DOCSLIB.ORG

Mouse Lmbr1l Conditional Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Lmbr1l Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Lmbr1l Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Lmbr1l conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Lmbr1l gene (NCBI Reference Sequence: NM_029098 ; Ensembl: ENSMUSG00000022999 ) is located on Mouse chromosome 15. 17 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 17 (Transcript: ENSMUST00000023736). Exon 2~3 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Lmbr1l gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-349E22 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 an ENU-induced allele exhibit altered lymphopoiesis and lymphoid activation. Exon 2 starts from about 4.98% of the coding region. The knockout of Exon 2~3 will result in frameshift of the gene. The size of intron 1 for 5'-loxP site insertion: 2628 bp, and the size of intron 3 for 3'-loxP site insertion: 1019 bp. The size of effective cKO region: ~2165 bp. The cKO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 6 17 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Lmbr1l 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(8665bp) | A(21.85% 1893) | C(25.27% 2190) | T(26.68% 2312) | G(26.2% 2270) Note: The sequence of homologous arms and cKO region is analyzed to determine the GC content. Significant high GC-content regions are found. It may be difficult to construct this targeting vector. 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% chr15 - 98915472 98918471 3000 browser details YourSeq 83 2106 2204 3000 89.8% chr4 - 123270303 123270400 98 browser details YourSeq 82 2095 2200 3000 86.7% chr4 - 128739127 128739231 105 browser details YourSeq 80 2084 2200 3000 83.5% chr11 + 101127474 101127585 112 browser details YourSeq 78 2106 2200 3000 91.6% chr2 - 30411535 30558846 147312 browser details YourSeq 78 2107 2200 3000 89.3% chr17 + 31673974 31674066 93 browser details YourSeq 77 2106 2200 3000 88.3% chr15 - 99906022 99906115 94 browser details YourSeq 77 2095 2200 3000 86.7% chr15 + 74929242 75177896 248655 browser details YourSeq 75 2106 2200 3000 87.3% chrX - 152283063 152283156 94 browser details YourSeq 75 2106 2200 3000 87.3% chr2 - 125869028 125869121 94 browser details YourSeq 75 2104 2200 3000 86.5% chr15 - 10494526 10494621 96 browser details YourSeq 75 2106 2200 3000 88.9% chr8 + 106067049 106067142 94 browser details YourSeq 75 2095 2200 3000 87.4% chr6 + 140405297 140405401 105 browser details YourSeq 75 2106 2204 3000 89.5% chr1 + 150567831 150567929 99 browser details YourSeq 73 2110 2200 3000 90.2% chr4 - 119243601 119243691 91 browser details YourSeq 73 2106 2200 3000 86.2% chr4 - 117396492 117396585 94 browser details YourSeq 73 2106 2200 3000 86.2% chr17 - 21578081 21578174 94 browser details YourSeq 73 2106 2200 3000 86.2% chr10 - 19608491 19608584 94 browser details YourSeq 73 2106 2200 3000 87.8% chr15 + 81169570 81169663 94 browser details YourSeq 72 2106 2194 3000 91.1% chr11 - 84339811 84479714 139904 Note: The 3000 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 3000 1 3000 3000 100.0% chr15 - 98910307 98913306 3000 browser details YourSeq 265 2264 2649 3000 88.7% chr5 - 76895227 76895605 379 browser details YourSeq 264 2240 2612 3000 90.4% chr11 + 97339592 97340006 415 browser details YourSeq 240 2255 2605 3000 90.8% chr10 - 59245338 59245909 572 browser details YourSeq 223 2066 2439 3000 91.2% chr17 - 35735334 35735933 600 browser details YourSeq 221 2234 2587 3000 91.1% chr11 - 95439788 95440230 443 browser details YourSeq 209 2253 2544 3000 90.2% chr8 - 70474603 70474885 283 browser details YourSeq 209 2040 2439 3000 85.8% chr17 - 27835450 27835793 344 browser details YourSeq 205 2045 2390 3000 89.6% chr14 - 31031920 31032285 366 browser details YourSeq 204 2067 2843 3000 84.8% chr3 - 103363326 103363976 651 browser details YourSeq 199 2072 2439 3000 86.5% chr2 - 39112311 39112628 318 browser details YourSeq 199 2044 2649 3000 83.3% chr16 - 13873789 13874267 479 browser details YourSeq 195 2136 2843 3000 92.0% chr4 - 120471537 120472381 845 browser details YourSeq 193 2072 2429 3000 91.1% chrX - 74507841 74508426 586 browser details YourSeq 192 2040 2843 3000 83.9% chr17 - 71401072 71401402 331 browser details YourSeq 192 2314 2626 3000 90.7% chr11 - 4733410 4733783 374 browser details YourSeq 191 2249 2601 3000 86.2% chr19 - 11952608 11952908 301 browser details YourSeq 190 2151 2843 3000 86.0% chr11 - 84927426 84928046 621 browser details YourSeq 182 2136 2439 3000 89.9% chr2 - 119143452 119144109 658 browser details YourSeq 178 2459 2748 3000 91.2% chr4 - 129366043 129438783 72741 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: Lmbr1l limb region 1 like [ Mus musculus (house mouse) ] Gene ID: 74775, updated on 19-Oct-2019 Gene summary Official Symbol Lmbr1l provided by MGI Official Full Name limb region 1 like provided by MGI Primary source MGI:MGI:1289247 See related Ensembl:ENSMUSG00000022999 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 Limr; AA415653; D15Ertd735e; 1110013E13Rik Expression Broad expression in testis adult (RPKM 85.7), thymus adult (RPKM 30.7) and 20 other tissues See more Orthologs human all Genomic context Location: 15 F1; 15 55.1 cM See Lmbr1l in Genome Data Viewer Exon count: 18 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (98903918..98918098, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 15 NC_000081.5 (98734352..98748529, complement) Chromosome 15 - NC_000081.6 Page 5 of 8 https://www.alphaknockout.com Transcript information: This gene has 8 transcripts Gene: Lmbr1l ENSMUSG00000022999 Description limb region 1 like [Source:MGI Symbol;Acc:MGI:1289247] Gene Synonyms 1110013E13Rik, D15Ertd735e Location Chromosome 15: 98,903,917-98,918,231 reverse strand. GRCm38:CM001008.2 About this gene This gene has 8 transcripts (splice variants), 206 orthologues, 1 paralogue, 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 Lmbr1l-201 ENSMUST00000023736.9 2304 489aa ENSMUSP00000023736.8 Protein coding CCDS27811 Q9D1E5 TSL:1 GENCODE basic APPRIS P1 Lmbr1l-205 ENSMUST00000127548.1 970 No protein - Retained intron - - TSL:3 Lmbr1l-203 ENSMUST00000123950.8 687 No protein - Retained intron - - TSL:3 Lmbr1l-208 ENSMUST00000231087.1 562 No protein - Retained intron - - - Lmbr1l-207 ENSMUST00000135051.2 547 No protein - Retained intron - - TSL:5 Lmbr1l-206 ENSMUST00000128818.1 380 No protein - Retained intron - - TSL:2 Lmbr1l-202 ENSMUST00000109127.7 2548 No protein - lncRNA - - TSL:1 Lmbr1l-204 ENSMUST00000126159.1 656 No protein - lncRNA - - TSL:3 Page 6 of 8 https://www.alphaknockout.com 34.31 kb Forward strand 98.90Mb 98.91Mb 98.92Mb Genes Gm49442-201 >lncRNA (Comprehensive set... Contigs AC161165.5 > Genes (Comprehensive set... < Dhh-201protein coding < Lmbr1l-201protein coding < Rhebl1-207protein coding < Lmbr1l-202lncRNA < Rhebl1-206protein coding < Lmbr1l-208retained intron < Lmbr1l-206retained intron < Dhh-202protein coding < Lmbr1l-203retained intron < Lmbr1l-204lncRNA < Lmbr1l-205retained intron < Lmbr1l-207retained intron Regulatory Build 98.90Mb 98.91Mb 98.92Mb Reverse strand 34.31 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding processed transcript RNA gene Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000023736 < Lmbr1l-201protein coding Reverse strand 14.31 kb ENSMUSP00000023... Transmembrane heli... Low complexity (Seg) Coiled-coils (Ncoils) Prints Lipocalin-interacting membrane receptor Pfam LMBR1-like membrane protein PANTHER Lipocalin-interacting membrane receptor PTHR12625:SF2 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant splice region variant synonymous variant Scale bar 0 60 120 180 240 300 360 420 489 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
Load more

Recommended publications
  • University of Copenhagen, Copenhagen, Denmark, Citation: Pereira J, Johnson WE, O’Brien SJ, 8
    Evolutionary genomics and adaptive evolution of the hedgehog gene family (Shh, Ihh and Dhh) in vertebrates Pereira, Joana; Johnson, Warren E.; O'Brien, Stephen J.; Jarvis, Erich D; Zhang, Guojie; Gilbert, M. Thomas P.; Vasconcelos, Vitor; Antunes, Agostinho Published in: PloS one DOI: 10.1371/journal.pone.0074132 Publication date: 2014 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Pereira, J., Johnson, W. E., O'Brien, S. J., Jarvis, E. D., Zhang, G., Gilbert, M. T. P., Vasconcelos, V., & Antunes, A. (2014). Evolutionary genomics and adaptive evolution of the hedgehog gene family (Shh, Ihh and Dhh) in vertebrates. PloS one, 9(12), [e74132]. https://doi.org/10.1371/journal.pone.0074132 Download date: 24. sep.. 2021 RESEARCH ARTICLE Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (Shh, Ihh and Dhh) in Vertebrates Joana Pereira1¤, Warren E. Johnson2, Stephen J. O’Brien3,4, Erich D. Jarvis5, Guojie Zhang6, M. Thomas P. Gilbert7, Vitor Vasconcelos1,8, Agostinho Antunes1,8* 1. CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal, 2. Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia, United States of America, 3. Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia, 4. Oceanographic Center, N. Ocean Drive, Nova Southeastern University, Ft. Lauderdale, Florida, United States of America, 5. Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, United States of America, 6. BGI-Shenzhen, Beishan Industrial Zoon, Yantian District, Shenzhen, China, 7.
    [Show full text]
  • Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-Like Mouse Models: Tracking the Role of the Hairless Gene
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2006 Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene Yutao Liu University of Tennessee - Knoxville Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Life Sciences Commons Recommended Citation Liu, Yutao, "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino- like Mouse Models: Tracking the Role of the Hairless Gene. " PhD diss., University of Tennessee, 2006. https://trace.tennessee.edu/utk_graddiss/1824 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Yutao Liu entitled "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Life Sciences. Brynn H. Voy, Major Professor We have read this dissertation and recommend its acceptance: Naima Moustaid-Moussa, Yisong Wang, Rogert Hettich Accepted for the Council: Carolyn R.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Distinguishing Pleiotropy from Linked QTL Between Milk Production Traits
    Cai et al. Genet Sel Evol (2020) 52:19 https://doi.org/10.1186/s12711-020-00538-6 Genetics Selection Evolution RESEARCH ARTICLE Open Access Distinguishing pleiotropy from linked QTL between milk production traits and mastitis resistance in Nordic Holstein cattle Zexi Cai1*†, Magdalena Dusza2†, Bernt Guldbrandtsen1, Mogens Sandø Lund1 and Goutam Sahana1 Abstract Background: Production and health traits are central in cattle breeding. Advances in next-generation sequencing technologies and genotype imputation have increased the resolution of gene mapping based on genome-wide association studies (GWAS). Thus, numerous candidate genes that afect milk yield, milk composition, and mastitis resistance in dairy cattle are reported in the literature. Efect-bearing variants often afect multiple traits. Because the detection of overlapping quantitative trait loci (QTL) regions from single-trait GWAS is too inaccurate and subjective, multi-trait analysis is a better approach to detect pleiotropic efects of variants in candidate genes. However, large sample sizes are required to achieve sufcient power. Multi-trait meta-analysis is one approach to deal with this prob- lem. Thus, we performed two multi-trait meta-analyses, one for three milk production traits (milk yield, protein yield and fat yield), and one for milk yield and mastitis resistance. Results: For highly correlated traits, the power to detect pleiotropy was increased by multi-trait meta-analysis com- pared with the subjective assessment of overlapping of single-trait QTL confdence intervals. Pleiotropic efects of lead single nucleotide polymorphisms (SNPs) that were detected from the multi-trait meta-analysis were confrmed by bivariate association analysis. The previously reported pleiotropic efects of variants within the DGAT1 and MGST1 genes on three milk production traits, and pleiotropic efects of variants in GHR on milk yield and fat yield were con- frmed.
    [Show full text]
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
    [Show full text]
  • Human Social Genomics in the Multi-Ethnic Study of Atherosclerosis
    Getting “Under the Skin”: Human Social Genomics in the Multi-Ethnic Study of Atherosclerosis by Kristen Monét Brown A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Epidemiological Science) in the University of Michigan 2017 Doctoral Committee: Professor Ana V. Diez-Roux, Co-Chair, Drexel University Professor Sharon R. Kardia, Co-Chair Professor Bhramar Mukherjee Assistant Professor Belinda Needham Assistant Professor Jennifer A. Smith © Kristen Monét Brown, 2017 [email protected] ORCID iD: 0000-0002-9955-0568 Dedication I dedicate this dissertation to my grandmother, Gertrude Delores Hampton. Nanny, no one wanted to see me become “Dr. Brown” more than you. I know that you are standing over the bannister of heaven smiling and beaming with pride. I love you more than my words could ever fully express. ii Acknowledgements First, I give honor to God, who is the head of my life. Truly, without Him, none of this would be possible. Countless times throughout this doctoral journey I have relied my favorite scripture, “And we know that all things work together for good, to them that love God, to them who are called according to His purpose (Romans 8:28).” Secondly, I acknowledge my parents, James and Marilyn Brown. From an early age, you two instilled in me the value of education and have been my biggest cheerleaders throughout my entire life. I thank you for your unconditional love, encouragement, sacrifices, and support. I would not be here today without you. I truly thank God that out of the all of the people in the world that He could have chosen to be my parents, that He chose the two of you.
    [Show full text]
  • Sea Anemone Genome Reveals the Gene Repertoire and Genomic Organization of the Eumetazoan Ancestor
    Lawrence Berkeley National Laboratory Lawrence Berkeley National Laboratory Title Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor Permalink https://escholarship.org/uc/item/3b01p9bc Authors Putnam, Nicholas H. Srivastava, Mansi Hellsten, Uffe et al. Publication Date 2007 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor Nicholas H. Putnam[1], Mansi Srivastava[2], Uffe Hellsten[1], Bill Dirks[2], Jarrod Chapman[1], Asaf Salamov[1], Astrid Terry[1], Harris Shapiro[1], Erika Lindquist[1], Vladimir V. Kapitonov[3], Jerzy Jurka[3], Grigory Genikhovich[4], Igor Grigoriev[1], JGI Sequencing Team[1], Robert E. Steele[5], John Finnerty[6], Ulrich Technau[4], Mark Q. Martindale[7], Daniel S. Rokhsar[1,2] [1] Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 [2] Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California, Berkeley CA 94720 [3] Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043 [4] Sars International Centre for Marine Molecular Biology, University of Bergen, Thormoeøhlensgt 55; 5008, Bergen, Norway [5] Department of Biological Chemistry and the Developmental Biology Center, University of California, Irvine, CA 92697 [6] Department of Biology, Boston University, Boston, MA 02215 [7] Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI 96813 Abstract Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the Cnidaria, the oldest eumetazoan phylum. Here we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet anemone Nematostella vectensis.
    [Show full text]
  • Gene Expression Changes in Goat Testes During Development and in Sperm During the Breeding and Non-Breeding Seasons: a Novel Male Fertility Test?
    Gene Expression Changes in Goat Testes During Development and in Sperm During the Breeding and Non-breeding Seasons: A Novel Male Fertility Test? Azure N. Faucette2, Desiree Rucker1, Lou Nuti1, David W. Forrest2, Nancy H. Ing2, Gary R. Newton1,3 Prairie View A&M University, Cooperative Agriculture Research Center1 and Texas AgriLife Research2 Objectives 2. Activities 1. To analyze alterations in gene expression in the goat testes during Ejaculates were collected from mature Alpine and Boer bucks ( n = 4 bucks each) development. in October (peak breeding) and April ( not peak breeding). RNA was isolated from 2. To analyze alterations in gene products in goat sperm between sperm, fluorescently labeled and hybridized to Agilent bovine microarrays. Gene breeding and non-breeding seasons products that were differentially expressed between months (p < 0.05) are reported in the Table. Selected genes are being analyzed with real time PCR in ongoing 1. Activities studies. Goat testes were harvested from five Alpine bucks at 0, 2, 4, 6, and 8 months of age. Tissues were fixed in paraformaldehyde and used for in situ hybridization . In addition, tissues were frozen and RNA isolated for mRNA analyses by Northern blotting. Gene products chosen as Microarrays detect altered mRNAs in sperm markers for testis cells: Gene Name Abbr. Fold SOX 9 – Sertoli cells change* STRA8 and Heat shock protein A8 (HSPA-8) – early germ cells Zinc finger CCHC domain containing 6 ZCCHC6 4.1 Protamine 1 (PRM1) – maturing germ cells Microcephalin 1 MCPH1 3.6 Heat shock protein
    [Show full text]
  • Large-Scale Genome-Wide Association Analysis of Bipolar Disorder Identifies a New Susceptibility Locus Near ODZ4
    LETTERS Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4 Psychiatric GWAS Consortium Bipolar Disorder Working Group1 We conducted a combined genome-wide association study our association study of bipolar disorder from 16,731 samples and a (GWAS) of 7,481 individuals with bipolar disorder (cases) and replication sample of 46,918 individuals. 9,250 controls as part of the Psychiatric GWAS Consortium. We received primary genotype and phenotype data (Table 1, Our replication study tested 34 SNPs in 4,496 independent Supplementary Note and Supplementary Table 1). Results have cases with bipolar disorder and 42,422 independent controls been reported singly6,7,9–11 and in combinations8,9,12 in seven publi- and found that 18 of 34 SNPs had P < 0.05, with 31 of 34 SNPs cations with case and control overlap. We divided the data into having signals with the same direction of effect (P = 3.8 × 11 case and control groupings and assigned each individual to only 10−7). An analysis of all 11,974 bipolar disorder cases and one group (Table 1). The final dataset comprised 7,481 unique cases 51,792 controls confirmed genome-wide significant evidence and 9,250 unique controls. Cases had the following diagnoses: bipolar of association for CACNA1C and identified a new intronic disorder type 1 (n = 6,289; 84%), bipolar disorder type 2 (n = 824; variant in ODZ4. We identified a pathway comprised of 11%) and schizoaffective disorder bipolar (n = 263; 4%), and there subunits of calcium channels enriched in bipolar disorder were 105 individuals with other bipolar diagnoses (1%).
    [Show full text]
  • A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression
    Supplementary Materials A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression Table S1. Statistically significant DEGs (Adj. p-value < 0.01) derived from meta-analysis for samples irradiated with high doses of HZE particles, collected 6-24 h post-IR not common with any other meta- analysis group. This meta-analysis group consists of 3 DEG lists obtained from DGEA, using a total of 11 control and 11 irradiated samples [Data Series: E-MTAB-5761 and E-MTAB-5754]. Ensembl ID Gene Symbol Gene Description Up-Regulated Genes ↑ (2425) ENSG00000000938 FGR FGR proto-oncogene, Src family tyrosine kinase ENSG00000001036 FUCA2 alpha-L-fucosidase 2 ENSG00000001084 GCLC glutamate-cysteine ligase catalytic subunit ENSG00000001631 KRIT1 KRIT1 ankyrin repeat containing ENSG00000002079 MYH16 myosin heavy chain 16 pseudogene ENSG00000002587 HS3ST1 heparan sulfate-glucosamine 3-sulfotransferase 1 ENSG00000003056 M6PR mannose-6-phosphate receptor, cation dependent ENSG00000004059 ARF5 ADP ribosylation factor 5 ENSG00000004777 ARHGAP33 Rho GTPase activating protein 33 ENSG00000004799 PDK4 pyruvate dehydrogenase kinase 4 ENSG00000004848 ARX aristaless related homeobox ENSG00000005022 SLC25A5 solute carrier family 25 member 5 ENSG00000005108 THSD7A thrombospondin type 1 domain containing 7A ENSG00000005194 CIAPIN1 cytokine induced apoptosis inhibitor 1 ENSG00000005381 MPO myeloperoxidase ENSG00000005486 RHBDD2 rhomboid domain containing 2 ENSG00000005884 ITGA3 integrin subunit alpha 3 ENSG00000006016 CRLF1 cytokine receptor like
    [Show full text]
  • Reciprocal Mouse and Human Limb Phenotypes Caused by Gain- and Loss-Of-Function Mutations Affecting Lmbr1
    Copyright 2001 by the Genetics Society of America Reciprocal Mouse and Human Limb Phenotypes Caused by Gain- and Loss-of-Function Mutations Affecting Lmbr1 Richard M. Clark,* Paul C. Marker,*,1 Erich Roessler,† Amalia Dutra,‡ John C. Schimenti,§ Maximilian Muenke† and David M. Kingsley*,** *Department of Developmental Biology, Stanford University, Stanford, California 94305-5327, †Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-1852, ‡Cytogenetic and Confocal Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, §The Jackson Laboratory, Bar Harbor, Maine 04609 and **Howard Hughes Medical Institute, Stanford University, Stanford, California 94305-5327 Manuscript received March 20, 2001 Accepted for publication June 1, 2001 ABSTRACT The major locus for dominant preaxial polydactyly in humans has been mapped to 7q36. In mice the dominant Hemimelic extra toes (Hx) and Hammertoe (Hm) mutations map to a homologous chromosomal region and cause similar limb defects. The Lmbr1 gene is entirely within the small critical intervals recently defined for both the mouse and human mutations and is misexpressed at the exact time that the mouse Hx phenotype becomes apparent during limb development. This result suggests that Lmbr1 may underlie preaxial polydactyly in both mice and humans. We have used deletion chromosomes to demonstrate that the dominant mouse and human limb defects arise from gain-of-function mutations and not from haploinsufficiency. Furthermore, we created a loss-of-function mutation in the mouse Lmbr1 gene that causes digit number reduction (oligodactyly) on its own and in trans to a deletion chromosome. The loss of digits that we observed in mice with reduced Lmbr1 activity is in contrast to the gain of digits observed in Hx mice and human polydactyly patients.
    [Show full text]
  • Overlapping BXSB Congenic Intervals, in Combination with Microarray Gene Expression, Reveal Novel Lupus Candidate Genes
    Genes and Immunity (2006) 7, 250–263 & 2006 Nature Publishing Group All rights reserved 1466-4879/06 $30.00 www.nature.com/gene ORIGINAL ARTICLE Overlapping BXSB congenic intervals, in combination with microarray gene expression, reveal novel lupus candidate genes MEK Haywood1, SJ Rose1, S Horswell2, MJ Lees1,GFu3, MJ Walport4 and BJ Morley1 1Rheumatology Section, Division of Medicine, Imperial College Faculty of Medicine, London, UK; 2Medical Research Council, Clinical Sciences Centre, Hammersmith Hospital, London, UK; 3Oxitec Limited, Oxford, UK and 4The Wellcome Trust, London, UK The BXSB mouse strain is an important model of glomerulonephritis observed in systemic lupus erythematosus (SLE). Linkage studies have successfully identified disease-susceptibility intervals; however, extracting the identity of the susceptibility gene(s) in such regions is the crucial next step. Congenic mouse strains present a defined genetic resource that is highly amenable to microarray analysis. We have performed microarray analysis using a series of chromosome 1 BXSB congenic mice with partially overlapping disease-susceptibility intervals. Simultaneous comparison of the four congenic lines allowed the identification of expression differences associated with both the initiation and progression of disease. Thus, we have identified a number of novel SLE disease gene candidates and have confirmed the identity of Ifi202 as a disease candidate in the BXSB strain. Sequencing of the promoter regions of Gas5 has revealed polymorphisms in the BXSB strain, which may account for the differential expression profile. Furthermore, the combination of the microarray results with the different phenotypes of these mice has allowed the identification of a number of expression differences that do not necessarily map to the congenic interval, but may be implicated in disease pathways.
    [Show full text]