ArticleNature communications2018
High-resolution TADs reveal DNA sequences underlying genome organization in flies.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 654 papers.
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654 citing papers in PubMed.
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- Chromosomal inversions modulate 3D chromatin interactions and regulatory architecture inResearch square · 2026Article
- Sequential-GAM constructs the single-cell geometric 3D genome structure.Nucleic acids research · 2026Article
- 3D genome organization in tissue regeneration involves long-range chromatin loops.Science advances · 2026Article
- Drosophila Rumpelstiltskin regulates Polycomb cis and trans interactions and Homie barrier activity.Epigenetics & chromatin · 2026Article
594 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
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 .
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