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Nat Commun. 2018 Jan 15;9(1):189. doi: 10.1038/s41467-017-02525-w.

High-resolution TADs reveal DNA sequences underlying genome organization in flies.

Author information

1
Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany.
2
Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany.
3
University of Freiburg, Department of Computer Science, Georges-Köhler-Allee 106, 79110, Freiburg, Germany.
4
Max Planck Institute of Biochemistry and Computational Biology, Am Klopferspitz 18, 82152, Martinsried, Germany.
5
Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany. manke@ie-freiburg.mpg.de.

Abstract

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 .

PMID:
29335486
PMCID:
PMC5768762
DOI:
10.1038/s41467-017-02525-w
[Indexed for MEDLINE]
Free PMC Article

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