Chromatin insulator factors involved in long-range DNA interactions and their role in the folding of the Drosophila genome

Autor: Stephanie Dejardin, Adrien Gamot, Jutta Vogelmann, Nicolas Nègre, Antoine Le Gall, Marcelo Nollmann, Frédéric Allemand, Gilles Labesse, Emmanuel Margeat, Martin Cohen-Gonsaud, Olivier Cuvier
Přispěvatelé: Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie moléculaire eucaryote (LBME), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), French National Research Agency [ANR-2010-BLAN-1221 01], France-BioImaging infrastructure [ANR-10-INSB-04], French Infrastructure for Integrated Structural Biology [ANR-10-INSB-05-01], European Project: 260787,EC:FP7:ERC,ERC-2010-StG_20091118,SMINSULATOR(2010), Vogelmann, Jutta, Le Gall, Antoine, Nöllmann, Marcelo, Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Jazyk: angličtina
Rok vydání: 2014
Předmět:
Cancer Research
[SDV]Life Sciences [q-bio]
Genome
Insect
Gene Expression
Biochemistry
chemistry.chemical_compound
Nuclear Matrix-Associated Proteins
Nucleic Acids
Transcriptional regulation
Drosophila Proteins
Gene Regulatory Networks
Genetics (clinical)
Genetics
Chromosome Biology
adn
Nuclear Proteins
Genomics
drosophila
Chromatin
3. Good health
Cell biology
DNA-Binding Proteins
Drosophila melanogaster
Insulator Elements
Epigenetics
Microtubule-Associated Proteins
Research Article
lcsh:QH426-470
Protein domain
Biophysics
Biology
DNA-binding protein
Protein–protein interaction
Genome-Wide Association Studies
Animals
Electrophoretic mobility shift assay
Eye Proteins
Enhancer
Molecular Biology
Ecology
Evolution
Behavior and Systematics
Biology and Life Sciences
Computational Biology
DNA
Cell Biology
Genome Analysis
lcsh:Genetics
chemistry
chromatine
Zdroj: PLoS Genetics
PLoS Genetics, 2014, 10 (8), ⟨10.1371/journal.pgen.1004544⟩
PLoS Genetics, Vol 10, Iss 8, p e1004544 (2014)
Plos Genetics 8 (10), . (2014)
PLoS Genetics, Public Library of Science, 2014, 10 (8), ⟨10.1371/journal.pgen.1004544⟩
ISSN: 1553-7390
1553-7404
DOI: 10.1371/journal.pgen.1004544⟩
Popis: Chromatin insulators are genetic elements implicated in the organization of chromatin and the regulation of transcription. In Drosophila, different insulator types were characterized by their locus-specific composition of insulator proteins and co-factors. Insulators mediate specific long-range DNA contacts required for the three dimensional organization of the interphase nucleus and for transcription regulation, but the mechanisms underlying the formation of these contacts is currently unknown. Here, we investigate the molecular associations between different components of insulator complexes (BEAF32, CP190 and Chromator) by biochemical and biophysical means, and develop a novel single-molecule assay to determine what factors are necessary and essential for the formation of long-range DNA interactions. We show that BEAF32 is able to bind DNA specifically and with high affinity, but not to bridge long-range interactions (LRI). In contrast, we show that CP190 and Chromator are able to mediate LRI between specifically-bound BEAF32 nucleoprotein complexes in vitro. This ability of CP190 and Chromator to establish LRI requires specific contacts between BEAF32 and their C-terminal domains, and dimerization through their N-terminal domains. In particular, the BTB/POZ domains of CP190 form a strict homodimer, and its C-terminal domain interacts with several insulator binding proteins. We propose a general model for insulator function in which BEAF32/dCTCF/Su(HW) provide DNA specificity (first layer proteins) whereas CP190/Chromator are responsible for the physical interactions required for long-range contacts (second layer). This network of organized, multi-layer interactions could explain the different activities of insulators as chromatin barriers, enhancer blockers, and transcriptional regulators, and suggest a general mechanism for how insulators may shape the organization of higher-order chromatin during cell division.
Author Summary Chromatin insulators mediate specific long-range DNA interactions required for the three dimensional organization of the interphase nucleus and for transcription regulation, but the mechanisms underlying the formation of these interactions is currently unknown. In this manuscript, we investigate the molecular associations between different protein components of insulators (BEAF32, CP190 and Chromator) by biochemical and biophysical means, and develop a novel biophysical assay to determine what factors are necessary and essential for the formation of long-range DNA interactions (LRI). Importantly, we show that CP190 and Chromator are able to mediate LRIs between specifically-bound BEAF32 nucleoprotein complexes. This ability of CP190 and Chromator to establish LRI requires specific contacts between BEAF32 and their C-terminal domains, and dimerization through their N-terminal domains. In particular, the BTB/POZ domains of CP190 form a strict homodimer. We propose a general model for insulator function in which BEAF32/dCTCF/Su(HW) provide DNA specificity, whereas CP190/Chromator are responsible for the physical interactions required for long-range contacts. This network of organized, multi-layer interactions could explain the different activities of insulators, and suggest a general mechanism for how insulators may shape the organization of higher-order chromatin during cell division.
Databáze: OpenAIRE
Externí odkaz: