DOCSLIB.ORG

The EF-Handome: Combining Comparative Genomic Study Using Famdbtool, a New Bioinformatics Tool, and the Network of Expertise of the European Calcium Society

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The EF-Handome: Combining Comparative Genomic Study Using Famdbtool, a New Bioinformatics Tool, and the Network of Expertise of the European Calcium Society View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biochimica et Biophysica Acta 1742 (2004) 179–183 http://www.elsevier.com/locate/bba Review The EF-Handome: combining comparative genomic study using FamDBtool, a new bioinformatics tool, and the network of expertise of the European Calcium Society Jacques Haiech*, Saad B.M. Moulhaye, Marie-Claude Kilhoffer UMR 7034 CNRS and IFR 85 Gilbert Laustriat, 74, route du Rhin, 67401 ILLKIRCH France Received 9 August 2004; received in revised form 1 October 2004; accepted 4 October 2004 Available online 20 October 2004 Abstract By combining a bioinformatics tool (FamDBTool) and the expertise of a network of calcium binding proteins specialists (European Calcium Society), we aim to accelerate and to rationalize the curation of the public general biological database such as Swissprot and Entrez Gene with respect to specific protein families. In this paper, we show the feasibility of such rationale in order to set and to curate the human, mouse and rat sets of EF-Hand genes, the EF-Handome. D 2004 Elsevier B.V. All rights reserved. Keywords: EF-Handome; FamDBtool; European Calcium Society 1. Introduction in the human genome. Most of these genes present orthologs in mouse and rat. The proteins coded by these Calcium is one of the most important second mes- genes are divided in several subfamilies based on sequence sengers in eukaryotic cells, and probably also in similarities. prokaryotic cells [1,2]. Upon cellular stimulation, the One of the largest subfamily is constituted by the S100 cytosolic calcium concentration undergoes either a tran- proteins (see http://www.unizh.ch/ ~kispi/clinchem/calzium/ sient increase or a set of calcium oscillations. In order to index.html). Although several EF-hand databases exist decipher such calcium signals, the cell possesses calcium- (http://www.structbio.vanderbilt.edu/cabp_database/), it is binding proteins that are able to detect either a transient difficult to obtain all the curated information in one increase in the calcium concentration amplitude or a unique location. In order to fulfill this aim, we have frequency type signal [3]. developed a new bioinformatics tool, FamDBtool, that EF-hand proteins represent the most abundant family of allows us to create an individual database for a given such eukaryotic calcium binding proteins [4,5].These protein family. This tool will be described elsewhere proteins evolve from an ancestral domain of 36 amino and can be obtained upon request. We have used this acids composed of two alpha helical domains and one tool to build an EF-hand protein database (the EF- calcium-binding loop. More than 200 genes coding for Handome) [6] that collects the human, mouse and rat proteins containing at least one EF-hand domain are found genes. This database is used as a working tool among the members of the European Calcium Society (ECS) not only to allow a group of experts to help in the curation of the data from the public databases, but also * Corresponding author. Tel.: +33 388 676889; fax: +33 388 664633. to share information and resources. The database is E-mail address: [email protected] (J. Haiech). accessible through the web server of the ECS (http:// 0167-4889/$ - see front matter D 2004 Elsevier B.V. All rights reserved. doi:10.1016/j.bbamcr.2004.10.001 180 J. Haiech et al. / Biochimica et Biophysica Acta 1742 (2004) 179–183 www.ulb.ac.be/assoc/ecs/ or upon request to haiech@ the gene form is hyperlinked and allows the access to the pharma.u-strasbg.fr). primary database. Several tools have been implemented in order to curate the database and to check the coherency of the data. 2. Building the database Then the database is expanded by searching for genes that present similarities to the starting set of genes. The The EF-Hand database is built from a list of user prevents the integration of new genes in the database Swissprot/TREMBL or RefSeq Identity numbers (Id list). that are not biologically pertinent. Therefore, the database Then, the information needed to fill the different tables may be steadily increased upon user supervision. and fields of the database is obtained from the main The entire database or some specific genes are updated public databases. The collected information for each gene upon user request. Complete description of the database is is presented in Fig. 1. described in the Master Thesis (FamDBTool, S. Moul- The form is divided into four parts, namely (i) general haye) that can be obtained upon request (haiech@pharma. information (locusId from the NCBI Entrez gene database, u-strasbg.fr). orthologous genes in mouse and rat and paralogous genes), (ii) gene information (contig description using the informa- tion from the UCSC Genome Bioinformatics Site http:// 3. The EF-Hand database www.genome.ucsc.edu/index.html?org=Human & db=hg17 & hgsid=34709571), (iii) mRNA information from the The EF-Hand database contains 230 human genes, 180 RefSeq database and (iv) the protein information from the mouse genes and 74 rat genes using the assembly hg17, UNIPROT database. All information displayed in blue in mm5 and rn3 from the UCSC center. These differences are Fig. 1. Gene form for the S100a3 human gene. J. Haiech et al. / Biochimica et Biophysica Acta 1742 (2004) 179–183 181 correlated with the level of completion and annotations of Table 2 the corresponding genomes. EF-Hand human genes separated by less than 100,000 base pairs Table 1 summarizes the number of human EF-Hand Name LocusID Contig Number of genes by chromosome. of gene Amino acids Three chromosomes present a higher number of EF-Hands S100A10 6281 chr1:148767467–148780369 96 genes than the others, namely chromosome 1, 2 and 15. S100A11 6282 chr1:148817055–148823584 105 THH 7062 chr1:148892937–148899629 1898 Some of the genes are located close together. We REPETIN 126638 chr1:148940296–148943438 784 consider genes to form a cluster when the distance between HORNERIN 0 chr1:148998628–149008802 2850 them was less than 100,000 base pairs. Eight putative FILAGGRIN 2312 chr1:149098662–149101005 591 clusters were found. Table 2 presents the information on FLJ22843 388698 chr1:149142696–149144433 213 these clusters. C1orf10 49860 chr1:149193792–149200801 495 S100A9 6280 chr1:150142403–150147572 114 A putative cluster was considered as a real cluster when S100A12 6283 chr1:150158257–150162148 91 such a cluster also exists regarding the mouse ortholog genes. S100A8 6279 chr1:150174582–150177622 93 One cluster does not fulfill this rule (RYR1-ACTN4 on S100A7L1 338324 chr1:150201073–150209776 100 chromosome 19). The most important cluster is on chromo- S100A7L2 127482 chr1:150222610–150223878 101 some 1 and all genes concerned are part of the S100 family. S100A7 6278 chr1:150242294–150247210 100 S100A6 6277 chr1:150319149–150322576 90 The family of human genes coding for proteins with a S100 S100A5 6276 chr1:150321696–150328314 92 like domain is composed of 29 genes; 23 of those genes are S100A4 6275 chr1:150328171–150332355 101 localized in chromosome 1. An excellent review has been S100A3 6274 chr1:150331882–150335807 101 published recently on this family [7] (Table 3). S100A2 6273 chr1:150345660–150352379 97 Fig. 2 represents the localization of these genes on S100A16 140576 chr1:150391440–150399587 103 S100A14 57402 chr1:150398807–150402863 104 chromosome 1. S100A13 6284 chr1:150404447–150412021 98 In fact, this cluster is composed of two subclusters: S100A1 6271 chr1:150412946–150418586 93 ! The S100A9 cluster from S100A1 to S100A9 genes on GUCA1A 2978 chr6:42230152–42256770 200 the dog chromosome 7, GUCA1B 2979 chr6:42259531–42271536 200 ! CALML5 51806 chr10:5529661–5532510 146 The S100A10 cluster starting from the loricrin gene to CALML3 810 chr10:5555924–5559225 148 S100A10 localized on dog chromosome 17. CABP4 57010 chr11:66978394–66984261 275 CABP2 51475 chr11:67041994–67048443 219 DUOX1 53905 chr15:43137248–43174830 1551 Table 1 DUOX2 50506 chr15:43171145–43194651 1548 EF-Hand human genes found on the different human chromosome (Assembly Build 35 from NCBI) FLJ20481 54947 chr16:54099455–54175650 427 CAPNS2 84290 chr16:54157085–54160093 248 Chromosome Chromosome Gene EF-Hand MRCL3 10627 chr18:3236528–3247233 170 size (Mb) number genes MRLC2 103910 chr18:3251135–3269179 172 1 246 2544 42 RYR1 6261 chr19:43,615,203–43,771,042 5038 2 243 1772 19 ACTN4 81 chr19:43829167–43914010 911 3 199 1406 11 4 191 1036 9 5 181 1233 9 6 170 1247 10 7 158 1383 12 The cluster S100A10 contains the small proline-rich 8 146 942 4 9 136 1100 5 protein clusters involved in the keratinisation and cornifi- 10 135 1003 4 cation of the epidermis [8,9]. The genes in this cluster (with 11 134 1692 9 the exception of S100A10 and S100A11) code for large 12 132 1278 6 proteins with repeated domains carrying the S100 specific 13 113 506 1 EF-hand motif at the N-terminus. It is a matter of discussion 14 105 1168 5 15 100 895 13 to consider the S100 domains of those proteins as members 16 90 1107 8 of the S100 family. 17 81 1421 6 The gap between the two clusters is smaller in human 18 76 396 3 than in mouse and rat. A rat S100 gene localized in 19 63 1621 12 this gap has been cloned and does not present an ortholog 20 63 724 6 21 46 355 2 with human or mouse gene (S100 ventral prostate, 22 49 707 3 NM_176076). X 153 1149 7 Fig. 3 compares these two clusters in human and Y 50 251 1 mouse.
Load more

Recommended publications
  • PARSANA-DISSERTATION-2020.Pdf
    DECIPHERING TRANSCRIPTIONAL PATTERNS OF GENE REGULATION: A COMPUTATIONAL APPROACH by Princy Parsana A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2020 © 2020 Princy Parsana All rights reserved Abstract With rapid advancements in sequencing technology, we now have the ability to sequence the entire human genome, and to quantify expression of tens of thousands of genes from hundreds of individuals. This provides an extraordinary opportunity to learn phenotype relevant genomic patterns that can improve our understanding of molecular and cellular processes underlying a trait. The high dimensional nature of genomic data presents a range of computational and statistical challenges. This dissertation presents a compilation of projects that were driven by the motivation to efficiently capture gene regulatory patterns in the human transcriptome, while addressing statistical and computational challenges that accompany this data. We attempt to address two major difficulties in this domain: a) artifacts and noise in transcriptomic data, andb) limited statistical power. First, we present our work on investigating the effect of artifactual variation in gene expression data and its impact on trans-eQTL discovery. Here we performed an in-depth analysis of diverse pre-recorded covariates and latent confounders to understand their contribution to heterogeneity in gene expression measurements. Next, we discovered 673 trans-eQTLs across 16 human tissues using v6 data from the Genotype Tissue Expression (GTEx) project. Finally, we characterized two trait-associated trans-eQTLs; one in Skeletal Muscle and another in Thyroid. Second, we present a principal component based residualization method to correct gene expression measurements prior to reconstruction of co-expression networks.
    [Show full text]
  • Annexin A2 Flop-Out Mediates the Non-Vesicular Release of Damps/Alarmins from C6 Glioma Cells Induced by Serum-Free Conditions
    cells Article Annexin A2 Flop-Out Mediates the Non-Vesicular Release of DAMPs/Alarmins from C6 Glioma Cells Induced by Serum-Free Conditions Hayato Matsunaga 1,2,† , Sebok Kumar Halder 1,3,† and Hiroshi Ueda 1,4,* 1 Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan; [email protected] (H.M.); [email protected] (S.K.H.) 2 Department of Medical Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan 3 San Diego Biomedical Research Institute, San Diego, CA 92121, USA 4 Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan * Correspondence: [email protected]; Tel.: +81-75-753-4536 † These authors contributed equally to this work. Abstract: Prothymosin alpha (ProTα) and S100A13 are released from C6 glioma cells under serum- free conditions via membrane tethering mediated by Ca2+-dependent interactions between S100A13 and p40 synaptotagmin-1 (Syt-1), which is further associated with plasma membrane syntaxin-1 (Stx-1). The present study revealed that S100A13 interacted with annexin A2 (ANXA2) and this interaction was enhanced by Ca2+ and p40 Syt-1. Amlexanox (Amx) inhibited the association between S100A13 and ANXA2 in C6 glioma cells cultured under serum-free conditions in the in situ proximity ligation assay. In the absence of Amx, however, the serum-free stress results in a flop-out of ANXA2 Citation: Matsunaga, H.; Halder, through the membrane, without the extracellular release. The intracellular delivery of anti-ANXA2 S.K.; Ueda, H. Annexin A2 Flop-Out antibody blocked the serum-free stress-induced cellular loss of ProTα, S100A13, and Syt-1.
    [Show full text]
  • RNA Expression Patterns in Serum Microvesicles from Patients With
    Noerholm et al. BMC Cancer 2012, 12:22 http://www.biomedcentral.com/1471-2407/12/22 RESEARCHARTICLE Open Access RNA expression patterns in serum microvesicles from patients with glioblastoma multiforme and controls Mikkel Noerholm1,2*, Leonora Balaj1, Tobias Limperg1,3, Afshin Salehi1,4, Lin Dan Zhu1, Fred H Hochberg1, Xandra O Breakefield1, Bob S Carter1,4 and Johan Skog1,2 Abstract Background: RNA from exosomes and other microvesicles contain transcripts of tumour origin. In this study we sought to identify biomarkers of glioblastoma multiforme in microvesicle RNA from serum of affected patients. Methods: Microvesicle RNA from serum from patients with de-novo primary glioblastoma multiforme (N = 9) and normal controls (N = 7) were analyzed by microarray analysis. Samples were collected according to protocols approved by the Institutional Review Board. Differential expressions were validated by qRT-PCR in a separate set of samples (N = 10 in both groups). Results: Expression profiles of microvesicle RNA correctly separated individuals in two groups by unsupervised clustering. The most significant differences pertained to down-regulated genes (121 genes > 2-fold down) in the glioblastoma multiforme patient microvesicle RNA, validated by qRT-PCR on several genes. Overall, yields of microvesicle RNA from patients was higher than from normal controls, but the additional RNA was primarily of size < 500 nt. Gene ontology of the down-regulated genes indicated these are coding for ribosomal proteins and genes related to ribosome production. Conclusions: Serum microvesicle RNA from patients with glioblastoma multiforme has significantly down- regulated levels of RNAs coding for ribosome production, compared to normal healthy controls, but a large overabundance of RNA of unknown origin with size < 500 nt.
    [Show full text]
  • Effect of Human S100A13 Gene Silencing on FGF-1 Transportation in Human Endothelial Cells Renxian Cao,1* Bin Yan,2 Huiling Yang,2 Xuyu Zu,2 Gebo Wen,1* Jing Zhong2
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector J Formos Med Assoc 2010;109(9):632–640 Contents lists available at ScienceDirect Volume 109 Number 9 September 2010 ISSN 0929 6646 Journal of the Journal of the Formosan Medical Association Formosan Medical Association Knockdown of miR-21 as a novel approach for leukemia therapy Fluoroquinolone prophylaxis—an Asian perspective Downregulation of S100A13 blocks FGF-1 release Application of head-up tilt table testing in children Formosan Medical Association Journal homepage: http://www.jfma-online.com Taipei, Taiwan Original Article Effect of Human S100A13 Gene Silencing on FGF-1 Transportation in Human Endothelial Cells Renxian Cao,1* Bin Yan,2 Huiling Yang,2 Xuyu Zu,2 Gebo Wen,1* Jing Zhong2 Background/Purpose: The S100 protein is part of a Ca2+ binding protein superfamily that contains an EF- hand domain, which is involved in the onset and progression of many human diseases, especially the pro- liferation and metastasis of tumors. S100A13, a new member of the S100 protein family, is a requisite component of the fibroblast growth factor-1 (FGF-1) protein release complex, and is involved in human tumorigenesis by interacting with FGF-1 and interleukin-1. In this study, experiments were designed to determine the direct role of S100A13 in FGF-1 protein release and transportation. Methods: We successfully constructed the lentiviral vectors containing shRNA targeting the human S100A13 gene. Human umbilical vein endothelial cells (HUVECs) were transfected with lentiviral RNAi vectors for S100A13. Then immunofluorescence staining, real-time quantitative polymerase chain reac- tion and Western blotting were used to detect the inhibition efficiency of the vectors and to monitor the release and transportation of FGF-1 protein.
    [Show full text]
  • Ectopic Expression of Peripheral-Tissue Antigens in the Thymic Epithelium: Probabilistic, Monoallelic, Misinitiated
    Ectopic expression of peripheral-tissue antigens in the thymic epithelium: Probabilistic, monoallelic, misinitiated Jennifer Villasen˜ or, Whitney Besse, Christophe Benoist, and Diane Mathis* Section on Immunology and Immunogenetics, Joslin Diabetes Center, Department of Medicine, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA 02215 Contributed by Diane Mathis, August 14, 2008 (sent for review July 18, 2008) Thymic medullary epithelial cells (MECs) express a broad repertoire operate by opening large, contiguous regions to the influence of of peripheral-tissue antigens (PTAs), many of which depend on the other positive and negative regulators. transcriptional regulatory factor Aire. Although Aire is known to The precise role of PTAs in the maturation and function of be critically important for shaping a self-tolerant T cell repertoire, MECs remains controversial. Currently, two models vie for its role in MEC maturation and function remains poorly under- acceptance. The ‘‘terminal differentiation’’ model proposes a stood. Using a highly sensitive and reproducible single-cell PCR hierarchy of PTA transcript expression based on the state of assay, we demonstrate that individual Aire-expressing MECs tran- MEC differentiation: as these cells mature from an scribe a subset of PTA genes in a probabilistic fashion, with no signs AireϪCD80loMHC-IIlo (MEClo) stage to the end-stage of preferential coexpression of genes characteristic of particular AireϩCD80hiMHC-IIhi (MEChi), they would transcribe more extrathymic epithelial cell lineages. In addition, Aire-dependent and more PTA genes, each MEChi expressing a large and diverse PTA genes in MECs are transcribed monoallelically or biallelically in subset of the full repertoire, in a more or less random fashion (3).
    [Show full text]
  • Fine Mapping Studies of Quantitative Trait Loci for Baseline Platelet Count in Mice and Humans
    Fine mapping studies of quantitative trait loci for baseline platelet count in mice and humans A thesis submitted in fulfillment of the requirements for the degree of Doctor of Philosophy Melody C Caramins December 2010 University of New South Wales ORIGINALITY STATEMENT ‘I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.’ Signed …………………………………………….............. Date …………………………………………….............. This thesis is dedicated to my father. Dad, thanks for the genes – and the environment! ACKNOWLEDGEMENTS “Nothing can come out of nothing, any more than a thing can go back to nothing.” - Marcus Aurelius Antoninus A PhD thesis is never the work of one person in isolation from the world at large. I would like to thank the following people, without whom this work would not have existed. Thank you firstly, to all my teachers, of which there have been many. Undoubtedly, the greatest debt is owed to my supervisor, Dr Michael Buckley.
    [Show full text]
  • S41467-020-18249-3.Pdf
    ARTICLE https://doi.org/10.1038/s41467-020-18249-3 OPEN Pharmacologically reversible zonation-dependent endothelial cell transcriptomic changes with neurodegenerative disease associations in the aged brain Lei Zhao1,2,17, Zhongqi Li 1,2,17, Joaquim S. L. Vong2,3,17, Xinyi Chen1,2, Hei-Ming Lai1,2,4,5,6, Leo Y. C. Yan1,2, Junzhe Huang1,2, Samuel K. H. Sy1,2,7, Xiaoyu Tian 8, Yu Huang 8, Ho Yin Edwin Chan5,9, Hon-Cheong So6,8, ✉ ✉ Wai-Lung Ng 10, Yamei Tang11, Wei-Jye Lin12,13, Vincent C. T. Mok1,5,6,14,15 &HoKo 1,2,4,5,6,8,14,16 1234567890():,; The molecular signatures of cells in the brain have been revealed in unprecedented detail, yet the ageing-associated genome-wide expression changes that may contribute to neurovas- cular dysfunction in neurodegenerative diseases remain elusive. Here, we report zonation- dependent transcriptomic changes in aged mouse brain endothelial cells (ECs), which pro- minently implicate altered immune/cytokine signaling in ECs of all vascular segments, and functional changes impacting the blood–brain barrier (BBB) and glucose/energy metabolism especially in capillary ECs (capECs). An overrepresentation of Alzheimer disease (AD) GWAS genes is evident among the human orthologs of the differentially expressed genes of aged capECs, while comparative analysis revealed a subset of concordantly downregulated, functionally important genes in human AD brains. Treatment with exenatide, a glucagon-like peptide-1 receptor agonist, strongly reverses aged mouse brain EC transcriptomic changes and BBB leakage, with associated attenuation of microglial priming. We thus revealed tran- scriptomic alterations underlying brain EC ageing that are complex yet pharmacologically reversible.
    [Show full text]
  • BMC Genomics Biomed Central
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Springer - Publisher Connector BMC Genomics BioMed Central Research article Open Access Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data Juan Jose Lozano1,2,5, Marta Soler3, Raquel Bermudo3, David Abia1, Pedro L Fernandez4, Timothy M Thomson*3 and Angel R Ortiz*1,2 Address: 1Bioinformatics Unit, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain, 2Department of Physiology and Biophysics, Mount Sinai School of Medicine, One Gustave Levy Pl., New York, NY 10029, USA, 3Instituto de Biología Molecular, Consejo Superior de Investigaciones Científicas, c. Jordi Girona 18–26, 08034 Barcelona, Spain, 4Departament de Anatomía Patològica, Hospital Clínic, and Institut de Investigacions Biomèdiques August Pi i Sunyer, c. Villarroel 170, 08036 Barcelona, Spain and 5Center for Genome Regulation, Barcelona (Spain) Email: Juan Jose Lozano - [email protected]; Marta Soler - [email protected]; Raquel Bermudo - [email protected]; David Abia - [email protected]; Pedro L Fernandez - [email protected]; Timothy M Thomson* - [email protected]; Angel R Ortiz* - [email protected] * Corresponding authors Published: 17 August 2005 Received: 17 January 2005 Accepted: 17 August 2005 BMC Genomics 2005, 6:109 doi:10.1186/1471-2164-6-109 This article is available from: http://www.biomedcentral.com/1471-2164/6/109 © 2005 Lozano et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    [Show full text]
  • Epidermal Wnt Signalling Regulates Transcriptome Heterogeneity and Proliferative Fate in Neighbouring Cells
    bioRxiv preprint doi: https://doi.org/10.1101/152637; this version posted June 20, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Title: Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells Arsham Ghahramani1,2 , Giacomo Donati2,3 , Nicholas M. Luscombe1,4,5,† and Fiona M. Watt2,† 1The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom 2King’s College London, Centre for Stem Cells and Regenerative Medicine, 28th 8 Floor, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, United Kingdom 3Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy 4UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom 5Okinawa Institute of Science & Technology Graduate University, Okinawa 904-0495, Japan † Correspondence to: [email protected] and [email protected] Abstract: Canonical Wnt/beta-catenin signalling regulates self-renewal and lineage selection within the mouse epidermis. Although the transcriptional response of keratinocytes that receive a Wnt signal is well characterised, little is known about the mechanism by which keratinocytes in proximity to the Wnt- receiving cell are co-opted to undergo a change in cell fate. To address this, we performed single-cell mRNA-Seq on mouse keratinocytes co-cultured with and without the presence of beta-catenin activated neighbouring cells. We identified seven distinct cell states in cultures that had not been exposed to the beta-catenin stimulus and show that the stimulus redistributes wild type subpopulation proportions.
    [Show full text]
  • Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
    Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement.
    [Show full text]
  • Jiang Et Al., 2015. Molecular [Profiling of Activated Olfactory Neurons
    ART ic LE s Molecular profiling of activated olfactory neurons identifies odorant receptors for odors in vivo Yue Jiang1–3, Naihua Natalie Gong1, Xiaoyang Serene Hu1, Mengjue Jessica Ni1, Radhika Pasi1 & Hiroaki Matsunami1,4 The mammalian olfactory system uses a large family of odorant receptors (ORs) to detect and discriminate amongst a myriad of volatile odor molecules. Understanding odor coding requires comprehensive mapping between ORs and corresponding odors. We developed a means of high-throughput in vivo identification of OR repertoires responding to odorants using phosphorylated ribosome immunoprecipitation of mRNA from olfactory epithelium of odor-stimulated mice followed by RNA-Seq. This approach screened the endogenously expressed ORs against an odor in one set of experiments using awake and freely behaving mice. In combination with validations in a heterologous system, we identified sets of ORs for two odorants, acetophenone and 2,5-dihydro-2,4,5-trimethylthiazoline (TMT), encompassing 69 OR-odorant pairs. We also identified shared amino acid residues specific to the acetophenone or TMT receptors and developed models to predict receptor activation by acetophenone. Our results provide a method for understanding the combinatorial coding of odors in vivo. In mammals, olfactory sensation starts with the detection of odor lig- early gene expression, such as c-Fos and Egr-1, which is widely used ands predominantly by ORs, a large family of seven transmembrane G to mark active neurons15,18,19. However, unlike immediate early gene protein–coupled receptors (GPCRs)1,2. ORs are individually expressed expression, phosphorylated S6 has the advantage of being physically in olfactory sensory neurons (OSNs) located in the olfactory epithe- associated with mRNA species expressed in the activated neurons.
    [Show full text]
  • Probing the S100 Protein Family Through Genomic and Functional Analysis$
    Genomics 84 (2004) 10–22 www.elsevier.com/locate/ygeno Probing the S100 protein family through genomic and functional analysis$ Timothy Ravasi,a,b,* Kenneth Hsu,c Jesse Goyette,c Kate Schroder,a Zheng Yang,c Farid Rahimi,c Les P. Miranda,b,1 Paul F. Alewood,b David A. Hume,a,b and Carolyn Geczyc a SRC for Functional and Applied Genomics, CRC for Chronic Inflammatory Diseases, University of Queensland, Brisbane 4072, QLD, Australia b Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, QLD, Australia c Cytokine Research Unit, School of Medical Sciences, University of New South Wales, Sydney 2052, NSW, Australia Received 25 November 2003; accepted 2 February 2004 Available online 10 May 2004 Abstract The EF-hand superfamily of calcium binding proteins includes the S100, calcium binding protein, and troponin subfamilies. This study represents a genome, structure, and expression analysis of the S100 protein family, in mouse, human, and rat. We confirm the high level of conservation between mammalian sequences but show that four members, including S100A12, are present only in the human genome. We describe three new members of the S100 family in the three species and their locations within the S100 genomic clusters and propose a revised nomenclature and phylogenetic relationship between members of the EF-hand superfamily. Two of the three new genes were induced in bone-marrow-derived macrophages activated with bacterial lipopolysaccharide, suggesting a role in inflammation. Normal human and murine tissue distribution profiles indicate that some members of the family are expressed in a specific manner, whereas others are more ubiquitous.
    [Show full text]