DOCSLIB.ORG

Proteomic and Genomic Analysis of PITX2 Interacting and Regulating Networks

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Proteomic and Genomic Analysis of PITX2 Interacting and Regulating Networks FEBS Letters 583 (2009) 638–642 journal homepage: www.FEBSLetters.org Proteomic and genomic analysis of PITX2 interacting and regulating networks Yue Huang a, Kan Huang a, Goran Boskovic d, Yulia Dementieva e, James Denvir f, Donald A. Primerano a,d, Guo-Zhang Zhu a,b,c,* a Biomedical Science Graduate Program, Marshall University, Huntington, WV 25755, USA b Department of Biological Sciences, One John Marshall Drive, Marshall University, Huntington, WV 25755, USA c Cell Differentiation and Development Center, Marshall University, Huntington, WV 25755, USA d Department of Biochemistry and Microbiology, Marshall University, Huntington, WV 25755, USA e Department of Mathematics, Marshall University, Huntington, WV 25755, USA f Department of Statistics, West Virginia University, Morgantown, WV 26506, USA article info abstract Article history: Pituitary homeobox 2 (PITX2) is a homeodomain transcription factor that has a substantial role in Received 18 October 2008 cell proliferation and differentiation in various tissues. In this report, we have conducted a system- Revised 20 December 2008 atic study, using proteomic and genomic approaches, to characterize PITX2-interacting proteins and Accepted 15 January 2009 PITX2-regulating genes. We identified four novel PITX2-associated protein partners Y box binding Available online 25 January 2009 factor-1, heterogeneous ribonucleoprotein K, nucleolin and heterogeneous nuclear ribonucleopro- Edited by Lukas Huber tein U in mass spectrometry analysis. We also found that overexpression of PITX2 upregulated 868 genes (2–25-fold) and downregulated 191 genes (2–15-fold) in DNA microarray analysis. These data provide an insightful perspective for further studying PITX2 function and mechanism of action. Keywords: PITX2 YB-1 Structured summary: b-Catenin MINT-6823857: PITX2 (uniprotkb:Q99697) physically interacts (MI:0218) with hnRNP K (uni- Proliferation protkb:P61978), YB-1 (uniprotkb:P67809), Nucleolin (uniprotkb:P19338) and hnRNP U (uni- Differentiation protkb:Q00839) by anti tag coimmunoprecipitation (MI:0007) MINT-6823877: PITX2 (uniprotkb:Q99697) physically interacts (MI:0218) with beta catenin (uni- protkb:P35222), hnRNP U (uniprotkb:Q00839), Nucleolin (uniprotkb:P19338), YB-1 (uniprotkb:P67809) and hnRNP K (uniprotkb:P61978) by anti tag coimmunoprecipitation (MI:0007) MINT-6823902: YB-1 (uniprotkb:P67809) physically interacts (MI:0218) with PITX2 (uniprotkb:Q99697) by anti bait coimmunoprecipitation (MI:0006) Ó 2009 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. 1. Introduction during the development of cardiac outflow tract [3]. Mutations of PITX2 have been identified in several human disorders, such as Transcription factor pituitary homeobox 2 (PITX2) is a member Axenfeld–Rieger syndrome, iridogoniodysgenesis syndrome and of the homeobox gene family. A number of studies have demon- sporadic Peter syndrome [6,7]. Pitx2-deficient mice are embryonic strated that PITX2 has a diverse role in cell proliferation, differen- lethal and show severe defects in heart, eye, pituitary gland and tiation, hematopoiesis and organogenesis [1–4]. During early tooth organogenesis [3]. Previous studies have shown that PITX2 embryogenesis, PITX2 is a key regulator in the establishment of cooperates with b-catenin and LEF/TCF and thus regulates cell embryo left-right asymmetry [5]. In response to Wnt and other proliferation by directly activating transcription of cyclin Ds and growth factors, PITX2 regulates cell-type specific cell proliferation c-myc [3,8,9]. Besides b-catenin and LEF/TCF, other functional binding partners of PITX2, such as nuclear factor-1 (NF-1), high mobility group-17 (HMG-17), MEF2A, Pit-1 and glial cells missing Abbreviations: PITX2, pituitary homeobox 2; YB-1, Y box binding factor-1; hnRNP U, heterogeneous nuclear ribonucleoprotein U; hnRNP K, heterogeneous a (GcMa), have also been reported [1,10–13]. ribonucleoprotein K; NF-1, nuclear factor-1; HMG-17, high mobility group-17; In this study, we analyzed the co-immunoprecipitated protein GcMa, glial cells missing a; PLOD, procollagen lysyl hydroxylase complex of PITX2 by mass spectrometry and successfully identified * Corresponding author. Address: Department of Biological Sciences, One John four proteins, Y box binding factor-1 (YB-1), nucleolin, heteroge- Marshall Drive, Marshall University, Huntington, WV 25755, USA. Fax: +1 304 696 7136. neous ribonucleoprotein K (hnRNP K) and heterogeneous nuclear E-mail address: [email protected] (G.-Z. Zhu). ribonucleoprotein U (hnRNP U), as novel PITX2-interacting 0014-5793/$34.00 Ó 2009 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. doi:10.1016/j.febslet.2009.01.028 Y. Huang et al. / FEBS Letters 583 (2009) 638–642 639 partners. We also investigated the regulatory effects of PITX2 by mum missed cleavages: 2; peptide mass tolerance: ±1–2 Da; frag- examining gene expression profile of HEK293 cells with transient ment mass tolerance: ±0.8–1 Da) on the non-redundant fasta overexpression of PITX2. Our result indicated that 868 genes and database obtained from the National Center for Biotechnology 191 genes were upregulated and downregulated more than Information (NCBI) and Swissprot database. The peptides and twofold, respectively. Many of these regulated genes have previ- proteins with significant Mowse score (P < 0.05), except trypsins, ously been linked to cell proliferation, cell differentiation, and were reported. organogenesis of muscle and eye. Taken together, our findings pro- vide an insightful perspective on PITX2 function and related molec- 2.4. RNA preparation ular mechanism. HEK293 cells were transiently transfected with pEGFP-NFLAG- PITX2c or pEGFP-N1. Forty eight hours after transfection, cells were 2. Materials and methods harvested for total RNA extraction by using TRI Reagent (Ambion). RNA quality was assessed by electrophoretic analysis on an Agilent 2.1. Cell culture Model 2100 Bioanalyzer. All RNA samples used in this study had RNA Integrity Numbers greater than 8.0. HEK293 cells were obtained from American Type Culture Col- lection (ATCC, Rockville, MD) and cultured in Dulbecco’s modified 2.5. Microarray analysis Eagle’s medium with 4.5 g/l glucose, 10% fetal bovine serum, and penicillin-streptomycin (100 IU/ml) at 37 °C in a humidified atmo- We employed a balanced block design with dye swap using four sphere with 5% CO2. biological replicates from HEK293 cells transfected with either pEGFP-N1 or pEGFP-NFLAG-PITX2c. For microarray probes, total RNA (250 ng) was used as the template for synthesis of internally 2.2. Immunoprecipitation and immunoblotting labeled cRNAs using Agilent QuickAmp Labeling kit and cyanine 3-CTP and cyanine 5-CTP (Perkin–Elmer, Waltham, MA) and a The open reading frame of human PITX2c, along with a FLAG modified QuickAmp protocol [14]. A total of 825 ng of cyanine 3- epitope inserted between Met1 and Asn2, was amplified by PCR with and cyanine5-labeled cRNAs was combined and hybridized onto 0 the following primers: forward primer (5 -ACTGaagcttgccaccATG- Agilent Whole Human Genome 4 Â 44 K microarrays at 65 °C for GATTACAAGGATGACGACGATAAGAACTGCATGAAAGGCCCGCTTCA- 17 h and then washed according to the manufacturer’s protocol. 0 C-3 , HindIII and Kozak site in lowercase) and reverse primer Slides were scanned on Agilent DNA Microarray Scanner. (50-AGCTggtacctcaCACGGGCCGGTCCACTG-30, KpnI site and stop co- don in lowercase). The PCR product was cloned into the HindIII/KpnI 2.6. Statistical analysis of microarray data sites of the vector pEGFP-N1 (Clontech). The resulting construct pEGFP-NFLAG-PITX2c, along with the control vector pEGFP-N1, Data were lowess-normalized and extracted from arrays using was transfected into HEK293 cells using FugeneHD transfection re- Agilent Feature Extraction v9.5. Features for which both channels agent (Roche). The cells were observed 24 and 48 h post-transfec- had low signal were excluded. Log2 expression ratios of PITX2- tion, and no significant difference of cell growth and cell viability overexpressed to control samples were imported to the Multiple was noticed between the test and control groups. Cells were then Experiment Viewer (MeV) v4.0 to perform statistical analysis lysed in immunoprecipitation buffer (50 mM Tris–HCl pH 7.4, [15]. Values were compared for significant deviation from zero 150 mM NaCl, 5 mM EDTA, 1% Triton X-100) after 48 h of initial using one-class Significance Analysis of Microarrays (SAM) [16]. transfection. For nuclear protein extraction, cells were incubated Only probes for which at least three replicates passed the low sig- in hypotonic buffer (10 mM HEPES, 10 mM KCl, 1.5 mM MgCl2, nal filter were included. SAM was performed with the maximum 0.5 mM DTT) for 10 min before adding of 0.5% CA-630. Cell nuclei number of unique permutation, and delta was chosen to give 0% re- were then isolated by centrifugation. Nuclear proteins were ex- ported 90th percentile False Discovery Rate (FDR). Data for signif- tracted by the immunoprecipitation buffer. Cell lysates were pre- icantly differentially expressed genes are shown in Supplementary cleared by protein G beads (Pierce) for 2 h at 4 °C, and then incubated Table 1. Raw data from the microarray experiment are available at with anti-FLAG M2 conjugated-agarose beads (Sigma) or rabbit anti- the NCBI Gene Expression Omnibus with Accession No. GSE13216. YB-1 (Epitomics) for 2 h or overnight at 4 °C. The beads were washed five times using the immunoprecipitation buffer. To eliminate
Load more

Recommended publications
  • Pitx2 Prevents Susceptibility to Atrial Arrhythmias by Inhibiting Left-Sided Pacemaker Specification
    Pitx2 prevents susceptibility to atrial arrhythmias by inhibiting left-sided pacemaker specification Jun Wanga, Elzbieta Klysika, Subeena Soodb, Randy L. Johnsonc, Xander H. T. Wehrensb,d, and James F. Martina,1 aInstitute of Biosciences and Technology, Texas A&M System Health Science Center, Houston, TX 77030; Departments of bMolecular Physiology and Biophysics and dMedicine (in Cardiology), Baylor College of Medicine, Houston, TX 77030; and cDepartment of Biochemistry and Molecular Biology, MD Anderson Cancer Center, Houston, TX 77030 Edited by Eric N. Olson, University of Texas Southwestern, Dallas, TX, and approved April 16, 2010 (received for review October 30, 2009) Atrial fibrillation (AF), the most prevalent sustained cardiac arrhyth- part through Nodal signaling. Pitx2c is the major downstream mia, often coexists with the related arrhythmia atrial flutter (AFL). effector of the Nodal pathway (10). Limitations in effectiveness and safety of current therapies make an Recent genome-wide association studies identified sequence understanding of the molecular mechanism underlying AF more variants on chromosome 4q25 that were associated with in- urgent. Genome-wide association studies implicated a region of creased risk for AF in multiple human populations (11–13). human chromosome 4q25 in familial AF and AFL, ≈150 kb distal to Moreover, the 4q25 variants were strongly associated with AF the Pitx2 homeobox gene, a developmental left–right asymmetry cases diagnosed at an earlier age (<60 years) and with recurrence (LRA) gene. To investigate the significance of the 4q25 variants, we after ablation therapy (14). In a small Icelandic cohort, the se- used mouse models to investigate Pitx2 in atrial arrhythmogenesis quence variants also were strongly associated with AFL (11).
    [Show full text]
  • Galnt11 Is a Novel Galnac-Transferase That
    Yale University EliScholar – A Digital Platform for Scholarly Publishing at Yale Yale Medicine Thesis Digital Library School of Medicine January 2012 Galnt11 Is A Novel Galnac-Transferase That Glycosylates Notch1 Receptor To Specify Between Motor And Sensory Ciliary Fates In The eV rtebrate Left-Right Organizer Marko Boskovski Yale School of Medicine, [email protected] Follow this and additional works at: http://elischolar.library.yale.edu/ymtdl Recommended Citation Boskovski, Marko, "Galnt11 Is A Novel Galnac-Transferase That Glycosylates Notch1 Receptor To Specify Between Motor And Sensory Ciliary Fates In The eV rtebrate Left-Right Organizer" (2012). Yale Medicine Thesis Digital Library. 1696. http://elischolar.library.yale.edu/ymtdl/1696 This Open Access Thesis is brought to you for free and open access by the School of Medicine at EliScholar – A Digital Platform for Scholarly Publishing at Yale. It has been accepted for inclusion in Yale Medicine Thesis Digital Library by an authorized administrator of EliScholar – A Digital Platform for Scholarly Publishing at Yale. For more information, please contact [email protected]. Galnt11 is a Novel GalNAc-transferase that Glycosylates Notch1 Receptor to Specify Between Motor and Sensory Ciliary Fates in the Vertebrate Left-Right Organizer A Thesis Submitted to the Yale University School of Medicine In Partial Fulfillment of the Requirements for the Degree of Doctor of Medicine by Marko T. Boskovski 2012 ABSTRACT GALNT11 IS A NOVEL GALNAC-TRANSFERASE THAT GLYCOSYLATES NOTCH1 RECEPTOR TO SPECIFY BETWEEN MOTOR AND SENSORY CILIARY FATES IN THE VERTEBRATE LEFT-RIGHT ORGANIZER. Marko T. Boskovski, Mustafa Khokha and Martina Brueckner. Section of Cardiology, Department of Pediatrics, Yale University, School of Medicine, New Haven, CT.
    [Show full text]
  • Wnt/Lef1 Signaling Acts Via Pitx2 to Regulate Somite Myogenesis
    Developmental Biology 337 (2010) 211–219 Contents lists available at ScienceDirect Developmental Biology journal homepage: www.elsevier.com/developmentalbiology Wnt/Lef1 signaling acts via Pitx2 to regulate somite myogenesis Muhammad Abu-Elmagd a, Lesley Robson b, Dylan Sweetman a, Julia Hadley c, Philippa Francis-West c,⁎, Andrea Münsterberg a,⁎ a University of East Anglia, School of Biological Sciences, Norwich, NR4 7TJ Earlham Road, UK b Queen Mary University of London, Neuroscience, Barts and The London SMD, E1 2AD London, UK c Craniofacial Development, The Dental Institute, King's College London, Guy's Campus, London, SE1 9RT, UK article info abstract Article history: Wnt signaling has been implicated in somite, limb, and branchial arch myogenesis but the mechanisms and Received for publication 23 February 2009 roles are not clear. We now show that Wnt signaling via Lef1 acts to regulate the number of premyogenic Revised 18 September 2009 cells in somites but does not regulate myogenic initiation in the limb bud or maintenance in the first or Accepted 14 October 2009 second branchial arch. We have also analysed the function and regulation of a putative downstream Available online 20 October 2009 transcriptional target of canonical Wnt signaling, Pitx2. We show that loss-of-function of Pitx2 decreases the Keywords: number of myogenic cells in the somite, whereas overexpression increases myocyte number particularly in Chicken embryo the epaxial region of the myotome. Increased numbers of mitotic cells were observed following Wnt signaling overexpression of Pitx2 or an activated form of Lef1, suggesting an effect on cell proliferation. In addition, Myogenesis we show that Pitx2 expression is regulated by canonical Wnt signaling in the epaxial somite and second Lef1 branchial arch, but not in the limb or the first branchial arch.
    [Show full text]
  • Rbpj-Dependent and -Independent Notch2 Signaling Regulates
    RBPJ-DEPENDENT AND -INDEPENDENT NOTCH2 SIGNALING REGULATES CILIARY BODY DEVELOPMENT IN THE MOUSE EYE By Yi Zhou B.S., Tsinghua University, 2010 Submitted to the graduate degree program in Anatomy and Cell Biology and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy. ________________________________ Ting Xie, Ph.D., Co-Chair ________________________________ William Kinsey, Ph.D., Co-Chair ________________________________ Dale Abrahamson, Ph.D. ________________________________ Peter Smith, Ph.D. ________________________________ Jerry Workman, Ph.D. Date Defended: Jan 6th, 2016 The Dissertation Committee for Yi Zhou certifies that this is the approved version of the following dissertation: RBPJ-DEPENDENT AND -INDEPENDENT NOTCH2 SIGNALING REGULATES CILIARY BODY DEVELOPMENT IN THE MOUSE EYE ________________________________ Ting Xie, Ph.D., Co-Chair ________________________________ William Kinsey, Ph.D., Co-Chair Date Approved: Jan 15th, 2016 ii ABSTRACT The ciliary body (CB) is a two-layered structure in the anterior eye, which is composed of the pigmented outer ciliary epithelium (OCE) and the non-pigmented inner ciliary epithelium (ICE). It is responsible for aqueous humor secretion and lens accommodation. Despite the important roles in maintaining normal eye functions, its development still remains poorly understood. The Notch signaling pathway is an evolutionarily conserved pathway that has diverse functions during tissue development and homeostasis. Canonical Notch signaling is mediated through the recombination signal binding protein for immunoglobulin kappa J region (RBPJ)-dependent transcription activation and repression. In this study, I have demonstrated that Notch2 and RBPJ are important regulators of CB development by conditionally deleting them in the developing CB.
    [Show full text]
  • Supplementary Table 2
    Supplementary Table 2. Differentially Expressed Genes following Sham treatment relative to Untreated Controls Fold Change Accession Name Symbol 3 h 12 h NM_013121 CD28 antigen Cd28 12.82 BG665360 FMS-like tyrosine kinase 1 Flt1 9.63 NM_012701 Adrenergic receptor, beta 1 Adrb1 8.24 0.46 U20796 Nuclear receptor subfamily 1, group D, member 2 Nr1d2 7.22 NM_017116 Calpain 2 Capn2 6.41 BE097282 Guanine nucleotide binding protein, alpha 12 Gna12 6.21 NM_053328 Basic helix-loop-helix domain containing, class B2 Bhlhb2 5.79 NM_053831 Guanylate cyclase 2f Gucy2f 5.71 AW251703 Tumor necrosis factor receptor superfamily, member 12a Tnfrsf12a 5.57 NM_021691 Twist homolog 2 (Drosophila) Twist2 5.42 NM_133550 Fc receptor, IgE, low affinity II, alpha polypeptide Fcer2a 4.93 NM_031120 Signal sequence receptor, gamma Ssr3 4.84 NM_053544 Secreted frizzled-related protein 4 Sfrp4 4.73 NM_053910 Pleckstrin homology, Sec7 and coiled/coil domains 1 Pscd1 4.69 BE113233 Suppressor of cytokine signaling 2 Socs2 4.68 NM_053949 Potassium voltage-gated channel, subfamily H (eag- Kcnh2 4.60 related), member 2 NM_017305 Glutamate cysteine ligase, modifier subunit Gclm 4.59 NM_017309 Protein phospatase 3, regulatory subunit B, alpha Ppp3r1 4.54 isoform,type 1 NM_012765 5-hydroxytryptamine (serotonin) receptor 2C Htr2c 4.46 NM_017218 V-erb-b2 erythroblastic leukemia viral oncogene homolog Erbb3 4.42 3 (avian) AW918369 Zinc finger protein 191 Zfp191 4.38 NM_031034 Guanine nucleotide binding protein, alpha 12 Gna12 4.38 NM_017020 Interleukin 6 receptor Il6r 4.37 AJ002942
    [Show full text]
  • NKX2-5: an Update on This Hypermutable Homeodomain Protein and Its Role in Human Congenital Heart Disease (CHD) Stella Marie Reamon-Buettner, Juergen T Borlak
    NKX2-5: An Update on this Hypermutable Homeodomain Protein and its Role in Human Congenital Heart Disease (CHD) Stella Marie Reamon-Buettner, Juergen T Borlak To cite this version: Stella Marie Reamon-Buettner, Juergen T Borlak. NKX2-5: An Update on this Hypermutable Home- odomain Protein and its Role in Human Congenital Heart Disease (CHD). Human Mutation, Wiley, 2010, 31 (11), pp.1185. 10.1002/humu.21345. hal-00585168 HAL Id: hal-00585168 https://hal.archives-ouvertes.fr/hal-00585168 Submitted on 12 Apr 2011 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. Human Mutation NKX2-5: An Update on this Hypermutable Homeodomain Protein and its Role in Human Congenital Heart Disease (CHD) For Peer Review Journal: Human Mutation Manuscript ID: humu-2010-0256.R1 Wiley - Manuscript type: Review Date Submitted by the 15-Jul-2010 Author: Complete List of Authors: Reamon-Buettner, Stella Marie; Fraunhofer Institute of Toxicology and Experimental Medicine, Molecular Medicine and Medical Biotechnology Borlak, Juergen; Fraunhofer Institute of Toxicology and Experimental Medicine, Molecular Medicine and Medical Biotechnology heart development, congenital heart disease, cardiac Key Words: malformations, transcription factors, NKX2-5, mutations John Wiley & Sons, Inc.
    [Show full text]
  • 6810.Full.Pdf
    The Journal of Neuroscience, September 1, 2001, 21(17):6810–6819 Conserved Function of Caenorhabditis elegans UNC-30 and Mouse Pitx2 in Controlling GABAergic Neuron Differentiation Joby J. Westmoreland,1 Jason McEwen,3 Billie A. Moore,1 Yishi Jin,3 and Brian G. Condie1,2 1Institute of Molecular Medicine and Genetics and 2Departments of Medicine and Cellular Biology and Anatomy, Medical College of Georgia, Augusta, Georgia 30912, and 3Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California 95064 We are taking a cross-species approach to identify genes that of the mouse and human genes coding for the 67 kDa gluta- are required for mammalian GABAergic neuron differentiation. mate decarboxylase (Gad1) also contain binding sites matching On the basis of homeodomain similarity, the vertebrate Pitx the UNC-30/Pitx2 consensus binding site sequence. We show genes appear to be orthologs of unc-30,aCaenorhabditis that these sites specifically bind to Pitx2 protein in vitro and that elegans gene necessary for differentiation of the GABAergic in transfected neuroblastoma cells, the Pitx2 binding sites con- phenotype of type D neurons. One of the Pitx genes, Pitx2,is tribute to the basal activity of the Gad1 promoter. Furthermore, expressed in regions of GABAergic neurogenesis in the mam- in cotransfection experiments, we find that Pitx2 strongly acti- malian brain. These observations led us to test the functional vates the Gad1 promoter. These results indicate that Pitx2 may conservation of the mouse Pitx2 and worm unc-30 genes using regulate Gad1 expression in mammals, suggesting a new role a rescue assay.
    [Show full text]
  • PLEIOTROPIC and ISOFORM-SPECIFIC FUNCTIONS of PITX2 in BRAIN DEVELOPMENT by Mindy Rachelle Waite a Dissertation Submitted In
    PLEIOTROPIC AND ISOFORM-SPECIFIC FUNCTIONS OF PITX2 IN BRAIN DEVELOPMENT by Mindy Rachelle Waite A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Cellular and Molecular Biology) in The University of Michigan 2012 Doctoral Committee: Associate Professor Donna M. Martin, Chair Professor Gregory R. Dressler Professor Sue O’Shea Associate Professor Philip J. Gage Associate Professor Robert C. Thompson Yesterday is but a dream, tomorrow but a vision. But today well lived makes every yesterday a dream of happiness, and every tomorrow a vision of hope. Look well, therefore, to This Day. -Sanskrit Proverb © Mindy Rachelle Waite 2012 ACKNOWLEDGMENTS I would like to thank Dr. Donna Martin for her unwavering mentorship and support. Donna, I can never repay you enough for taking me in as one of your own and building my skillset from the ground up. You really put your heart and soul into teaching me how to do research, write, speak, and even work in a team setting. Thank you so much for the skills and self-confidence which will be necessary for my future successes. I will never forget our first “data dance” and promise to think of you every time I see red ink. I would also like to thank the rest of my lab. Liz, Jennifer, Joe, Wanda, Kaia, and Jillian – what would I have ever done without you guys? Graduate school can be a frustrating, lonely experience for some, but not for me. Every day I worked with my friends. Thank you for your unconditional support and delightful shenanigans.
    [Show full text]
  • Single-Cell Transcriptome Analysis During Cardiogenesis Reveals Basis for Organ Level
    bioRxiv preprint doi: https://doi.org/10.1101/365734; this version posted July 9, 2018. 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-ND 4.0 International license. Single-cell transcriptome analysis during cardiogenesis reveals basis for organ level developmental anomalies T. Yvanka de Soysa1,2, Sanjeev S. Ranade1,2, Satoshi Okawa3, Srikanth Ravichandran3, Yu Huang1,2, Hazel T. Salunga1,2, Amelia Schricker1,2, Antonio Del Sol3, Casey A. Gifford1,2*, Deepak Srivastava1,2,4,5* Affiliations: 1Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA 2Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA 3Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg Departments of 4Pediatrics, and 5Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA *Corresponding author: [email protected], [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/365734; this version posted July 9, 2018. 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-ND 4.0 International license. Organogenesis involves integration of myriad cell types with reciprocal interactions, each progressing through successive stages of lineage specification and differentiation. Establishment of unique gene networks within each cell dictates fate determination, and mutations of transcription factors that drive such networks can result in birth defects.
    [Show full text]
  • CREB-Dependent Transcription in Astrocytes: Signalling Pathways, Gene Profiles and Neuroprotective Role in Brain Injury
    CREB-dependent transcription in astrocytes: signalling pathways, gene profiles and neuroprotective role in brain injury. Tesis doctoral Luis Pardo Fernández Bellaterra, Septiembre 2015 Instituto de Neurociencias Departamento de Bioquímica i Biologia Molecular Unidad de Bioquímica y Biologia Molecular Facultad de Medicina CREB-dependent transcription in astrocytes: signalling pathways, gene profiles and neuroprotective role in brain injury. Memoria del trabajo experimental para optar al grado de doctor, correspondiente al Programa de Doctorado en Neurociencias del Instituto de Neurociencias de la Universidad Autónoma de Barcelona, llevado a cabo por Luis Pardo Fernández bajo la dirección de la Dra. Elena Galea Rodríguez de Velasco y la Dra. Roser Masgrau Juanola, en el Instituto de Neurociencias de la Universidad Autónoma de Barcelona. Doctorando Directoras de tesis Luis Pardo Fernández Dra. Elena Galea Dra. Roser Masgrau In memoriam María Dolores Álvarez Durán Abuela, eres la culpable de que haya decidido recorrer el camino de la ciencia. Que estas líneas ayuden a conservar tu recuerdo. A mis padres y hermanos, A Meri INDEX I Summary 1 II Introduction 3 1 Astrocytes: physiology and pathology 5 1.1 Anatomical organization 6 1.2 Origins and heterogeneity 6 1.3 Astrocyte functions 8 1.3.1 Developmental functions 8 1.3.2 Neurovascular functions 9 1.3.3 Metabolic support 11 1.3.4 Homeostatic functions 13 1.3.5 Antioxidant functions 15 1.3.6 Signalling functions 15 1.4 Astrocytes in brain pathology 20 1.5 Reactive astrogliosis 22 2 The transcription
    [Show full text]
  • Notch Signaling Regulates Left
    Downloaded from genesdev.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH COMMUNICATION (3) induction of an evolutionarily conserved cascade of Notch signaling regulates left– gene expression in the left LPM, and (4) transformation right asymmetry of these left–right asymmetric signals into morphologi- cal asymmetries of the visceral organs. In mice, genera- determination by inducing tion of the initial asymmetric signal requires directional Nodal expression fluid flow on the ventral surface of the node (Nonaka et al. 2002). This fluid flow is generated by motile mono- Luke T. Krebs,1,4 Naomi Iwai,2,3,4 cilia on cells of the node, and the presence of nodal cilia is conserved in other vertebrates (Essner et al. 2002). Shigenori Nonaka,2,3 Ian C. Welsh,1 Yu Lan,1,5 1,5 2 However, the mechanism by which directional fluid Rulang Jiang, Yukio Saijoh, flow at the node specifies orientation of the left–right Timothy P. O’Brien,1 Hiroshi Hamada,2,3,6 and axis is controversial (Stern and Wolpert 2002; Tabin and Thomas Gridley1,7 Vogan 2003). In addition, the mechanism for transfer of the initial asymmetric signal from the node to the LPM 1The Jackson Laboratory, Bar Harbor, Maine 04609, USA; is unknown. 2Developmental Genetics Group, Graduate School of Frontier The Notch signaling pathway is an evolutionarily con- Biosciences, Osaka University, Osaka 565-0871, Japan; served intercellular signaling mechanism. Mutations in 3CREST (Core Research for Evolutional Science and Notch pathway components disrupt embryonic develop- Technology), Japan Science and Technology Corporation (JST), ment in diverse multicellular organisms and cause in- Osaka 565-0871, Japan herited disease syndromes in humans (Artavanis-Tsako- nas et al.
    [Show full text]
  • Supplementary File Table S1
    Supplementary file Table S1 Grouping of Homeobox genes according to their main known function. Anatomical Structure Morphogenesis EN1, HOXC10, HOXC13, HOXD3, LBX1, SIX2, SIX4 Organ Morphogenesis CDX1, CDX2, HOXA11, HOXA13, ISL1, LHX1, PAX3, PDHX, PITX2, PITX3, PROX1, SIX6 Body Pattern Formation ALX3, EMX2, HHEX, HOXA11, HOXA2, HOXA4, HOXA5, HOXA6, HOXB1, HOXB5, HOXB6, HOXC5, HOXD10, HOXD8, LMX1B, PITX2 Ectoderm Development PROX1, VAX2 Endoderm Development HOXC11 Brain & Nervous System Development Brain Development ALX1, DLX2, EMX2 Nervous System Development: ARX, DLX5, DLX6, HOXD10, LBX1, LHX1, OTP, PAX3, PHOX2A, PHOX2B Skeletal Development: ALX3, ALX4, DLX3, DLX5, DLX6, EN1, HOXA11, HOXA13, HOXA2, HOXB6, HOXD10, HOXD13, MSX2 Muscle Development: BARX2, MKX, SIRT1, SIRT2, SIX1 Other Homeobox Genes Involved In BARX1, CDX4, CUX1, DLX1, EMX1, EN2, Multicellular Organismal HOXA1, HOXA7, HOXA9, HOXB13, HOXB2, Development: HOXB3, HOXB4, HOXB7, HOXB8, HOXB9, HOXC12, HOXC8, HOXC9, HOXD1, HOXD11, HOXD12, HOXD9, ISL2, LBX2, LMX1A, MEIS1, NKX3-1, OTX1, TLX1, VAX1, VSX1, VSX2 Homeobox Genes Involved In Cell ARX, EMX2, HHEX, HLX, HOPX, LBX1, LHX1, Differentiation: LMX1B, MIXL1, OTP, PHOX2A, SIRT1, VSX2 Other Genes: PHTF1, SIRT3, SIRT6, SIRT7, ZHX1, ZHX2 Homeobox genes include two subsets of genes coding for transcription factors involved in multiple functions. The clustered HOX genes are indicated in bold. Supplementary file Figure S2 5’ Spatial collinearity 3’ HOXA Chr. 7p15.3 HOXB Chr. 17q21.3 HOXC Chr. 12q13.3 HOXD Chr. 2q31 13 12 11 10 9 8 7 6 5 4 3 2 1 Paralogous HOX groups Distribution of the 39 human HOX genes in four clusters located in different chromosomal regions*. Blue indicates anterior HOX genes. Yellow, paralogy group 3 Hox genes, green and purple indicatete central HOX genes and Red the posterior HOX genes.
    [Show full text]