKAP6, AKAP8, CBFA2T3, AKAP7, AKAP9, RAB32 ARFGEF2, CMYA5, EZR, MAP2, MYO7A, MYRIP, NBEA, NF2, SPHKAP, SYNM, WASF1 CaM Endogenous ligands & CALM1, CALM2, EF-hand domain CALM3 containingH CaMKK calcium/calmodulin- CAMKK1, CAMKK2 dependent protein kinase kinaseC CB CalbindinC CALB1, CALB2 CK1 Casein kinase 1C CSNK1A1, CSNK1D, CSNK1E, CSNK1G1, CSNK1G2, CSNK1G3 CRHR Corticotropin releasing CRHR1, CRHR2 hormone receptorsH DAGL Diacylglycerol lipaseC DAGLA, DAGLB DGK Diacylglycerol kinasesH DGKB,
    [Show full text]
  • Recent Natural Selection Identifies a Genetic Variant in a Regulatory Subunit of Protein Phosphatase 2A That Associates with Altered Cancer Risk and Survival Lukasz F
    Published OnlineFirst September 22, 2009; DOI: 10.1158/1078-0432.CCR-09-0797 Susceptibility and Prevention Recent Natural Selection Identifies a Genetic Variant in a Regulatory Subunit of Protein Phosphatase 2A that Associates with Altered Cancer Risk and Survival Lukasz F. Grochola,1 Alexei Vazquez,2,3,4 Elisabeth E. Bond,1 Peter Würl,5 Helge Taubert,6 Thomas H. Müller,7 Arnold J. Levine,2,3 and Gareth L. Bond1 Abstract Purpose: A regulated p53-dependent stress response is crucial in suppressing tumor for- mation and mediating the response to commonly used cancer therapeutics. However, little is known about the human, inherited genetics of this important signaling pathway. Experimental Design: Studies of human genetic variants in the p53 tumor suppressor gene and MDM2 oncogene have shown that single nucleotide polymorphisms (SNP) can affect p53 signaling, confer cancer risk, and alter outcome, and also suggest that the pathway is under evolutionary selective pressure. Here, we attempt to accelerate the identification of functional p53 pathway SNPs by incorporating these characteristics into an analysis of 142 genes that are known to affect p53 signaling. Results: We report that a genomic scan for recent natural selection denotes that of the 142 genes studied, the PPP2R5E gene that encodes a regulatory subunit of the tumor suppressing protein phosphatase 2A resides in a naturally selected genomic region. We go on to show that a selected SNPin PPP2R5E (ε-SNP2) associates with significant allelic differences in the onset (up to 19.2 years; P = 0.0002) and risk (odds ratio, up to 8.1; P = 0.0009) of soft tissue sarcoma development, as well as overall survival (relative risk, up to 3.04; P = 0.026).
    [Show full text]
  • Regulation of the Phosphoprotein Phosphatase 2A System and Its Modulation During Oxidative Stress: a Potential Therapeutic Target?
    Pharmacology & Therapeutics 198 (2019) 68–89 Contents lists available at ScienceDirect Pharmacology & Therapeutics journal homepage: www.elsevier.com/locate/pharmthera Regulation of the phosphoprotein phosphatase 2A system and its modulation during oxidative stress: A potential therapeutic target? I.S. Elgenaidi, J.P. Spiers ⁎ Department of Pharmacology and Therapeutics, Trinity College Dublin, Ireland article info abstract Phosphoprotein phosphatases are of growing interest in the pathophysiology of many diseases and are often the Keywords:: neglected partner of protein kinases. One family member, PP2A, accounts for dephosphorylation of ~55-70% of all Ischaemia serine/threonine phosphosites. Interestingly, dysregulation of kinase signalling is a hallmark of many diseases in PP2A HIF1α which an increase in oxidative stress is also noted. With this in mind, we assess the evidence to support oxidative CIP2A stress-mediated regulation of the PP2A system SMAPs In this article, we first present an overview of the PP2A system before providing an analysis of the regulation hypoxia of PP2A by endogenous inhibitors, post translational modification, and miRNA. Next, a detailed critique of data miRNA implicating reactive oxygen species, ischaemia, ischaemia-reperfusion, and hypoxia in regulating the PP2A holoenzyme and associated regulators is presented. Finally, the pharmacological targeting of PP2A, its endoge- nous inhibitors, and enzymes responsible for its post-translational modification are covered. There is extensive evidence that oxidative stress modulates multiple components of the PP2A system, however, most of the data pertains to the catalytic subunit of PP2A. Irrespective of the underlying aetiology, free radical- mediated attenuation of PP2A activity is an emerging theme. However, in many instances, a dichotomy exists, which requires clarification and mechanistic insight.
    [Show full text]
  • High-Resolution Map and Imprinting Analysis of the Gtl2–Dnchc1 Domain on Mouse Chromosome 12
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Genomics 87 (2006) 225 – 235 www.elsevier.com/locate/ygeno High-resolution map and imprinting analysis of the Gtl2–Dnchc1 domain on mouse chromosome 12 Sascha Tierling a, Simone Dalbert a, Sandra Schoppenhorst a,1, Chen-En Tsai b,2, Sven Oliger a, Anne C. Ferguson-Smith b, Martina Paulsen a,*,Jo¨rn Walter a a Genetik/Epigenetik, FR 8.3 Biowissenschaften, Universita¨t des Saarlandes, Postfach 151150, D-66041 Saarbru¨cken, Germany b Department of Anatomy, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK Received 2 June 2005; accepted 27 September 2005 Available online 23 November 2005 Abstract The imprinted Dlk1 –Dio3 region on mouse chromosome 12 contains six imprinted genes and a number of maternally expressed snoRNAs and miRNAs. Here we present a high-resolution sequence analysis of the 1.1-Mb segment telomeric to Gtl2 in mouse and a homology comparison to the human. Ppp2r5c and Dnchc1 at the telomeric end of the analyzed sequence are biallelically expressed, suggesting that the imprinted domain does not extend beyond the paternally expressed Dio3 gene. RT-PCR experiments support the predicted presence of a maternally expressed intergenic transcript(s) encompassing Gtl2, Rian, and Mirg. These maternally expressed genes, and also the intergenic transcript(s), show pronounced expression in the adult mouse brain, whereas the paternally transcribed Dio3 and the nonimprinted Ppp2r5c and Dnchc1 are expressed in different tissues. Hence, tissue-specific coregulation of maternally expressed genes might be an important feature of this domain.
    [Show full text]
  • Genetic Risk Factors for PTSD: a Gene-Set Analysis of Neurotransmitter Receptors
    Genetic Risk Factors for PTSD: A Gene-Set Analysis of Neurotransmitter Receptors Michael Lewis Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Psychology Russell T. Jones Bruce H. Scarpa-Friedman Margaret T. Davis Rachel A. Diana May 12, 2020 Blacksburg, VA Keywords: PTSD, Gene-set analysis, GSA-SNP2, Neurotransmitter receptors, serotonin, glutamate, intracellular signaling Genetic Risk Factors for PTSD: A Gene-Set Analysis of Neurotransmitter Receptors Michael Lewis Abstract (Academic) PTSD is a moderately heritable disorder that causes intense and chronic suffering in afflicted individuals. The pathogenesis of PTSD is not well understood, and genetic mechanisms are particularly elusive. Neurotransmitter systems are thought to contribute to PTSD etiology and are the targets of most pharmacotherapies used to treat PTSD, including the only two FDA approved options and a wide array of off-label options. However, the degree to which variations in genes which encode for and regulate neurotransmitter receptors increase risk of developing PTSD is unclear. Recently, large collaborative groups of PTSD genetics researchers have completed genome-wide association studies (GWAS) using massive sample sizes and have made summary statistics available for public use. In 2018, a new technique for high-powered analysis of GWAS summary statistics called GSA-SNP2 was introduced. In order to explore the relationship between PTSD and genetic variants in widely theorized molecular targets, this study applied GSA-SNP2 to manually curated neurotransmitter receptor gene-sets. Curated gene-sets included nine total “neurotransmitter receptor group” gene-sets and 45 total “receptor subtype” gene-sets.
    [Show full text]
  • Genome-Wide Dissection of Microrna Functions and Cotargeting Networks Using Gene-Set Signatures
    Genome-wide dissection of microRNA functions and cotargeting networks using gene-set signatures The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Tsang, John S., Margaret S. Ebert, and Alexander van Oudenaarden. “Genome-wide Dissection of MicroRNA Functions and Cotargeting Networks Using Gene Set Signatures.” Molecular Cell 38.1 (2010): 140–153. As Published http://dx.doi.org/10.1016/j.molcel.2010.03.007 Publisher Elsevier Version Author's final manuscript Citable link http://hdl.handle.net/1721.1/76631 Terms of Use Creative Commons Attribution-Noncommercial-Share Alike 3.0 Detailed Terms http://creativecommons.org/licenses/by-nc-sa/3.0/ NIH Public Access Author Manuscript Mol Cell. Author manuscript; available in PMC 2011 June 9. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Mol Cell. 2010 April 9; 38(1): 140±153. doi:10.1016/j.molcel.2010.03.007. Genome-wide dissection of microRNA functions and co- targeting networks using gene-set signatures John S. Tsang1,2, Margaret S. Ebert3,4, and Alexander van Oudenaarden2,3,4 1 Graduate Program in Biophysics, Harvard University, Cambridge, MA 2 Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 3 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 4 Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA SUMMARY MicroRNAs are emerging as important regulators of diverse biological processes and pathologies in animals and plants. While hundreds of human miRNAs are known, only a few have known functions.
    [Show full text]
  • Functional and Genomic Analyses of Alpha-Solenoid Proteins
    Functional and Genomic Analyses of Alpha-Solenoid Proteins David Fournier1, Gareth A. Palidwor2, Sergey Shcherbinin3, Angelika Szengel1, Martin H. Schaefer1, Carol Perez-Iratxeta2, Miguel A. Andrade-Navarro1* 1 Max-Delbru¨ck Center for Molecular Medicine, Berlin, Germany, 2 Ottawa Hospital Research Institute, Ottawa, Ontario, Canada, 3 The University of British Columbia, Vancouver, British Columbia, Canada Abstract Alpha-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some alpha-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of alpha-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of alpha-solenoids. Unexpectedly, we identified occurrences of alpha-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known alpha-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that alpha-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of alpha-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that alpha-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of alpha-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity.
    [Show full text]
  • Evolvability of Proteomes: Predicting Protein Function In
    Evolvability of proteomes: Predicting protein function in the light of evolution Inaugural-Dissertation to obtain the academic degree Doctor rerum naturalium (Dr. rer. nat.) submitted to the Department of Biology, Chemistry and Pharmacy of Freie Universität Berlin by David Fournier from Oullins, France 2014 1 Time period: October 2009 - March 2014 Supervisor: Dr. Miguel Andrade Institute: Max Delbrück Center für Molekulare Medizin, Berlin Buch 1st Reviewer: Prof. Dr. Udo Heinemann, Freie Universität 2nd Reviewer: Prof. Dr. Erich Wanker Date of defense: 04/04/2014 2 Acknowledgements First of all, I would like to thank Miguel Andrade for supervising my work, this has been a great time all along these years thinking about these evolutionary scenarios. Thank you not only for the scientific direction but also the great management. Thank you to all the CBDMers, with whom I had very good connections and lots of fun talking with. I have a special thought for all my colleagues who participated to the Marathon Staffel and other running events in Berlin all these years. That was really a lot of fun to be part of this. Moreover, I salute all my colleagues and friends who joined the weekly experimental lab procedure of wine tasting. I would like to thank Alexandre Budria and Yves Clément for helpful comments and suggestions to the thesis. I thank all collaborators who have participated to the articles I was involved in. I thank especially Prof. Dr. Erich Wanker for providing very interesting data and also for stimulating discussions. Thanks to Alexandre, Prof. Dr. Detlev Ganten and Russ Hodge for their great motivation to organize the seminar on evolutionary medicine.
    [Show full text]
  • Rabbit Anti-PPP2R5C/FITC Conjugated Antibody-SL11991R
    SunLong Biotech Co.,LTD Tel: 0086-571- 56623320 Fax:0086-571- 56623318 E-mail:[email protected] www.sunlongbiotech.com Rabbit Anti-PPP2R5C/FITC Conjugated antibody SL11991R-FITC Product Name: Anti-PPP2R5C/FITC Chinese Name: FITC标记的蛋白质磷酸酶2调节亚基5C/PP2A-B56-γ抗体 2A5G_HUMAN; B' alpha regulatory subunit; B56G; KIAA0044; MGC23064; PP2A B subunit B' gamma isoform; PP2A B subunit B56 gamma isoform; PP2A B subunit isoform B''-gamma; PP2A B subunit isoform B56-gamma; PP2A B subunit isoform PR61-gamma; PP2A B subunit isoform R5-gamma; PP2A B subunit PR61 gamma isoform; PP2A B subunit R5 gamma isoform; Ppp2r5c; PR61G; Protein phosphatase 2 Alias: regulatory subunit B (B56) gamma isoform; Protein phosphatase 2 regulatory subunit B' gamma; Renal carcinoma antigen NY REN 29; Renal carcinoma antigen NY-REN-29; Serine/threonine protein phosphatase 2A 56 kDa regulatory subunit gamma isoform; Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform; 2A5G_HUMAN. Organism Species: Rabbit Clonality: Polyclonal React Species: Human,Mouse,Rat,Dog,Cow,Horse,Rabbit,Sheep, ICC=1:50-200IF=1:50-200 Applications: not yet tested in other applications. optimalwww.sunlongbiotech.com dilutions/concentrations should be determined by the end user. Molecular weight: 61kDa Form: Lyophilized or Liquid Concentration: 1mg/ml immunogen: KLH conjugated synthetic peptide derived from human PPP2R5C (390-435aa) 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.
    [Show full text]