DOCSLIB.ORG

Mouse Cnksr3 Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Cnksr3 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Cnksr3 Knockout Project (CRISPR/Cas9) Objective: To create a Cnksr3 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Cnksr3 gene (NCBI Reference Sequence: NM_172546 ; Ensembl: ENSMUSG00000015202 ) is located on Mouse chromosome 10. 13 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 13 (Transcript: ENSMUST00000015346). Exon 2~4 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 3.18% of the coding region. Exon 2~4 covers 27.33% of the coding region. The size of effective KO region: ~7944 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 13 Legends Exon of mouse Cnksr3 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 4 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(22.7% 454) | C(22.15% 443) | T(29.75% 595) | G(25.4% 508) 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(22.4% 448) | C(21.55% 431) | T(35.7% 714) | G(20.35% 407) Note: The 2000 bp section downstream of Exon 4 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 - 7160808 7162807 2000 browser details YourSeq 65 1440 1516 2000 92.3% chr7 - 139124628 139124704 77 browser details YourSeq 64 1443 1516 2000 93.3% chr9 - 46368520 46368593 74 browser details YourSeq 64 1441 1516 2000 92.2% chr16 - 31077102 31077177 76 browser details YourSeq 64 1443 1516 2000 93.3% chr14 + 41044777 41044850 74 browser details YourSeq 63 1444 1516 2000 93.2% chr5 + 112897242 112897314 73 browser details YourSeq 63 1442 1516 2000 92.0% chr14 + 118808121 118808195 75 browser details YourSeq 63 1440 1516 2000 88.2% chr1 + 76305205 76305280 76 browser details YourSeq 62 1445 1516 2000 93.1% chrX - 74852312 74852383 72 browser details YourSeq 62 1445 1516 2000 93.1% chr7 - 117825012 117825083 72 browser details YourSeq 62 1441 1516 2000 90.8% chr2 - 161046582 161046657 76 browser details YourSeq 62 1445 1516 2000 93.1% chr18 - 67446756 67446827 72 browser details YourSeq 62 1443 1516 2000 91.9% chr1 - 132699078 132699151 74 browser details YourSeq 62 1445 1516 2000 93.1% chrX + 74780727 74780798 72 browser details YourSeq 62 1441 1516 2000 90.8% chr8 + 127576594 127576669 76 browser details YourSeq 62 1438 1516 2000 89.8% chr8 + 74984392 74984470 79 browser details YourSeq 62 1445 1516 2000 93.1% chr17 + 34389294 34389365 72 browser details YourSeq 62 1443 1516 2000 91.9% chr15 + 8793146 8793219 74 browser details YourSeq 62 1445 1516 2000 93.1% chr14 + 51004061 51004132 72 browser details YourSeq 62 1444 1516 2000 93.2% chr1 + 62289922 62289995 74 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 - 7150864 7152863 2000 browser details YourSeq 951 788 1844 2000 95.7% chr7 - 113663544 113664622 1079 browser details YourSeq 941 789 1844 2000 94.8% chr11 - 61229120 61230195 1076 browser details YourSeq 935 657 1844 2000 93.3% chr11 - 82686321 82687396 1076 browser details YourSeq 933 789 1844 2000 95.8% chr13 - 103286890 103353221 66332 browser details YourSeq 932 773 1844 2000 94.4% chr3 + 32840837 32842078 1242 browser details YourSeq 931 803 1844 2000 95.0% chr6 + 34837161 34838224 1064 browser details YourSeq 930 658 1844 2000 93.7% chr1 + 163026933 163028167 1235 browser details YourSeq 927 787 1844 2000 94.8% chr11 - 72236017 72237093 1077 browser details YourSeq 927 803 1844 2000 95.4% chr16 + 35520715 35521770 1056 browser details YourSeq 926 787 1844 2000 94.4% chr9 - 74566371 74567452 1082 browser details YourSeq 925 801 1844 2000 94.6% chr4 - 40562576 40563646 1071 browser details YourSeq 924 792 1844 2000 94.4% chr5 - 103899287 103900366 1080 browser details YourSeq 923 756 1844 2000 94.1% chr10 - 37058562 37059671 1110 browser details YourSeq 923 790 1844 2000 94.2% chr6 + 89620684 89621756 1073 browser details YourSeq 921 787 1844 2000 94.3% chr10 - 14370792 14371872 1081 browser details YourSeq 921 803 1844 2000 94.7% chrX + 151216933 151217994 1062 browser details YourSeq 921 789 1844 2000 94.6% chr11 + 55954302 55955382 1081 browser details YourSeq 920 803 1844 2000 95.2% chr1 - 9836565 9837633 1069 browser details YourSeq 920 789 1844 2000 94.0% chr7 + 6845928 6847018 1091 Note: The 2000 bp section downstream of Exon 4 is BLAT searched against the genome. No significant similarity is found. Page 5 of 8 https://www.alphaknockout.com Gene and protein information: Cnksr3 Cnksr family member 3 [ Mus musculus (house mouse) ] Gene ID: 215748, updated on 12-Aug-2019 Gene summary Official Symbol Cnksr3 provided by MGI Official Full Name Cnksr family member 3 provided by MGI Primary source MGI:MGI:2674130 See related Ensembl:ENSMUSG00000015202 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 Magi1; BC024086; 6820402C05 Expression Ubiquitous expression in cerebellum adult (RPKM 8.5), bladder adult (RPKM 8.3) and 28 other tissues See more Orthologs human all Genomic context Location: 10; 10 A1 See Cnksr3 in Genome Data Viewer Exon count: 14 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (7119061..7212237, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (3134304..3227479) Chromosome 10 - NC_000076.6 Page 6 of 8 https://www.alphaknockout.com Transcript information: This gene has 2 transcripts Gene: Cnksr3 ENSMUSG00000015202 Description Cnksr family member 3 [Source:MGI Symbol;Acc:MGI:2674130] Gene Synonyms Magi1 Location Chromosome 10: 7,119,063-7,212,237 reverse strand. GRCm38:CM001003.2 About this gene This gene has 2 transcripts (splice variants), 103 orthologues, 6 paralogues and is a member of 1 Ensembl protein family. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Cnksr3-201 ENSMUST00000015346.11 3447 555aa ENSMUSP00000015346.5 Protein coding CCDS56690 Q8BMA3 TSL:1 GENCODE basic APPRIS P1 Cnksr3-202 ENSMUST00000150282.1 2554 314aa ENSMUSP00000115863.1 Protein coding - Q8BMA3 TSL:1 GENCODE basic 113.17 kb Forward strand 7.12Mb 7.14Mb 7.16Mb 7.18Mb 7.20Mb 7.22Mb Contigs < AC161889.5 < AC099593.6 Genes (Comprehensive set... < Cnksr3-202protein coding < Cnksr3-201protein coding Regulatory Build 7.12Mb 7.14Mb 7.16Mb 7.18Mb 7.20Mb 7.22Mb Reverse strand 113.17 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000015346 < Cnksr3-201protein coding Reverse strand 93.17 kb ENSMUSP00000015... MobiDB lite Low complexity (Seg) Superfamily Sterile alpha motif/pointed domain superfamily PDZ superfamily SMART Sterile alpha motif domain PDZ domain Pfam CRIC domain PDZ domain Connector enhancer of kinase suppressor of ras 2 Sterile alpha motif domain PROSITE profiles Sterile alpha motif domain PDZ domain CRIC domain PANTHER PTHR12844:SF43 PTHR12844 Gene3D 2.30.42.10 Sterile alpha motif/pointed domain superfamily CDD cd09511 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant splice region variant synonymous variant Scale bar 0 60 120 180 240 300 360 420 480 555 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
Load more

Recommended publications
  • Molecular Effects of Isoflavone Supplementation Human Intervention Studies and Quantitative Models for Risk Assessment
    Molecular effects of isoflavone supplementation Human intervention studies and quantitative models for risk assessment Vera van der Velpen Thesis committee Promotors Prof. Dr Pieter van ‘t Veer Professor of Nutritional Epidemiology Wageningen University Prof. Dr Evert G. Schouten Emeritus Professor of Epidemiology and Prevention Wageningen University Co-promotors Dr Anouk Geelen Assistant professor, Division of Human Nutrition Wageningen University Dr Lydia A. Afman Assistant professor, Division of Human Nutrition Wageningen University Other members Prof. Dr Jaap Keijer, Wageningen University Dr Hubert P.J.M. Noteborn, Netherlands Food en Consumer Product Safety Authority Prof. Dr Yvonne T. van der Schouw, UMC Utrecht Dr Wendy L. Hall, King’s College London This research was conducted under the auspices of the Graduate School VLAG (Advanced studies in Food Technology, Agrobiotechnology, Nutrition and Health Sciences). Molecular effects of isoflavone supplementation Human intervention studies and quantitative models for risk assessment Vera van der Velpen Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Friday 20 June 2014 at 13.30 p.m. in the Aula. Vera van der Velpen Molecular effects of isoflavone supplementation: Human intervention studies and quantitative models for risk assessment 154 pages PhD thesis, Wageningen University, Wageningen, NL (2014) With references, with summaries in Dutch and English ISBN: 978-94-6173-952-0 ABSTRact Background: Risk assessment can potentially be improved by closely linked experiments in the disciplines of epidemiology and toxicology.
    [Show full text]
  • Genome-Wide Association Study of Diabetic Kidney Disease Highlights Biology Involved in Glomerular Basement Membrane Collagen
    CLINICAL RESEARCH www.jasn.org Genome-Wide Association Study of Diabetic Kidney Disease Highlights Biology Involved in Glomerular Basement Membrane Collagen Rany M. Salem ,1 Jennifer N. Todd,2,3,4 Niina Sandholm ,5,6,7 Joanne B. Cole ,2,3,4 Wei-Min Chen,8 Darrell Andrews,9 Marcus G. Pezzolesi,10 Paul M. McKeigue,11 Linda T. Hiraki,12 Chengxiang Qiu,13 Viji Nair,14 Chen Di Liao,12 Jing Jing Cao,12 Erkka Valo ,5,6,7 Suna Onengut-Gumuscu,8 Adam M. Smiles,15 Stuart J. McGurnaghan,16 Jani K. Haukka,5,6,7 Valma Harjutsalo,5,6,7,17 Eoin P. Brennan,9 Natalie van Zuydam,18,19 Emma Ahlqvist,20 Ross Doyle,9 Tarunveer S. Ahluwalia ,21 Maria Lajer,21 Maria F. Hughes,9 Jihwan Park,13 Jan Skupien,15 Athina Spiliopoulou,11 Andrew Liu,22 Rajasree Menon,14,23 Carine M. Boustany-Kari,24 Hyun M. Kang,23,25 Robert G. Nelson,26 Ronald Klein,27 Barbara E. Klein,27 Kristine E. Lee ,27 Xiaoyu Gao,28 Michael Mauer,29 Silvia Maestroni,30 Maria Luiza Caramori,29 Ian H. de Boer ,31 Rachel G. Miller,32 Jingchuan Guo ,32 Andrew P. Boright,12 David Tregouet,33,34 Beata Gyorgy,33,34 Janet K. Snell-Bergeon,35 David M. Maahs,36 Shelley B. Bull ,37 Angelo J. Canty,38 Colin N.A. Palmer,39 Lars Stechemesser,40 Bernhard Paulweber,40 Raimund Weitgasser,40,41 Jelizaveta Sokolovska,42 Vita Rovıte,43 Valdis Pırags, 42,44 Edita Prakapiene,45 Lina Radzeviciene,46 Rasa Verkauskiene,46 Nicolae Mircea Panduru,6,47 Leif C.
    [Show full text]
  • Genome-Wide Association and Trans-Ethnic Meta-Analysis for Advanced Diabetic Kidney Disease: Family Investigation of Nephropathy and Diabetes (FIND)
    RESEARCH ARTICLE Genome-Wide Association and Trans-ethnic Meta-Analysis for Advanced Diabetic Kidney Disease: Family Investigation of Nephropathy and Diabetes (FIND) Sudha K. Iyengar1☯*, John R. Sedor2,3☯*, Barry I. Freedman4☯*, W. H. Linda Kao5†, Matthias Kretzler6, Benjamin J. Keller6, Hanna E. Abboud7†, Sharon G. Adler8, Lyle G. Best9, Donald W. Bowden10, Allison Burlock6, Yii-Der Ida Chen11, Shelley A. Cole12, Mary E. Comeau13, Jeffrey M. Curtis14, Jasmin Divers13, Christiane Drechsler15, Ravi Duggirala12, Robert C. Elston1, Xiuqing Guo11, Huateng Huang16, Michael Marcus Hoffmann17, Barbara V. Howard18, Eli Ipp19, Paul L. Kimmel20, Michael J. Klag21, William C. Knowler14, Orly F. Kohn22, Tennille S. Leak6, David J. Leehey23, Man Li24, Alka Malhotra14, Winfried März25, Viji Nair6, Robert G. Nelson14, Susanne B. Nicholas26, Stephen J. O’Brien27, Madeleine V. Pahl28, Rulan S. Parekh29, Marcus G. Pezzolesi30, Rebekah S. Rasooly31, Charles N. Rotimi32, Jerome I. Rotter11, Jeffrey R. Schelling2, Michael F. Seldin33, Vallabh O. Shah34, Adam M. Smiles35, Michael W. Smith36, Kent D. Taylor11, Farook Thameem37¤, Denyse P. Thornley-Brown38, Barbara J. Truitt1, OPEN ACCESS Christoph Wanner39, E. Jennifer Weil14, Cheryl A. Winkler40, Philip G. Zager41, Robert P. Igo, Jr1‡, Robert L. Hanson14‡, Carl D. Langefeld11‡, Family Investigation of Citation: Iyengar SK, Sedor JR, Freedman BI, Kao Nephropathy and Diabetes (FIND)¶ WHL, Kretzler M, Keller BJ, et al. (2015) Genome- Wide Association and Trans-ethnic Meta-Analysis for 1 Department of Epidemiology & Biostatistics, Case Western Reserve University, Cleveland, Ohio, Advanced Diabetic Kidney Disease: Family United States of America, 2 Departments of Medicine, Case Western Reserve University, Cleveland, Ohio, Investigation of Nephropathy and Diabetes (FIND).
    [Show full text]
  • Integrated Analysis of Gene Expression Changes Associated
    Miao et al. Lipids in Health and Disease (2019) 18:92 https://doi.org/10.1186/s12944-019-1032-5 RESEARCH Open Access Integrated analysis of gene expression changes associated with coronary artery disease Liu Miao1 , Rui-Xing Yin1,2,3* , Feng Huang1,2,3, Shuo Yang1, Wu-Xian Chen1 and Jin-Zhen Wu1 Abstract Background: This study investigated the pathways and genes involved in coronary artery disease (CAD) and the associated mechanisms. Methods: Two array data sets of GSE19339 and GSE56885 were downloaded. The limma package was used to analyze the differentially expressed genes (DEGs) in normal and CAD specimens. Examination of DEGs through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and Gene Ontology annotation was achieved by Database for Annotation, Visualization and Integrated Discovery (DAVID). The Cytoscape software facilitated the establishment of the protein-protein interaction (PPI) network and Molecular Complex Detection (MCODE) was performed for the significant modules. Results: We identified 413 DEGs (291 up-regulated and 122 down-regulated). Approximately 256 biological processes, only 1 cellular component, and 21 molecular functions were identified by GO analysis and 10 pathways were enriched by KEGG. Moreover, 264 protein pairs and 64 nodes were visualized by the PPI network. After the MCODE analysis, the top 4 high degree genes, including interleukin 1 beta (IL1B, degree = 29), intercellular adhesion molecule 1 (ICAM1, degree = 25), Jun proto-oncogene (JUN, degree = 23) and C-C motif chemokine ligand 2 (CCL2, degree = 20) had been identified to validate in RT-PCR and Cox proportional hazards regression between CAD and normals. Conclusions: The relative expression of IL1B, ICAM1 and CCL2 was higher in CAD than in normal controls (P <0.05–0.
    [Show full text]
  • Role of PDZ-Binding Motif from West Nile Virus NS5 Protein on Viral
    www.nature.com/scientificreports OPEN Role of PDZ‑binding motif from West Nile virus NS5 protein on viral replication Emilie Giraud1*, Chloé Otero del Val2, Célia Caillet‑Saguy2, Nada Zehrouni2, Cécile Khou5, Joël Caillet4, Yves Jacob3, Nathalie Pardigon5 & Nicolas Wolf2 West Nile virus (WNV) is a Flavivirus, which can cause febrile illness in humans that may progress to encephalitis. Like any other obligate intracellular pathogens, Flaviviruses hijack cellular protein functions as a strategy for sustaining their life cycle. Many cellular proteins display globular domain known as PDZ domain that interacts with PDZ‑Binding Motifs (PBM) identifed in many viral proteins. Thus, cellular PDZ‑containing proteins are common targets during viral infection. The non‑structural protein 5 (NS5) from WNV provides both RNA cap methyltransferase and RNA polymerase activities and is involved in viral replication but its interactions with host proteins remain poorly known. In this study, we demonstrate that the C‑terminal PBM of WNV NS5 recognizes several human PDZ‑ containing proteins using both in vitro and in cellulo high‑throughput methods. Furthermore, we constructed and assayed in cell culture WNV replicons where the PBM within NS5 was mutated. Our results demonstrate that the PBM of WNV NS5 is important in WNV replication. Moreover, we show that knockdown of the PDZ‑containing proteins TJP1, PARD3, ARHGAP21 or SHANK2 results in the decrease of WNV replication in cells. Altogether, our data reveal that interactions between the PBM of NS5 and PDZ‑containing proteins afect West Nile virus replication. Arboviruses include numerous human and animal pathogens that are important global health threats responsible for arboviroses.
    [Show full text]
  • UNIVERSITY of CALIFORNIA Los Angeles a Sterile Alpha Motif
    UNIVERSITY OF CALIFORNIA Los Angeles A Sterile Alpha Motif Domain Network Involved in Kidney Development A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biochemistry and Molecular Biology by Catherine Nicole Leettola 2015 ABSTRACT OF THE DISSERTATION A Sterile Alpha Motif Domain Network Involved in Kidney Development by Catherine Nicole Leettola Doctor of Philosophy in Biochemistry and Molecular Biology University of California, Los Angeles, 2015 Professor James U. Bowie, Chair Cystic kidney diseases including polycystic kidney disease (PKD) and nephronophthisis (NPHP) are the most common genetic disorders leading to end-stage renal failure in humans. Animal models and human cases of PKD and NPHP have implicated the sterile alpha motif (SAM) domain containing proteins bicaudal C homolog 1 (BICC1) and ankyrin repeat and SAM- domain containing protein 6 (ANKS6) as being involved in these conditions and important for renal development. SAM domains are known protein-protein interaction domains that are capable of binding each other to form polymers and heterodimers. Using a negGFP native gel assay, we have identified the SAM domain of the previously uncharacterized protein ankyrin repeat and SAM-domain containing protein 3 (ANKS3) as a direct binding partner of the BICC1 and ANKS6 SAM domains. We found the ANKS3 SAM domain to polymerize with moderate affinity and determined the ANKS6 SAM domain can bind to a single end of this polymer. Crystal structures of the ANKS3 SAM domain polymer and the ANKS3 SAM-ANKS6 SAM ii heterodimer are presented to reveal typical ML-EH SAM domain interaction interfaces with a pronounced charge complementarity.
    [Show full text]
  • Transparent Machine Learning for Multi-Omics Analysis of Mental Disorders
    UPTEC X20 015 Examensarbete 30 hp Juni 2020 Transparent Machine Learning for Multi-Omics Analysis of Mental Disorders Stella Belin Abstract Transparent Machine Learning for Multi-Omics Analysis of Mental Disorders Stella Belin Teknisk- naturvetenskaplig fakultet UTH-enheten Schizophrenia and bipolar disorder are two severe mental disorders that affect more than 65 million individuals worldwide. The aim of this Besöksadress: project was to find co-prediction mechanisms for genes associated with Ångströmlaboratoriet Lägerhyddsvägen 1 schizophrenia and bipolar disorder using a multi-omics data set and a Hus 4, Plan 0 transparent machine learning approach. The overall purpose of the project was to further understand the biological mechanisms of these Postadress: complex disorders. In this work, publicly available multi-omics data Box 536 751 21 Uppsala collected from post-mortem brain tissue were used. The omics types included were gene expression, DNA methylation, and SNP array data. The Telefon: data consisted of samples from individuals with schizophrenia, bipolar 018 – 471 30 03 disorder, and healthy controls. Individuals with schizophrenia or Telefax: bipolar disorder were considered as a combined CASE class. 018 – 471 30 00 Using machine learning techniques, a multi-omics pipeline was developed Hemsida: to integrate these data in a manner such that all types were adequately http://www.teknat.uu.se/student represented. A feature selection was performed on methylation and SNP data, where the most important sites were estimated and mapped to their corresponding genes. Next, those genes were intersected with the gene expression data, and another feature selection was performed on the gene expression data. The most important genes were used to develop an interpretable rule-based model with an accuracy of 88%.
    [Show full text]
  • Promoter Methylation of Genes in and Around the Candidate Lung Cancer Susceptibility Locus 6Q23-25
    Research Article Promoter Methylation of Genes in and around the Candidate Lung Cancer Susceptibility Locus 6q23-25 Mathewos Tessema,1 Randy Willink,1 Kieu Do,1 Yang Y. Yu,1 Wayne Yu,3 Emi O. Machida,3 Malcolm Brock,3 Leander Van Neste,4 Christine A. Stidley,2 Stephen B. Baylin,3 and Steven A. Belinsky1 1Lung Cancer Program, Lovelace Respiratory Research Institute; 2Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico; 3Cancer Biology Division, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland; and 4Department of Molecular Biotechnology, Faculty of Biosciences Engineering, Ghent University, Ghent, Belgium Abstract epithelium of smokers include loss of heterozygosity (LOH) at chromosomes 3p21, 9p21, and 17p13 (3). Within these areas of Chromosomal aberrations associated with lung cancer are allelic loss, inactivation of the remaining allele by promoter frequently observed in the long arm of chromosome 6. A hypermethylation of RASSF1A and p16 genes and by mutation of candidate susceptibility locus at 6q23-25 for lung cancer was the p53 gene is commonly seen in non–small cell lung cancers recently identified; however, no tumor suppressor genes (NSCLC) (4). Methylation of the p16 gene is one of the earliest inactivated by mutation have been identified in this locus. changes in lung cancer development, occurring in the field of Genetic, epigenetic, gene expression, and in silico screening epithelial damage induced by carcinogens within tobacco and approaches were used to select 43 genes located in 6q12-27 increasing in prevalence during histologic progression of adeno- for characterization of methylation status. Twelve (28%) genes carcinoma and squamous cell carcinoma (5–7).
    [Show full text]
  • Frequent Loss-Of-Heterozygosity in CRISPR-Cas9–Edited Early Human Embryos
    Frequent loss-of-heterozygosity in CRISPR-Cas9–edited COLLOQUIUM PAPER early human embryos Gregorio Alanis-Lobatoa, Jasmin Zohrenb, Afshan McCarthya, Norah M. E. Fogartya,c, Nada Kubikovad,e, Emily Hardmana, Maria Grecof, Dagan Wellsd,g, James M. A. Turnerb, and Kathy K. Niakana,h,1 aHuman Embryo and Stem Cell Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom; bSex Chromosome Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom; cCentre for Stem Cells and Regenerative Medicine, Guy’s Campus, King’s College London, SE1 9RT London, United Kingdom; dNuffield Department of Women’s and Reproductive Health, John Radcliffe Hospital, University of Oxford, OX3 9DU Oxford, United Kingdom; eJesus College, University of Oxford, OX1 3DW Oxford, United Kingdom; fAncient Genomics Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom; gJuno Genetics, OX4 4GE Oxford, United Kingdom; and hThe Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EG Cambridge, United Kingdom Edited by Barbara J. Meyer, University of California, Berkeley, CA, and approved October 31, 2020 (received for review June 5, 2020) CRISPR-Cas9 genome editing is a promising technique for clinical homozygous WT embryos in both cases was not associated with applications, such as the correction of disease-associated alleles in use of the provided repair template for gene correction. Instead, somatic cells. The use of this approach has also been discussed in the authors suggest that in edited embryos the WT maternal the context of heritable editing of the human germ line. However, allele served as a template for the high-fidelity homology di- studies assessing gene correction in early human embryos report rected repair (HDR) pathway to repair the double-strand lesion low efficiency of mutation repair, high rates of mosaicism, and the caused by the Cas9 protein in the paternal allele (8).
    [Show full text]
  • Chromatin Conformation Links Distal Target Genes to CKD Loci
    BASIC RESEARCH www.jasn.org Chromatin Conformation Links Distal Target Genes to CKD Loci Maarten M. Brandt,1 Claartje A. Meddens,2,3 Laura Louzao-Martinez,4 Noortje A.M. van den Dungen,5,6 Nico R. Lansu,2,3,6 Edward E.S. Nieuwenhuis,2 Dirk J. Duncker,1 Marianne C. Verhaar,4 Jaap A. Joles,4 Michal Mokry,2,3,6 and Caroline Cheng1,4 1Experimental Cardiology, Department of Cardiology, Thoraxcenter Erasmus University Medical Center, Rotterdam, The Netherlands; and 2Department of Pediatrics, Wilhelmina Children’s Hospital, 3Regenerative Medicine Center Utrecht, Department of Pediatrics, 4Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology, 5Department of Cardiology, Division Heart and Lungs, and 6Epigenomics Facility, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands ABSTRACT Genome-wide association studies (GWASs) have identified many genetic risk factors for CKD. However, linking common variants to genes that are causal for CKD etiology remains challenging. By adapting self-transcribing active regulatory region sequencing, we evaluated the effect of genetic variation on DNA regulatory elements (DREs). Variants in linkage with the CKD-associated single-nucleotide polymorphism rs11959928 were shown to affect DRE function, illustrating that genes regulated by DREs colocalizing with CKD-associated variation can be dysregulated and therefore, considered as CKD candidate genes. To identify target genes of these DREs, we used circular chro- mosome conformation capture (4C) sequencing on glomerular endothelial cells and renal tubular epithelial cells. Our 4C analyses revealed interactions of CKD-associated susceptibility regions with the transcriptional start sites of 304 target genes. Overlap with multiple databases confirmed that many of these target genes are involved in kidney homeostasis.
    [Show full text]
  • CNKSR3 (NM 173515) Human Tagged ORF Clone – RC209167
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC209167 CNKSR3 (NM_173515) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: CNKSR3 (NM_173515) Human Tagged ORF Clone Tag: Myc-DDK Symbol: CNKSR3 Synonyms: CNK3; CNK3/IPCEF1; MAGI1 Vector: pCMV6-Entry (PS100001) E. coli Selection: Kanamycin (25 ug/mL) Cell Selection: Neomycin This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 5 CNKSR3 (NM_173515) Human Tagged ORF Clone – RC209167 ORF Nucleotide >RC209167 ORF sequence Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGGAACCCGTGACCAAGTGGAGCCCCAAACAAGTGGTGGACTGGACTAGAGGGTTGGATGACTGCCTGC AACAATATGTCCACAAGTTTGAACGAGAGAAGATCAACGGCGAGCAGCTGCTGCAGATTTCCCATCAGGA CCTGGAGGAGCTGGGGGTCACACGGATCGGACACCAGGAGCTTGTGTTGGAGGCTGTGGACCTTCTCTGT GCACTGAATTATGGCCTCGAAACTGATAACATGAAGAACTTGGTTCTGAAACTGAGAGCATCTTCCCACA ATTTACAGAATTACATAAGTAGCCGACGGAAAAGTCCCGCTTACGATGGCAACACCTCCCGCAAGGCCCC CAATGAGTTCCTGACCTCGGTGGTGGAGCTCATCGGCGCCGCCAAGGCCCTGCTGGCGTGGCTGGACCGG GCTCCGTTTACAGGGATCACTGATTTCTCAGTCACGAAGAACAAAATTATCCAGCTTTGCTTGGACCTGA CCACTACAGTCCAGAAGGATTGCTTTGTAGCGGAAATGGAGGATAAAGTTTTAACTGTGGTCAAGGTTTT AAATGGCATCTGTGACAAAACAATCCGATCTACCACAGATCCTGTGATGAGCCAGTGTGCATGTCTGGAG
    [Show full text]
  • Identification and Functional Characterization of the Novel Mineralocorticoid Receptor Target Gene Cnksr3
    Identification and Functional Characterization of the Novel Mineralocorticoid Receptor Target Gene Cnksr3 vorgelegt von Diplom-Ingenieur Tim Ziera Von der Fakultät III - Prozesswissenschaften der Technischen Universität Berlin zur Erlangung des akademischen Grades Doktor der Ingenieurwissenschaften - Dr.-Ing. - genehmigte Dissertation Promotionsausschuss: Vorsitzender: Prof. Dr. U. Stahl Berichter: Prof. Dr. R. Lauster Berichter: PD. Dr. K. Prelle Berichter: Prof. Dr. L.-A. Garbe Tag der wissenschaftlichen Aussprache: 23.10.2009 Berlin 2009 D83 Keywords Aldosterone, Epithelial Na+ Channel, Chromatin Immunoprecipitation (ChIP), Microarray, Reporter Gene Assay, Ussing Chamber, Site-Directed Mutagenesis Abstract Abstract The mineralocorticoid receptor (MR) is a ligand-dependent transcription factor mainly expressed in epithelial cells at the distal nephron and distal colon where it regulates salt and water homeostasis. MR expression and function is also found in several non-epithelial tissues particularly in the cardiovascular system. Dysregulation of aldosterone-MR signaling is frequently involved in hypertension and cardiac failure. While therapeutic benefits of MR antagonists in the above noted diseases are undisputed, the molecular mechanisms of action remain to be fully elucidated. Activated by aldosterone the MR elicits most of its physiological actions by altering gene expression of target genes including genes that modulate the activity of the epithelial sodium channel (ENaC) in the kidney. In the recent years a number of gene expression studies have been carried out to identify primary MR target genes. The search for MR target genes is yet hampered by the ubiquitously expressed glucocorticoid receptor (GR). Both MR and GR can be activated by aldosterone and cortisol, albeit at different concentrations. Hence, the current knowledge of MR target genes is likely to be mixed with actual GR target genes.
    [Show full text]