DOCSLIB.ORG

Mouse Casp8ap2 Conditional Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Casp8ap2 Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Casp8ap2 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Casp8ap2 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Casp8ap2 gene (NCBI Reference Sequence: NM_011997 ; Ensembl: ENSMUSG00000028282 ) is located on Mouse chromosome 4. 11 exons are identified, with the ATG start codon in exon 2 and the TAG stop codon in exon 10 (Transcript: ENSMUST00000029950). Exon 4 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Casp8ap2 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-75H14 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 disruption of this gene die before implantation. Exon 4 starts from about 2.12% of the coding region. The knockout of Exon 4 will result in frameshift of the gene. The size of intron 3 for 5'-loxP site insertion: 819 bp, and the size of intron 4 for 3'-loxP site insertion: 639 bp. The size of effective cKO region: ~601 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 3 4 5 11 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Casp8ap2 Homology arm cKO region loxP site Page 2 of 7 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(7101bp) | A(26.6% 1889) | C(19.39% 1377) | T(33.71% 2394) | G(20.29% 1441) 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 7 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% chr4 + 32627817 32630816 3000 browser details YourSeq 200 233 2212 3000 94.4% chr9 + 119785036 120133031 347996 browser details YourSeq 198 217 2211 3000 94.7% chr1 - 36716383 36848910 132528 browser details YourSeq 195 1897 2209 3000 91.2% chr9 + 101083164 101083802 639 browser details YourSeq 167 1919 2218 3000 89.6% chr8 + 33568937 33569494 558 browser details YourSeq 163 1900 2199 3000 89.8% chr2 - 155344489 155345098 610 browser details YourSeq 156 1892 2173 3000 94.4% chr2 + 154395889 154396541 653 browser details YourSeq 143 1874 2052 3000 92.1% chrX + 101777446 101777622 177 browser details YourSeq 142 1873 2044 3000 89.4% chr3 - 86018030 86018191 162 browser details YourSeq 139 1875 2052 3000 87.8% chr1 - 130617574 130617737 164 browser details YourSeq 136 1890 2053 3000 91.9% chr11 - 100987614 100987789 176 browser details YourSeq 136 1914 2314 3000 96.0% chr4 + 44224587 44225157 571 browser details YourSeq 134 1882 2052 3000 90.4% chr3 - 34633244 34633423 180 browser details YourSeq 133 1895 2212 3000 84.5% chr1 - 64958186 64958359 174 browser details YourSeq 132 1895 2200 3000 91.3% chr12 - 86869234 86869800 567 browser details YourSeq 132 1899 2052 3000 95.2% chr10 - 128022502 128022657 156 browser details YourSeq 132 1893 2048 3000 95.3% chr7 + 30048749 30049296 548 browser details YourSeq 131 1882 2044 3000 88.7% chr8 - 114901617 114901770 154 browser details YourSeq 131 1874 2050 3000 86.5% chr3 - 116580897 116581059 163 browser details YourSeq 130 1888 2044 3000 89.8% chr8 + 69211933 69212083 151 Note: The 3000 bp section upstream of Exon 4 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% chr4 + 32631418 32634417 3000 browser details YourSeq 259 810 1550 3000 80.9% chr9 + 57843631 57844518 888 browser details YourSeq 235 1419 2552 3000 91.3% chr11 - 6205222 6459959 254738 browser details YourSeq 203 862 1439 3000 86.1% chr10 - 4200403 4351547 151145 browser details YourSeq 186 840 1216 3000 87.2% chr13 - 28892793 28893214 422 browser details YourSeq 183 880 1216 3000 84.8% chr7 - 64407649 64408020 372 browser details YourSeq 167 807 1542 3000 81.0% chrX - 100712861 100713499 639 browser details YourSeq 161 805 1214 3000 88.9% chrX + 100961971 100962437 467 browser details YourSeq 159 810 1195 3000 89.3% chr2 + 61552959 61553386 428 browser details YourSeq 146 863 1216 3000 89.4% chr6 + 112977397 112977808 412 browser details YourSeq 142 2424 2768 3000 84.9% chr1 + 49465745 49465989 245 browser details YourSeq 133 879 1163 3000 88.9% chr5 - 144096500 144096840 341 browser details YourSeq 129 2428 2573 3000 94.6% chr4 + 5397236 5397382 147 browser details YourSeq 128 2427 2575 3000 93.3% chr7 - 141575782 141575930 149 browser details YourSeq 128 2428 2576 3000 94.0% chr15 - 17199210 17199364 155 browser details YourSeq 128 2428 2575 3000 94.0% chr19 + 32998579 32998728 150 browser details YourSeq 127 2427 2575 3000 93.3% chr5 - 64725548 64725705 158 browser details YourSeq 127 2424 2573 3000 92.7% chr9 + 15289739 15289889 151 browser details YourSeq 126 879 1216 3000 86.7% chr7 - 29772136 29772535 400 browser details YourSeq 125 2427 2575 3000 93.3% chrX - 36419814 36419974 161 Note: The 3000 bp section downstream of Exon 4 is BLAT searched against the genome. No significant similarity is found. Page 4 of 7 https://www.alphaknockout.com Gene and protein information: Casp8ap2 caspase 8 associated protein 2 [ Mus musculus (house mouse) ] Gene ID: 26885, updated on 10-Oct-2019 Gene summary Official Symbol Casp8ap2 provided by MGI Official Full Name caspase 8 associated protein 2 provided by MGI Primary source MGI:MGI:1349399 See related Ensembl:ENSMUSG00000028282 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 FLASH; D4Ertd659e Expression Broad expression in CNS E11.5 (RPKM 6.6), placenta adult (RPKM 3.7) and 17 other tissues See more Orthologs human all Genomic context Location: 4 A5; 4 14.27 cM See Casp8ap2 in Genome Data Viewer Exon count: 12 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (32615470..32653271) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 4 NC_000070.5 (32702448..32740240) Chromosome 4 - NC_000070.6 Page 5 of 7 https://www.alphaknockout.com Transcript information: This gene has 5 transcripts Gene: Casp8ap2 ENSMUSG00000028282 Description caspase 8 associated protein 2 [Source:MGI Symbol;Acc:MGI:1349399] Gene Synonyms D4Ertd659e, FLASH Location Chromosome 4: 32,615,451-32,653,265 forward strand. GRCm38:CM000997.2 About this gene This gene has 5 transcripts (splice variants), 197 orthologues, is a member of 1 Ensembl protein family and is associated with 1 phenotype. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Casp8ap2-201 ENSMUST00000029950.9 6799 1962aa ENSMUSP00000029950.3 Protein coding CCDS18016 Q9WUF3 TSL:1 GENCODE basic APPRIS P2 Casp8ap2-205 ENSMUST00000178925.7 6557 1962aa ENSMUSP00000136016.1 Protein coding CCDS18016 Q9WUF3 TSL:5 GENCODE basic APPRIS P2 Casp8ap2-202 ENSMUST00000108178.1 1189 190aa ENSMUSP00000103813.1 Protein coding - B1AX75 TSL:5 GENCODE basic APPRIS ALT2 Casp8ap2-204 ENSMUST00000127619.1 595 No protein - lncRNA - - TSL:3 Casp8ap2-203 ENSMUST00000124278.7 300 No protein - lncRNA - - TSL:5 57.81 kb Forward strand 32.61Mb 32.62Mb 32.63Mb 32.64Mb 32.65Mb 32.66Mb Genes (Comprehensive set... Gm11933-201 >processed pseudogene Casp8ap2-202 >protein coding Mdn1-201 >protein coding Casp8ap2-203 >lncRNA Mdn1-211 >protein coding Casp8ap2-204 >lncRNA Mdn1-210 >lncRNA Casp8ap2-205 >protein coding Casp8ap2-201 >protein coding Contigs AL831746.5 > AL805973.6 > Genes < Gm11936-201processed pseudogene (Comprehensive set... Regulatory Build 32.61Mb 32.62Mb 32.63Mb 32.64Mb 32.65Mb 32.66Mb Reverse strand 57.81 kb Regulation Legend CTCF Open Chromatin Promoter Promoter Flank Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding RNA gene pseudogene Page 6 of 7 https://www.alphaknockout.com Transcript: ENSMUST00000029950 37.79 kb Forward strand Casp8ap2-201 >protein coding ENSMUSP00000029... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) PANTHER CASP8-associated protein 2 Gene3D 1.10.10.60 CDD cd12202 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend inframe insertion inframe deletion missense variant synonymous variant Scale bar 0 200 400 600 800 1000 1200 1400 1600 1962 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 7 of 7.
Load more

Recommended publications
  • By Submitted in Partial Satisfaction of the Requirements for Degree of in In
    Developments of Two Imaging based Technologies for Cell Biology Researches by Xiaowei Yan DISSERTATION Submitted in partial satisfaction of the requirements for degree of DOCTOR OF PHILOSOPHY in Biochemistry and Molecular Biology in the GRADUATE DIVISION of the UNIVERSITY OF CALIFORNIA, SAN FRANCISCO Approved: ______________________________________________________________________________Ronald Vale Chair ______________________________________________________________________________Jonathan Weissman ______________________________________________________________________________Orion Weiner ______________________________________________________________________________ ______________________________________________________________________________ Committee Members Copyright 2021 By Xiaowei Yan ii DEDICATION Everything happens for the best. To my family, who supported me with all their love. iii ACKNOWLEDGEMENTS The greatest joy of my PhD has been joining UCSF, working and learning with such a fantastic group of scientists. I am extremely grateful for all the support and mentorship I received and would like to thank: My mentor, Ron Vale, who is such a great and generous person. Thank you for showing me that science is so much fun and thank you for always giving me the freedom in pursuing my interest. I am grateful for all the guidance from you and thank you for always supporting me whenever I needed. You are a person full of wisdom, and I have been learning so much from you and your attitude to science, science community and even life will continue inspire me. Thank you for being my mentor and thank you for being such a great mentor. Everyone else in Vale lab, past and present, for making our lab a sweet home. I would like to give my special thank to Marvin (Marvin Tanenbaum) and Nico (Nico Stuurman), two other mentors for me in the lab. I would like to thank them for helping me adapt to our lab, for all the valuable advice and for all the happiness during the time that we work together.
    [Show full text]
  • Cytotoxic Effects and Changes in Gene Expression Profile
    Toxicology in Vitro 34 (2016) 309–320 Contents lists available at ScienceDirect Toxicology in Vitro journal homepage: www.elsevier.com/locate/toxinvit Fusarium mycotoxin enniatin B: Cytotoxic effects and changes in gene expression profile Martina Jonsson a,⁎,MarikaJestoib, Minna Anthoni a, Annikki Welling a, Iida Loivamaa a, Ville Hallikainen c, Matti Kankainen d, Erik Lysøe e, Pertti Koivisto a, Kimmo Peltonen a,f a Chemistry and Toxicology Research Unit, Finnish Food Safety Authority (Evira), Mustialankatu 3, FI-00790 Helsinki, Finland b Product Safety Unit, Finnish Food Safety Authority (Evira), Mustialankatu 3, FI-00790 Helsinki, c The Finnish Forest Research Institute, Rovaniemi Unit, P.O. Box 16, FI-96301 Rovaniemi, Finland d Institute for Molecular Medicine Finland (FIMM), University of Helsinki, P.O. Box 20, FI-00014, Finland e Plant Health and Biotechnology, Norwegian Institute of Bioeconomy, Høyskoleveien 7, NO -1430 Ås, Norway f Finnish Safety and Chemicals Agency (Tukes), Opastinsilta 12 B, FI-00521 Helsinki, Finland article info abstract Article history: The mycotoxin enniatin B, a cyclic hexadepsipeptide produced by the plant pathogen Fusarium,isprevalentin Received 3 December 2015 grains and grain-based products in different geographical areas. Although enniatins have not been associated Received in revised form 5 April 2016 with toxic outbreaks, they have caused toxicity in vitro in several cell lines. In this study, the cytotoxic effects Accepted 28 April 2016 of enniatin B were assessed in relation to cellular energy metabolism, cell proliferation, and the induction of ap- Available online 6 May 2016 optosis in Balb 3T3 and HepG2 cells. The mechanism of toxicity was examined by means of whole genome ex- fi Keywords: pression pro ling of exposed rat primary hepatocytes.
    [Show full text]
  • XIAO-DISSERTATION-2015.Pdf
    CELLULAR AND PROCESS ENGINEERING TO IMPROVE MAMMALIAN MEMBRANE PROTEIN EXPRESSION By Su Xiao A dissertation is submitted to Johns Hopkins University in conformity with the requirements for degree of Doctor of Philosophy Baltimore, Maryland May 2015 © 2015 Su Xiao All Rights Reserved Abstract Improving the expression level of recombinant mammalian proteins has been pursued for production of commercial biotherapeutics in industry, as well as for biomedical studies in academia, as an adequate supply of correctly folded proteins is a prerequisite for all structure and function studies. Presented in this dissertation are different strategies to improve protein functional expression level, especially for membrane proteins. The model protein is neurotensin receptor 1 (NTSR1), a hard-to- express G protein-coupled receptor (GPCR). GPCRs are integral membrane proteins playing a central role in cell signaling and are targets for most of the medicines sold worldwide. Obtaining adequate functional GPCRs has been a bottleneck in their structure studies because the expression of these proteins from mammalian cells is very low. The first strategy is the adoption of mammalian inducible expression system. A stable and inducible T-REx-293 cell line overexpressing an engineered rat NTSR1 was constructed. 2.5 million Functional copies of NTSR1 per cell were detected on plasma membrane, which is 167 fold improvement comparing to NTSR1 constitutive expression. The second strategy is production process development including suspension culture adaptation and induction parameter optimization. A further 3.5 fold improvement was achieved and approximately 1 milligram of purified functional NTSR1 per liter suspension culture was obtained. This was comparable yield to the transient baculovirus- insect cell system.
    [Show full text]
  • Supplementary Data
    SUPPLEMENTARY DATA A cyclin D1-dependent transcriptional program predicts clinical outcome in mantle cell lymphoma Santiago Demajo et al. 1 SUPPLEMENTARY DATA INDEX Supplementary Methods p. 3 Supplementary References p. 8 Supplementary Tables (S1 to S5) p. 9 Supplementary Figures (S1 to S15) p. 17 2 SUPPLEMENTARY METHODS Western blot, immunoprecipitation, and qRT-PCR Western blot (WB) analysis was performed as previously described (1), using cyclin D1 (Santa Cruz Biotechnology, sc-753, RRID:AB_2070433) and tubulin (Sigma-Aldrich, T5168, RRID:AB_477579) antibodies. Co-immunoprecipitation assays were performed as described before (2), using cyclin D1 antibody (Santa Cruz Biotechnology, sc-8396, RRID:AB_627344) or control IgG (Santa Cruz Biotechnology, sc-2025, RRID:AB_737182) followed by protein G- magnetic beads (Invitrogen) incubation and elution with Glycine 100mM pH=2.5. Co-IP experiments were performed within five weeks after cell thawing. Cyclin D1 (Santa Cruz Biotechnology, sc-753), E2F4 (Bethyl, A302-134A, RRID:AB_1720353), FOXM1 (Santa Cruz Biotechnology, sc-502, RRID:AB_631523), and CBP (Santa Cruz Biotechnology, sc-7300, RRID:AB_626817) antibodies were used for WB detection. In figure 1A and supplementary figure S2A, the same blot was probed with cyclin D1 and tubulin antibodies by cutting the membrane. In figure 2H, cyclin D1 and CBP blots correspond to the same membrane while E2F4 and FOXM1 blots correspond to an independent membrane. Image acquisition was performed with ImageQuant LAS 4000 mini (GE Healthcare). Image processing and quantification were performed with Multi Gauge software (Fujifilm). For qRT-PCR analysis, cDNA was generated from 1 µg RNA with qScript cDNA Synthesis kit (Quantabio). qRT–PCR reaction was performed using SYBR green (Roche).
    [Show full text]
  • Genome-Wide Screen of Cell-Cycle Regulators in Normal and Tumor Cells
    bioRxiv preprint doi: https://doi.org/10.1101/060350; this version posted June 23, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Genome-wide screen of cell-cycle regulators in normal and tumor cells identifies a differential response to nucleosome depletion Maria Sokolova1, Mikko Turunen1, Oliver Mortusewicz3, Teemu Kivioja1, Patrick Herr3, Anna Vähärautio1, Mikael Björklund1, Minna Taipale2, Thomas Helleday3 and Jussi Taipale1,2,* 1Genome-Scale Biology Program, P.O. Box 63, FI-00014 University of Helsinki, Finland. 2Science for Life laboratory, Department of Biosciences and Nutrition, Karolinska Institutet, SE- 141 83 Stockholm, Sweden. 3Science for Life laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden To identify cell cycle regulators that enable cancer cells to replicate DNA and divide in an unrestricted manner, we performed a parallel genome-wide RNAi screen in normal and cancer cell lines. In addition to many shared regulators, we found that tumor and normal cells are differentially sensitive to loss of the histone genes transcriptional regulator CASP8AP2. In cancer cells, loss of CASP8AP2 leads to a failure to synthesize sufficient amount of histones in the S-phase of the cell cycle, resulting in slowing of individual replication forks. Despite this, DNA replication fails to arrest, and tumor cells progress in an elongated S-phase that lasts several days, finally resulting in death of most of the affected cells.
    [Show full text]
  • Discrepancies Between Human DNA, Mrna and Protein Reference
    Database, 2016, 1–15 doi: 10.1093/database/baw124 Original article Original article Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population Matsuyuki Shirota1,2,3 and Kengo Kinoshita2,3,4,* 1Graduate School of Medicine, Tohoku University, Sendai, Miyagi 9808575, Japan, 2Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 9808575, Japan, 3Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi 9808579, Japan, 4Institute for Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 9808575, Japan *Corresponding author: Tel: þ81227957179; Fax: þ81227957179; Email: [email protected] Citation details: Shirota,M. and Kinoshita,K. Discrepancies between human DNA, mRNA and protein reference se- quences and their relation to single nucleotide variants in the human population. Database (2016) Vol. 2016: article ID baw124; doi:10.1093/database/baw124. Received 5 May 2016; Revised 6 July 2016; Accepted 4 August 2016 Abstract The protein coding sequences of the human reference genome GRCh38, RefSeq mRNA and UniProt protein databases are sometimes inconsistent with each other, due to poly- morphisms in the human population, but the overall landscape of the discordant se- quences has not been clarified. In this study, we comprehensively listed the discordant bases and regions between the GRCh38, RefSeq and UniProt reference sequences, based on the genomic coordinates of GRCh38. We observed that the RefSeq sequences are more likely to represent the major alleles than GRCh38 and UniProt, by assigning the al- ternative allele frequencies of the discordant bases. Since some reference sequences have minor alleles, functional and structural annotations may be performed based on rare alleles in the human population, thereby biasing these analyses.
    [Show full text]
  • Anti-FLASH Antibody (ARG54381)
    Product datasheet [email protected] ARG54381 Package: 50 μg anti-FLASH antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes FLASH Tested Reactivity Hu Tested Application ICC/IF, WB Specificity This antibody recognizes human and mouse FLASH (220kDa). Host Rabbit Clonality Polyclonal Isotype IgG Target Name FLASH Antigen Species Human Immunogen Peptide corresponding to aa 1253-1268 of human FLASH (accession no. AF165161). This sequence differs by one amino acid from that of mouse. Conjugation Un-conjugated Alternate Names CASP8-associated protein 2; FLASH; FLICE-associated huge protein; CED-4; RIP25 Application Instructions Application table Application Dilution ICC/IF Assay-dependent WB Assay-dependent Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control HeLa Calculated Mw 223 kDa Properties Form Liquid Purification Immunoaffinity chroma-tography Buffer PBS (pH 7.4) and 0.02% Sodium azide Preservative 0.02% Sodium azide Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C or below. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. www.arigobio.com 1/2 Note For laboratory research only, not for drug, diagnostic or other use. Bioinformation Database links GeneID: 9994 Human Swiss-port # Q9UKL3 Human Gene Symbol CASP8AP2 Gene Full Name caspase 8 associated protein 2 Background A mammalian homologue of CED-4 has been identified and designated FLASH (FLICE-associated huge protein).
    [Show full text]
  • Gene Section Review
    Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST-CNRS Gene Section Review CASP8AP2 (caspase 8 associated protein 2) Rocío Juárez-Velázquez, Patricia Pérez-Vera Laboratorio de Cultivo de Tejidos, Departamento de Genética Humana, Instituto Nacional de Pediatria, Mexico, Mexico; [email protected] Published in Atlas Database: March 2015 Online updated version : http://AtlasGeneticsOncology.org/Genes/CASP8AP2ID926ch6q15.html Printable original version : http://documents.irevues.inist.fr/bitstream/handle/2042/62522/03-2015-CASP8AP2ID926ch6q15.pdf DOI: 10.4267/2042/62522 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2016 Atlas of Genetics and Cytogenetics in Oncology and Haematology multiple transcript variants encoding the same Abstract protein. CASP8AP2 was initially identified as a pro- Protein apoptotic protein that transmits an apoptosis indication through the death-inducing signaling Description complex. Size 1982 amino acids; 222,658 kDa protein. More recently, diverse functions have been It contains a motif structurally related to described including TNF-induced NF-kappaB CED4/Apaf1 (602233) and a C-terminal death activation, cell-cycle progression and cell division, effector domain (DED)-recruiting domain (DRD); a regulation of histone gene transcription and histone NCOA2-binding domain (position 1709-1982aa); a mRNA processing. SUMO interaction motifs: SIM1 (position 1683- Keywords 1687aa), SIM2 (position 1737-1741aa, SIM3
    [Show full text]
  • Systems-Wide Rnai Analysis of CASP8AP2/FLASH Shows
    Hummon et al. Molecular Cancer 2012, 11:1 http://www.molecular-cancer.com/content/11/1/1 RESEARCH Open Access Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells Amanda B Hummon1,3, Jason J Pitt2, Jordi Camps1, Georg Emons1,5, Susan B Skube3, Konrad Huppi2, Tamara L Jones2, Tim Beissbarth4, Frank Kramer4, Marian Grade1,5, Michael J Difilippantonio1,6, Thomas Ried1 and Natasha J Caplen2* Abstract Background: Colorectal carcinomas (CRC) carry massive genetic and transcriptional alterations that influence multiple cellular pathways. The study of proteins whose loss-of-function (LOF) alters the growth of CRC cells can be used to further understand the cellular processes cancer cells depend upon for survival. Results: A small-scale RNAi screen of ~400 genes conducted in SW480 CRC cells identified several candidate genes as required for the viability of CRC cells, most prominently CASP8AP2/FLASH. To understand the function of this gene in maintaining the viability of CRC cells in an unbiased manner, we generated gene specific expression profiles following RNAi. Silencing of CASP8AP2/FLASH resulted in altered expression of over 2500 genes enriched for genes associated with cellular growth and proliferation. Loss of CASP8AP2/FLASH function was significantly associated with altered transcription of the genes encoding the replication-dependent histone proteins as a result of the expression of the non-canonical polyA variants of these transcripts. Silencing of CASP8AP2/FLASH also mediated enrichment of changes in the expression of targets of the NFB and MYC transcription factors.
    [Show full text]
  • Alterations of the Pro-Survival Bcl-2 Protein Interactome in Breast Cancer
    bioRxiv preprint doi: https://doi.org/10.1101/695379; this version posted July 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Alterations of the pro-survival Bcl-2 protein interactome in 2 breast cancer at the transcriptional, mutational and 3 structural level 4 5 Simon Mathis Kønig1, Vendela Rissler1, Thilde Terkelsen1, Matteo Lambrughi1, Elena 6 Papaleo1,2 * 7 1Computational Biology Laboratory, Danish Cancer Society Research Center, 8 Strandboulevarden 49, 2100, Copenhagen 9 10 2Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo 11 Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, 12 Denmark 13 14 Abstract 15 16 Apoptosis is an essential defensive mechanism against tumorigenesis. Proteins of the B-cell 17 lymphoma-2 (Bcl-2) family regulates programmed cell death by the mitochondrial apoptosis 18 pathway. In response to intracellular stresses, the apoptotic balance is governed by interactions 19 of three distinct subgroups of proteins; the activator/sensitizer BH3 (Bcl-2 homology 3)-only 20 proteins, the pro-survival, and the pro-apoptotic executioner proteins. Changes in expression 21 levels, stability, and functional impairment of pro-survival proteins can lead to an imbalance 22 in tissue homeostasis. Their overexpression or hyperactivation can result in oncogenic effects. 23 Pro-survival Bcl-2 family members carry out their function by binding the BH3 short linear 24 motif of pro-apoptotic proteins in a modular way, creating a complex network of protein- 25 protein interactions.
    [Show full text]
  • Genetic-Linkage Mapping of Complex Hereditary Disorders to a Whole-Genome Molecular-Interaction Network
    Downloaded from genome.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Methods Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network Ivan Iossifov,1 Tian Zheng,2 Miron Baron,3 T. Conrad Gilliam,4 and Andrey Rzhetsky4,5,6 1Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA; 2Department of Statistics, Columbia University, New York, New York 10027, USA; 3Department of Psychiatry, Columbia University, New York, New York 10032, USA; 4Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA; 5Department of Medicine, Institute for Genomics & Systems Biology, Computation Institute, University of Chicago, Chicago, Illinois 60637, USA Common hereditary neurodevelopmental disorders such as autism, bipolar disorder, and schizophrenia are most likely both genetically multifactorial and heterogeneous. Because of these characteristics traditional methods for genetic analysis fail when applied to such diseases. To address the problem we propose a novel probabilistic framework that combines the standard genetic linkage formalism with whole-genome molecular-interaction data to predict pathways or networks of interacting genes that contribute to common heritable disorders. We apply the model to three large genotype–phenotype data sets, identify a small number of significant candidate genes for autism (24), bipolar disorder (21), and schizophrenia (25), and
    [Show full text]
  • Prognostic Relevance of Genetic Variations in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma
    2495 Review Article Prognostic relevance of genetic variations in T-cell acute lymphoblastic leukemia/lymphoblastic lymphoma Hui Yu1,2#, Yuxin Du1,2#, Ji Xu3, Mingzhi Zhang1,2 1Department of Oncology, 2Lymphoma Diagnosis and Treatment Center of Henan Province, Zhengzhou University First Affiliated Hospital, Zhengzhou 450052, China; 3Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China Contributions: (I) Conception and design: All authors; (II) Administrative support: None; (III) Provision of study materials or patients: None; (IV) Collection and assembly of data: None; (V) Data analysis and interpretation: None; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. #These authors contributed equally to this work. Correspondence to: Dr. Mingzhi Zhang. Department of Oncology, Zhengzhou University First Affiliated Hospital, Lymphoma Diagnosis and Treatment Center of Henan Province, No. 1 Jianshe East Road, Zhengzhou 450052, China. Email: [email protected]. Abstract: T-cell acute lymphoblastic leukemia (ALL) and lymphoblastic lymphoma (LBL) are highly aggressive malignant tumors. With the current intensive treatment regimens, event-free survival (EFS) rates of up to 60–90% can be achieved, but the survival rate of relapsed patients remains poor—only approximately 3–12%. Therefore, precise and effective prognostic parameters are highly needed to further improve survival rates along with reduced acute and long-term toxicities, including the rate of secondary malignancies. In addition, gene mutations can be used as therapeutic targets. This review highlights several gene mutations with a high frequency or a strong influence associated with favorable or unfavorable aspects of prognosis— NOTCH1, FBXW7, PTEN, LOH6q, CASP8AP2, c-MYC, IL-7, CALM-AF10, and CDKN2A/B—and indicates that the actual incidence of mutations in T-ALL/LBL is much higher than currently recognized.
    [Show full text]