DOCSLIB.ORG

Examination of the Transcription Factors Acting in Bone Marrow

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Examination of the Transcription Factors Acting in Bone Marrow THESIS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY (PHD) Examination of the transcription factors acting in bone marrow derived macrophages by Gergely Nagy Supervisor: Dr. Endre Barta UNIVERSITY OF DEBRECEN DOCTORAL SCHOOL OF MOLECULAR CELL AND IMMUNE BIOLOGY DEBRECEN, 2016 Table of contents Table of contents ........................................................................................................................ 2 1. Introduction ............................................................................................................................ 5 1.1. Transcriptional regulation ................................................................................................... 5 1.1.1. Transcriptional initiation .................................................................................................. 5 1.1.2. Co-regulators and histone modifications .......................................................................... 8 1.2. Promoter and enhancer sequences guiding transcription factors ...................................... 11 1.2.1. General transcription factors .......................................................................................... 11 1.2.2. The ETS superfamily ..................................................................................................... 17 1.2.3. The AP-1 and CREB proteins ........................................................................................ 20 1.2.4. Other promoter specific transcription factor families .................................................... 26 1.3. Nuclear receptors ............................................................................................................... 31 1.4. Transcription factors in macrophage development ........................................................... 37 1.5. NGS methods in functional genomics ............................................................................... 40 1.5.1. Getting and aligning raw NGS data ............................................................................... 40 1.5.2. The determination of read and motif enrichments ......................................................... 43 2. Aims of the study ................................................................................................................. 47 3. Materials and Methods ......................................................................................................... 49 3.1. The differentiation of bone marrow derived macrophage (BMDM) cells ........................ 49 3.2. Chromatin immunoprecipitation coupled with next-generation sequencing .................... 49 3.3. ChIP-seq analysis .............................................................................................................. 51 3.3.1. Primary analysis ............................................................................................................. 51 3.3.2. The determination of nucleosome-free regions (NFRs) ................................................. 51 3.3.3. Peak prediction ............................................................................................................... 52 2 3.3.4. Secondary analyses ........................................................................................................ 52 3.4. Global run-on sequencing (GRO-seq) ............................................................................... 53 3.5. GRO-seq analysis .............................................................................................................. 54 3.5.1. Primary analysis ............................................................................................................. 54 3.5.2. The determination of transcripts .................................................................................... 54 3.5.3. The annotation of transcripts .......................................................................................... 56 3.5.4. The expressional analysis of nascent transcripts ............................................................ 56 3.5.5. The annotation of RXR-bound regulatory regions ......................................................... 57 3.6. RNA-seq ............................................................................................................................ 57 3.7. RNA-seq analysis .............................................................................................................. 58 3.8. Domain predictions based on the CTCF and RAD21 “co-peaks” .................................... 59 3.9. Chromosome conformation capture (3C) .......................................................................... 59 3.10. 3C-sequencing ................................................................................................................. 60 3.11. 3C-seq analysis ................................................................................................................ 60 3.12. The phylogenetic comparison of AP-1/CREB related bZIP proteins ............................. 61 4. Results .................................................................................................................................. 62 4.1. Determining the putative regulatory regions of macrophages based on histone coverage information ............................................................................................................................... 62 4.2. Determining macrophage specific transcription factors from NFR predictions ............... 67 4.3. The examination of histone patterns near PU.1 binding sites ........................................... 71 4.4. Combining NFR data to get further putative regulators .................................................... 75 4.5. The examination of the RXR cistrome in macrophages ................................................... 78 4.6. The determination of the nascent transcriptome of macrophages ..................................... 82 4.7. The examination of the gene expressional changes of TFs upon RXR activation ............ 85 4.8. The annotation of the putative regulatory regions .......................................................... 100 3 4.9. Putative binding elements of the annotated RXR peaks ................................................. 106 4.10. The examination of functional domains ........................................................................ 107 5. Discussion .......................................................................................................................... 114 6. Keywords / kulcsszavak ..................................................................................................... 119 7. Summary ............................................................................................................................ 120 Összefoglalás .......................................................................................................................... 121 8. Abbreviations ..................................................................................................................... 122 9. Acknowledgements ............................................................................................................ 131 10. References ........................................................................................................................ 132 4 1. Introduction 1.1. Transcriptional regulation 1.1.1. Transcriptional initiation Transcriptional initiation, elongation and termination are main steps of nascent RNA synthesis. As once RNA polymerase has been launched, it runs along the gene, of these steps – in our present knowledge – initiation may provide the most extended regulatory possibilities. In eukaryotes, the pre-initiation complex (PIC) assembled on the transcription factor binding sites (TFBSs) of the promoter of protein coding genes is composed of transcription factors (TFs), their co-regulators, as well as RNA polymerase II (Pol II) (Figure 1) (Green, Trends Biochem Sci., 2000; Grünberg and Hahn, Trends Biochem Sci., 2013). Pol II also is a complex built up from RNA polymerase II B (RPB1-12) subunits coded by Polr2a- k genes (Ruprich-Robert and Thuriaux, Nucleic Acids Res., 2010). To launch Pol II, not only the presence of a large number of regulatory proteins (Tsai and Nussinov, Biochem J., 2011), but also their enzymatic activity is needed: beside the multiple serine phosphorylation on the carboxy-terminal domain (CTD) of RPB1, helicase and topoisomerase activities are also indispensable to start PolII (Heidemann et al., Biochim Biophys Acta., 2013; Baranello et al., Transcription, 2013). Once PIC has been formed, PolII synthesizes truncated and elongated transcripts in an abortive and productive manner, respectively (Dvir, Biochim Biophys Acta., 2002; Mandal et al., PNAS, 2004; Core et al., Science, 2008; Gaertner and Zeitlinger, Development, 2014). This former property may be needed for further regulatory functions, e.g. the operation of short transcripts in some comparable ways as happens in prokaryotes. In E. coli, the abortive transcript of bacteriophage T7 gene 10 has an antiterminator effect thus facilitating the expression of the further promoterless genes of the polycistron located directly downstream (Lee et al., Nucleic Acids Res., 2010). In eukaryotes, the ratio of the truncated and elongated 5 transcripts correlates with gene expression (Core et al., Science, 2008), but the possible roles of the short products still remain mostly unknown (Seila et
Load more

Recommended publications
  • Supplementary Materials: Evaluation of Cytotoxicity and Α-Glucosidase Inhibitory Activity of Amide and Polyamino-Derivatives of Lupane Triterpenoids
    Supplementary Materials: Evaluation of cytotoxicity and α-glucosidase inhibitory activity of amide and polyamino-derivatives of lupane triterpenoids Oxana B. Kazakova1*, Gul'nara V. Giniyatullina1, Akhat G. Mustafin1, Denis A. Babkov2, Elena V. Sokolova2, Alexander A. Spasov2* 1Ufa Institute of Chemistry of the Ufa Federal Research Centre of the Russian Academy of Sciences, 71, pr. Oktyabrya, 450054 Ufa, Russian Federation 2Scientific Center for Innovative Drugs, Volgograd State Medical University, Novorossiyskaya st. 39, Volgograd 400087, Russian Federation Correspondence Prof. Dr. Oxana B. Kazakova Ufa Institute of Chemistry of the Ufa Federal Research Centre of the Russian Academy of Sciences 71 Prospeсt Oktyabrya Ufa, 450054 Russian Federation E-mail: [email protected] Prof. Dr. Alexander A. Spasov Scientific Center for Innovative Drugs of the Volgograd State Medical University 39 Novorossiyskaya st. Volgograd, 400087 Russian Federation E-mail: [email protected] Figure S1. 1H and 13C of compound 2. H NH N H O H O H 2 2 Figure S2. 1H and 13C of compound 4. NH2 O H O H CH3 O O H H3C O H 4 3 Figure S3. Anticancer screening data of compound 2 at single dose assay 4 Figure S4. Anticancer screening data of compound 7 at single dose assay 5 Figure S5. Anticancer screening data of compound 8 at single dose assay 6 Figure S6. Anticancer screening data of compound 9 at single dose assay 7 Figure S7. Anticancer screening data of compound 12 at single dose assay 8 Figure S8. Anticancer screening data of compound 13 at single dose assay 9 Figure S9. Anticancer screening data of compound 14 at single dose assay 10 Figure S10.
    [Show full text]
  • 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.
    [Show full text]
  • Supplemental Materials ZNF281 Enhances Cardiac Reprogramming
    Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7
    [Show full text]
  • Transcriptional Control of Tissue-Resident Memory T Cell Generation
    Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2019 © 2019 Filip Cvetkovski All rights reserved ABSTRACT Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Tissue-resident memory T cells (TRM) are a non-circulating subset of memory that are maintained at sites of pathogen entry and mediate optimal protection against reinfection. Lung TRM can be generated in response to respiratory infection or vaccination, however, the molecular pathways involved in CD4+TRM establishment have not been defined. Here, we performed transcriptional profiling of influenza-specific lung CD4+TRM following influenza infection to identify pathways implicated in CD4+TRM generation and homeostasis. Lung CD4+TRM displayed a unique transcriptional profile distinct from spleen memory, including up-regulation of a gene network induced by the transcription factor IRF4, a known regulator of effector T cell differentiation. In addition, the gene expression profile of lung CD4+TRM was enriched in gene sets previously described in tissue-resident regulatory T cells. Up-regulation of immunomodulatory molecules such as CTLA-4, PD-1, and ICOS, suggested a potential regulatory role for CD4+TRM in tissues. Using loss-of-function genetic experiments in mice, we demonstrate that IRF4 is required for the generation of lung-localized pathogen-specific effector CD4+T cells during acute influenza infection. Influenza-specific IRF4−/− T cells failed to fully express CD44, and maintained high levels of CD62L compared to wild type, suggesting a defect in complete differentiation into lung-tropic effector T cells.
    [Show full text]
  • Mouse Population-Guided Resequencing Reveals That Variants in CD44 Contribute to Acetaminophen-Induced Liver Injury in Humans
    Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Mouse population-guided resequencing reveals that variants in CD44 contribute to acetaminophen-induced liver injury in humans Alison H. Harrill,1,2,12 Paul B. Watkins,3,12 Stephen Su,6 Pamela K. Ross,2 David E. Harbourt,5 Ioannis M. Stylianou,7 Gary A. Boorman,8 Mark W. Russo,3 Richard S. Sackler,9 Stephen C. Harris,11 Philip C. Smith,5 Raymond Tennant,8 Molly Bogue,7 Kenneth Paigen,7 Christopher Harris,9,10 Tanupriya Contractor,9 Timothy Wiltshire,5 Ivan Rusyn,1,2,14 and David W. Threadgill1,4,13,14,15 1Curriculum in Toxicology, University of North Carolina, Chapel Hill, North Carolina 27599, USA; 2Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, USA; 3Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, North Carolina 27599, USA; 4Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599, USA; 5School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA; 6Department of Mouse Genetics, Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA; 7The Jackson Laboratory, Bar Harbor, Maine 04609, USA; 8National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA; 9Verto Institute Research Laboratories, New Brunswick, New Jersey 08903, USA; 10Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA; 11Purdue Pharma L.P., Stamford, Connecticut 06901, USA; 12Hamner-UNC Center for Drug Safety Sciences, The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709, USA; 13Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA Interindividual variability in response to chemicals and drugs is a common regulatory concern.
    [Show full text]
  • Has Critical Roles in Epithelial Dysfunction in Airway Disease
    JBC Papers in Press. Published on May 1, 2017 as Manuscript M117.775304 The latest version is at http://www.jbc.org/cgi/doi/10.1074/jbc.M117.775304 EHF has critical roles in airway epithelial dysfunction Ets Homologous Factor (EHF) has critical roles in epithelial dysfunction in airway disease Sara L Fossum1,2, Michael J. Mutolo1,2, Antonio Tugores3, Sujana Ghosh1,2, Scott H. Randell4, Lisa C. Jones4, Shih-Hsing Leir1,2,5, Ann Harris1,2,5 1Human Molecular Genetics Program, Lurie Children’s Research Center, Chicago, IL 60614, USA, 2Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, 3 Unidad de Investigación, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de Gran Canaria, Spain, 4Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA, 5 Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44016, USA Running title: EHF has critical roles in airway epithelial dysfunction Downloaded from To whom correspondence should be addressed: Ann Harris, Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio, 44106; Email: [email protected] http://www.jbc.org/ Keywords: genomics, gene regulation, epithelium, lung, transcription factor at University of North Carolina Chapel Hill on August 16, 2019 ABSTRACT The airway epithelium forms a barrier between the internal and external environments. The airway epithelium plays a critical role Epithelial dysfunction is critical in the pathology in lung function in both normal and pathological of many respiratory diseases including cystic states.
    [Show full text]
  • Hepatitis C Virus As a Unique Human Model Disease to Define
    viruses Review Hepatitis C Virus as a Unique Human Model Disease to Define Differences in the Transcriptional Landscape of T Cells in Acute versus Chronic Infection David Wolski and Georg M. Lauer * Liver Center at the Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA * Correspondence: [email protected]; Tel.: +1-617-724-7515 Received: 27 June 2019; Accepted: 23 July 2019; Published: 26 July 2019 Abstract: The hepatitis C virus is unique among chronic viral infections in that an acute outcome with complete viral elimination is observed in a minority of infected patients. This unique feature allows direct comparison of successful immune responses with those that fail in the setting of the same human infection. Here we review how this scenario can be used to achieve better understanding of transcriptional regulation of T-cell differentiation. Specifically, we discuss results from a study comparing transcriptional profiles of hepatitis C virus (HCV)-specific CD8 T-cells during early HCV infection between patients that do and do not control and eliminate HCV. Identification of early gene expression differences in key T-cell differentiation molecules as well as clearly distinct transcriptional networks related to cell metabolism and nucleosomal regulation reveal novel insights into the development of exhausted and memory T-cells. With additional transcriptional studies of HCV-specific CD4 and CD8 T-cells in different stages of infection currently underway, we expect HCV infection to become a valuable model disease to study human immunity to viruses. Keywords: viral hepatitis; hepatitis C virus; T cells; transcriptional regulation; transcription factors; metabolism; nucleosome 1.
    [Show full text]
  • Sexual Dimorphism in Brain Transcriptomes of Amami Spiny Rats (Tokudaia Osimensis): a Rodent Species Where Males Lack the Y Chromosome Madison T
    Ortega et al. BMC Genomics (2019) 20:87 https://doi.org/10.1186/s12864-019-5426-6 RESEARCHARTICLE Open Access Sexual dimorphism in brain transcriptomes of Amami spiny rats (Tokudaia osimensis): a rodent species where males lack the Y chromosome Madison T. Ortega1,2, Nathan J. Bivens3, Takamichi Jogahara4, Asato Kuroiwa5, Scott A. Givan1,6,7,8 and Cheryl S. Rosenfeld1,2,8,9* Abstract Background: Brain sexual differentiation is sculpted by precise coordination of steroid hormones during development. Programming of several brain regions in males depends upon aromatase conversion of testosterone to estrogen. However, it is not clear the direct contribution that Y chromosome associated genes, especially sex- determining region Y (Sry), might exert on brain sexual differentiation in therian mammals. Two species of spiny rats: Amami spiny rat (Tokudaia osimensis) and Tokunoshima spiny rat (T. tokunoshimensis) lack a Y chromosome/Sry, and these individuals possess an XO chromosome system in both sexes. Both Tokudaia species are highly endangered. To assess the neural transcriptome profile in male and female Amami spiny rats, RNA was isolated from brain samples of adult male and female spiny rats that had died accidentally and used for RNAseq analyses. Results: RNAseq analyses confirmed that several genes and individual transcripts were differentially expressed between males and females. In males, seminal vesicle secretory protein 5 (Svs5) and cytochrome P450 1B1 (Cyp1b1) genes were significantly elevated compared to females, whereas serine (or cysteine) peptidase inhibitor, clade A, member 3 N (Serpina3n) was upregulated in females. Many individual transcripts elevated in males included those encoding for zinc finger proteins, e.g.
    [Show full text]
  • Local Genetic and Environmental Factors in Asthma Disease Pathogenesis: Chronicity and Persistence Mechanisms
    Eur Respir J 2007; 29: 793–803 DOI: 10.1183/09031936.00087506 CopyrightßERS Journals Ltd 2007 SERIES ‘‘GENETICS OF ASTHMA AND COPD IN THE POSTGENOME ERA’’ Edited by E. von Mutius, M. Kabesch and F. Kauffmann Number 4 in this Series Local genetic and environmental factors in asthma disease pathogenesis: chronicity and persistence mechanisms S.T. Holgate*, D.E. Davies*, R.M. Powell*, P.H. Howarth*, H.M. Haitchi# and J.W. Holloway" ABSTRACT: While asthma is an inflammatory disorder of the airways usually associated with AFFILIATIONS atopy, an important additional component is involvement of the epithelium and underlying *Allergy and Inflammation Research, Division of Infection, Inflammation mesenchyme acting as a trophic unit (EMTU). and Repair, In addition to allergens, a wide range of environmental factors interact with the EMTU, such as #IIR Division and virus infections, environmental tobacco smoke and pollutants, to initiate tissue damage and "Division of Human Genetics, School aberrant repair responses that are translated into remodelling of the airways. While candidate of Medicine, Southampton General Hospital, Southampton, UK. gene association studies have revealed polymorphic variants that influence asthmatic inflamma- tion, positional cloning of previously unknown genes is identifying a high proportion of novel CORRESPONDENCE genes in the EMTU. S.T. Holgate Dipeptidyl peptidase (DPP) 10 and disintegrin and metalloproteinase (ADAM)33 are newly Allergy and Inflammation Research MP810 identified genes strongly associated with asthma that are preferentially expressed in the airway Level D epithelium and underlying mesenchyme, respectively. Centre Block Also of increasing importance is the recognition that genes associated with asthma and atopy Southampton General Hospital have important interactions with the environment through epigenetic mechanisms that influence Southampton SO16 6YD UK their expression.
    [Show full text]
  • Combinatorial Bzip Dimers Display Complex DNA-Binding Specificity Landscapes
    Combinatorial bZIP dimers display complex DNA-binding specificity landscapes The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Rodriguez-Martinez, Jose A et al. “Combinatorial bZIP Dimers Display Complex DNA-Binding Specificity Landscapes.” eLife 6 (2017): n. pag. As Published http://dx.doi.org/10.7554/eLife.19272 Publisher eLife Sciences Publications, Ltd. Version Final published version Citable link http://hdl.handle.net/1721.1/110147 Terms of Use Creative Commons Attribution 4.0 International License Detailed Terms http://creativecommons.org/licenses/by-nc/4.0/ RESEARCH ARTICLE Combinatorial bZIP dimers display complex DNA-binding specificity landscapes Jose´ A Rodrı´guez-Martı´nez1†, Aaron W Reinke2†, Devesh Bhimsaria1,3†, Amy E Keating2,4, Aseem Z Ansari1,5* 1Department of Biochemistry, University of Wisconsin-Madison, Madison, United States; 2Department of Biology, Massachusetts Institute of Technology, Cambridge, United States; 3Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, Unites States; 4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States; 5The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States Abstract How transcription factor dimerization impacts DNA-binding specificity is poorly understood. Guided by protein dimerization properties, we examined DNA binding specificities of 270 human bZIP pairs. DNA interactomes of 80 heterodimers and 22 homodimers revealed that 72% of heterodimer motifs correspond to conjoined half-sites preferred by partnering monomers. Remarkably, the remaining motifs are composed of variably-spaced half-sites (12%) or ‘emergent’ sites (16%) that cannot be readily inferred from half-site preferences of partnering monomers.
    [Show full text]
  • SUPPLEMENTARY NOTE Co-Activation of GR and NFKB
    SUPPLEMENTARY NOTE Co-activation of GR and NFKB alters the repertoire of their binding sites and target genes. Nagesha A.S. Rao1*, Melysia T. McCalman1,*, Panagiotis Moulos2,4, Kees-Jan Francoijs1, 2 2 3 3,5 Aristotelis Chatziioannou , Fragiskos N. Kolisis , Michael N. Alexis , Dimitra J. Mitsiou and 1,5 Hendrik G. Stunnenberg 1Department of Molecular Biology, Radboud University Nijmegen, the Netherlands 2Metabolic Engineering and Bioinformatics Group, Institute of Biological Research and Biotechnology, National Hellenic Research Foundation, Athens, Greece 3Molecular Endocrinology Programme, Institute of Biological Research and Biotechnology, National Hellenic Research Foundation, Greece 4These authors contributed equally to this work 5 Corresponding authors E-MAIL: [email protected] ; TEL: +31-24-3610524; FAX: +31-24-3610520 E-MAIL: [email protected] ; TEL: +30-210-7273741; FAX: +30-210-7273677 Running title: Global GR and NFKB crosstalk Keywords: GR, p65, genome-wide, binding sites, crosstalk SUPPLEMENTARY FIGURES/FIGURE LEGENDS AND SUPPLEMENTARY TABLES 1 Rao118042_Supplementary Fig. 1 A Primary transcript Mature mRNA TNF/DMSO TNF/DMSO 8 12 r=0.74, p< 0.001 r=0.61, p< 0.001 ) 2 ) 10 2 6 8 4 6 4 2 2 0 Fold change (mRNA) (log Fold change (primRNA) (log 0 −2 −2 −2 0 2 4 −2 0 2 4 Fold change (RNAPII) (log2) Fold change (RNAPII) (log2) B chr5: chrX: 56 _ 104 _ DMSO DMSO 1 _ 1 _ 56 _ 104 _ TA TA 1 _ 1 _ 56 _ 104 _ TNF TNF Cluster 1 1 _ Cluster 2 1 _ 56 _ 104 _ TA+TNF TA+TNF 1 _ 1 _ CCNB1 TSC22D3 chr20: chr17: 25 _ 33 _ DMSO DMSO 1 _ 1 _ 25 _ 33 _ TA TA 1 _ 1 _ 25 _ 33 _ TNF TNF Cluster 3 1 _ Cluster 4 1 _ 25 _ 33 _ TA+TNF TA+TNF 1 _ 1 _ GPCPD1 CCL2 chr6: chr22: 77 _ 35 _ DMSO DMSO 1 _ 77 _ 1 _ 35 _ TA TA 1 _ 1 _ 77 _ 35 _ TNF Cluster 5 Cluster 6 TNF 1 _ 1 _ 77 _ 35 _ TA+TNF TA+TNF 1 _ 1 _ TNFAIP3 DGCR6 2 Supplementary Figure 1.
    [Show full text]
  • Chloride Channels Regulate Differentiation and Barrier Functions
    RESEARCH ARTICLE Chloride channels regulate differentiation and barrier functions of the mammalian airway Mu He1†*, Bing Wu2†, Wenlei Ye1, Daniel D Le2, Adriane W Sinclair3,4, Valeria Padovano5, Yuzhang Chen6, Ke-Xin Li1, Rene Sit2, Michelle Tan2, Michael J Caplan5, Norma Neff2, Yuh Nung Jan1,7,8, Spyros Darmanis2*, Lily Yeh Jan1,7,8* 1Department of Physiology, University of California, San Francisco, San Francisco, United States; 2Chan Zuckerberg Biohub, San Francisco, United States; 3Department of Urology, University of California, San Francisco, San Francisco, United States; 4Division of Pediatric Urology, University of California, San Francisco, Benioff Children’s Hospital, San Francisco, United States; 5Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Heaven, United States; 6Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, United States; 7Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States; 8Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States *For correspondence: Abstract The conducting airway forms a protective mucosal barrier and is the primary target of [email protected] (MH); [email protected] airway disorders. The molecular events required for the formation and function of the airway (SD); mucosal barrier, as well as the mechanisms by which barrier dysfunction leads to early onset airway [email protected] (LYJ) diseases,
    [Show full text]