A GO catalogue of human DNA-binding transcription factors.

Journal: Biochimica et biophysica acta. Gene regulatory mechanisms
Published Date: Oct 18, 2021

Abstract

To control gene transcription, DNA-binding transcription factors recognise specific sequence motifs in gene regulatory regions. A complete and reliable GO annotation of all DNA-binding transcription factors is key to investigating the delicate balance of gene regulation in response to environmental and developmental stimuli. The need for such information is demonstrated by the many lists of transcription factors that have been produced over the past decade. The COST Action Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) Consortium brought together experts in the field of transcription with the aim of providing high quality and interoperable gene regulatory data. The Gene Ontology (GO) Consortium provides strict definitions for gene product function, including factors that regulate transcription. The collaboration between the GREEKC and GO Consortia has enabled the application of those definitions to produce a new curated catalogue of over 1400 human DNA-binding transcription factors, that can be accessed at https://www.ebi.ac.uk/QuickGO/targetset/dbTF. This catalogue has facilitated an improvement in the GO annotation of human DNA-binding transcription factors and led to the GO annotation of almost sixty thousand DNA-binding transcription factors in over a hundred species. Thus, this work will aid researchers investigating the regulation of transcription in both biomedical and basic science.

Authors

  • Ruth C Lovering
    Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London, WC1E 6JF, UK. r.lovering@ucl.ac.uk.
  • Pascale Gaudet
    Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland, Department of Medicine and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA, School of Information, University of South Florida, Tampa, FL, 33647, USA, Genomics Division, Lawrence Berkeley National Lab, 1 Cyclotron Rd., Berkeley, 94720 CA USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland, ETH Zurich, Department of Computer Science, Universitätstr. 19, 8092 Zürich, Switzerland, SIB Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zürich, Switzerland and University College London, Gower St, London WC1E 6BT, UK.
  • Marcio L Acencio
    Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim NO-7491, Norway. Electronic address: marcio.acencio@uni.lu.
  • Alex Ignatchenko
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom. Electronic address: alexsign@ebi.ac.uk.
  • Arttu Jolma
    Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada. Electronic address: arttu.jolma@gmail.com.
  • Oriol Fornes
    Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Vancouver, BC, V5Z 4H4, Canada. oriol@cmmt.ubc.ca.
  • Martin Kuiper
    Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
  • Ivan V Kulakovskiy
    Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia. Electronic address: ivan.kulakovskiy@gmail.com.
  • Astrid Lægreid
    Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
  • Maria J Martin
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Colin Logie
    Molecular Biology Department, Faculty of Science, Radboud University, PO box 9101, 6500HB Nijmegen, the Netherlands.

Keywords

External Resources

Popular Topics
Recent Journals