The Suppressive Effects of 1,25-Dihydroxyvitamin D3 and Vitamin D Receptor on Brown Adipocyte Differentiation and Mitochondrial Respiration

Total Page:16

File Type:pdf, Size:1020Kb

The Suppressive Effects of 1,25-Dihydroxyvitamin D3 and Vitamin D Receptor on Brown Adipocyte Differentiation and Mitochondrial Respiration University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Masters Theses Graduate School 8-2014 The Suppressive Effects of 1,25-dihydroxyvitamin D3 and Vitamin D Receptor on Brown Adipocyte Differentiation and Mitochondrial Respiration Carolyn Jeanne Ricciardi University of Tennessee - Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_gradthes Part of the Molecular, Genetic, and Biochemical Nutrition Commons Recommended Citation Ricciardi, Carolyn Jeanne, "The Suppressive Effects of 1,25-dihydroxyvitamin D3 and Vitamin D Receptor on Brown Adipocyte Differentiation and Mitochondrial Respiration. " Master's Thesis, University of Tennessee, 2014. https://trace.tennessee.edu/utk_gradthes/2876 This Thesis is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Masters Theses by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a thesis written by Carolyn Jeanne Ricciardi entitled "The Suppressive Effects of 1,25-dihydroxyvitamin D3 and Vitamin D Receptor on Brown Adipocyte Differentiation and Mitochondrial Respiration." I have examined the final electronic copy of this thesis for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Master of Science, with a major in Nutrition. Ling Zhao, Major Professor We have read this thesis and recommend its acceptance: Jay Whelan, Guoxun Chen Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) The Suppressive Effects of 1,25-dihydroxyvitamin D3 and Vitamin D Receptor on Brown Adipocyte Differentiation and Mitochondrial Respiration A Thesis Presented for the Master of Science Degree The University of Tennessee, Knoxville Carolyn Jeanne Ricciardi August 2014 Copyright © 2014 by Carolyn J. Ricciardi All rights reserved. ii DEDICATION To my mother, Jennifer Fuller-Ricciardi, and my father, Charles Ricciardi, who have been my motivation, my support system, and my biggest fans. iii ACKNOWLEDGEMENTS I’d like to thank my advisor Dr. Ling Zhao and my committee members Dr. Whelan and Dr. Chen for their guidance and expertise over the past two years. I’d also like to thank my lab partners and classmates Matt Goff, Megan Johnstone, Vaishali Keshani, Jaanki Purohit, Pan Hu, and Jiyoung Bae for their willingness to help me with my studies and research. Finally, many thanks to my Tennessee friends for their unconditional support throughout graduate school. iv ABSTRACT The vitamin D system plays a role in metabolism regulation. It has been reported that 1,25(OH)2D3 [1,25-dihydroxyvitamin D] suppresses 3T3-L1 adipocyte differentiation. Vitamin D receptor (VDR) knockout mice showed increased energy expenditure whereas mice with adipose-specific VDR over expression showed decreased energy expenditure. Brown adipose tissue (BAT), which functions in non-shivering thermogenesis by uncoupling ATP synthesis from oxidation, plays important roles in energy expenditure. However, the effects of 1,25(OH)2D3 on brown adipocyte differentiation and mitochondrial respiration have not been studied. Reported here is the mRNA expression of VDR, UCP1, and CYP27B1 (1α[alpha]- hydroxylase) in two mice models of obesity; and the down regulation of mRNA of VDR, CYP24A1 (24-hyrdoxylase), and CYP27B1 during brown adipocyte differentiation in vitro. 1,25(OH)2D3 dose-dependently suppressed brown adipocyte differentiation, as revealed by oil red O (ORO) stained cell morphology, ORO absorbance, and brown adipocyte marker gene expression. Moreover, cellular bioenergetics measurements showed that 1,25(OH)2D3 suppressed isoproterenol-stimulated oxygen consumption rates (OCR), maximal OCR and OCR from proton leak, but had no effects on ATP-generating OCR and spare respiration capacity in brown adipocytes. Consistently, over-expression of VDR also suppressed brown adipocyte differentiation. Furthermore, both 1,25(OH)2D3 and VDR over expression suppressed PPARγ [gamma] transactivation in brown preadipocytes. Taken together, the results demonstrate the suppressive effects of 1,25(OH)2D3/VDR signaling on brown adipocyte differentiation and mitochondrial respiration and suggest a role of 1,25(OH)2D3/VDR signaling in regulating BAT function for obesity treatment and prevention. v Keywords: Vitamin D receptor, brown adipocyte, UCP1, mitochondrial respiration vi TABLE OF CONTENTS CHAPTER I Introduction ................................................................................................... 1 CHAPTER II Literature Review ........................................................................................ 4 2.1 Overview of Vitamin D ............................................................................................. 4 2.1.1 Vitamin D Structure and Function ..................................................................... 4 2.1.2 Dietary and Non-dietary Sources of Vitamin D ................................................. 6 2.1.3 Vitamin D Metabolism and Transportation……………………………………6 2.1.4 Vitamin D and Energy Metabolism……………………………………………7 2.2 Brown Adipose Tissue: Significance and Nutritional Regulation .......................... 12 2.2.1 Brown Adipose Tissue Function ...................................................................... 12 2.2.2 Brown Adipose Development..……………………………………………….13 2.2.3 Brown Adipose Tissue Activation……………………………………………17 2.2.4 Regulation of Brown Adipose Mass by Nutritional and Non-nutritional Regulators………………………………...…………………………………..18 2.3 The Research Gap………………………………………………………………..21 CHAPTER III Materials and Methods .............................................................................. 22 3.1.1 Reagents ........................................................................................................... 22 3.1.2 Animals ............................................................................................................. 22 3.1.3 Cell Culture and differentiation ....................................................................... 22 3.1.4 Western Blot Analysis ...................................................................................... 23 3.1.5 RNA preparation and quantitative real time PCR analysis .............................. 24 3.1.6 MTT Assay ....................................................................................................... 24 3.1.7 Analysis of mitochondrial content by MitoTracker green staining .................. 25 3.1.8 Reporter Gene Assays………………………………………………………...25 3.1.9 Cell respiration measurements ......................................................................... 26 3.1.10 Statistical Analysis ......................................................................................... 27 CHAPTER IV Results, Discussion, and Future Directions ............................................. 28 4.1 Results ..................................................................................................................... 28 4.1.1 VDR, CYP24A1 and CYP27B1 mRNA expression in the BAT of mice model of obesity and during brown adipocyte differentiation in cultured cells……………28 4.1.2 Effects of 1,25(OH)2D3 on the vitamin D system during brown adipocyte differentiation ………………………………………………………………..28 4.1.3 Effects of 1,25(OH)2D3 on brown adipocyte lipid accumulation, mRNA expression, and mitochondrial content……...………………………………..29 4.1.4 Brown adipocyte time sensitivity to 1,25(OH)2D3 treatment………………...30 4.1.5 Effects of 1,25(OH)2D3 on mitochondrial respiration in brown adipocytes…..31 4.1.6 Effects of over-expression of VDR on brown adipocyte differentiation……...31 4.1.7 1,25(OH)2D3/VDR suppresses PPARγ transactivation in brown preadipocytes…………………………………………………………..32 4.2 Discussion………………………………………………………………………….32 4.3 Future Directions…………………………………………………………………...36 LIST OF REFERENCES…………………………………………………………………39 APPENDIX……………………………………………………………………………….48 Vita………………………………………………………………………………………..60 vii LIST OF FIGURES Figure 1 Endogenous metabolism of Vitamin D3…...…………………………………...…......49 Figure 2 mRNA expression of VDR, CYP27B1, and UCP1 in mice models of obesity.............50 Figure 3 mRNA expression of VDR, CYP24A1 and CYP27B1 during brown adipocyte differentiation…………………………………………………………………………………….51 Figure 41,25(OH)2D3 dose-dependently suppresses brown adipocyte differentiation………….52 Figure 4A-C 1,25(OH)2D3 dose-dependently suppresses brown adipocyte differentiation…….53 Figure 4D 1,25(OH)2D3 dose-dependently suppresses brown adipocyte differentiation……….54 Figure 4E-F 1,25(OH)2D3 dose-dependently suppresses brown adipocyte differentiation..........55 Figure 5 Effects of 1,25(OH)2D3 treatment timing on brown adipocyte differentiation..............56 Figure 6 Effects of 1,25(OH)2D3 on mitochondrial respiration in brown adipocytes..................57 Figure 7 Over-expression of VDR suppresses brown adipocyte differentiation..........................58 Figure 8 1,25(OH)2D3/VDR suppress PPARγ transactivation in brown preadipocytes………...59 viii CHAPTER I INTRODUCTION Obesity, physiologically, is a result of hyperplasia and/or hypertrophy of lipid storing adipose tissue [1]. It is defined clinically as having a body mass index ≥30kg/m2 and is currently a major health concern
Recommended publications
  • Role of Estrogen Receptor Beta and the Isoflavone Genistein
    WCP2018 OR28-3 Oral session White-to-brown adipose differentiation: role of estrogen receptor beta and the isoflavone genistein Alessandra Bitto, Federica Mannino, Natasha Irrera, Giovanni Pallio, Domenica Altavilla, Francesco Squadrito Clinical and experimental medicine, University of Messina, Italy The two types of fat cells in mammals brown and white have different functions. White adipose tissue (WAT) stores excess energy in the form of triglyceride and releases free fatty acids during caloric deficiency. Brown adipose tissue (BAT) on the other hand can dissipate energy through thermogenesis. Genistein can have an effect on energy expenditure UCP (uncoupling protein) expression and protect against the obesogenic effect of a high calorie diet. The effect of genistein in inducing white-to-brown transdifferentiation was investigated in 3T3-L1 cells differentiated into white adipocytes with a specific medium (DMEM 10% calf serum 1% penicillin/streptomycin 500 uM 3isobutyl1 methylxanthine 10ug/ml insulin 250 nM dexmethasone 8 ug/ml biotin and 4 ug/ml pantothenic acid). Fully differentiated white adipocytes were treated after 10 days with different genistein doses (10-50-100-200 uM) for 24-48h or left untreated. Two specific ER-beta and PPAR-gamma receptor inhibitors were also used to understand if genistein effects are mediated by the estrogen or the PPAR receptor. Also a CRISPR/Cas9 approach was used to delete either ER-beta or PPAR-gamma to clarify which receptor is involved in genistein action. Intracellular lipid accumulation was determined by oil-red-O staining after 24 and 48hours of treatment. The expression of UCP1 estrogen receptor alpha and beta PPARalpha and gamma DIO2 (Type II iodothyronine deiodinase) PRDM16 (PR domain containing 16) and CIDEA (cell death inducing DNA fragmentation factor) were evaluated by qPCR after 24 and 48hours of genistein treatment.
    [Show full text]
  • The Title of the Dissertation
    UNIVERSITY OF CALIFORNIA SAN DIEGO Novel network-based integrated analyses of multi-omics data reveal new insights into CD8+ T cell differentiation and mouse embryogenesis A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biology by Kai Zhang Committee in charge: Professor Wei Wang, Chair Professor Pavel Arkadjevich Pevzner, Co-Chair Professor Vineet Bafna Professor Cornelis Murre Professor Bing Ren 2018 Copyright Kai Zhang, 2018 All rights reserved. The dissertation of Kai Zhang is approved, and it is accept- able in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California San Diego 2018 iii EPIGRAPH The only true wisdom is in knowing you know nothing. —Socrates iv TABLE OF CONTENTS Signature Page ....................................... iii Epigraph ........................................... iv Table of Contents ...................................... v List of Figures ........................................ viii List of Tables ........................................ ix Acknowledgements ..................................... x Vita ............................................. xi Abstract of the Dissertation ................................. xii Chapter 1 General introduction ............................ 1 1.1 The applications of graph theory in bioinformatics ......... 1 1.2 Leveraging graphs to conduct integrated analyses .......... 4 1.3 References .............................. 6 Chapter 2 Systematic
    [Show full text]
  • Letters to the Editor
    LETTERS TO THE EDITOR The closely related rare and severe acute myeloid leukemias carrying EVI1 or PRDM16 rearrangements share singular biological features In a recent issue of Haematologica , Matsuo et al .1 pinpoint the pejorative effect of EVI1 overexpression in 18 acute myeloid leukemias (AML) with MLL rearrangements. However, EVI1 overexpression has also been reported in patients with translocations involving chromosome 3 and the EVI1 gene. 2,3 Because of the poor prognosis associated to these anomalies, it is important to investigate them at an early stage in order to adapt patient management. Indeed, previous reports 4-6 and the 2008 WHO classification 7 indi - cate that EVI1-rearranged (EVI1-r) AML display typical fea - tures, such as absence of thrombopenia, atypical megakary - Figure 1. Algorithm for the suspicion of EVI1 and PRDM16 AMLs. ocytes and multilineage dysplasia 2-4 which can be detected by current diagnostic reference methods. In this line, we compared a cohort of 17 EVI1-r AML, aged between 8 and 79-years old (median 54 years) to 1822 other cases of AML months. diagnosed in the same laboratory over 14 years. At diagno - This study consolidates the unusual base-line character - sis, there were similar hemoglobin levels or white blood istics and clinical features of EVI1-r AML cases. Moreover, cell counts in both groups. Median platelet counts were it indicates a very low rate of MPO expression in EVI1-r 9 9 123x10 /L, higher than 100x10 /L in 53% of EVI1-r AML AML patients. It is interesting to note that relationships patients, compared to 25% in the control AML population have been reported between EVI1 expression and MPO (P=0.02).
    [Show full text]
  • Regulation of Adult Neurogenesis in Mammalian Brain
    International Journal of Molecular Sciences Review Regulation of Adult Neurogenesis in Mammalian Brain 1,2, 3, 3,4 Maria Victoria Niklison-Chirou y, Massimiliano Agostini y, Ivano Amelio and Gerry Melino 3,* 1 Centre for Therapeutic Innovation (CTI-Bath), Department of Pharmacy & Pharmacology, University of Bath, Bath BA2 7AY, UK; [email protected] 2 Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK 3 Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy; [email protected] (M.A.); [email protected] (I.A.) 4 School of Life Sciences, University of Nottingham, Nottingham NG7 2HU, UK * Correspondence: [email protected] These authors contributed equally to this work. y Received: 18 May 2020; Accepted: 7 July 2020; Published: 9 July 2020 Abstract: Adult neurogenesis is a multistage process by which neurons are generated and integrated into existing neuronal circuits. In the adult brain, neurogenesis is mainly localized in two specialized niches, the subgranular zone (SGZ) of the dentate gyrus and the subventricular zone (SVZ) adjacent to the lateral ventricles. Neurogenesis plays a fundamental role in postnatal brain, where it is required for neuronal plasticity. Moreover, perturbation of adult neurogenesis contributes to several human diseases, including cognitive impairment and neurodegenerative diseases. The interplay between extrinsic and intrinsic factors is fundamental in regulating neurogenesis. Over the past decades, several studies on intrinsic pathways, including transcription factors, have highlighted their fundamental role in regulating every stage of neurogenesis. However, it is likely that transcriptional regulation is part of a more sophisticated regulatory network, which includes epigenetic modifications, non-coding RNAs and metabolic pathways.
    [Show full text]
  • ETV6 Mutations in Early Immature Human T Cell Leukemias
    Published December 12, 2011 Brief Definitive Report ETV6 mutations in early immature human T cell leukemias Pieter Van Vlierberghe,1 Alberto Ambesi-Impiombato,1 Arianne Perez-Garcia,1 J. Erika Haydu,1 Isaura Rigo,1 Michael Hadler,1 Valeria Tosello,1 Giusy Della Gatta,1 Elisabeth Paietta,4 Janis Racevskis,4 Peter H. Wiernik,4 Selina M. Luger,5 Jacob M. Rowe,6 Montserrat Rue,7 and Adolfo A. Ferrando1,2,3 1Institute for Cancer Genetics, 2Department of Pediatrics, and 3Department of Pathology, Columbia University Medical Center, New York, NY 10032 4Montefiore Medical Center North, Bronx, New York, NY 10467 5Hematologic Malignancies and Stem Cell Transplant Program, Hematology-Oncology Division, University of Pennsylvania Medical Center, Philadelphia, PA 19104 6 Rambam Medical Center, Haifa 31096, Israel Downloaded from 7Department of Basic Medical Sciences, University of Lleida, Lleida 25003, Spain Early immature T cell acute lymphoblastic leukemias (T-ALLs) account for 5–10% of pediatric T-ALLs and are associated with poor prognosis. However, the genetic defects that drive the biology of these tumors remain largely unknown. In this study, analysis of micro- array gene expression signatures in adult T-ALL demonstrated a high prevalence of early immature leukemias and revealed a close relationship between these tumors and myeloid jem.rupress.org leukemias. Many adult immature T-ALLs harbored mutations in myeloid-specific oncogenes and tumor suppressors including IDH1, IDH2, DNMT3A, FLT3, and NRAS. Moreover, we identifiedETV6 mutations as a novel genetic lesion uniquely present in immature adult T-ALL. Our results demonstrate that early immature adult T-ALL represents a heterogeneous category of leukemias characterized by the presence of overlapping myeloid and T-ALL on May 30, 2015 characteristics, and highlight the potential role of ETV6 mutations in these tumors.
    [Show full text]
  • Single Cell Regulatory Landscape of the Mouse Kidney Highlights Cellular Differentiation Programs and Disease Targets
    ARTICLE https://doi.org/10.1038/s41467-021-22266-1 OPEN Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets Zhen Miao 1,2,3,8, Michael S. Balzer 1,2,8, Ziyuan Ma 1,2,8, Hongbo Liu1,2, Junnan Wu 1,2, Rojesh Shrestha 1,2, Tamas Aranyi1,2, Amy Kwan4, Ayano Kondo 4, Marco Pontoglio 5, Junhyong Kim6, ✉ Mingyao Li 7, Klaus H. Kaestner2,4 & Katalin Susztak 1,2,4 1234567890():,; Determining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response. Here, we profile open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We reveal key cell type-specific transcription factors and major gene- regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrates that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells follow a more complex differentiation, where Hfn4a is associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease implicates critical cell types, developmental stages, genes, and regulatory mechanisms. The single cell multi-omics atlas reveals key chromatin remodeling events and gene expression dynamics associated with kidney development. 1 Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA. 2 Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
    [Show full text]
  • Table S1. Complete Gene Expression Data from Human Diabetes RT² Profiler™ PCR Array Receptors, Transporters & Channels* A
    Table S1. Complete gene expression data from Human Diabetes RT² Profiler™ PCR Array Position Unigene GenBank Symbol Description FC Average Ct Receptors, Transporters & Channels* NGT GDM A01 Hs,5447 NM_000352 ABCC8 ATP-binding cassette, sub-family C (CFTR/MRP), member 8 0.93 35.00 35.00 A04 0Hs,2549 NM_000025 ADRB3 Adrenergic, beta-3-, receptor 0.88 34.92 35.00 A07 Hs,1307 NM_000486 AQP2 Aquaporin 2 (collecting duct) 0.93 35.00 35.00 A09 30Hs,5117 NM_001123 CCR2 Chemokine (C-C motif) receptor 2 1.00 26.28 26.17 A10 94Hs,5916 396NM_006139 CD28 CD28 molecule 0.81 34.51 34.71 A11 29Hs,5126 NM_001712 CEACAM1 Carcinoembryonic antigen-related cell adhesion molecule 1 1.31 26.08 25.59 B01 82Hs,2478 NM_005214 CTLA4 (biliaryCytotoxic glycoprotein) T-lymphocyte -associated protein 4 0.53 30.90 31.71 B11 24Hs,208 NM_000160 GCGR Glucagon receptor 0.93 35.00 35.00 C01 Hs,3891 NM_002062 GLP1R Glucagon-like peptide 1 receptor 0.93 35.00 35.00 C07 03Hs,6434 NM_000201 ICAM1 Intercellular adhesion molecule 1 0.84 28.74 28.89 D02 47Hs,5134 NM_000418 IL4R Interleukin 4 receptor 0.64 34.22 34.75 D06 57Hs,4657 NM_000208 INSR Insulin receptor 0.93 35.00 35.00 E05 44Hs,4312 NM_006178 NSF N-ethylmaleimide-sensitive factor 0.48 28.42 29.37 F08 79Hs,2961 NM_004578 RAB4A RAB4A, member RAS oncogene family 0.88 20.55 20.63 F10 69Hs,7287 NM_000655 SELL Selectin L 0.97 23.89 23.83 F11 56Hs,3806 NM_001042 SLC2A4 Solute carrier family 2 (facilitated glucose transporter), member 4 0.77 34.72 35.00 F12 91Hs,5111 NM_003825 SNAP23 Synaptosomal-associated protein, 23kDa 3.90
    [Show full text]
  • Nrf1 and Nrf2 Positively and C-Fos and Fra1 Negatively Regulate the Human Antioxidant Response Element-Mediated Expression of NAD(P)H:Quinone Oxidoreductase1 Gene
    Proc. Natl. Acad. Sci. USA Vol. 93, pp. 14960–14965, December 1996 Pharmacology Nrf1 and Nrf2 positively and c-Fos and Fra1 negatively regulate the human antioxidant response element-mediated expression of NAD(P)H:quinone oxidoreductase1 gene RADJENDIRANE VENUGOPAL AND ANIL K. JAISWAL* Department of Pharmacology, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111 Communicated by Y. W. Kan, University of California, San Francisco, CA, August 5, 1996 (received for review February 21, 1996) ABSTRACT Twenty-four base pairs of the human anti- (c-Jun, Jun-D, and Jun-B) form homodimers among them- oxidant response element (hARE) are required for high basal selves and heterodimers with c-Fos and Fra (Fra1 and Fra2) transcription of the NAD(P)H:quinone oxidoreductase1 proteins and bind to the TRE (a single AP1 binding site) and (NQO1) gene and its induction in response to xenobiotics and regulate the expression of target genes (6). Nrf1 and Nrf2 are antioxidants. hARE is a unique cis-element that contains one recently identified NF-E2-related factors that bind to the perfect and one imperfect AP1 element arranged as inverse sequence GCTGAGTCATGATGAGTCA (7, 8). The Nrf1 repeats separated by 3 bp, followed by a ‘‘GC’’ box. We report and Nrf2 contain 742 and 589 amino acids, respectively. Both here that Jun, Fos, Fra, and Nrf nuclear transcription factors these proteins display marked homology to the NF-E2, which bind to the hARE. Overexpression of cDNA derived combi- regulates expression of globin genes in developing erythroid nations of the nuclear proteins Jun and Fos or Jun and Fra1 cells through interaction with upstream AP1-like recognition repressed hARE-mediated chloramphenicol acetyltransferase sites (9).
    [Show full text]
  • Transcription Factors Recognize DNA Shape Without Nucleotide Recognition
    bioRxiv preprint doi: https://doi.org/10.1101/143677; this version posted May 29, 2017. 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. Transcription+factors+recognize+DNA+shape+without+nucleotide+recognition++ Md.$Abul$Hassan$Samee1,$Benoit$G.$Bruneau1,2,$Katherine$S.$Pollard$1,3$ 1:$Gladstone$Institutes,$1650$Owens$St.,$San$Francisco,$CA$94158$ 2:$$Department$of$Pediatrics$and$Cardiovascular$Research$Institute,$University$of$California,$ San$Francisco,$CA$94158$ 3:$Division$of$Bioinformatics,$Institute$for$Human$Genetics,$and$Institute$for$Computational$ Health$Sciences,$University$of$California,$San$Francisco,$CA$94158$ $ + bioRxiv preprint doi: https://doi.org/10.1101/143677; this version posted May 29, 2017. 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+ We$hypothesized$that$transcription$factors$(TFs)$recognize$DNA$shape$without$nucleotide$ sequence$recognition.$Motivating$an$independent$role$for$shape,$many$TF$binding$sites$lack$ a$sequenceZmotif,$DNA$shape$adds$specificity$to$sequenceZmotifs,$and$different$sequences$ can$ encode$ similar$ shapes.$ We$ therefore$ asked$ if$ binding$ sites$ of$ a$ TF$ are$ enriched$ for$ specific$patterns$of$DNA$shapeZfeatures,$e.g.,$helical$twist.$We$developed$ShapeMF,$which$ discovers$ these$ shapeZmotifs$ de%novo%without$ taking$ sequence$ information$ into$ account.$
    [Show full text]
  • Downregulation of Prdm16 Is Critical for HOXB4-Mediated Benign HSC Expansion in Vivo Hui Yu University of Tennessee Health Science Center
    University of Tennessee Health Science Center UTHSC Digital Commons Theses and Dissertations (ETD) College of Graduate Health Sciences 12-2014 Downregulation of Prdm16 Is Critical for HOXB4-mediated Benign HSC Expansion In Vivo Hui Yu University of Tennessee Health Science Center Follow this and additional works at: https://dc.uthsc.edu/dissertations Part of the Medical Genetics Commons, and the Medical Molecular Biology Commons Recommended Citation Yu, Hui , "Downregulation of Prdm16 Is Critical for HOXB4-mediated Benign HSC Expansion In Vivo" (2014). Theses and Dissertations (ETD). Paper 307. http://dx.doi.org/10.21007/etd.cghs.2014.0367. This Dissertation is brought to you for free and open access by the College of Graduate Health Sciences at UTHSC Digital Commons. It has been accepted for inclusion in Theses and Dissertations (ETD) by an authorized administrator of UTHSC Digital Commons. For more information, please contact [email protected]. Downregulation of Prdm16 Is Critical for HOXB4-mediated Benign HSC Expansion In Vivo Document Type Dissertation Degree Name Doctor of Philosophy (PhD) Program Biochemistry Track Therapeutics and Cell Signaling Research Advisor Brian P. Sorrentino, MD Committee Suzanne J. Baker, PhD Wing H. Leung, MD, PhD Janet F. Partridge, PhD Lawrence M. Pfeffer, PhD DOI 10.21007/etd.cghs.2014.0367 This dissertation is available at UTHSC Digital Commons: https://dc.uthsc.edu/dissertations/307 DOWNREGULATION OF PRDM16 IS CRITICAL FOR HOXB4-MEDIATED BENIGN HSC EXPANSION IN VIVO A Dissertation Presented for The Graduate Studies Council The University of Tennessee Health Science Center In Partial Fulfillment Of the Requirements for the Degree Doctor of Philosophy From The University of Tennessee By Hui Yu December 2014 Copyright © 2014 by Hui Yu All rights reserved ii DEDICATION This dissertation is dedicated to my parents, Guoquan Yu and Yan Xu, my husband, Satish Kumar Nandakumar and my precious daughter Emma Satish for all their love and support.
    [Show full text]
  • Modeling Enhancer-Promoter Interactions with Attention-Based Neural Networks
    bioRxiv preprint doi: https://doi.org/10.1101/219667; this version posted November 14, 2017. 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. Article Modeling Enhancer-Promoter Interactions with Attention-Based Neural Networks Weiguang Mao 1,2, Dennis Kostka 1,2,3 and Maria Chikina 1,2* 1 Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh 2 Joint Carnegie Mellon - University of Pittsburgh Ph.D. Program in Computational Biology 3 Department of Developmental Biology, School of Medicine, University of Pittsburgh * Correspondence: [email protected] Academic Editor: name Version November 9, 2017 submitted to Cells 1 Abstract: Background: Gene regulatory sequences play critical roles in ensuring tightly controlled 2 RNA expression patterns that are essential in a large variety of biological processes. Specifically, 3 enhancer sequences drive expression of their target genes, and the availability of genome-wide 4 maps of enhancer-promoter interactions has opened up the possibility to use machine learning 5 approaches to extract and interpret features that define these interactions in different biological 6 contexts. Methods: Inspired by machine translation models we develop an attention-based neural 7 network model, EPIANN, to predict enhancer-promoter interactions based on DNA sequences. Codes 8 and data are available at https://github.com/wgmao/EPIANN. Results: Our approach accurately 9 predicts enhancer-promoter interactions across six cell lines. In addition, our method generates 10 pairwise attention scores at the sequence level, which specify how short regions in the enhancer and 11 promoter pair-up to drive the interaction prediction.
    [Show full text]
  • Influence of DNA Methylation on Transcription Factor Binding
    Influence of DNA methylation on transcription factor binding Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Silvia Domcke aus München, Deutschland Basel, 2017 Originaldokument gespeichert auf dem Dokumentenserver der Universität Basel edoc.unibas.ch Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. Dirk Schübeler und Dr. François Spitz. Basel, den 18.04.2017 Prof. Dr. Martin Spiess (Dekan) "While Occam's razor is a useful tool in the physical sciences, it can be a very dangerous implement in biology. It is thus very rash to use simplicity and elegance as a guide in biological research. While DNA could be claimed to be both simple and elegant, it must be remembered that DNA almost certainly originated fairly close to the origin of life when things were necessarily simple or they would not have got going. Biologists must constantly keep in mind that what they see was not designed, but rather evolved." ---- Francis Crick in 'What mad Pursuit' (1988) ---- i ii Acknowledgements This thesis would not have been possible without the support and contribution of many people. I would like to thank my PhD advisor Dirk Schübeler for giving me the opportunity to work in his group and for many excellent as well as thought- provoking scientific discussions. I especially appreciate that it was always possible to get critical input and advice while still having a lot of freedom and flexibility. For direct contributions to this study I would like to thank the co-authors of the published manuscript, in particular Anaïs Bardet.
    [Show full text]