Mouse Lim2 Conditional Knockout Project (CRISPR/Cas9)
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Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins
International Journal of Molecular Sciences Article Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins M. Quadir Siddiqui 1,† , Maulik D. Badmalia 1,† and Trushar R. Patel 1,2,3,* 1 Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; [email protected] (M.Q.S.); [email protected] (M.D.B.) 2 Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive, Calgary, AB T2N 4N1, Canada 3 Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada * Correspondence: [email protected] † These authors contributed equally to the work. Abstract: Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and func- tions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share Citation: Siddiqui, M.Q.; Badmalia, similarities with transcriptional regulators and have positively charged electrostatic patches, which M.D.; Patel, T.R. -
Variants in PAX6, PITX3 and HSF4 Causing Autosomal Dominant Congenital Cataracts ✉ ✉ Vanita Berry 1,2 , Alex Ionides2, Nikolas Pontikos 1,2, Anthony T
www.nature.com/eye ARTICLE OPEN Variants in PAX6, PITX3 and HSF4 causing autosomal dominant congenital cataracts ✉ ✉ Vanita Berry 1,2 , Alex Ionides2, Nikolas Pontikos 1,2, Anthony T. Moore2, Roy A. Quinlan3 and Michel Michaelides 1,2 © Crown 2021 BACKGROUND: Lens development is orchestrated by transcription factors. Disease-causing variants in transcription factors and their developmental target genes are associated with congenital cataracts and other eye anomalies. METHODS: Using whole exome sequencing, we identified disease-causing variants in two large British families and one isolated case with autosomal dominant congenital cataract. Bioinformatics analysis confirmed these disease-causing mutations as rare or novel variants, with a moderate to damaging pathogenicity score, with testing for segregation within the families using direct Sanger sequencing. RESULTS: Family A had a missense variant (c.184 G>A; p.V62M) in PAX6 and affected individuals presented with nuclear cataract. Family B had a frameshift variant (c.470–477dup; p.A160R*) in PITX3 that was also associated with nuclear cataract. A recurrent missense variant in HSF4 (c.341 T>C; p.L114P) was associated with congenital cataract in a single isolated case. CONCLUSIONS: We have therefore identified novel variants in PAX6 and PITX3 that cause autosomal dominant congenital cataract. Eye; https://doi.org/10.1038/s41433-021-01711-x INTRODUCTION consistent with early developmental effects as would be Cataract the opacification of the eye lens is the most common, but anticipated for PAX6 and PITX3 transcription factors. Recently, treatable cause of blindness in the world (https://www.who.int/ we have found two novel mutations in the transcription factors publications-detail/world-report-on-vision). -
Relative Impact of Multi-Layered Genomic Data on Gene Expression
Sohn et al. BMC Systems Biology 2013, 7(Suppl 6):S9 http://www.biomedcentral.com/1752-0509/7/S6/S9 RESEARCH Open Access Relative impact of multi-layered genomic data on gene expression phenotypes in serous ovarian tumors Kyung-Ah Sohn1†, Dokyoon Kim2,3†, Jaehyun Lim2,4, Ju Han Kim2,4* From 24th International Conference on Genome Informatics (GIW 2013) Singapore, Singapore. 16-18 December 2013 Abstract Background: The emerging multi-layers of genomic data have provided unprecedented opportunities for cancer research, especially for the association study between gene expressions and other types of genomic features. No previous approaches, however, provide an adequate statistical framework for or global analysis on the relative impact of different genomic feature layers to gene expression phenotypes. Methods: We propose an integrative statistical framework based on a sparse regression to model the impact of multi-layered genomic features on gene expression traits. The proposed approach can be regarded as an integrative expression Quantitative Traits Loci approach in which not only the genetic variations of SNPs or copy number variations but also other features in both genomic and epigenomic levels are used to explain the expression of genes. To highlight the validity of the proposed approach, the TCGA ovarian cancer dataset was analysed as a pilot task. Results: The analysis shows that our integrative approach has consistently superior power in predicting gene expression levels compared to that from each single data type-based analysis. Moreover, the proposed method has the advantage of producing a substantially reduced number of spurious associations. We provide an interesting characterization of genes in terms of its genomic association patterns. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
RNA Sequencing and Bioinformatics Analysis of Human Lens Epithelial
Wang et al. BMC Ophthalmology (2021) 21:152 https://doi.org/10.1186/s12886-021-01915-5 RESEARCH ARTICLE Open Access RNA sequencing and bioinformatics analysis of human lens epithelial cells in age-related cataract Zhongying Wang1†, Dongmei Su2†, Shanhe Liu1, Guiqian Zheng1, Gaobo Zhang1, Tingsong Cui1,XuMa2*, Zhaoyi Sun1* and Shanshan Hu1* Abstract Background: Age-related cataract (ARC) is the main cause of blindness in older individuals but its specific pathogenic mechanism is unclear. This study aimed to identify differentially expressed genes (DEGs) associated with ARC and to improve our understanding of the disease mechanism. Methods: Anterior capsule samples of the human lens were collected from ARC patients and healthy controls and used for RNA sequencing to detect DEGs. Identified DEGs underwent bioinformatics analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Subsequently, reverse transcription quantitative RT-qPCR was used to validate the different expression levels of selected genes. Results: A total of 698 up-regulated DEGs and 414 down-regulated DEGs were identified in ARC patients compared with controls by transcriptome analysis. Through GO and KEGG bioinformatics analysis, the functions of significantly DEGs and their possible molecular mechanisms were determined. Sequencing results were verified by RT-qPCR as being accurate and reliable. Conclusions: This study identified several genes associated with ARC, which improves our knowledge of the disease mechanism. Keywords: Age-related cataract, Differentially expressed genes, Bioinformatics analysis, Pathogenic genes Background alternative effective methods are necessary to prevent and Age-related cataract (ARC) is a common visual disorder treat the occurrence and development of ARC. -
Subterranean Mammals Show Convergent Regression in Ocular Genes and Enhancers, Along with Adaptation to Tunneling
RESEARCH ARTICLE Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling Raghavendran Partha1, Bharesh K Chauhan2,3, Zelia Ferreira1, Joseph D Robinson4, Kira Lathrop2,3, Ken K Nischal2,3, Maria Chikina1*, Nathan L Clark1* 1Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United States; 2UPMC Eye Center, Children’s Hospital of Pittsburgh, Pittsburgh, United States; 3Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, United States; 4Department of Molecular and Cell Biology, University of California, Berkeley, United States Abstract The underground environment imposes unique demands on life that have led subterranean species to evolve specialized traits, many of which evolved convergently. We studied convergence in evolutionary rate in subterranean mammals in order to associate phenotypic evolution with specific genetic regions. We identified a strong excess of vision- and skin-related genes that changed at accelerated rates in the subterranean environment due to relaxed constraint and adaptive evolution. We also demonstrate that ocular-specific transcriptional enhancers were convergently accelerated, whereas enhancers active outside the eye were not. Furthermore, several uncharacterized genes and regulatory sequences demonstrated convergence and thus constitute novel candidate sequences for congenital ocular disorders. The strong evidence of convergence in these species indicates that evolution in this environment is recurrent and predictable and can be used to gain insights into phenotype–genotype relationships. DOI: https://doi.org/10.7554/eLife.25884.001 *For correspondence: [email protected] (MC); [email protected] (NLC) Competing interests: The Introduction authors declare that no The subterranean habitat has been colonized by numerous animal species for its shelter and unique competing interests exist. -
The Human Genome Project
TO KNOW OURSELVES ❖ THE U.S. DEPARTMENT OF ENERGY AND THE HUMAN GENOME PROJECT JULY 1996 TO KNOW OURSELVES ❖ THE U.S. DEPARTMENT OF ENERGY AND THE HUMAN GENOME PROJECT JULY 1996 Contents FOREWORD . 2 THE GENOME PROJECT—WHY THE DOE? . 4 A bold but logical step INTRODUCING THE HUMAN GENOME . 6 The recipe for life Some definitions . 6 A plan of action . 8 EXPLORING THE GENOMIC LANDSCAPE . 10 Mapping the terrain Two giant steps: Chromosomes 16 and 19 . 12 Getting down to details: Sequencing the genome . 16 Shotguns and transposons . 20 How good is good enough? . 26 Sidebar: Tools of the Trade . 17 Sidebar: The Mighty Mouse . 24 BEYOND BIOLOGY . 27 Instrumentation and informatics Smaller is better—And other developments . 27 Dealing with the data . 30 ETHICAL, LEGAL, AND SOCIAL IMPLICATIONS . 32 An essential dimension of genome research Foreword T THE END OF THE ROAD in Little has been rapid, and it is now generally agreed Cottonwood Canyon, near Salt that this international project will produce Lake City, Alta is a place of the complete sequence of the human genome near-mythic renown among by the year 2005. A skiers. In time it may well And what is more important, the value assume similar status among molecular of the project also appears beyond doubt. geneticists. In December 1984, a conference Genome research is revolutionizing biology there, co-sponsored by the U.S. Department and biotechnology, and providing a vital of Energy, pondered a single question: Does thrust to the increasingly broad scope of the modern DNA research offer a way of detect- biological sciences. -
35Th International Society for Animal Genetics Conference 7
35th INTERNATIONAL SOCIETY FOR ANIMAL GENETICS CONFERENCE 7. 23.16 – 7.27. 2016 Salt Lake City, Utah ABSTRACT BOOK https://www.asas.org/meetings/isag2016 INVITED SPEAKERS S0100 – S0124 https://www.asas.org/meetings/isag2016 epigenetic modifications, such as DNA methylation, and measuring different proteins and cellular metab- INVITED SPEAKERS: FUNCTIONAL olites. These advancements provide unprecedented ANNOTATION OF ANIMAL opportunities to uncover the genetic architecture GENOMES (FAANG) ASAS-ISAG underlying phenotypic variation. In this context, the JOINT SYMPOSIUM main challenge is to decipher the flow of biological information that lies between the genotypes and phe- notypes under study. In other words, the new challenge S0100 Important lessons from complex genomes. is to integrate multiple sources of molecular infor- T. R. Gingeras* (Cold Spring Harbor Laboratory, mation (i.e., multiple layers of omics data to reveal Functional Genomics, Cold Spring Harbor, NY) the causal biological networks that underlie complex traits). It is important to note that knowledge regarding The ~3 billion base pairs of the human DNA rep- causal relationships among genes and phenotypes can resent a storage devise encoding information for be used to predict the behavior of complex systems, as hundreds of thousands of processes that can go on well as optimize management practices and selection within and outside a human cell. This information is strategies. Here, we describe a multi-step procedure revealed in the RNAs that are composed of 12 billion for inferring causal gene-phenotype networks underly- nucleotides, considering the strandedness and allelic ing complex phenotypes integrating multi-omics data. content of each of the diploid copies of the genome. -
Molvis Template
Molecular Vision 3: 5, 1997 <http://www.emory.edu/molvis/v3/steele> © Molecular Vision Received 24 Mar 1997 | Accepted 2 May 1997 | Published 7 May 1997 Identification of a mutation in the MP19 gene, Lim2, in the cataractous mouse mutant To3 Ernest C. Steele, Jr.,1 Stefan Kerscher,2 Mary F. Lyon,2 Peter H. Glenister,2 Jack Favor,3 JianHua Wang,1 and Robert L. Church1* 1Emory Eye Center, Emory University School of Medicine, Department of Ophthalmology, Atlanta, GA, USA, 2MRC Mammalian Genetics Unit, Harwell, Didcot, Oxfordshire OX11 ORD, United Kingdom, and 3Institute of Mammalian Genetics, GSF - National Research Center for the Environment and Health, D-85758 Neuherberg, Germany Purpose: Lim2, the gene encoding the second most abundant lens specific integral membrane protein, MP19, has recently been proposed as an ideal candidate gene for the cataractous mouse mutant, To3. The aim of this study was to screen the Lim2 gene in the To3 mutant for a genetic lesion that was correlated and consistent with the mutant phenotype. Methods: Genomic DNA was isolated from both normal mouse parental strains as well as the heterozygous and homozygous To3 cataract mutant. PCR was used to generate overlapping fragments of the entire Lim2 gene from these DNAs. The coding regions, including splice junctions and the translational termination site, of these fragments were then sequenced. Results: A single G -> T transversion was identified within the first coding exon of the Lim2 gene in the To3 mutant DNA. This DNA change results in the nonconservative substitution of a valine for the normally encoded glycine at amino acid 15 of the MP19 polypeptide. -
UNIVERSITY of CALIFORNIA, IRVINE Gene Regulatory
UNIVERSITY OF CALIFORNIA, IRVINE Gene Regulatory Mechanisms in Epithelial Specification and Function DISSERTATION submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biomedical Sciences by Rachel Herndon Klein Dissertation Committee: Professor Bogi Andersen, M.D., Chair Professor Xing Dai, Ph.D. Professor Anand Ganesan, M.D. Professor Ali Mortazavi, Ph.D Professor Kyoko Yokomori, Ph.D 2015 © 2015 Rachel Herndon Klein DEDICATION To My parents, my sisters, my husband, and my friends for your love and support, and to Ben with all my love. ii TABLE OF CONTENTS Page LIST OF FIGURES iv LIST OF TABLES vi ACKNOWLEDGMENTS vii CURRICULUM VITAE viii-ix ABSTRACT OF THE DISSERTATION x-xi CHAPTER 1: INTRODUCTION 1 CHAPTER 2: Cofactors of LIM domain (CLIM) proteins regulate corneal epithelial progenitor cell function through noncoding RNA H19 22 CHAPTER 3: KLF7 regulates the corneal epithelial progenitor cell state acting antagonistically to KLF4 49 CHAPTER 4: GRHL3 interacts with super enhancers and the neuronal repressor REST to regulate keratinocyte differentiation and migration 77 CHAPTER 5: Methods 103 CHAPTER 6: Summary and Conclusions 111 REFERENCES 115 iii LIST OF FIGURES Page Figure 1-1. Structure and organization of the epidermis. 3 Figure 1-2. Structure of the limbus, and cornea epithelium. 4 Figure 1-3. Comparison of H3K4 methylating SET enzymes between S. cerevisiae, D. melanogaster, and H. sapiens. 18 Figure 1-4. The WRAD complex associates with Trithorax SET enzymes. 18 Figure 1-5. Model for GRHL3, PcG, and TrX –mediated regulation of epidermal differentiation genes. 19 Figure 2-1. Microarray gene expression analysis of postnatal day 3 (P3) whole mouse corneas reveals genes and pathways with altered expression in K14-DN-Clim mice. -
Mouse Models of Congenital Cataract
Mouse models of JOCHEN GRAW congenital cataract Abstract approach to collecting murine cataract mutations was initiated about 20 years ag02 Mouse mutants affecting lens development using paternal treatment of germ cells by X-raT are excellent models for corresponding human and later ethylnitrosourea.3 Among the disorders. The mutant aphakia has been offspring, dominant cataract mutations were characterised by bilaterally aphakic eyes identified by slit lamp observations and (Varnum and Stevens, J Hered 1968;59:147-50); subsequent genetic confirmation. The the corresponding gene was mapped to Neuherberg collection of cataracts contains now chromosome 19 (Varnum and Stevens, Mouse about 150 lines of independent origin and News Lett 1975;53:35). Recent investigations in distinct phenotypes.4,s our laboratory refined the linkage of 0.6 cM proximal to the marker D19Mitl0. Several candidate genes have been excluded (Chukl, Mouse models affecting early eye and lens FgfS, Lbpl, Npm3, Pax2, Pitx3). The Cat3 development mutations are characterised by vacuolated One of the most important genes in eye lenses caused by alterations in the initial development is the paired-box gene Pax6, which secondary lens fibre cell differentiation. is affected in various alleles of the mouse and Secondary malformations develop at the rat Small eye (Sey) mutants.6,7 In homozygous cornea and iris, but the retina remains Sey mice, eyes and nasal cavities do not unaffected. The mutation has been mapped to develop; the animals die soon after birth. The chromosome 10 close to the markers DlOMit41 histological analysis of homozygous mutants and DI0Mit95. Several candidate genes have demonstrated the presence of optic vesicles, but been excluded (Den, Elk3, Lde, MellS, Tr2-11). -
An RNA-Seq-Based Resource for Pain and Sensory Neuroscience Research
bioRxiv preprint doi: https://doi.org/10.1101/165431; this version posted October 13, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Title: Comparative transcriptome profiling of the human and mouse dorsal root ganglia: An RNA-seq-based resource for pain and sensory neuroscience research Short Title: Human and mouse DRG comparative transcriptomics Pradipta Ray 1, 2 #, Andrew Torck 1 , Lilyana Quigley 1, Andi Wangzhou 1, Matthew Neiman 1, Chandranshu Rao 1, Tiffany Lam 1, Ji-Young Kim 1, Tae Hoon Kim 2, Michael Q. Zhang 2, Gregory Dussor 1 and Theodore J. Price 1, # 1 The University of Texas at Dallas, School of Behavioral and Brain Sciences 2 The University of Texas at Dallas, Department of Biological Sciences # Corresponding authors Theodore J Price Pradipta Ray School of Behavioral and Brain Sciences School of Behavioral and Brain Sciences The University of Texas at Dallas The University of Texas at Dallas BSB 14.102G BSB 10.608 800 W Campbell Rd 800 W Campbell Rd Richardson TX 75080 Richardson TX 75080 972-883-4311 972-883-7262 [email protected] [email protected] Number of pages: 27 Number of figures: 9 Number of tables: 8 Supplementary Figures: 4 Supplementary Files: 6 Word count: Abstract = 219; Introduction = 457; Discussion = 1094 Conflict of interest: The authors declare no conflicts of interest Patient anonymity and informed consent: Informed consent for human tissue sources were obtained by Anabios, Inc. (San Diego, CA). Human studies: This work was approved by The University of Texas at Dallas Institutional Review Board (MR 15-237).