DOCSLIB.ORG

The Role of Iroquois 3 and 5 in Limb Bud Pattern Formation and Morphogenesis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Role of Iroquois 3 and 5 in Limb Bud Pattern Formation and Morphogenesis The Role of Iroquois 3 and 5 in Limb Bud Pattern Formation and Morphogenesis by Danyi Li A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Graduate Department of Molecular Genetics University of Toronto © Copyright by Danyi Li (2014) The Role of Iroquois 3 and 5 in Limb Bud Pattern Formation and Morphogenesis Danyi Li Doctor of Philosophy Graduate Department of Molecular Genetics University of Toronto 2014 Abstract Limb skeletal pattern heavily relies on graded Sonic hedgehog (Shh) signaling. As a morphogen and growth cue, Shh regulates identities of posterior limb elements including the ulna/fibula and digits 2 through 5. In contrast, proximal and anterior structures including the humerus/femur, radius/tibia and digit 1 are regarded as Shh-independent and the mechanisms governing their pattern formation are unclear. Here I show that patterning of the proximal and anterior limb skeleton involves an early specification phase dependent on two transcription factors, Irx3 and Irx5 (Irx3/5). They are expressed in the anterior margin of the limb field to regulate expression of the key anterior prepattern gene Gli3 and specify the anterior population during limb initiation. The early specification phase is followed by a late modulation phase during which Shh signaling negatively regulates these anterior elements. In addition, Irx3/5 also play a role in limb bud morphogenesis. Irx3/5-DKO hindlimb buds are small with abnormal shape due to prolonged cell cycle time and division defects including anaphase bridge and altered cell division orientation in the anterior hindlimb field. Therefore, pattern formation of anterior limb skeletal elements requires functions of Irx3/5 during limb bud initiation for the specification and expansion of anterior population followed by negative modulation by Shh signaling. ii Acknowledgments I would like to take this opportunity to gratefully acknowledge the following people for their contributions and support throughout my graduate study. To my supervisors Dr. Chi-chung Hui and Dr. Sevan Hopyan, who gave me the chance to work on this exciting and challenging project and provide me with continuous guidance and opportunities to help me learn to be a scientist and become a better person, thank you for all the things that you have done for me. What you have taught me will benefit me in my future career and throughout my life. To my committee members Dr. Sabine Cordes and Dr. Andrew Spence, who gave me valuable comments and suggestions on my work, thank you for your attentiveness and scientific expertise. I am very lucky to work with a group of people who are always willing to help and make my time in the lab so enjoyable. To Mary Zhang, Rong Mo, Vijitha Puviindran and Kendra Sturgeon, thank you for your help from maintaining mouse colonies to mutant analysis and molecular experiments. I want to thank Dr. Rui Sakuma and Niki Vakili for initiating this project. To Olena Zhulyn, Wenqi Yin, Dr. Sue Li, Dr. Han Kim, Dr. Kelvin Law, Dr. Kimberly Lau, Dr. Steven Deimling, Dr. Hirotaka Tao and Laurie Wyngaarden, thank you for all the scientific and non-scientific discussions and sharing experience from experimental techniques to good food and sale discount. I especially thank Olena for helping with the flow cytometry experiment and brain storm on my manuscript development. I also want to thank Gregory Anderson from the Henkelman lab for collaboration on OPT analysis. I am also grateful to my family and friends who are always by my side cheering for my success and accomplishment and encouraging me to get through my “dark time”. iii Table of Contents Abstract ii Acknowledgment iii List of Tables vii List of Figures viii List of Videos x List of Abbreviations xi Chapter 1 INTRODUCTION 1 1 Introduction 1 1.1 An overview of vertebrate limb development and pattern formation 1 1.1.1 Limb induction 1 1.1.2 AER and limb PD pattern formation 2 1.1.3 ZPA and limb AP pattern formation 3 1.1.4 Self-regulated feedback loop between the AER and ZPA 4 1.1.5 Proliferative expansion, determination and differentiation 4 1.2 Limb AP pattern formation 5 1.2.1 Prepatterning the limb bud and Shh-activation network 5 1.2.2 Limb AP pattern formation after Shh activation 7 1.3 Cell biology of limb bud morphogenesis 9 1.3.1 Cell proliferation and cell death 9 1.3.2 Oriented cell behavior 10 1.4 Iroquois homeobox (Irx) genes 11 1.4.1 Discovery and genomic organization 11 1.4.2 Functions of Irx genes in development 12 1.4.3 Irx3 and Irx5 have novel functions in mouse hindlimb development 14 1.5 Thesis rational and outline 16 Chapter 2 Irx3/5 interact with Shh signaling for anterior limb pattern formation 22 2 Chapter 2 23 2.1 Summary 23 2.2 Introduction 23 2.3 Materials and Methods 24 2.3.1 Mice and genotyping 24 2.3.2 Cre activity induction via tamoxifen administration 25 2.3.3 Western blot 25 2.3.4 Cartilage staining 25 2.3.5 Quantification of limb bud frontal area plane 26 2.3.6 Section immunofluorescence 26 2.3.7 Whole-mount in situ hybridization 26 2.3.8 RNA isolation and real-time quantitative PCR 27 2.3.9 Chromatin immunoprecipitation 27 2.3.10 Quantification of location of Shh domain in limb buds and percentage of limb bud frontal plane area expressing Gli1 27 2.4 Results 28 2.4.1 Irx3/5 are required prior to limb bud outgrowth 28 iv 2.4.2 Irx3/5 regulate AP prepattern to promote proximal and anterior hindlimb progenitors 29 2.4.3 Irx3 binds to Gli3 limb enhancer and regulates Gli3 expression in hindlimb buds 30 2.4.4 Early genetic interaction between Irx3/5 and Gli3 is essential for signaling center establishment 31 2.4.5 Irx3/5-dependent anterior progenitor population contributes to preaxial polydactyly 32 2.4.6 Requirement of Irx3/5 in forelimb AP pattern formation is revealed in Kif7-/- background 32 2.4.7 Forelimb bud displays lower Shh signaling activity than that of the hindlimb 33 2.4.8 Reducing Shh signaling rescues anterior skeletal formation in the Irx3/5-DKO hindlimb 33 2.5 Discussion 34 2.5.1 A biphasic model for limb anterior pattern formation 34 2.5.2 Irx3/5 are key determinants of anterior population in early hindlimb field 35 Chapter 3 Limb bud morphogenesis requires regulation of cell proliferation by Irx3/5 in the anterior hindlimb field 49 3 Chapter 3 50 3.1 Summary 50 3.2 Introduction 50 3.3 Materials and Methods 52 3.3.1 Mice 52 3.3.2 OPT and limb bud morphology analysis 52 3.3.3 Double-pulse chasing analysis and cell cycle time estimation 52 3.3.4 Flow cytometry 53 3.3.5 Live imaging 53 3.3.6 Orientation of cell division 54 3.4 Results 54 3.4.1 Irx3/5-DKO hindlimb buds are small and display abnormal shape 54 3.4.2 Prolonged cell cycle time in the anterior hindlimb field of Irx3/5-DKO embryos during limb initiation 55 3.4.3 Live imaging data revealed multiple cell division defects in initiating Irx3/5-DKO hindimb buds 56 3.5 Discussion 57 Chapter 4 Conclusion and Future Experiments 68 4 Chapter 4 68 4.1 Thesis summary 68 4.2 Irx3 and Irx5 are novel anterior limb determinants 69 4.2.1 Identifying the molecular mechanism of anterior specification by Irx3/5 70 4.2.2 Fate mapping of Irx3/5-expressing cells may reveal the origin of anterior limb structures 72 4.3 Genetic interaction between Irx3/5 and Gli3 is required for signaling center establishment and limb outgrowth 74 4.4 Early specification and progressive modulation of anterior limb elements by Irx3/5 and Shh signaling 76 v 4.5 Difference between forelimb and hindlimb development 77 4.6 Irx3/5 regulate limb bud morphogenesis in multiple aspects 78 4.7 Conclusion remarks 79 References 84 vi List of Tables Table 3.1 Shape information of E10.0 forelimb buds 61 Table 3.2 Shape information of E10.0 and E10.5 hindlimb buds 61 vii List of Figures Figure 1.1 An overview of mouse limb bud outgrowth and AP pattern formation 18 Figure 1.2 Oriented cell behavior in limb bud morphogenesis 19 Figure 1.3 Iroquois homeobox genes 20 Figure 1.4 Expression of Irx3/5 during forelimb and hindlimb development 20 Figure 1.5 Irx3/5-DKO embryos display hindlimb specific phenotype 21 Figure 2.1 Irx3/5 are required prior to limb bud outgrowth for the formation of anterior-distal hindlimb elements 36 Figure 2.2 Morphogenesis, cell proliferation and cell death in Irx3/5-DKO hindlimb buds 37 Figure 2.3 Irx3/5 regulate hindlimb bud prepattern 38 Figure 2.4 Irx3/5-DKO hindlimb buds are primed to form Shh-responding elements 39 Figure 2.5 Irx3/5 regulate Gli3 expression in limb 40 Figure 2.6 Early genetic interaction between Irx3/5 and Gli3 is required for signaling center establishment and limb bud outgrowth 41 Figure 2.7 Irx3/5-dependent anterior progenitor population contributes to preaxial polydactyly 42 Figure 2.8 Irx3/5 are required for the formation of anterior forelimb elements in Kif7-/- background 42 Figure 2.9 Irx3/5 are involved in forelimb development 43 Figure 2.10 Shh domain is more posteriorly restricted in the forelimb bud than hindlimb 44 Figure 2.11 Forelimb bud displays lower Shh signaling activity than that of the hindlimb 45 Figure 2.12 Reducing Shh signaling in Irx3/5-DKO hindlimb buds rescues anterior pattern formation 46 Figure 2.13 Prepattern and limb bud size are not rescued in Irx3/5-DKO;Shh+/- hindlimbs 47 Figure 2.14 A biphasic model of limb anterior pattern formation 47 Figure 3.1 Surface renderings of E10.5 control and Irx3/5-DKO embryos viewed from the right 60 Figure 3.2 Dorsal and lateral views of forelimb bud isosurfaces at E10.0 61 Figure 3.3 Dorsal and lateral views of hindlimb bud isosurfaces at E10.0 and
Load more

Recommended publications
  • Sorbonne Université́
    Sorbonne Université́ École Doctorale ED515 – Complexité́ du vivant INSERM UMRS 933 : Physiopathologie des maladies génétiques d'expression pédiatrique Mécanismes physiopathologiques impliqués dans la différenciation du tractus génital masculin Matthieu Peycelon Thèse de Doctorat de Génétique Humaine Dirigée par Pr. Jean-Pierre Siffroi Présentée et soutenue publiquement le 19 décembre 2019 Devant un jury composé de : Brigitte BENZACKEN PU-PH Université Paris 13 Rapporteur Anne-Françoise SPINOIT Professeur Université de Gand Rapporteur Irène NETCHINE PU-PH Université Paris 6 Examinateur Nicolas KALFA PU-PH Université de Montpellier Examinateur Alaa EL GHONEIMI PU-PH Université Paris 7 Président Jean-Pierre SIFFROI PU-PH Université Paris 6 Directeur de thèse Sorbonne Université́ École Doctorale ED515 – Complexité́ du vivant INSERM UMRS 933 : Physiopathologie des maladies génétiques d'expression pédiatrique Mécanismes physiopathologiques impliqués dans la différenciation du tractus génital masculin Matthieu Peycelon Thèse de Doctorat de Génétique Humaine Dirigée par Pr. Jean-Pierre Siffroi Présentée et soutenue publiquement le 19 décembre 2019 Devant un jury composé de : Brigitte BENZACKEN PU-PH Université Paris 13 Rapporteur Anne-Françoise SPINOIT Professeur Université de Gand Rapporteur Irène NETCHINE PU-PH Université Paris 6 Examinateur Nicolas KALFA PU-PH Université de Montpellier Examinateur Alaa EL GHONEIMI PU-PH Université Paris 7 Président Jean-Pierre SIFFROI PU-PH Université Paris 6 Directeur de thèse Ce travail de thèse a été réalisé́ sous la direction du Professeur Jean-Pierre Siffroi, au sein de l’unité́ mixte de recherche INSERM / Sorbonne Université UMR_S933 dirigée par le Professeur Serge Amselem. Adresse : Département de Génétique Médicale, Hôpital Armand Trousseau ; 26 avenue du Docteur Arnold Netter, 75012, Paris.
    [Show full text]
  • Overlap of Vitamin a and Vitamin D Target Genes with CAKUT- Related Processes [Version 1; Peer Review: 1 Approved with Reservations]
    F1000Research 2021, 10:395 Last updated: 21 JUL 2021 BRIEF REPORT Overlap of vitamin A and vitamin D target genes with CAKUT- related processes [version 1; peer review: 1 approved with reservations] Ozan Ozisik1, Friederike Ehrhart 2,3, Chris T Evelo 2, Alberto Mantovani4, Anaı̈s Baudot 1,5 1Aix Marseille University, Inserm, MMG, Marseille, 13385, France 2Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6200 MD, The Netherlands 3Department of Bioinformatics, NUTRIM/MHeNs, Maastricht University, Maastricht, 6200 MD, The Netherlands 4Istituto Superiore di Sanità, Rome, 00161, Italy 5Barcelona Supercomputing Center (BSC), Barcelona, 08034, Spain v1 First published: 18 May 2021, 10:395 Open Peer Review https://doi.org/10.12688/f1000research.51018.1 Latest published: 18 May 2021, 10:395 https://doi.org/10.12688/f1000research.51018.1 Reviewer Status Invited Reviewers Abstract Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) are a 1 group of abnormalities affecting the kidneys and their outflow tracts, which include the ureters, the bladder, and the urethra. CAKUT version 1 patients display a large clinical variability as well as a complex 18 May 2021 report aetiology, as only 5% to 20% of the cases have a monogenic origin. It is thereby suspected that interactions of both genetic and 1. Elena Menegola, Università degli Studi di environmental factors contribute to the disease. Vitamins are among the environmental factors that are considered for CAKUT aetiology. In Milano, Milan, Italy this study, we collected vitamin A and vitamin D target genes and Any reports and responses or comments on the computed their overlap with CAKUT-related gene sets.
    [Show full text]
  • Table S1 the Four Gene Sets Derived from Gene Expression Profiles of Escs and Differentiated Cells
    Table S1 The four gene sets derived from gene expression profiles of ESCs and differentiated cells Uniform High Uniform Low ES Up ES Down EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol 269261 Rpl12 11354 Abpa 68239 Krt42 15132 Hbb-bh1 67891 Rpl4 11537 Cfd 26380 Esrrb 15126 Hba-x 55949 Eef1b2 11698 Ambn 73703 Dppa2 15111 Hand2 18148 Npm1 11730 Ang3 67374 Jam2 65255 Asb4 67427 Rps20 11731 Ang2 22702 Zfp42 17292 Mesp1 15481 Hspa8 11807 Apoa2 58865 Tdh 19737 Rgs5 100041686 LOC100041686 11814 Apoc3 26388 Ifi202b 225518 Prdm6 11983 Atpif1 11945 Atp4b 11614 Nr0b1 20378 Frzb 19241 Tmsb4x 12007 Azgp1 76815 Calcoco2 12767 Cxcr4 20116 Rps8 12044 Bcl2a1a 219132 D14Ertd668e 103889 Hoxb2 20103 Rps5 12047 Bcl2a1d 381411 Gm1967 17701 Msx1 14694 Gnb2l1 12049 Bcl2l10 20899 Stra8 23796 Aplnr 19941 Rpl26 12096 Bglap1 78625 1700061G19Rik 12627 Cfc1 12070 Ngfrap1 12097 Bglap2 21816 Tgm1 12622 Cer1 19989 Rpl7 12267 C3ar1 67405 Nts 21385 Tbx2 19896 Rpl10a 12279 C9 435337 EG435337 56720 Tdo2 20044 Rps14 12391 Cav3 545913 Zscan4d 16869 Lhx1 19175 Psmb6 12409 Cbr2 244448 Triml1 22253 Unc5c 22627 Ywhae 12477 Ctla4 69134 2200001I15Rik 14174 Fgf3 19951 Rpl32 12523 Cd84 66065 Hsd17b14 16542 Kdr 66152 1110020P15Rik 12524 Cd86 81879 Tcfcp2l1 15122 Hba-a1 66489 Rpl35 12640 Cga 17907 Mylpf 15414 Hoxb6 15519 Hsp90aa1 12642 Ch25h 26424 Nr5a2 210530 Leprel1 66483 Rpl36al 12655 Chi3l3 83560 Tex14 12338 Capn6 27370 Rps26 12796 Camp 17450 Morc1 20671 Sox17 66576 Uqcrh 12869 Cox8b 79455 Pdcl2 20613 Snai1 22154 Tubb5 12959 Cryba4 231821 Centa1 17897
    [Show full text]
  • Supplemental Materials ZNF281 Enhances Cardiac Reprogramming
    Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7
    [Show full text]
  • Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. 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. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. 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. Abstract The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes.
    [Show full text]
  • Methylome and Transcriptome Maps of Human Visceral and Subcutaneous
    www.nature.com/scientificreports OPEN Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal Received: 9 April 2019 Accepted: 11 June 2019 key epigenetic diferences at Published: xx xx xxxx developmental genes Stephen T. Bradford1,2,3, Shalima S. Nair1,3, Aaron L. Statham1, Susan J. van Dijk2, Timothy J. Peters 1,3,4, Firoz Anwar 2, Hugh J. French 1, Julius Z. H. von Martels1, Brodie Sutclife2, Madhavi P. Maddugoda1, Michelle Peranec1, Hilal Varinli1,2,5, Rosanna Arnoldy1, Michael Buckley1,4, Jason P. Ross2, Elena Zotenko1,3, Jenny Z. Song1, Clare Stirzaker1,3, Denis C. Bauer2, Wenjia Qu1, Michael M. Swarbrick6, Helen L. Lutgers1,7, Reginald V. Lord8, Katherine Samaras9,10, Peter L. Molloy 2 & Susan J. Clark 1,3 Adipocytes support key metabolic and endocrine functions of adipose tissue. Lipid is stored in two major classes of depots, namely visceral adipose (VA) and subcutaneous adipose (SA) depots. Increased visceral adiposity is associated with adverse health outcomes, whereas the impact of SA tissue is relatively metabolically benign. The precise molecular features associated with the functional diferences between the adipose depots are still not well understood. Here, we characterised transcriptomes and methylomes of isolated adipocytes from matched SA and VA tissues of individuals with normal BMI to identify epigenetic diferences and their contribution to cell type and depot-specifc function. We found that DNA methylomes were notably distinct between diferent adipocyte depots and were associated with diferential gene expression within pathways fundamental to adipocyte function. Most striking diferential methylation was found at transcription factor and developmental genes. Our fndings highlight the importance of developmental origins in the function of diferent fat depots.
    [Show full text]
  • Ann. Anim. Sci., Vol. 19, No. 2 (2019) 343–357 DOI: 10.2478/Aoas-2019-0004
    Ann. Anim. Sci., Vol. 19, No. 2 (2019) 343–357 DOI: 10.2478/aoas-2019-0004 FTO AND IRX3 GENES ARE NOT PROMISING MARKERS FOR OBESITY IN LABRADOR RETRIEVER DOGS* * Adrian Grzemski1, Monika Stachowiak1, Krzysztof Flisikowski2, Monika Mankowska1, Paulina Krzeminska1, Maciej Gogulski3, Roman Aleksiewicz4, Maciej Szydlowski1, Marek Switonski1, Joanna Nowacka-Woszuk1♦ 1Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wołyńska 33, 60-637 Poznań, Poland 2Chair of Livestock Biotechnology, Technische Universität München, Liesel-Beckmannstr. 1, 85354 Freising, Germany 3University Centre for Veterinary Medicine, Poznan University of Life Sciences, Szydłowska 43, 60-656 Poznań, Poland 4Department of Internal Medicine and Veterinary Diagnostics, Poznan University of Life Sciences, Wołyńska 35, 60-637 Poznań, Poland ♦Corresponding author: [email protected] Abstract Obesity is a serious problem in numerous dog breeds, but knowledge of its hereditary background is scarce. On the contrary, numerous DNA polymorphisms associated with human obesity have been identified, with the strongest effect being demonstrated forFTO gene. We used targeted next- generation sequencing (tNGS) to search for polymorphisms in the region harboring FTO and IRX3 in 32 Labrador dogs. Moreover, we investigated the selected regions of FTO and IRX3, ortholo- gous to the human regions associated with obesity, in 165 Labradors. For all dogs, the following information was available: age, sex, gonadal status, body weight, and body conformation score (BCS). The use of tNGS revealed 12,217 polymorphisms, but none of these obtained significance when lean and obese dogs were compared. Study of two SNPs in the 5’-flanking region of FTO in 165 dogs – creating two upstream reading frames (uORFs) – also showed no association with body weight and BCS but suggested the need for improvement in FTO annotation.
    [Show full text]
  • Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
    Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol .
    [Show full text]
  • Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant
    Appendix 2. Significantly Differentially Regulated Genes in Term Compared With Second Trimester Amniotic Fluid Supernatant Fold Change in term vs second trimester Amniotic Affymetrix Duplicate Fluid Probe ID probes Symbol Entrez Gene Name 1019.9 217059_at D MUC7 mucin 7, secreted 424.5 211735_x_at D SFTPC surfactant protein C 416.2 206835_at STATH statherin 363.4 214387_x_at D SFTPC surfactant protein C 295.5 205982_x_at D SFTPC surfactant protein C 288.7 1553454_at RPTN repetin solute carrier family 34 (sodium 251.3 204124_at SLC34A2 phosphate), member 2 238.9 206786_at HTN3 histatin 3 161.5 220191_at GKN1 gastrokine 1 152.7 223678_s_at D SFTPA2 surfactant protein A2 130.9 207430_s_at D MSMB microseminoprotein, beta- 99.0 214199_at SFTPD surfactant protein D major histocompatibility complex, class II, 96.5 210982_s_at D HLA-DRA DR alpha 96.5 221133_s_at D CLDN18 claudin 18 94.4 238222_at GKN2 gastrokine 2 93.7 1557961_s_at D LOC100127983 uncharacterized LOC100127983 93.1 229584_at LRRK2 leucine-rich repeat kinase 2 HOXD cluster antisense RNA 1 (non- 88.6 242042_s_at D HOXD-AS1 protein coding) 86.0 205569_at LAMP3 lysosomal-associated membrane protein 3 85.4 232698_at BPIFB2 BPI fold containing family B, member 2 84.4 205979_at SCGB2A1 secretoglobin, family 2A, member 1 84.3 230469_at RTKN2 rhotekin 2 82.2 204130_at HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 81.9 222242_s_at KLK5 kallikrein-related peptidase 5 77.0 237281_at AKAP14 A kinase (PRKA) anchor protein 14 76.7 1553602_at MUCL1 mucin-like 1 76.3 216359_at D MUC7 mucin 7,
    [Show full text]
  • Identification of Transcriptional Mechanisms Downstream of Nf1 Gene Defeciency in Malignant Peripheral Nerve Sheath Tumors Daochun Sun Wayne State University
    Wayne State University DigitalCommons@WayneState Wayne State University Dissertations 1-1-2012 Identification of transcriptional mechanisms downstream of nf1 gene defeciency in malignant peripheral nerve sheath tumors Daochun Sun Wayne State University, Follow this and additional works at: http://digitalcommons.wayne.edu/oa_dissertations Recommended Citation Sun, Daochun, "Identification of transcriptional mechanisms downstream of nf1 gene defeciency in malignant peripheral nerve sheath tumors" (2012). Wayne State University Dissertations. Paper 558. This Open Access Dissertation is brought to you for free and open access by DigitalCommons@WayneState. It has been accepted for inclusion in Wayne State University Dissertations by an authorized administrator of DigitalCommons@WayneState. IDENTIFICATION OF TRANSCRIPTIONAL MECHANISMS DOWNSTREAM OF NF1 GENE DEFECIENCY IN MALIGNANT PERIPHERAL NERVE SHEATH TUMORS by DAOCHUN SUN DISSERTATION Submitted to the Graduate School of Wayne State University, Detroit, Michigan in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY 2012 MAJOR: MOLECULAR BIOLOGY AND GENETICS Approved by: _______________________________________ Advisor Date _______________________________________ _______________________________________ _______________________________________ © COPYRIGHT BY DAOCHUN SUN 2012 All Rights Reserved DEDICATION This work is dedicated to my parents and my wife Ze Zheng for their continuous support and understanding during the years of my education. I could not achieve my goal without them. ii ACKNOWLEDGMENTS I would like to express tremendous appreciation to my mentor, Dr. Michael Tainsky. His guidance and encouragement throughout this project made this dissertation come true. I would also like to thank my committee members, Dr. Raymond Mattingly and Dr. John Reiners Jr. for their sustained attention to this project during the monthly NF1 group meetings and committee meetings, Dr.
    [Show full text]
  • Differentially Methylated Genes
    10/30/2013 Disclosures Key Rheumatoid Arthritis-Associated Pathogenic Pathways Revealed by Integrative Analysis of RA Omics Datasets Consultant: IGNYTA Funding: Rheumatology Research Foundation By John W. Whitaker, Wei Wang and Gary S. Firestein DNA methylation and gene regulation The RA methylation signature in FLS DNA methylation – DNMT1 (maintaining methylation) OA – DNMT3a, 3b (de novo methylation) RA % of CpG methylation: 0% 100% Nakano et al. 2013 ARD AA06 AANAT AARS ABCA6 ABCC12 ABCG1 ABHD8 ABL2 ABR ABRA ACACA ACAN ACAP3 ACCSL ACN9 ACOT7 ACOX2 ACP5 ACP6 ACPP ACSL1 ACSL3 ACSM5 ACVRL1 ADAM10 ADAM32 ADAM33 ADAMTS12 ADAMTS15 ADAMTS19 ADAMTS4 ADAT3 ADCK4 ADCK5 ADCY2 ADCY3 ADCY6 ADORA1 ADPGK ADPRHL1 ADTRP AFAP1 AFAP1L2 AFF3 AFG3L1P AGAP11 AGER AGTR1 AGXT AIF1L AIM2 AIRE AJUBA AK4 AKAP12 AKAP2 AKR1C2 AKR1E2 AKT2 ALAS1 ALDH1L1-AS1 ALDH3A1 ALDH3B1 ALDH8A1 ALDOB ALDOC ALOX12 ALPK3 ALS2CL ALX4 AMBRA1 AMPD2 AMPD3 ANGPT1 ANGPT2 ANGPTL5 ANGPTL6 ANK1 ANKMY2 ANKRD29 ANKRD37 ANKRD53 ANO3 ANO6 ANO7 ANP32C ANXA6 ANXA8L2 AP1G1 AP2A2 AP2M1 AP5B1 APBA2 APC APCDD1 APOBEC3B APOBEC3G APOC1 APOH APOL6 APOLD1 APOM AQP1 AQP10 AQP6 AQP9 ARAP1 ARHGAP24 ARHGAP42 ARHGEF19 ARHGEF25 ARHGEF3 ARHGEF37 ARHGEF7 ARL4C ARL6IP 5 ARL8B ARMC3 ARNTL2 ARPP21 ARRB1 ARSI ASAH2B ASB10 ASB2 ASCL2 ASIC4 ASPH ATF3 ATF7 ATL1 ATL3 ATP10A ATP1A1 ATP1A4 ATP2C1 ATP5A1 ATP5EP2 ATP5L2 ATP6V0CP3 ATP6V1C1 ATP6V1E2 ATXN7L1 ATXN7L2 AVPI1 AXIN2 B3GNT7 B3GNT8 B3GNTL1 BACH1 BAG3 Differential methylated genes in RA FLS BAIAP2L2 BANP BATF BATF2 BBS2 BCAS4 BCAT1 BCL7C BDKRB2 BEGAIN BEST1 BEST3
    [Show full text]
  • Strand Breaks for P53 Exon 6 and 8 Among Different Time Course of Folate Depletion Or Repletion in the Rectosigmoid Mucosa
    SUPPLEMENTAL FIGURE COLON p53 EXONIC STRAND BREAKS DURING FOLATE DEPLETION-REPLETION INTERVENTION Supplemental Figure Legend Strand breaks for p53 exon 6 and 8 among different time course of folate depletion or repletion in the rectosigmoid mucosa. The input of DNA was controlled by GAPDH. The data is shown as ΔCt after normalized to GAPDH. The higher ΔCt the more strand breaks. The P value is shown in the figure. SUPPLEMENT S1 Genes that were significantly UPREGULATED after folate intervention (by unadjusted paired t-test), list is sorted by P value Gene Symbol Nucleotide P VALUE Description OLFM4 NM_006418 0.0000 Homo sapiens differentially expressed in hematopoietic lineages (GW112) mRNA. FMR1NB NM_152578 0.0000 Homo sapiens hypothetical protein FLJ25736 (FLJ25736) mRNA. IFI6 NM_002038 0.0001 Homo sapiens interferon alpha-inducible protein (clone IFI-6-16) (G1P3) transcript variant 1 mRNA. Homo sapiens UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15 GALNTL5 NM_145292 0.0001 (GALNT15) mRNA. STIM2 NM_020860 0.0001 Homo sapiens stromal interaction molecule 2 (STIM2) mRNA. ZNF645 NM_152577 0.0002 Homo sapiens hypothetical protein FLJ25735 (FLJ25735) mRNA. ATP12A NM_001676 0.0002 Homo sapiens ATPase H+/K+ transporting nongastric alpha polypeptide (ATP12A) mRNA. U1SNRNPBP NM_007020 0.0003 Homo sapiens U1-snRNP binding protein homolog (U1SNRNPBP) transcript variant 1 mRNA. RNF125 NM_017831 0.0004 Homo sapiens ring finger protein 125 (RNF125) mRNA. FMNL1 NM_005892 0.0004 Homo sapiens formin-like (FMNL) mRNA. ISG15 NM_005101 0.0005 Homo sapiens interferon alpha-inducible protein (clone IFI-15K) (G1P2) mRNA. SLC6A14 NM_007231 0.0005 Homo sapiens solute carrier family 6 (neurotransmitter transporter) member 14 (SLC6A14) mRNA.
    [Show full text]