Cdx) Transcription Factors1
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ATRX Induction by Mutant Huntingtin Via Cdx2 Modulates Heterochromatin Condensation and Pathology in Huntington’S Disease
Cell Death and Differentiation (2012) 19, 1109–1116 & 2012 Macmillan Publishers Limited All rights reserved 1350-9047/12 www.nature.com/cdd ATRX induction by mutant huntingtin via Cdx2 modulates heterochromatin condensation and pathology in Huntington’s disease J Lee1,2, YK Hong3, GS Jeon4, YJ Hwang4, KY Kim4, KH Seong4, M-K Jung4, DJ Picketts5, NW Kowall1,2, KS Cho3 and H Ryu*,1,2,4 Aberrant chromatin remodeling is involved in the pathogenesis of Huntington’s disease (HD) but the mechanism is not known. Herein, we report that mutant huntingtin (mtHtt) induces the transcription of alpha thalassemia/mental retardation X linked (ATRX), an ATPase/helicase and SWI/SNF-like chromatin remodeling protein via Cdx-2 activation. ATRX expression was elevated in both a cell line model and transgenic model of HD, and Cdx-2 occupancy of the ATRX promoter was increased in HD. Induction of ATRX expanded the size of promyelocytic leukemia nuclear body (PML-NB) and increased trimethylation of H3K9 (H3K9me3) and condensation of pericentromeric heterochromatin, while knockdown of ATRX decreased PML-NB and H3K9me3 levels. Knockdown of ATRX/dXNP improved the hatch rate of fly embryos expressing mtHtt (Q127). ATRX/dXNP overexpression exacerbated eye degeneration of eye-specific mtHtt (Q127) expressing flies. Our findings suggest that transcriptional alteration of ATRX by mtHtt is involved in pericentromeric heterochromatin condensation and contributes to the pathogenesis of HD. Cell Death and Differentiation (2012) 19, 1109–1116; doi:10.1038/cdd.2011.196; published -
KLF2 Induced
UvA-DARE (Digital Academic Repository) The transcription factor KLF2 in vascular biology Boon, R.A. Publication date 2008 Link to publication Citation for published version (APA): Boon, R. A. (2008). The transcription factor KLF2 in vascular biology. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:23 Sep 2021 Supplementary data: Genes induced by KLF2 Dekker et al. LocusLink Accession Gene Sequence Description Fold p-value ID number symbol change (FDR) 6654 AK022099 SOS1 cDNA FLJ12037 fis, clone HEMBB1001921. 100.00 5.9E-09 56999 AF086069 ADAMTS9 full length insert cDNA clone YZ35C05. 100.00 1.2E-09 6672 AF085934 SP100 full length insert cDNA clone YR57D07. 100.00 6.7E-13 9031 AF132602 BAZ1B Williams Syndrome critical region WS25 mRNA, partial sequence. -
Homeobox Gene Expression Profile in Human Hematopoietic Multipotent
Leukemia (2003) 17, 1157–1163 & 2003 Nature Publishing Group All rights reserved 0887-6924/03 $25.00 www.nature.com/leu Homeobox gene expression profile in human hematopoietic multipotent stem cells and T-cell progenitors: implications for human T-cell development T Taghon1, K Thys1, M De Smedt1, F Weerkamp2, FJT Staal2, J Plum1 and G Leclercq1 1Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Ghent, Belgium; and 2Department of Immunology, Erasmus Medical Center, Rotterdam, The Netherlands Class I homeobox (HOX) genes comprise a large family of implicated in this transformation proces.14 The HOX-C locus transcription factors that have been implicated in normal and has been primarily implicated in lymphomas.15 malignant hematopoiesis. However, data on their expression or function during T-cell development is limited. Using degener- Hematopoietic cells are derived from stem cells that reside in ated RT-PCR and Affymetrix microarray analysis, we analyzed fetal liver (FL) in the embryo and in the adult bone marrow the expression pattern of this gene family in human multipotent (ABM), which have the unique ability to self-renew and thereby stem cells from fetal liver (FL) and adult bone marrow (ABM), provide a life-long supply of blood cells. T lymphocytes are a and in T-cell progenitors from child thymus. We show that FL specific type of hematopoietic cells that play a major role in the and ABM stem cells are similar in terms of HOX gene immune system. They develop through a well-defined order of expression, but significant differences were observed between differentiation steps in the thymus.16 Several transcription these two cell types and child thymocytes. -
Angiogenic Patterning by STEEL, an Endothelial-Enriched Long
Angiogenic patterning by STEEL, an endothelial- enriched long noncoding RNA H. S. Jeffrey Mana,b, Aravin N. Sukumara,b, Gabrielle C. Lamc,d, Paul J. Turgeonb,e, Matthew S. Yanb,f, Kyung Ha Kub,e, Michelle K. Dubinskya,b, J. J. David Hob,f, Jenny Jing Wangb,e, Sunit Dasg,h, Nora Mitchelli, Peter Oettgeni, Michael V. Seftonc,d,j, and Philip A. Marsdena,b,e,f,1 aInstitute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada; bKeenan Research Centre for Biomedical Science in the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, University of Toronto, Toronto, ON M5B 1T8, Canada; cDonnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E2, Canada; dInstitute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; eDepartment of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; fDepartment of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; gArthur and Sonia Labatt Brain Tumour Research Institute, Hospital for SickKids, University of Toronto, Toronto, ON M5G 1X8, Canada; hDivision of Neurosurgery and Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada; iDepartment of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115; and jDepartment of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada Edited by Napoleone Ferrara, University of California, San Diego, La Jolla, CA, and approved January 24, 2018 (received for review August 28, 2017) Endothelial cell (EC)-enriched protein coding genes, such as endothelial formation in vitro and blood vessel formation in vivo. -
The Gli2 Transcription Factor Is Required for Normal Mouse Mammary Gland Development
Developmental Biology 238, 133–144 (2001) doi:10.1006/dbio.2001.0410, available online at http://www.idealibrary.com on The Gli2 Transcription Factor Is Required for Normal Mouse Mammary Gland Development Michael T. Lewis,*,1,2 Sarajane Ross,*,3 Phyllis A. Strickland,* Charles W. Sugnet,* Elsa Jimenez,* Chi-chung Hui,† and Charles W. Daniel* *Department of Biology, Sinsheimer Laboratories, University of California, Santa Cruz, California 95064; and †The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada The hedgehog signal transduction network performs critical roles in mediating cell–cell interactions during embryogenesis and organogenesis. Loss-of-function or misexpression mutation of hedgehog network components can cause birth defects, skin cancer, and other tumors. The Gli gene family (Gli1, Gli2, and Gli3) encodes zinc finger transcription factors that act as mediators of hedgehog signal transduction. In this study, we investigate the role of Gli2 in mammary gland development. Mammary expression of Gli2 is developmentally regulated in a tissue compartment-specific manner. Expression is exclusively stromal during virgin stages of development but becomes both epithelial and stromal during pregnancy and lactation. The null phenotype with respect to both ductal and alveolar development was examined by transplantation rescue of embryonic mammary glands into physiologically normal host females. Glands derived from both wild type and null embryo donors showed ductal outgrowths that developed to equivalent extents in virgin hosts. However, in null transplants, ducts were frequently distended or irregularly shaped and showed a range of histological alterations similar to micropap- illary ductal hyperplasias in the human breast. Alveolar development during pregnancy was not overtly affected by loss of Gli2 function. -
ASCL2 Expression Contributes to Gastric Tumor Migration and Invasion by Downregulating Mir223 and Inducing EMT
MOLECULAR MEDICINE REPORTS 18: 3751-3759, 2018 ASCL2 expression contributes to gastric tumor migration and invasion by downregulating miR223 and inducing EMT QINGSONG ZUO*, JIE WANG*, CHAO CHEN, YONG ZHANG, DIAN-XU FENG, RONGHUA ZHAO and TENG CHEN Department of General Surgery, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, P.R. China Received May 15, 2017; Accepted November 23, 2017 DOI: 10.3892/mmr.2018.9363 Abstract. Achaete-scute homolog 2 (ASCL2), a basic results of the present study demonstrated that ASCL2 was able helix-loop-helix transcription factor, serves an essential role in to downregulate the expression level of miR223, contribute to the maintenance of adult intestinal stem cells and the growth EMT and promote gastric tumor metastasis, which indicated of gastric cancer (GC). However, the function of ASCL2 in that ASCL2 may serve as a therapeutic target in the treatment the metastasis of GC is poorly understood. The present study of GC. aimed to evaluate the effect of ASCL2 expression on gastric tumor metastasis. ASCL2 protein expression was detected in Introduction 32 cases of gastric metastasis and its relevant primary tumors using western blotting and immunohistochemistry. The Gastric cancer (GC) is the second most common cause of data suggested that the expression of ASCL2 was highest in cancer-associated mortality in the world, and the incidence metastatic tumors, among adjacent normal tissues, primary GC is highest in East Asia, Eastern Europe and parts of Latin gastric tumors and gastric metastatic tumors. Furthermore, America (1,2). However, the precise mechanisms underlying ASCL2-overexpressing GC cell lines MKN1-ASCL2 and gastric carcinogenesis are not yet completely understood (3). -
Isolation and Characterization of BEN, a Member of the TFII-I Family of DNA-Binding Proteins Containing Distinct Helix–Loop–Helix Domains
Isolation and characterization of BEN, a member of the TFII-I family of DNA-binding proteins containing distinct helix–loop–helix domains Dashzeveg Bayarsaihan and Frank H. Ruddle* Department of Molecular, Cellular, and Developmental Biology, Kline Biology Tower, Yale University, 266 Whitney Avenue, New Haven, CT 06520 Contributed by Frank H. Ruddle, May 4, 2000 The transcriptional regulation of the Hoxc8 gene is controlled during paraxial mesoderm at the 14th somite, and in the lateral plate early mouse embryogenesis by an enhanceosome-like control region, mesoderm at the 12th somite. Later in development, posterior termed the early enhancer (EE), located 3 kb upstream from the Hoxc8 expression of Hoxc8 decreases, whereas intense expression is translation start site. The EE is involved in establishing the posterior maintained at previously determined anterior limits within the expression pattern of Hoxc8 at embryonic day (E) 8.5–9.0. Genetic and thorax (somites and lateral plate mesoderm) and in the brachial biochemical data have shown that nuclear factors interact with this region (neural tube) (7). region in a sequence-specific manner. We have used a yeast one- Transgenic reporter analysis was used to identify cis-regulatory hybrid screen in a search for transcription factors that bind to EE domains critical for the normal expression of Hoxc8. Two distinct motifs and have isolated a novel murine DNA-binding protein, termed genomic regions were identified that regulate the early and late BEN (binding factor for early enhancer). The ORF of BEN encodes a phases of Hoxc8 expression (5, 6). The early phase is regulated by protein of 1072 amino acids and contains six helix–loop–helix do- DNA elements located 3 kb upstream from the translation start site mains, a hydrophobic leucine zipper-like motif, and a serine-rich of the gene, whereas the late expression is regulated by elements repeat. -
The Human Gene Map for Performance and Health-Related Fitness Phenotypes: the 2006–2007 Update
BASIC SCIENCES The Human Gene Map for Performance and Health-Related Fitness Phenotypes: The 2006–2007 Update MOLLY S. BRAY1, JAMES M. HAGBERG2, LOUIS PE´ RUSSE3, TUOMO RANKINEN4, STEPHEN M. ROTH2, BERND WOLFARTH5, and CLAUDE BOUCHARD4 1USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX; 2Department of Kinesiology, School of Public Health, University of Maryland, College Park, MD; 3Division of Kinesiology, Department of Preventive Medicine, Laval University, Ste-Foy, Que´bec, CANADA; 4Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA; and 5Preventive and Rehabilitative Sports Medicine, Technical University Munich, Munich, GERMANY ABSTRACT BRAY, M. S., J. M. HAGBERG, L. PE´ RUSSE, T. RANKINEN, S. M. ROTH, B. WOLFARTH, and C. BOUCHARD. The Human Gene Map for Performance and Health-Related Fitness Phenotypes: The 2006–2007 Update. Med. Sci. Sports Exerc., Vol. 41, No. 1, pp. 34–72, 2009. This update of the human gene map for physical performance and health-related fitness phenotypes covers the research advances reported in 2006 and 2007. The genes and markers with evidence of association or linkage with a performance or a fitness phenotype in sedentary or active people, in responses to acute exercise, or for training-induced adaptations are positioned on the map of all autosomes and sex chromosomes. Negative studies are reviewed, but a gene or a locus must be supported by at least one positive study before being inserted on the map. A brief discussion on the nature of the evidence and on what to look for in assessing human genetic studies of relevance to fitness and performance is offered in the introduction, followed by a review of all studies published in 2006 and 2007. -
Supplemental Figure 1 Supplemental Figure 1. Flow Cytometry
Supplemental Figure 1 Initial neutrophil isolation sample Single cells Live 83.4% 99.6% 99.1% W - SC SC S S FSC FSC FSC-H Live/ dead CD45 positive 100% SC S CD16 PE cy7 CD16 CD45+ CD16+ CD66b+ neutrophils 98.1% CD45 V500 CD16 PerCP cy5.5 Supplemental Figure 1. Flow cytometry with gating strategey depicted confirms 98.1% purity of CD66b/CD16 double positive neutrophils. Supplemental Figure 1. Flow cytometry with gating strategy depicted confirms 98.1% purity of CD66b/CD16 double positive neutrophils. (a) (b) Supplemental Figure 2 A. B. (c) (d) -2000 bp 0 2000bp Position relative to TSS Supplemental Fig 2. a) No response to CpG in qRTPCR. b) Healthy volunteer neutrophils do not produce NETs via sytox green assay in response to pathogen ligands at 1 hour or immediately following live organism challenge supporting this time point for ATAC-seq. (PMA is a positive control)Supplemental(ligand donors Fign=4ure, live 2organism. A. Representativedonors n=2) c) Representative QC plots demonstratingQC plots demonstrating librarylibrary prepprep resultsresults inin expected insert size expecteddistribution and insertd) reads sizeare distributionenriched around andtranscription B. readsstart aresites enriched(TSS). around transcription start sites (TSS). Supplemental Figure 3. LTA BGP LPS HMGB1 FLAG E. coli R848 S. aureus Supplemental Fig 3. Quality control for DiffBind method of identification of differentially accessible regions of chromatin. Correlation heat maps and principal component analysis (PCA) of differentially accessible chromatin. We found that for any given challenge across donors, stimulated samples cluster together, control samples cluster Supplementaltogether, and the stimulated Figandurecontrol 3.cluster Qualityaway from controleach other, forsuggesting DiffBindhigh quality methoddata and accessibleof identificationchromatin region ofidentification differentiallythat allows for analysis accessibleof four healthy donor regionsdata. -
Genome-Wide DNA Methylation Analysis Reveals Molecular Subtypes of Pancreatic Cancer
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 17), pp: 28990-29012 Research Paper Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer Nitish Kumar Mishra1 and Chittibabu Guda1,2,3,4 1Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA 2Bioinformatics and Systems Biology Core, University of Nebraska Medical Center, Omaha, NE, 68198, USA 3Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA 4Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA Correspondence to: Chittibabu Guda, email: [email protected] Keywords: TCGA, pancreatic cancer, differential methylation, integrative analysis, molecular subtypes Received: October 20, 2016 Accepted: February 12, 2017 Published: March 07, 2017 Copyright: Mishra et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Pancreatic cancer (PC) is the fourth leading cause of cancer deaths in the United States with a five-year patient survival rate of only 6%. Early detection and treatment of this disease is hampered due to lack of reliable diagnostic and prognostic markers. Recent studies have shown that dynamic changes in the global DNA methylation and gene expression patterns play key roles in the PC development; hence, provide valuable insights for better understanding the initiation and progression of PC. In the current study, we used DNA methylation, gene expression, copy number, mutational and clinical data from pancreatic patients. -
Drosophila Pax6 Promotes Development of the Entire Eye-Antennal Disc, Thereby Ensuring Proper Adult Head Formation
PAPER Drosophila Pax6 promotes development of the entire COLLOQUIUM eye-antennal disc, thereby ensuring proper adult head formation Jinjin Zhua, Sneha Palliyila, Chen Ranb, and Justin P. Kumara,1 aDepartment of Biology, Indiana University, Bloomington, IN 47405; and bDepartment of Biology, Stanford University, Stanford, CA 94305 Edited by Ellen V. Rothenberg, California Institute of Technology, Pasadena, CA, and accepted by Editorial Board Member Neil H. Shubin February 17, 2017 (received for review July 26, 2016) Paired box 6 (Pax6) is considered to be the master control gene for molecular battle among GRNs allows for the subdivision of the eye development in all seeing animals studied so far. In vertebrates, eye-antennal disc to be maintained within a single continuous it is required not only for lens/retina formation but also for the cellular field (13–16). Of the GRNs that are known to operate development of the CNS, olfactory system, and pancreas. Although within the eye-antennal disc, the retinal determination (RD) Pax6 plays important roles in cell differentiation, proliferation, and network, which controls eye development, is the best studied (17). patterning during the development of these systems, the underlying At the core of the RD network lie the Paired box 6 (Pax6) genes mechanism remains poorly understood. In the fruit fly, Drosophila eyeless (ey)andtwin of eyeless (toy), the SIX family member sine melanogaster, Pax6 also functions in a range of tissues, including oculis (so), the transcriptional coactivator eyes absent (eya), and the the eye and brain. In this report, we describe the function of Pax6 in Ski/Sno family member dachshund (dac)(17). -
Adjusting the Molecular Clock: the Importance of Circadian Rhythms in the Development of Glioblastomas and Its Intervention As a Therapeutic Strategy
International Journal of Molecular Sciences Review Adjusting the Molecular Clock: The Importance of Circadian Rhythms in the Development of Glioblastomas and Its Intervention as a Therapeutic Strategy Paula M. Wagner 1,2,†,César G. Prucca 1,2,† , Beatriz L. Caputto 1,2 and Mario E. Guido 1,2,* 1 CIQUIBIC-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba 5000, Argentina; [email protected] (P.M.W.); [email protected] (C.G.P.); [email protected] (B.L.C.) 2 Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba 5000, Argentina * Correspondence: [email protected] † Equal contribution. Abstract: Gliomas are solid tumors of the central nervous system (CNS) that originated from different glial cells. The World Health Organization (WHO) classifies these tumors into four groups (I-IV) with increasing malignancy. Glioblastoma (GBM) is the most common and aggressive type of brain tumor classified as grade IV. GBMs are resistant to conventional therapies with poor prognosis after diagnosis even when the Stupp protocol that combines surgery and radiochemotherapy is applied. Nowadays, few novel therapeutic strategies have been used to improve GBM treatment, looking for higher efficiency and lower side effects, but with relatively modest results. The circadian timing system temporally organizes the physiology and behavior of most organisms and daily regulates several cellular processes in organs, tissues, and even in individual cells, including tumor cells. The Citation: Wagner, P.M.; Prucca, C.G.; Caputto, B.L.; Guido, M.E. Adjusting potentiality of the function of the circadian clock on cancer cells modulation as a new target for novel the Molecular Clock: The Importance treatments with a chronobiological basis offers a different challenge that needs to be considered in of Circadian Rhythms in the further detail.