DOCSLIB.ORG

(12) Patent Application Publication (10) Pub. No.: US 2002/0177218 A1 Fang Et Al

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

US 2002O177218A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2002/0177218 A1 Fang et al. (43) Pub. Date: Nov. 28, 2002 (54) METHODS OF DETECTING MULTIPLE DNA Publication Classification BINDING PROTEIN AND DNA INTERACTIONS IN A SAMPLE, AND (51) Int. Cl." ....................................................... C12N 1/20 DEVICES, SYSTEMS AND KITS FOR (52) U.S. Cl. .......................................................... 435/252.3 PRACTICING THE SAME (57) ABSTRACT (76) Inventors: Yu Fang, Fremont, CA (US); Methods for detecting the presence of at least one, usually Xiao-Yang Wang, Mountain View, CA a plurality of, DNA binding proteins, e.g., transcription (US); Pierre Turpin, San Francisco, factors, in a Sample, both qualitatively and quantitatively, are CA (US) provided. In the Subject methods, a Substrate having one or Correspondence Address: more DNA probes immobilized on a surface thereof, one for each DNA binding protein of interest, is contacted with a BOZICEVIC, FIELD & FRANCIS LLP Sample under conditions Sufficient for binding complexes of 200 MIDDLEFIELD RID the probes and their respective DNA binding proteins to be SUTE 200 produced. The Sample may be purified with respect to one or MENLO PARK, CA 94025 (US) more DNA binding proteins or be a cellular/nuclear extract. (21) Appl. No.: 10/113,877 Resultant binding complexes on the Surface of the Substrate are then detected and related to the presence of the DNA (22) Filed: Mar. 29, 2002 binding protein-DAN interations of interest in the Sample. Also provided are devices and Systems for use in practicing Related U.S. Application Data the subject methods. The subject methods find use in a variety of different applications, e.g., detecting the presence (60) Provisional application No. 60/280,658, filed on Mar. of a transcription factor in a Sample, the Study of transcrip 30, 2001. Provisional application No. 60/314,330, tion factor profiles in response to a given Stimulus, Screening filed on Aug. 20, 2001. for therapeutic agents, and the like. Patent Application Publication Nov. 28, 2002. Sheet 1 of 13 US 2002/0177218 A1 Patent Application Publication Nov. 28, 2002. Sheet 2 of 13 US 2002/0177218 A1 Figure 2 33... : Add callysates: : 33 33r & 3. Extract 3. -- iii-inding Targon sing & antibody and ash E:: resilts 33: 3. i-C Patent Application Publication Nov. 28, 2002 Sheet 3 of 13 US 2002/0177218A1 Figure 3a - Eli » (« EMSA O. 10 COO NFkB p50 concentration, uM Patent Application Publication Nov. 28, 2002 Sheet 4 of 13 US 2002/0177218A1 Figure 3b 1 2 3 4 5 6 7 8 9 O 11 12 13 -& & 8.33. 48 88: Patent Application Publication Nov. 28, 2002 Sheet 5 of 13 US 2002/0177218 A1 Figure 4a i. .8 O hutant oligo . i. s f:3. i.2 3.1 a 5 sag 10 g 20 g 30 ug 25 g 5 g. 100 ng 200ng - t Dose of Helge NPt. NE Dose of competition oligo 30 g of HeLa NFa. NE Patent Application Publication Nov. 28, 2002. Sheet 6 of 13 US 2002/0177218 A1 Figure 4b Wild-type oligo f O Mutant 1.4 5 gig is 20 g 3 g 25 ng 5 ng 1 ng 200ng l- - Dose of Jurka NE Dose of competition oligo 30 g of Jurkat NE Patent Application Publication Nov. 28, 2002 Sheet 7 of 13 US 2002/0177218A1 Figure 4c a Wild-type oligo Mutant oligo ... 3 i 1.8- . D O.0 a. l org 5 pig 10 pg 20g 30 g 25 mg 50 fig 100 g 200ng l- l Dose of HeLaf PMANE Dose of competition oligo 30g of HeLat PMANE Patent Application Publication Nov. 28, 2002 Sheet 8 of 13 US 2002/0177218 A1 Figure 5 NFkB p50 dsDNA-coated ATF-2 dsDNA-coated c-Fos dsDNA-coated Patent Application Publication Nov. 28, 2002 Sheet 9 of 13 US 2002/0177218 A1 Figure 6 0.84 6 . NFke p50 NFkB pe;5 e-Rei c-ress CR-3- AF-2 Patent Application Publication Nov. 28, 2002. Sheet 10 of 13 US 2002/0177218 A1 Figure 7 2.2. O5 O to a lar its to - i. Transcription Factor Patent Application Publication Nov. 28, 2002. Sheet 11 of 13 US 2002/0177218 A1 Figure 8 1.25 Wies O, 7 5 O. 5 O 0.25 OOO p53 c-Myb c-Myc Max USF1 USF2, Transcription Factor Raji U-937 Nucl. Extr. Patent Application Publication Nov. 28, 2002 Sheet 12 of 13 US 2002/0177218 A1 Figure 9: 48 DBP Transfactor Glass Array (format3.0) 48 DBP TransFactor Glass Array (Format3.0) A - B Each chamber: P50 SMAD4 ISGF-3g P50 SMAD4 ISGF-3g c-Fos Pit SA3 cos Pi Si A3 Oct-1 ERHSF-1 Oct-1 ERHSF-1 MYO) Pax-5 P. A MYO Pax-5 P.I. -2x6 wt & mut oligos -6 Ab. cocktail -fluorescent 2nd Ab. 55 c-Myth MA) P65 c-Myb MA) REB-E2F. SA: CREB-1 E2F-1 SA GATA TRb1 CTCF A GATA TRb1 croF JunB RXRb ETS-1 A JunB RXRb ETS-1 c-Re MAX STAT6 e-Rei AXSAT& ATF2 prbSTAT5 ATF2 prb STAT5 160 ARPPAR P160 ARPPAR SRF-1 GR RF-5 SRF-1 GRIRF-5 -24 DBP-DNA 1 side C-1 SAT C-ta PSA Sp1 PS3 NF-ATc1 Sp1 P53 NF-ATc1 -2 conditions/slide AP-2 YY1PR AP-2 YY1PR C-Myc EGR C/EBPa AC-Myc EGRC/EBPa -less extracts -less Ab. A369RAORES PARYINGEN BOT Patent Application Publication Nov. 28, 2002. Sheet 13 of 13 US 2002/0177218 A1 Figure 10 3000 Comparison of Single Antibody versus Mixing Antibodies 2so g2 9 200 CD 2 c 1500 C 9) O I 1000 500 Single Mix Single Mix Single Mix Single Mix Single Mix Single Mix Antibody NF-kBp50 EGR c-Rei Max SRF-1 ATF2 Transcription Factor Hela-TNFO K562+PMA Raji Raji U937 Jurkat Nuclear Extract A B C D E F US 2002/0177218 A1 Nov. 28, 2002 METHODS OF DETECTING MULTIPLE DNA with a biotinylated dis-DNA probe and an antibody for the BINDING PROTEIN AND DNA INTERACTIONS IN transcription factor. The resultant mixture is then transferred A SAMPLE, AND DEVICES, SYSTEMS AND KITS to anti-lgG coated microWells, and the presence of DNA/ FOR PRACTICING THE SAME transcription factor/antibody complexes are detected chro mogenically with AP conjugated Streptavidin. There are CROSS-REFERENCE TO RELATED disdvantages with this method, including the fact that reac APPLICATIONS tions are performed in more than one container and the lack 0001 Pursuant to 35 U.S.C. S 119 (e), this application of Specificity with respect to the detection of active V. claims priority to the filing date of U.S. Provisional Patent inactive transcription factor, leading to decreased Sensitivity. Application Serial No. 60/280,658 filed Mar. 30, 2001 and 0008. Yet another transcription factor assay is reported in U.S. Provisional Patent Application Serial No. 60/314,330 Renard et al., Nucleic Acids Res. (Feb. 15, 2001) 29:E21, filed Aug. 20, 2001; the disclosures of which are herein which article describes a calorimetric assay that employs a incorporated by reference. substrate bound oligonucleotide which includes an NFKB consensus binding Sequence, where both purified Samples INTRODUCTION and cell extracts are assayed. In the assays reported in this document, only a Single transcription factor, NFKB, is FIELD OF THE INVENTION assayed. 0002 The field of this invention is DNAbinding proteins, 0009. There is continued interest in the development of particularly transcription factors. new ELISA based assays for transcription factors and analo gous DNA binding proteins. Of particular interest would be BACKGROUND OF THE INVENTION the development of Such an assay that could be employed to detect multiple transcription factors in a single Sample, 0003) The study of the interactions between a DNA including a cellular or nuclear extract, where the assay is binding protein and DNA is one of the most rapidly growing more sensitive than EMSA. areas of molecular biology. Transcription factors, a Subset of DNA binding proteins, are at the heart of the regulation and 0010 Relevant Literature control of gene expression, replication, and recombination. 0011 Benotmane, et al. (1997) Analytical Biochemistry Because of their important roles, inhibition and Stimulation 250:181-185; Gubler et al., Biotechniques (1995) 18:1011 of transcription factor binding to DNA is of great interest in 1014; Hibma et al., Nucleic Acids Res. (1994) 22: 3806 the discovery of potential targets for new drugs. 3807; McKay et al., Anal. Biochem (1998) 1:28:34; Mollo, 0004 Several different protocols have been developed to Methods Mol. Biol. (2000) 130:235-246; Renard et al., Nuc. study DNA-protein interactions, such as DNA-protein pho Acids Res. (Feb. 15, 2001) 29:E21; and Revzin, Biotech tocrosslinking, South-western blotting, in Vivo reporting niques (1989) 7:346-355. See also: (a) U.S. Pat. Nos. system and the electrophoretic mobility shift assay (EMSA). 4.963,658; 4.978,608; 5,011,770; (b) WO95/30026; WO EMSA is one of the most powerful tools to study the 98/08096; WO 99/19510; WO 01/73115; and (c) EPO 620 functional relationship between a DNA binding protein and 439 and EP 1 136567. its cognate DNA site. However, the EMSA has some intrin sic disadvantages Such as radioactive usage, limitation of SUMMARY OF THE INVENTION Sample numbers and long assay time. These disadvantages 0012 Methods for detecting, both qualitatively and quan and the need for a high throughput format have led to the titatively, the presence of at least one, usually a plurality of, development of an enzyme-linked DNA-protein binding DNA binding proteins, e.g., transcription factors, in a assay to complement the traditional EMSA.
Recommended publications
  • Core Transcriptional Regulatory Circuitries in Cancer

    Core Transcriptional Regulatory Circuitries in Cancer

    Oncogene (2020) 39:6633–6646 https://doi.org/10.1038/s41388-020-01459-w REVIEW ARTICLE Core transcriptional regulatory circuitries in cancer 1 1,2,3 1 2 1,4,5 Ye Chen ● Liang Xu ● Ruby Yu-Tong Lin ● Markus Müschen ● H. Phillip Koeffler Received: 14 June 2020 / Revised: 30 August 2020 / Accepted: 4 September 2020 / Published online: 17 September 2020 © The Author(s) 2020. This article is published with open access Abstract Transcription factors (TFs) coordinate the on-and-off states of gene expression typically in a combinatorial fashion. Studies from embryonic stem cells and other cell types have revealed that a clique of self-regulated core TFs control cell identity and cell state. These core TFs form interconnected feed-forward transcriptional loops to establish and reinforce the cell-type- specific gene-expression program; the ensemble of core TFs and their regulatory loops constitutes core transcriptional regulatory circuitry (CRC). Here, we summarize recent progress in computational reconstitution and biologic exploration of CRCs across various human malignancies, and consolidate the strategy and methodology for CRC discovery. We also discuss the genetic basis and therapeutic vulnerability of CRC, and highlight new frontiers and future efforts for the study of CRC in cancer. Knowledge of CRC in cancer is fundamental to understanding cancer-specific transcriptional addiction, and should provide important insight to both pathobiology and therapeutics. 1234567890();,: 1234567890();,: Introduction genes. Till now, one critical goal in biology remains to understand the composition and hierarchy of transcriptional Transcriptional regulation is one of the fundamental mole- regulatory network in each specified cell type/lineage.
  • Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model

    Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model

    Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A.
  • 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

    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
  • Early B-Cell Factors Are Required for Specifying Multiple Retinal Cell Types and Subtypes from Postmitotic Precursors

    Early B-Cell Factors Are Required for Specifying Multiple Retinal Cell Types and Subtypes from Postmitotic Precursors

    11902 • The Journal of Neuroscience, September 8, 2010 • 30(36):11902–11916 Development/Plasticity/Repair Early B-Cell Factors Are Required for Specifying Multiple Retinal Cell Types and Subtypes from Postmitotic Precursors Kangxin Jin,1,2 Haisong Jiang,1,2 Zeqian Mo,3 and Mengqing Xiang1,2 1Center for Advanced Biotechnology and Medicine and Department of Pediatrics, 2Graduate Program in Molecular Genetics, Microbiology and Immunology, and 3Department of Cell Biology and Neuroscience, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854 The establishment of functional retinal circuits in the mammalian retina depends critically on the proper generation and assembly of six classes of neurons, five of which consist of two or more subtypes that differ in morphologies, physiological properties, and/or sublaminar positions. How these diverse neuronal types and subtypes arise during retinogenesis still remains largely to be defined at the molecular level. Here we show that all four family members of the early B-cell factor (Ebf) helix-loop-helix transcription factors are similarly expressedduringmouseretinogenesisinseveralneuronaltypesandsubtypesincludingganglion,amacrine,bipolar,andhorizontalcells, and that their expression in ganglion cells depends on the ganglion cell specification factor Brn3b. Misexpressed Ebfs bias retinal precursors toward the fates of non-AII glycinergic amacrine, type 2 OFF-cone bipolar and horizontal cells, whereas a dominant-negative Ebf suppresses the differentiation of these cells as well as ganglion cells. Reducing Ebf1 expression by RNA interference (RNAi) leads to an inhibitory effect similar to that of the dominant-negative Ebf, effectively neutralizes the promotive effect of wild-type Ebf1, but has no impact on the promotive effect of an RNAi-resistant Ebf1.
  • The Ciliogenic Transcription Factor RFX3 Regulates Early Midline Distribution of Guidepost Neurons Required for Corpus Callosum Development

    The Ciliogenic Transcription Factor RFX3 Regulates Early Midline Distribution of Guidepost Neurons Required for Corpus Callosum Development

    The Ciliogenic Transcription Factor RFX3 Regulates Early Midline Distribution of Guidepost Neurons Required for Corpus Callosum Development Carine Benadiba1,2, Dario Magnani3, Mathieu Niquille1, Laurette Morle´ 2, Delphine Valloton1, Homaira Nawabi2, Aouatef Ait-Lounis4, Belkacem Otsmane1, Walter Reith4, Thomas Theil3, Jean- Pierre Hornung1,Ce´cile Lebrand1,5.*, Be´ne´dicte Durand2.* 1 De´partement de Biologie Cellulaire et de Morphologie, University of Lausanne, Lausanne, Switzerland, 2 Centre de Ge´ne´tique et de Physiologie Mole´culaire et Cellulaire, CNRS UMR 5534, Universite´ Claude Bernard Lyon 1, Lyon, France, 3 Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom, 4 Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Centre Me´dical Universitaire, Geneva, Switzerland, 5 National Center of Competence in Research Robotics, Ecole Polytechnique Fe´de´rale, Lausanne, Switzerland Abstract The corpus callosum (CC) is the major commissure that bridges the cerebral hemispheres. Agenesis of the CC is associated with human ciliopathies, but the origin of this default is unclear. Regulatory Factor X3 (RFX3) is a transcription factor involved in the control of ciliogenesis, and Rfx3–deficient mice show several hallmarks of ciliopathies including left–right asymmetry defects and hydrocephalus. Here we show that Rfx3–deficient mice suffer from CC agenesis associated with a marked disorganisation of guidepost neurons required for axon pathfinding across the midline. Using transplantation assays, we demonstrate that abnormalities of the mutant midline region are primarily responsible for the CC malformation. Conditional genetic inactivation shows that RFX3 is not required in guidepost cells for proper CC formation, but is required before E12.5 for proper patterning of the cortical septal boundary and hence accurate distribution of guidepost neurons at later stages.
  • C-Myc Regulates Cell Proliferation During Lens Development

    C-Myc Regulates Cell Proliferation During Lens Development

    c-myc Regulates Cell Proliferation during Lens Development Gabriel R. Cavalheiro., Gabriel E. Matos-Rodrigues., Anielle L. Gomes, Paulo M. G. Rodrigues, Rodrigo A. P. Martins* Programa de Biologia Celular e do Desenvolvimento, Instituto de Cieˆncias Biome´dicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil Abstract Myc protooncogenes play important roles in the regulation of cell proliferation, growth, differentiation and survival during development. In various developing organs, c-myc has been shown to control the expression of cell cycle regulators and its misregulated expression is detected in many human tumors. Here, we show that c-myc gene (Myc) is highly expressed in developing mouse lens. Targeted deletion of c-myc gene from head surface ectoderm dramatically impaired ocular organogenesis, resulting in severe microphtalmia, defective anterior segment development, formation of a lens stalk and/or aphakia. In particular, lenses lacking c-myc presented thinner epithelial cell layer and growth impairment that was detectable soon after its inactivation. Defective development of c-myc-null lens was not caused by increased cell death of lens progenitor cells. Instead, c-myc loss reduced cell proliferation, what was associated with an ectopic expression of Prox1 and p27Kip1 proteins within epithelial cells. Interestingly, a sharp decrease in the expression of the forkhead box transcription factor Foxe3 was also observed following c-myc inactivation. These data represent the first description of the physiological roles played by a Myc family member in mouse lens development. Our findings support the conclusion that c- myc regulates the proliferation of lens epithelial cells in vivo and may, directly or indirectly, modulate the expression of classical cell cycle regulators in developing mouse lens.
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
  • Insulin/Glucose-Responsive Cells Derived from Induced Pluripotent Stem Cells: Disease Modeling and Treatment of Diabetes

    Insulin/Glucose-Responsive Cells Derived from Induced Pluripotent Stem Cells: Disease Modeling and Treatment of Diabetes

    Insulin/Glucose-Responsive Cells Derived from Induced Pluripotent Stem Cells: Disease Modeling and Treatment of Diabetes Sevda Gheibi *, Tania Singh, Joao Paulo M.C.M. da Cunha, Malin Fex and Hindrik Mulder * Unit of Molecular Metabolism, Lund University Diabetes Centre, Jan Waldenströms gata 35; Box 50332, SE-202 13 Malmö, Sweden; [email protected] (T.S.); [email protected] (J.P.M.C.M.d.C.); [email protected] (M.F.) * Correspondence: [email protected] (S.G.); [email protected] (H.M.) Supplementary Table 1. Transcription factors associated with development of the pancreas. Developmental Gene Aliases Function Ref. Stage SRY-Box Transcription Factor Directs the primitive endoderm SOX17 DE, PFE, PSE [1] 17 specification. Establishes lineage-specific transcriptional programs which leads DE, PFE, PSE, Forkhead Box A2; Hepatocyte to proper differentiation of stem cells FOXA2 PMPs, EPs, [2] Nuclear Factor 3-β into pancreatic progenitors. Regulates Mature β-cells expression of PDX1 gene and aids in maturation of β-cells A pleiotropic developmental gene which regulates growth, and Sonic Hedgehog Signaling differentiation of several organs. SHH DE [3] Molecule Repression of SHH expression is vital for pancreas differentiation and development Promotes cell differentiation, proliferation, and survival. Controls C-X-C Motif Chemokine the spatiotemporal migration of the Receptor 4; Stromal Cell- CXCR4 DE angioblasts towards pre-pancreatic [4] Derived Factor 1 Receptor; endodermal region which aids the Neuropeptide Y3 Receptor induction of PDX1 expression giving rise to common pancreatic progenitors Crucial for generation of pancreatic HNF1 Homeobox B HNF1B PFE, PSE, PMPs multipotent progenitor cells and [5] Hepatocyte Nuclear Factor 1-β NGN3+ endocrine progenitors Master regulator of pancreatic organogenesis.
  • RFX2 Antibody Cat

    RFX2 Antibody Cat

    RFX2 Antibody Cat. No.: 25-404 RFX2 Antibody Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human Antibody produced in rabbits immunized with a synthetic peptide corresponding a region IMMUNOGEN: of human RFX2. TESTED APPLICATIONS: ELISA, WB RFX2 antibody can be used for detection of RFX2 by ELISA at 1:1562500. RFX2 antibody APPLICATIONS: can be used for detection of RFX2 by western blot at 1 μg/mL, and HRP conjugated secondary antibody should be diluted 1:50,000 - 100,000. POSITIVE CONTROL: 1) 721_B Cell Lysate PREDICTED MOLECULAR 80 kDa WEIGHT: Properties PURIFICATION: Antibody is purified by peptide affinity chromatography method. CLONALITY: Polyclonal CONJUGATE: Unconjugated PHYSICAL STATE: Liquid September 30, 2021 1 https://www.prosci-inc.com/rfx2-antibody-25-404.html Purified antibody supplied in 1x PBS buffer with 0.09% (w/v) sodium azide and 2% BUFFER: sucrose. CONCENTRATION: batch dependent For short periods of storage (days) store at 4˚C. For longer periods of storage, store RFX2 STORAGE CONDITIONS: antibody at -20˚C. As with any antibody avoid repeat freeze-thaw cycles. Additional Info OFFICIAL SYMBOL: RFX2 ALTERNATE NAMES: RFX2, FLJ14226, ACCESSION NO.: NP_000626 PROTEIN GI NO.: 19743881 GENE ID: 5990 USER NOTE: Optimal dilutions for each application to be determined by the researcher. Background and References RFX2 is a member of transcription factors that contain a highly-conserved winged helix DNA binding domain. RFX2 is structurally related to regulatory factors X1, X3, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. This protein can bind to cis elements in the promoter of the IL-5 receptor alpha gene.This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA BACKGROUND: binding domain.
  • A Forkhead Gene, Foxe3, Is Essential for Lens Epithelial Proliferation and Closure of the Lens Vesicle

    A Forkhead Gene, Foxe3, Is Essential for Lens Epithelial Proliferation and Closure of the Lens Vesicle

    Downloaded from genesdev.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press A forkhead gene, FoxE3, is essential for lens epithelial proliferation and closure of the lens vesicle Åsa Blixt,1 Margit Mahlapuu,1 Marjo Aitola,2 Markku Pelto-Huikko,2 Sven Enerba¨ck,1 and Peter Carlsson1,3 1Department of Molecular Biology, Go¨teborg University, The Lundberg Laboratory, Medicinaregatan 9C, Box 462, S-405 30 Go¨teborg, Sweden; 2Department of Developmental Biology, Medical School, University of Tampere, Tampere, Finland In the mouse mutant dysgenetic lens (dyl) the lens vesicle fails to separate from the ectoderm, causing a fusion between the lens and the cornea. Lack of a proliferating anterior lens epithelium leads to absence of secondary lens fibers and a dysplastic, cataractic lens. We report the cloning of a gene, FoxE3, encoding a forkhead/winged helix transcription factor, which is expressed in the developing lens from the start of lens placode induction and becomes restricted to the anterior proliferating cells when lens fiber differentiation begins. We show that FoxE3 is colocalized with dyl in the mouse genome, that dyl mice have mutations in the part of FoxE3 encoding the DNA-binding domain, and that these mutations cosegregate with the dyl phenotype. During embryonic development, the primordial lens epithelium is formed in an apparently normal way in dyl mutants. However, instead of the proliferation characteristic of a normal lens epithelium, the posterior of these cells fail to divide and show signs of premature differentiation, whereas the most anterior cells are eliminated by apoptosis. This implies that FoxE3 is essential for closure of the lens vesicle and is a factor that promotes survival and proliferation, while preventing differentiation, in the lens epithelium.
  • Hypothetical Cytokinin-Binding Riboswitches in Arabidopsis Thaliana Jeremy Grojean1, Brian Downes2*

    Hypothetical Cytokinin-Binding Riboswitches in Arabidopsis Thaliana Jeremy Grojean1, Brian Downes2*

    Grojean and Downes Biology Direct 2010, 5:60 http://www.biology-direct.com/content/5/1/60 HYPOTHESIS Open Access Riboswitches as hormone receptors: hypothetical cytokinin-binding riboswitches in Arabidopsis thaliana Jeremy Grojean1, Brian Downes2* Abstract Background: Riboswitches are mRNA elements that change conformation when bound to small molecules. They are known to be key regulators of biosynthetic pathways in both prokaryotes and eukaryotes. Presentation of the Hypothesis: The hypothesis presented here is that riboswitches function as receptors in hormone perception. We propose that riboswitches initiate or integrate signaling cascades upon binding to classic signaling molecules. The molecular interactions for ligand binding and gene expression control would be the same as for biosynthetic pathways, but the context and the cadre of ligands to consider is dramatically different. The hypothesis arose from the observation that a compound used to identify adenine binding RNA sequences is chemically similar to the classic plant hormone, or growth regulator, cytokinin. A general tenet of the hypothesis is that riboswitch-binding metabolites can be used to make predictions about chemically related signaling molecules. In fact, all cell permeable signaling compounds can be considered as potential riboswitch ligands. The hypothesis is plausible, as demonstrated by a cursory review of the transcriptome and genome of the model plant Arabidopsis thaliana for transcripts that i) contain an adenine aptamer motif, and ii) are also predicted to be cytokinin- regulated. Here, one gene, CRK10 (for Cysteine-rich Receptor-like Kinase 10, At4g23180), contains an adenine aptamer-related sequence and is down-regulated by cytokinin approximately three-fold in public gene expression data.
  • The WRKY Transcription Factor Family in Model Plants and Crops

    The WRKY Transcription Factor Family in Model Plants and Crops

    Critical Reviews in Plant Sciences ISSN: 0735-2689 (Print) 1549-7836 (Online) Journal homepage: http://www.tandfonline.com/loi/bpts20 The WRKY Transcription Factor Family in Model Plants and Crops Fei Chen, Yue Hu, Alessandro Vannozzi, Kangcheng Wu, Hanyang Cai, Yuan Qin, Alison Mullis, Zhenguo Lin & Liangsheng Zhang To cite this article: Fei Chen, Yue Hu, Alessandro Vannozzi, Kangcheng Wu, Hanyang Cai, Yuan Qin, Alison Mullis, Zhenguo Lin & Liangsheng Zhang (2018): The WRKY Transcription Factor Family in Model Plants and Crops, Critical Reviews in Plant Sciences, DOI: 10.1080/07352689.2018.1441103 To link to this article: https://doi.org/10.1080/07352689.2018.1441103 Published online: 05 Mar 2018. Submit your article to this journal View related articles View Crossmark data Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=bpts20 CRITICAL REVIEWS IN PLANT SCIENCES https://doi.org/10.1080/07352689.2018.1441103 The WRKY Transcription Factor Family in Model Plants and Crops Fei Chena, Yue Hua, Alessandro Vannozzib, Kangcheng Wua, Hanyang Caia, Yuan Qina, Alison Mullisc, Zhenguo Linc, and Liangsheng Zhanga aState Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou, China; bDepartment of Agronomy, Food, Natural Resources, Animals, and Environment (DAFNAE), University of Padova, Legnaro, Italy; cDepartment of Biology, Saint Louis University, St Louis, Missouri, USA ABSTRACT KEYWORDS The WRKY gene family in flowering plants encodes a large group of transcription factors (TFs) that environmental stress; gene play essential roles in diverse stress responses, developmental, and physiological processes.