High-resolution TADs reveal DNA sequences underlying genome organization in flies
| Autor: | Vivek Bhardwaj, Thomas Manke, Bianca Habermann, Jose M. Villaveces, Asifa Akhtar, Fidel Ramírez, Kin Chung Lam, Björn Grüning, Laura Arrigoni |
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| Přispěvatelé: | Albert-Ludwigs-Universität Freiburg, Scionics Computer Innovation GmbH, Scionics Computer Innovation, Max Planck Institute of Immunobiology and Epigenetics (MPI-IE), Max-Planck-Gesellschaft, Max-Planck-Institut für Biochemie (MPIB), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Max-Planck-Institut für Biochemie = Max Planck Institute of Biochemistry (MPIB) |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
CCCTC-Binding Factor [SDV]Life Sciences [q-bio] Genome Insect Molecular Conformation Gene Expression General Physics and Astronomy Insulator (genetics) Genome Mice chemistry.chemical_compound 0302 clinical medicine Databases Genetic Drosophila Proteins lcsh:Science Genomic organization Genetics 0303 health sciences Multidisciplinary Chromosome Mapping Biological Evolution Chromatin DNA-Binding Proteins Drosophila melanogaster Science Genomics Computational biology Biology Article General Biochemistry Genetics and Molecular Biology DNA sequencing 03 medical and health sciences [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] Animals Humans Nucleotide Motifs Eye Proteins Gene Transcription factor 030304 developmental biology fungi General Chemistry Chromatin Assembly and Disassembly Chromosomes Insect 030104 developmental biology chemistry CTCF lcsh:Q Human genome Software 030217 neurology & neurosurgery DNA Transcription Factors |
| Zdroj: | Nature Communications Nature Communications, Nature Publishing Group, 2018, 9 (1), pp.189. ⟨10.1038/s41467-017-02525-w⟩ Nature Communications, Vol 9, Iss 1, Pp 1-15 (2018) Nature Communications, 2018, 9 (1), pp.189. ⟨10.1038/s41467-017-02525-w⟩ |
| ISSN: | 2041-1723 |
| DOI: | 10.1038/s41467-017-02525-w |
| Popis: | Despite an abundance of new studies about topologically associating domains (TADs), the role of genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer (hicexplorer.readthedocs.io) to annotate >2800 high-resolution (570 bp) TAD boundaries in Drosophila melanogaster. We identify eight DNA motifs enriched at boundaries, including a motif bound by the M1BP protein, and two new boundary motifs. In contrast to mammals, the CTCF motif is only enriched on a small fraction of boundaries flanking inactive chromatin while most active boundaries contain the motifs bound by the M1BP or Beaf-32 proteins. We demonstrate that boundaries can be accurately predicted using only the motif sequences at open chromatin sites. We propose that DNA sequence guides the genome architecture by allocation of boundary proteins in the genome. Finally, we present an interactive online database to access and explore the spatial organization of fly, mouse and human genomes, available at http://chorogenome.ie-freiburg.mpg.de. Although topologically associating domains (TADs) have been extensively investigated, it is not clear to what extent DNA sequence contributes to their formation. Here the authors develop software to identify high-resolution TAD boundaries and reveal their relationship to underlying DNA motifs. |
| Databáze: | OpenAIRE |
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