DOCSLIB.ORG

Mouse Cacna1b Conditional Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Cacna1b Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Cacna1b Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Cacna1b conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Cacna1b gene (NCBI Reference Sequence: NM_001042528 ; Ensembl: ENSMUSG00000004113 ) is located on Mouse chromosome 2. 47 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 47 (Transcript: ENSMUST00000041342). Exon 3 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Cacna1b gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-474E19 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 deficient in this gene exhibit defects in nociception, memory and learning. They also exhibit hyperactive and hyperaggressive behaviors as well as defects in the the sleep-wake cycle. Deficits in the sympathetic nervous system results in defects in circulatory regulation. Exon 3 starts from about 5.6% of the coding region. The knockout of Exon 3 will result in frameshift of the gene. The size of intron 2 for 5'-loxP site insertion: 3354 bp, and the size of intron 3 for 3'-loxP site insertion: 24245 bp. The size of effective cKO region: ~640 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 gRNA region 5' gRNA region 3' 1 3 47 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Cacna1b 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(7140bp) | A(20.63% 1473) | C(24.58% 1755) | T(27.65% 1974) | G(27.14% 1938) 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% chr2 - 24758672 24761671 3000 browser details YourSeq 166 652 847 3000 94.2% chr1 + 161140716 161140920 205 browser details YourSeq 153 652 840 3000 92.7% chr4 + 149447915 149448103 189 browser details YourSeq 152 652 945 3000 93.7% chr2 - 125262593 125262922 330 browser details YourSeq 152 656 846 3000 89.2% chr1 - 54586597 54586763 167 browser details YourSeq 150 656 836 3000 92.8% chr18 - 34278327 34278513 187 browser details YourSeq 148 656 842 3000 88.7% chr13 + 9007570 9007739 170 browser details YourSeq 146 650 835 3000 87.8% chr5 - 3597811 3597983 173 browser details YourSeq 146 652 844 3000 88.2% chr14 + 73016470 73016629 160 browser details YourSeq 145 661 839 3000 92.8% chr16 - 68573219 68573396 178 browser details YourSeq 145 657 845 3000 87.3% chr4 + 133819459 133819623 165 browser details YourSeq 143 662 842 3000 89.0% chr15 - 5889638 5889805 168 browser details YourSeq 143 662 842 3000 88.2% chr5 + 117496156 117496318 163 browser details YourSeq 142 653 845 3000 87.4% chr10 - 128910949 128911106 158 browser details YourSeq 142 656 845 3000 85.4% chrX + 135573471 135573642 172 browser details YourSeq 142 651 842 3000 89.1% chr2 + 142670970 142671151 182 browser details YourSeq 142 651 846 3000 91.3% chr18 + 18903468 18903666 199 browser details YourSeq 142 652 841 3000 88.7% chr12 + 36097560 36097739 180 browser details YourSeq 141 641 842 3000 88.8% chr12 - 3603741 3603938 198 browser details YourSeq 139 652 806 3000 92.9% chr4 - 54482231 54482383 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% chr2 - 24755032 24758031 3000 browser details YourSeq 177 271 580 3000 93.7% chr3 + 153946353 153946700 348 browser details YourSeq 176 262 585 3000 93.2% chr1 + 136387916 136388508 593 browser details YourSeq 160 261 589 3000 87.9% chr15 + 36411314 36411635 322 browser details YourSeq 154 266 585 3000 88.2% chr7 + 79389486 79389972 487 browser details YourSeq 151 215 421 3000 92.6% chr13 + 44853153 44853462 310 browser details YourSeq 146 257 422 3000 95.1% chr7 - 30116809 30116977 169 browser details YourSeq 146 262 424 3000 95.1% chr12 - 97190549 97190713 165 browser details YourSeq 145 257 421 3000 93.9% chr2 - 69246643 69246806 164 browser details YourSeq 145 264 480 3000 91.5% chr10 - 43894415 43894987 573 browser details YourSeq 144 261 423 3000 95.1% chr6 + 29297409 29297571 163 browser details YourSeq 144 273 580 3000 94.0% chr3 + 9275494 9275819 326 browser details YourSeq 144 257 425 3000 91.6% chr2 + 9851599 9851765 167 browser details YourSeq 144 261 422 3000 93.2% chr13 + 73638166 73638326 161 browser details YourSeq 143 262 421 3000 95.0% chr5 - 110574323 110574483 161 browser details YourSeq 143 260 423 3000 95.0% chr14 - 59955426 59955591 166 browser details YourSeq 143 261 418 3000 96.2% chr15 + 70865017 70865182 166 browser details YourSeq 143 260 425 3000 90.7% chr1 + 18256357 18256518 162 browser details YourSeq 142 261 422 3000 93.2% chrX + 57776383 57776543 161 browser details YourSeq 142 260 428 3000 92.9% chr7 + 139934755 139934930 176 Note: The 3000 bp section downstream of Exon 3 is BLAT searched against the genome. No significant similarity is found. Page 4 of 8 https://www.alphaknockout.com Gene and protein information: Cacna1b calcium channel, voltage-dependent, N type, alpha 1B subunit [ Mus musculus (house mouse) ] Gene ID: 12287, updated on 12-Aug-2019 Gene summary Official Symbol Cacna1b provided by MGI Official Full Name calcium channel, voltage-dependent, N type, alpha 1B subunit provided by MGI Primary source MGI:MGI:88296 See related Ensembl:ENSMUSG00000004113 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 BIII; Cav2.2; Cchn1a; AW050276; AW060892; AW822256; alpha(1B) Expression Biased expression in CNS E18 (RPKM 11.3), whole brain E14.5 (RPKM 9.4) and 8 other tissues See more Orthologs human all Genomic context Location: 2 A3; 2 16.58 cM See Cacna1b in Genome Data Viewer Exon count: 52 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (24603860..24763200, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (24461895..24618672, complement) Chromosome 2 - NC_000068.7 Page 5 of 8 https://www.alphaknockout.com Transcript information: This gene has 10 transcripts Gene: Cacna1b ENSMUSG00000004113 Description calcium channel, voltage-dependent, N type, alpha 1B subunit [Source:MGI Symbol;Acc:MGI:88296] Gene Synonyms Cav2.2, Cchn1a, alpha(1B) Location Chromosome 2: 24,603,887-24,763,152 reverse strand. GRCm38:CM000995.2 About this gene This gene has 10 transcripts (splice variants), 269 orthologues, 26 paralogues, is a member of 1 Ensembl protein family and is associated with 62 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Cacna1b- ENSMUST00000070864.13 9655 2288aa ENSMUSP00000063236.7 Protein coding CCDS15739 A2AIS0 TSL:5 202 GENCODE basic APPRIS P3 Cacna1b- ENSMUST00000041342.11 6984 2327aa ENSMUSP00000037416.5 Protein coding CCDS38065 O55017 TSL:1 201 GENCODE basic APPRIS ALT2 Cacna1b- ENSMUST00000102939.8 9736 2325aa ENSMUSP00000100003.2 Protein coding - A2AIR9 TSL:5 204 GENCODE basic APPRIS ALT2 Cacna1b- ENSMUST00000100348.9 7182 2328aa ENSMUSP00000097920.3 Protein coding - A2AIR7 TSL:5 203 GENCODE basic APPRIS ALT2 Cacna1b- ENSMUST00000114447.7 6987 2328aa ENSMUSP00000110090.1 Protein coding - A2AIR7 TSL:5 205 GENCODE basic APPRIS ALT2 Cacna1b- ENSMUST00000133892.1 684 228aa ENSMUSP00000115285.1 Protein coding - A2AIZ9 CDS 5' and 3' 209 incomplete TSL:3 Cacna1b- ENSMUST00000131861.1 523 168aa ENSMUSP00000141653.1 Protein coding - A0A0A6YWR0 CDS 5' 208 incomplete TSL:5 Cacna1b- ENSMUST00000155356.3 332 111aa ENSMUSP00000116674.2 Protein coding - F7C9S8 CDS 5' and 3' 210 incomplete TSL:5 Cacna1b- ENSMUST00000124183.1 308 102aa ENSMUSP00000114605.1 Protein coding - A2AJ01 CDS 5' and 3' 206 incomplete TSL:5 Cacna1b- ENSMUST00000125798.2 949 114aa ENSMUSP00000141767.1 Nonsense mediated - A0A0A6YWZ5 CDS 5' 207 decay incomplete TSL:5 Page 6 of 8 https://www.alphaknockout.com 179.27 kb Forward strand 24.60Mb 24.65Mb 24.70Mb 24.75Mb Genes Gm25455-201 >misc RNA Gm13459-201 >processed pseudogene (Comprehensive set... Contigs AL732546.13 > BX294112.6
Load more

Recommended publications
  • Genetic Associations Between Voltage-Gated Calcium Channels (Vgccs) and Autism Spectrum Disorder (ASD)
    Liao and Li Molecular Brain (2020) 13:96 https://doi.org/10.1186/s13041-020-00634-0 REVIEW Open Access Genetic associations between voltage- gated calcium channels and autism spectrum disorder: a systematic review Xiaoli Liao1,2 and Yamin Li2* Abstract Objectives: The present review systematically summarized existing publications regarding the genetic associations between voltage-gated calcium channels (VGCCs) and autism spectrum disorder (ASD). Methods: A comprehensive literature search was conducted to gather pertinent studies in three online databases. Two authors independently screened the included records based on the selection criteria. Discrepancies in each step were settled through discussions. Results: From 1163 resulting searched articles, 28 were identified for inclusion. The most prominent among the VGCCs variants found in ASD were those falling within loci encoding the α subunits, CACNA1A, CACNA1B, CACN A1C, CACNA1D, CACNA1E, CACNA1F, CACNA1G, CACNA1H, and CACNA1I as well as those of their accessory subunits CACNB2, CACNA2D3, and CACNA2D4. Two signaling pathways, the IP3-Ca2+ pathway and the MAPK pathway, were identified as scaffolds that united genetic lesions into a consensus etiology of ASD. Conclusions: Evidence generated from this review supports the role of VGCC genetic variants in the pathogenesis of ASD, making it a promising therapeutic target. Future research should focus on the specific mechanism that connects VGCC genetic variants to the complex ASD phenotype. Keywords: Autism spectrum disorder, Voltage-gated calcium
    [Show full text]
  • CACNB1 Antibody (C-Term) Blocking Peptide Synthetic Peptide Catalog # Bp16144b
    10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 CACNB1 Antibody (C-term) Blocking Peptide Synthetic peptide Catalog # BP16144b Specification CACNB1 Antibody (C-term) Blocking CACNB1 Antibody (C-term) Blocking Peptide - Peptide - Background Product Information The protein encoded by this gene belongs to Primary Accession Q02641 the calciumchannel beta subunit family. It plays an important role in thecalcium channel by modulating G protein inhibition, increasing CACNB1 Antibody (C-term) Blocking Peptide - Additional Information peakcalcium current, controlling the alpha-1 subunit membrane targetingand shifting the voltage dependence of activation and Gene ID 782 inactivation.Alternative splicing occurs at this locus and three transcriptvariants encoding Other Names three distinct isoforms have been identified. Voltage-dependent L-type calcium channel subunit beta-1, CAB1, Calcium channel CACNB1 Antibody (C-term) Blocking voltage-dependent subunit beta 1, CACNB1, Peptide - References CACNLB1 Format Jangsangthong, W., et al. Pflugers Arch. Peptides are lyophilized in a solid powder 459(3):399-411(2010)Olsen, J.V., et al. Cell format. Peptides can be reconstituted in 127(3):635-648(2006)Olsen, J.V., et al. Cell solution using the appropriate buffer as 127(3):635-648(2006)Lim, J., et al. Cell needed. 125(4):801-814(2006)Foell, J.D., et al. Physiol. Genomics 17(2):183-200(2004) Storage Maintain refrigerated at 2-8°C for up to 6 months. For long term storage store at -20°C. Precautions This product is for
    [Show full text]
  • An Integrated Genomic Analysis of Gene-Function Correlation on Schizophrenia Susceptibility Genes
    Journal of Human Genetics (2010) 55, 285–292 & 2010 The Japan Society of Human Genetics All rights reserved 1434-5161/10 $32.00 www.nature.com/jhg ORIGINAL ARTICLE An integrated genomic analysis of gene-function correlation on schizophrenia susceptibility genes Tearina T Chu and Ying Liu Schizophrenia is a highly complex inheritable disease characterized by numerous genetic susceptibility elements, each contributing a modest increase in risk for the disease. Although numerous linkage or association studies have identified a large set of schizophrenia-associated loci, many are controversial. In addition, only a small portion of these loci overlaps with the large cumulative pool of genes that have shown changes of expression in schizophrenia. Here, we applied a genomic gene-function approach to identify susceptibility loci that show direct effect on gene expression, leading to functional abnormalities in schizophrenia. We carried out an integrated analysis by cross-examination of the literature-based susceptibility loci with the schizophrenia-associated expression gene list obtained from our previous microarray study (Journal of Human Genetics (2009) 54: 665–75) using bioinformatic tools, followed by confirmation of gene expression changes using qPCR. We found nine genes (CHGB, SLC18A2, SLC25A27, ESD, C4A/C4B, TCP1, CHL1 and CTNNA2) demonstrate gene-function correlation involving: synapse and neurotransmission; energy metabolism and defense mechanisms; and molecular chaperone and cytoskeleton. Our findings further support the roles of these genes in genetic influence and functional consequences on the development of schizophrenia. It is interesting to note that four of the nine genes are located on chromosome 6, suggesting a special chromosomal vulnerability in schizophrenia.
    [Show full text]
  • Conotoxins As Tools to Understand the Physiological Function of Voltage-Gated Calcium (Cav) Channels
    marine drugs Review Conotoxins as Tools to Understand the Physiological Function of Voltage-Gated Calcium (CaV) Channels David Ramírez 1,2, Wendy Gonzalez 1,3, Rafael A. Fissore 4 and Ingrid Carvacho 5,* 1 Centro de Bioinformática y Simulación Molecular, Universidad de Talca, 3460000 Talca, Chile; [email protected] (D.R.); [email protected] (W.G.) 2 Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, 3460000 Talca, Chile 3 Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, 3460000 Talca, Chile 4 Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003, USA; rfi[email protected] 5 Department of Biology and Chemistry, Faculty of Basic Sciences, Universidad Católica del Maule, 3480112 Talca, Chile * Correspondence: [email protected]; Tel.: +56-71-220-3518 Received: 8 August 2017; Accepted: 4 October 2017; Published: 13 October 2017 Abstract: Voltage-gated calcium (CaV) channels are widely expressed and are essential for the completion of multiple physiological processes. Close regulation of their activity by specific inhibitors and agonists become fundamental to understand their role in cellular homeostasis as well as in human tissues and organs. CaV channels are divided into two groups depending on the membrane potential required to activate them: High-voltage activated (HVA, CaV1.1–1.4; CaV2.1–2.3) and Low-voltage activated (LVA, CaV3.1–3.3). HVA channels are highly expressed in brain (neurons), heart, and adrenal medulla (chromaffin cells), among others, and are also classified into subtypes which can be distinguished using pharmacological approaches. Cone snails are marine gastropods that capture their prey by injecting venom, “conopeptides”, which cause paralysis in a few seconds.
    [Show full text]
  • A Novel 2.3 Mb Microduplication of 9Q34. 3 Inserted Into 19Q13. 4 in A
    Hindawi Publishing Corporation Case Reports in Pediatrics Volume 2012, Article ID 459602, 7 pages doi:10.1155/2012/459602 Case Report A Novel 2.3 Mb Microduplication of 9q34.3 Inserted into 19q13.4 in a Patient with Learning Disabilities Shalinder Singh,1 Fern Ashton,1 Renate Marquis-Nicholson,1 Jennifer M. Love,1 Chuan-Ching Lan,1 Salim Aftimos,2 Alice M. George,1 and Donald R. Love1, 3 1 Diagnostic Genetics, LabPlus, Auckland City Hospital, P.O. Box 110031, Auckland 1148, New Zealand 2 Genetic Health Service New Zealand-Northern Hub, Auckland City Hospital, Private Bag 92024, Auckland 1142, New Zealand 3 School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand Correspondence should be addressed to Donald R. Love, [email protected] Received 1 July 2012; Accepted 27 September 2012 Academic Editors: L. Cvitanovic-Sojat, G. Singer, and V. C. Wong Copyright © 2012 Shalinder Singh et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Insertional translocations in which a duplicated region of one chromosome is inserted into another chromosome are very rare. We report a 16.5-year-old girl with a terminal duplication at 9q34.3 of paternal origin inserted into 19q13.4. Chromosomal analysis revealed the karyotype 46,XX,der(19)ins(19;9)(q13.4;q34.3q34.3)pat. Cytogenetic microarray analysis (CMA) identified a ∼2.3Mb duplication of 9q34.3 → qter, which was confirmed by Fluorescence in situ hybridisation (FISH).
    [Show full text]
  • Anti-Cav2.2 (Aa 851-867) Polyclonal Antibody (DPAB2869RM) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use
    Anti-CaV2.2 (aa 851-867) polyclonal antibody (DPAB2869RM) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Product Overview Rabbit Anti-Mouse Calcium Channel, Voltage-Dependent, N Type, Alpha 1B Subunit Polyclonal Antibody. Recognizes the ~210 kDa and the ~240 kDa forms of α1B-subunit of Cav2.2. Supplied with a control peptide. Antigen Description The N-type calcium channel is a type of voltage-dependent calcium channel. Like the others of this class, the α1 subunit forms the pore through which calcium enters the cell and determines most of the channel"s properties. The α1 subunit is also known as the calcium channel, voltage- dependent, N type, alpha 1B subunit (CACNA1B) or Cav2.2 which in humans is encoded by the CACNA1B gene. Specificity Mouse; rat Immunogen a synthetic peptide [(C)RHHRHRDRDKTSASTPA] corresponding to amino acids 851-867 of the α1B-subunit of rat brain voltage-gated calcium channels, conjugated to KLH Isotype IgG Source/Host Rabbit Species Reactivity Rat Conjugate Unconjugated Applications IHC, ICC, IB, IP Positive Control None Format Liquid. 50 μl antibody lyophilized from PBS, 5% sucrose, 1% BSA, pH. 7.4 and 40 μg control peptide lyophilized from PBS. Size 50 μl Preservative ≤0.1% Sodium Azide Storage -20℃ Ship Ambient Temperature Only Standard Handling 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 1 © Creative Diagnostics All Rights Reserved GENE INFORMATION Gene Name Cacna1b calcium channel, voltage-dependent,
    [Show full text]
  • CACNA1A Mutations with Clinical Relevance in Migraine Affect Cav2.1
    CACNA1A mutations with clinical relevance in migraine affect Ca V2.1 channel regulation by G proteins and SNAREs Selma A. Serra Pascual TESI DOCTORAL UPF / 2011 DIRECTORS DE LA TESI: Dr. José Manuel Fernández-Fernández Dr. Miguel Á. Valverde Departament de Ciències de la Salut i de la Vida A mi madre, al meu pare y a Miguel. En record del besavi Salvador i de l’ avi Pere. “¡Como el entomólogo a la caza de mariposas de vistosos matices, mi atención perseguía, en el vergel de la substancia gris, células de formas delicadas y elegantes, las misteriosas mariposas del alma, cuyo batir de alas quién sabe si esclarecerá algún día el secreto de la vida mental!” Santiago Ramón y Cajal (1852-1934). iii AGRADECIMIENTOS ¡Parece mentira que esta aventura haya llegado a su fin! La realización de esta tesis ha supuesto una gran inversión personal y económica. Por lo segundo, agradezco al Ministerio de Ciencia e Innovación y a la Marató de TV3 el haber financiado nuestros proyectos científicos, y en concreto al Ministerio, el haberme concedido una beca. Me gustaría pensar que a pesar de la crisis que estamos atravesando los políticos y la sociedad sigan apostando por la investigación y el desarrollo en el futuro, pues en ello reside la clave fundamental para el progreso “sostenible”. Son muchas las personas que han aportado su conocimiento e ideas y ofrecido su respaldo durante el desarrollo de mi tesis. Gracias a todos por haberme hecho crecer como científica y como persona, haber contribuido a realizar este sueño y compartido algunas tristezas pero también muchas alegrías.
    [Show full text]
  • Localized, Non-Random Differences in Chromatin Accessibility Between Homologous Metaphase Chromosomes Wahab a Khan1,3, Peter K Rogan2,3* and Joan HM Knoll1,3*
    Khan et al. Molecular Cytogenetics 2014, 7:70 http://www.molecularcytogenetics.org/content/7/1/70 RESEARCH Open Access Localized, non-random differences in chromatin accessibility between homologous metaphase chromosomes Wahab A Khan1,3, Peter K Rogan2,3* and Joan HM Knoll1,3* Abstract Background: Condensation differences along the lengths of homologous, mitotic metaphase chromosomes are well known. This study reports molecular cytogenetic data showing quantifiable localized differences in condensation between homologs that are related to differences in accessibility (DA) of associated DNA probe targets. Reproducible DA was observed for ~10% of locus-specific, short (1.5-5 kb) single copy DNA probes used in fluorescence in situ hybridization. Results: Fourteen probes (from chromosomes 1, 5, 9, 11, 15, 17, 22) targeting genic and intergenic regions were developed and hybridized to cells from 10 individuals with cytogenetically-distinguishable homologs. Differences in hybridization between homologs were non-random for 8 genomic regions (RGS7, CACNA1B, GABRA5, SNRPN, HERC2, PMP22:IVS3, ADORA2B:IVS1, ACR) and were not unique to known imprinted domains or specific chromosomes. DNA probes within CCNB1, C9orf66, ADORA2B:Promoter-Ex1, PMP22:IVS4-Ex 5, and intergenic region 1p36.3 showed no DA (equivalent accessibility), while OPCML showed unbiased DA. To pinpoint probe locations, we performed 3D-structured illumination microscopy (3D-SIM). This showed that genomic regions with DA had 3.3-fold greater volumetric, integrated probe intensities and broad distributions of probe depths along axial and lateral axes of the 2 homologs, compared to a low copy probe target (NOMO1) with equivalent accessibility. Genomic regions with equivalent accessibility were also enriched for epigenetic marks of open interphase chromatin (DNase I HS, H3K27Ac, H3K4me1) to a greater extent than regions with DA.
    [Show full text]
  • Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands That Promote Axonal Growth
    Research Article: New Research Development Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth Jeremy S. Toma,1 Konstantina Karamboulas,1,ª Matthew J. Carr,1,2,ª Adelaida Kolaj,1,3 Scott A. Yuzwa,1 Neemat Mahmud,1,3 Mekayla A. Storer,1 David R. Kaplan,1,2,4 and Freda D. Miller1,2,3,4 https://doi.org/10.1523/ENEURO.0066-20.2020 1Program in Neurosciences and Mental Health, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada, 2Institute of Medical Sciences University of Toronto, Toronto, Ontario M5G 1A8, Canada, 3Department of Physiology, University of Toronto, Toronto, Ontario M5G 1A8, Canada, and 4Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada Abstract Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are es- sential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, in- cluding known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesen- chymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons.
    [Show full text]
  • Phenotype Informatics
    Freie Universit¨atBerlin Department of Mathematics and Computer Science Phenotype informatics: Network approaches towards understanding the diseasome Sebastian Kohler¨ Submitted on: 12th September 2012 Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) am Fachbereich Mathematik und Informatik der Freien Universitat¨ Berlin ii 1. Gutachter Prof. Dr. Martin Vingron 2. Gutachter: Prof. Dr. Peter N. Robinson 3. Gutachter: Christopher J. Mungall, Ph.D. Tag der Disputation: 16.05.2013 Preface This thesis presents research work on novel computational approaches to investigate and characterise the association between genes and pheno- typic abnormalities. It demonstrates methods for organisation, integra- tion, and mining of phenotype data in the field of genetics, with special application to human genetics. Here I will describe the parts of this the- sis that have been published in peer-reviewed journals. Often in modern science different people from different institutions contribute to research projects. The same is true for this thesis, and thus I will itemise who was responsible for specific sub-projects. In chapter 2, a new method for associating genes to phenotypes by means of protein-protein-interaction networks is described. I present a strategy to organise disease data and show how this can be used to link diseases to the corresponding genes. I show that global network distance measure in interaction networks of proteins is well suited for investigat- ing genotype-phenotype associations. This work has been published in 2008 in the American Journal of Human Genetics. My contribution here was to plan the project, implement the software, and finally test and evaluate the method on human genetics data; the implementation part was done in close collaboration with Sebastian Bauer.
    [Show full text]
  • Downloaded from the European Nucleotide Archive (ENA; 126
    Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 5 September 2018 doi:10.20944/preprints201809.0082.v1 1 Article 2 Transcriptomics as precision medicine to classify in 3 vivo models of dietary-induced atherosclerosis at 4 cellular and molecular levels 5 Alexei Evsikov 1,2, Caralina Marín de Evsikova 1,2* 6 1 Epigenetics & Functional Genomics Laboratory, Department of Molecular Medicine, Morsani College of 7 Medicine, University of South Florida, Tampa, Florida, 33612, USA; 8 2 Department of Research and Development, Bay Pines Veteran Administration Healthcare System, Bay 9 Pines, FL 33744, USA 10 11 * Correspondence: [email protected]; Tel.: +1-813-974-2248 12 13 Abstract: The central promise of personalized medicine is individualized treatments that target 14 molecular mechanisms underlying the physiological changes and symptoms arising from disease. 15 We demonstrate a bioinformatics analysis pipeline as a proof-of-principle to test the feasibility and 16 practicality of comparative transcriptomics to classify two of the most popular in vivo diet-induced 17 models of coronary atherosclerosis, apolipoprotein E null mice and New Zealand White rabbits. 18 Transcriptomics analyses indicate the two models extensively share dysregulated genes albeit with 19 some unique pathways. For instance, while both models have alterations in the mitochondrion, the 20 biochemical pathway analysis revealed, Complex IV in the electron transfer chain is higher in mice, 21 whereas the rest of the electron transfer chain components are higher in the rabbits. Several fatty 22 acids anabolic pathways are expressed higher in mice, whereas fatty acids and lipids degradation 23 pathways are higher in rabbits.
    [Show full text]
  • Targeting Alternative Splicing As a Potential Therapy for Episodic Ataxia Type 2
    biomedicines Review Targeting Alternative Splicing as a Potential Therapy for Episodic Ataxia Type 2 1 2 2,3 4,5, Fanny Jaudon , Simona Baldassari , Ilaria Musante , Agnes Thalhammer y, Federico Zara 2,3 and Lorenzo A. Cingolani 1,4,* 1 Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; [email protected] 2 Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; [email protected] (S.B.); [email protected] (I.M.); [email protected] (F.Z.) 3 Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16126 Genoa, Italy 4 Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia (IIT), 16132 Genoa, Italy; [email protected] 5 IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy * Correspondence: [email protected] Present address: SISSA-Scuola Internazionale Superiore di Studi Avanzati, 34136 Trieste, Italy. y Received: 21 August 2020; Accepted: 4 September 2020; Published: 5 September 2020 Abstract: Episodic ataxia type 2 (EA2) is an autosomal dominant neurological disorder characterized by paroxysmal attacks of ataxia, vertigo, and nausea that usually last hours to days. It is caused by loss-of-function mutations in CACNA1A, the gene encoding the pore-forming α1 subunit of P/Q-type voltage-gated Ca2+ channels. Although pharmacological treatments, such as acetazolamide and 4-aminopyridine, exist for EA2, they do not reduce or control the symptoms in all patients. CACNA1A is heavily spliced and some of the identified EA2 mutations are predicted to disrupt selective isoforms of this gene. Modulating splicing of CACNA1A may therefore represent a promising new strategy to develop improved EA2 therapies.
    [Show full text]