KIRREL Is Differentially Expressed in Adipose Tissue from 'Fertil+'And 'Fertil
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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. -
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, -
Identification of Novel Kirrel3 Gene Splice Variants in Adult Human
Durcan et al. BMC Physiology 2014, 14:11 http://www.biomedcentral.com/1472-6793/14/11 RESEARCH ARTICLE Open Access Identification of novel Kirrel3 gene splice variants in adult human skeletal muscle Peter Joseph Durcan1, Johannes D Conradie1, Mari Van deVyver2 and Kathryn Helen Myburgh1* Abstract Background: Multiple cell types including trophoblasts, osteoclasts and myoblasts require somatic cell fusion events as part of their physiological functions. In Drosophila Melanogaster the paralogus type 1 transmembrane receptors and members of the immunoglobulin superfamily Kin of Irre (Kirre) and roughest (Rst) regulate myoblast fusion during embryonic development. Present within the human genome are three homologs to Kirre termed Kin of Irre like (Kirrel) 1, 2 and 3. Currently it is unknown if Kirrel3 is expressed in adult human skeletal muscle. Results: We investigated (using PCR and Western blot) Kirrel3 in adult human skeletal muscle samples taken at rest and after mild exercise induced muscle damage. Kirrel3 mRNA expression was verified by sequencing and protein presence via blotting with 2 different anti-Kirrel3 protein antibodies. Evidence for three alternatively spliced Kirrel3 mRNA transcripts in adult human skeletal muscle was obtained. Kirrel3 mRNA in adult human skeletal muscle was detected at low or moderate levels, or not at all. This sporadic expression suggests that Kirrel3 is expressed in a pulsatile manner. Several anti Kirrel3 immunoreactive proteins were detected in all adult human skeletal muscle samples analysed and results suggest the presence of different isoforms or posttranslational modification, or both. Conclusion: The results presented here demonstrate for the first time that there are at least 3 splice variants of Kirrel3 expressed in adult human skeletal muscle, two of which have never previously been identified in human muscle. -
KIRREL Is Differentially Expressed in Adipose Tissue From
KIRREL is differentially expressed in adipose tissue from “fertil+” and “fertil-” cows: in vitro role in ovary? Stéphanie Coyral-Castel, Christelle Ramé, Juliette Cognie, Jerôme Lecardonnel, Sylvain Marthey, Diane Esquerré, Christelle Hennequet-Antier, Sébastien Elis, Sébastien Fritz, Mekki Boussaha, et al. To cite this version: Stéphanie Coyral-Castel, Christelle Ramé, Juliette Cognie, Jerôme Lecardonnel, Sylvain Marthey, et al.. KIRREL is differentially expressed in adipose tissue from “fertil+” and “fertil-” cows: invitro role in ovary?. Reproduction -Cambridge- Supplement-, Society for Reproduction and Fertility, 2018, 155 (2), pp.181-196. 10.1530/REP-17-0649. hal-02625059 HAL Id: hal-02625059 https://hal.inrae.fr/hal-02625059 Submitted on 26 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Copyright Page 1 of 49Reproduction Advance Publication first posted on 23 November 2017 as Manuscript REP-17-0649 1 KIRREL is differentially expressed in adipose tissue from “fertil+” and “fertil-” cows: 2 in vitro role in ovary? 3 4 S Coyral-Castel1,2,3,4,5, -
Family of Neural Wiring Receptors in Bilaterians Defined by Phylogenetic, Biochemical, and Structural Evidence
Family of neural wiring receptors in bilaterians defined by phylogenetic, biochemical, and structural evidence Shouqiang Chenga,1, Yeonwoo Parkb,1, Justyna D. Kurletoa,c,1, Mili Jeond, Kai Zinnd, Joseph W. Thorntonb,e,f, and Engin Özkana,2 aDepartment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637; bCommittee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637; cFaculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; dDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125; eDepartment of Human Genetics, The University of Chicago, Chicago, IL 60637; and fDepartment of Ecology and Evolution, The University of Chicago, Chicago, IL 60637 Edited by Rachelle Gaudet, Harvard University, Cambridge, MA, and accepted by Editorial Board Member Jeremy Nathans April 8, 2019 (received for review November 5, 2018) The evolution of complex nervous systems was accompanied by the Most of the Dprs and DIPs that have been studied thus far are expansion of numerous protein families, including cell-adhesion expressed exclusively in the nervous system. In the pupal optic molecules, surface receptors, and their ligands. These proteins lobe, the larval ventral nerve cord, olfactory receptor neurons, and mediate axonal guidance, synapse targeting, and other neuronal the neuromuscular system, each Dpr and DIP is expressed in a wiring-related functions. Recently, 32 interacting cell surface pro- unique subset of neurons (5, 7–9). One Dpr is also expressed in teins belonging to two newly defined families of the Ig superfamily postsynaptic muscle cells (10). In the optic lobe, Dprs and DIPs (IgSF) in fruit flies were discovered to label different subsets of are expressed in distinctive combinations in different neuronal neurons in the brain and ventral nerve cord. -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
Human KIRREL / NEPH1 / KIRREL1 Protein (Fc Tag)
Human KIRREL / NEPH1 / KIRREL1 Protein (Fc Tag) Catalog Number: 15752-H02H General Information SDS-PAGE: Gene Name Synonym: NEPH1 Protein Construction: A DNA sequence encoding the human KIRREL (NP_060710.3) (Met1-Leu493) was expressed with the Fc region of human IgG1 at the C-terminus. Source: Human Expression Host: HEK293 Cells QC Testing Purity: > 95 % as determined by SDS-PAGE Endotoxin: Protein Description < 1.0 EU per μg of the protein as determined by the LAL method NEPH1 (KIRREL1) belongs to a family of three closely related Stability: transmembrane proteins of the Ig superfamily with a structure similar to that of nephrin. All three Neph proteins share a conserved podocin-binding ℃ Samples are stable for up to twelve months from date of receipt at -70 motif; mutation of a centrally located tyrosine residue dramatically lowers the affinity of Neph1 for podocin. Neph1 triggers AP-1 activation similarly to Gln 17 Predicted N terminal: nephrin but requires the presence of Tec family kinases for efficient Molecular Mass: transactivation. Neph1 consists of a signal peptide, five Ig-like C2-type domains with the middle domain overlapping with a PKD-like domain, an The recombinant human KIRREL/Fc comprises 715 amino acids and has a RGD sequence, a transmembrane domain and a cytoplasmic tail, which is predicted molecular mass of 78.8 kDa. The apparent molecular mass of the expressed in slit diaphragm domains of podocytes and in vertebrate and protein is approximately 96.1 kDa in SDS-PAGE under reducing conditions. invertebrate nervous systems. Neph1 is abundantly expressed in the kidney, specifically expressed in podocytes of kidney glomeruli, and plays a Formulation: significant role in the normal development and function of the glomerular permeability. -
Bioinformatics Tools for the Analysis of Gene-Phenotype Relationships Coupled with a Next Generation Chip-Sequencing Data Processing Pipeline
Bioinformatics Tools for the Analysis of Gene-Phenotype Relationships Coupled with a Next Generation ChIP-Sequencing Data Processing Pipeline Erinija Pranckeviciene Thesis submitted to the Faculty of Graduate and Postdoctoral Studies in partial fulfillment of the requirements for the Doctorate in Philosophy degree in Cellular and Molecular Medicine Department of Cellular and Molecular Medicine Faculty of Medicine University of Ottawa c Erinija Pranckeviciene, Ottawa, Canada, 2015 Abstract The rapidly advancing high-throughput and next generation sequencing technologies facilitate deeper insights into the molecular mechanisms underlying the expression of phenotypes in living organisms. Experimental data and scientific publications following this technological advance- ment have rapidly accumulated in public databases. Meaningful analysis of currently avail- able data in genomic databases requires sophisticated computational tools and algorithms, and presents considerable challenges to molecular biologists without specialized training in bioinfor- matics. To study their phenotype of interest molecular biologists must prioritize large lists of poorly characterized genes generated in high-throughput experiments. To date, prioritization tools have primarily been designed to work with phenotypes of human diseases as defined by the genes known to be associated with those diseases. There is therefore a need for more prioritiza- tion tools for phenotypes which are not related with diseases generally or diseases with which no genes have yet been associated in particular. Chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq) is a method of choice to study the gene regulation processes responsible for the expression of cellular phenotypes. Among publicly available computational pipelines for the processing of ChIP-Seq data, there is a lack of tools for the downstream analysis of composite motifs and preferred binding distances of the DNA binding proteins. -
NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer
Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 11-7-2018 Decipher Mechanisms by which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer Jairo Ramos [email protected] Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Clinical Epidemiology Commons Recommended Citation Ramos, Jairo, "Decipher Mechanisms by which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer" (2018). FIU Electronic Theses and Dissertations. 3872. https://digitalcommons.fiu.edu/etd/3872 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida DECIPHER MECHANISMS BY WHICH NUCLEAR RESPIRATORY FACTOR ONE (NRF1) COORDINATES CHANGES IN THE TRANSCRIPTIONAL AND CHROMATIN LANDSCAPE AFFECTING DEVELOPMENT AND PROGRESSION OF INVASIVE BREAST CANCER A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in PUBLIC HEALTH by Jairo Ramos 2018 To: Dean Tomás R. Guilarte Robert Stempel College of Public Health and Social Work This dissertation, Written by Jairo Ramos, and entitled Decipher Mechanisms by Which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer, having been approved in respect to style and intellectual content, is referred to you for judgment. -
The Intellectual Disability Gene Kirrel3 Regulates Target-Specific Mossy Fiber
SHORT REPORT The intellectual disability gene Kirrel3 regulates target-specific mossy fiber synapse development in the hippocampus E Anne Martin1†, Shruti Muralidhar1†, Zhirong Wang1, Die´ go Cordero Cervantes1, Raunak Basu1, Matthew R Taylor1, Jennifer Hunter1, Tyler Cutforth2, Scott A Wilke3, Anirvan Ghosh4, Megan E Williams1* 1Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, United States; 2Department of Neurology, Columbia University, New York City, United States; 3Neurobiology Section, Division of Biological Sciences, University of California, San Diego, San Diego, United States; 4Neuroscience Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland Abstract Synaptic target specificity, whereby neurons make distinct types of synapses with different target cells, is critical for brain function, yet the mechanisms driving it are poorly understood. In this study, we demonstrate Kirrel3 regulates target-specific synapse formation at hippocampal mossy fiber (MF) synapses, which connect dentate granule (DG) neurons to both CA3 and GABAergic neurons. Here, we show Kirrel3 is required for formation of MF filopodia; the structures that give rise to DG-GABA synapses and that regulate feed-forward inhibition of CA3 neurons. Consequently, loss of Kirrel3 robustly increases CA3 neuron activity in developing mice. Alterations in the Kirrel3 gene are repeatedly associated with intellectual disabilities, but the role of *For correspondence: megan. Kirrel3 at synapses remained largely unknown. Our findings demonstrate that subtle synaptic [email protected] changes during development impact circuit function and provide the first insight toward understanding the cellular basis of Kirrel3-dependent neurodevelopmental disorders. † These authors contributed DOI: 10.7554/eLife.09395.001 equally to this work Competing interests: The authors declare that no competing interests exist. -
Comparative Promoter Analysis Allows De Novo Identification of Specialized Cell Junction-Associated Proteins
Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins Clemens D. Cohen*, Andreas Klingenhoff†, Anissa Boucherot*, Almut Nitsche‡, Anna Henger*§, Bodo Brunner‡, Holger Schmid*, Monika Merkle*, Moin A. Saleem¶, Klaus-Peter Koller‡, Thomas Werner†, Hermann-Josef Gro¨ neʈ, Peter J. Nelson*,**, and Matthias Kretzler*§ *Medizinische Poliklinik, University of Munich, 80336 Munich, Germany; †Genomatix GmbH, 80335 Munich, Germany; ‡Sanofi-Aventis, 65926 Frankfurt, Germany; ¶Children’s Renal Unit, University of Bristol, Bristol BS10 5NB, United Kingdom; and ʈCellular and Molecular Pathology, German Cancer Research Center, 69120 Heidelberg, Germany Edited by Mark T. Groudine, Fred Hutchinson Cancer Research Center, Seattle, WA, and approved February 8, 2006 (received for review December 28, 2005) Shared transcription factor binding sites that are conserved in could also be used in bioinformatic analyses to detect genes distance and orientation help control the expression of gene heretofore not associated with the specific biologic process (5). products that act together in the same biological context. New To test these hypotheses, a unique tissue environment linked to bioinformatics approaches allow the rapid characterization of a specific biologic function was selected for a bioinformatic-driven shared promoter structures and can be used to find novel inter- analysis of promoter coregulation as outlined in Fig. 1. Glomerular acting molecules. Here, these principles are demonstrated by using epithelial cells, also referred to as podocytes, cover the fenestrated molecules linked to the unique functional unit of the glomerular capillaries of renal glomeruli in vertebrates and contribute to the slit diaphragm. An evolutionarily conserved promoter model was kidney filtration barrier (8). Podocytes have a complex phenotype generated by comparative genomics in the proximal promoter with interdigitating foot processes that are bridged by the final regions of the slit diaphragm-associated molecule nephrin. -
Kirrel3-Mediated Synapse Formation Is Attenuated by Disease-Associated Missense Variants 3 Abbreviated Title: Kirrel3 Variants Impair Its Function 4 5 Matthew R
bioRxiv preprint doi: https://doi.org/10.1101/2019.12.30.891085; this version posted December 30, 2019. 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-NC 4.0 International license. 1 2 Kirrel3-mediated synapse formation is attenuated by disease-associated missense variants 3 Abbreviated Title: Kirrel3 variants impair its function 4 5 Matthew R. Taylor1*, E. Anne Martin1*, Brooke Sinnen1, Rajdeep Trilokekar1, Emmanuelle Ranza2,3, 6 Stylianos E. Antonarakis2,4, Megan E. Williams1 7 8 1Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 9 84112, USA 10 2Service of Genetic Medicine, Geneva University Hospitals, Geneva, Switzerland 11 3Current address: Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland 12 4Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 13 Switzerland 14 * These authors contributed equally to this work 15 16 Correspondence should be addressed to Megan E. Williams at [email protected]. 17 18 Number of pages: 37 19 Number of figures: 6 20 Number of tables: 1 21 Abstract word count: 209 22 Introduction word count: 728 23 Discussion word count: 1562 24 25 Conflict of Interest Statement: The authors declare no competing financial interests. 26 27 Acknowledgements: This work was supported by grants from the National Institute of Mental Health 28 (R01 MH105426, M.E.W), Brain Research Foundation Fay/Frank Seed Grant (M.E.W), Childcare 29 Foundation (S.E.A), and an Autism Speaks Dennis Weatherstone Predoctoral Fellowship 10116 (E.A.M).