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

Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A. Grüning, José Villaveces, Bianca Habermann, Asifa Akhtar and Thomas Manke ()
Additional contact information
Fidel Ramírez: Max Planck Institute of Immunobiology and Epigenetics
Vivek Bhardwaj: Max Planck Institute of Immunobiology and Epigenetics
Laura Arrigoni: Max Planck Institute of Immunobiology and Epigenetics
Kin Chung Lam: Max Planck Institute of Immunobiology and Epigenetics
Björn A. Grüning: University of Freiburg, Department of Computer Science
José Villaveces: Max Planck Institute of Biochemistry and Computational Biology
Bianca Habermann: Max Planck Institute of Biochemistry and Computational Biology
Asifa Akhtar: Max Planck Institute of Immunobiology and Epigenetics
Thomas Manke: Max Planck Institute of Immunobiology and Epigenetics

Nature Communications, 2018, vol. 9, issue 1, 1-15

Abstract: 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 .

Date: 2018
References: Add references at CitEc
Citations: View citations in EconPapers (1)

Downloads: (external link)
https://www.nature.com/articles/s41467-017-02525-w Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-017-02525-w

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-017-02525-w

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().