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Journal Article

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

MPS-Authors

Ramirez,  Fidel
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Bhardwaj,  Vivek
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Arrigoni,  Laura
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Lam,  Kin Chung
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Akhtar,  Asifa
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

/persons/resource/persons50420

Manke,  Thomas
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

External Resource

https://www.nature.com/articles/s41467-017-02525-w
(Publisher version)

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Citation

Ramirez, F., Bhardwaj, V., Arrigoni, L., Lam, K. C., Grüning, B. A., Villaveces, J., et al. (2018). High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nature Communications, 9, 189. doi:10.1038/s41467-017-02525-w.


Cite as: https://hdl.handle.net/21.11116/0000-0003-6E0F-3
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 .