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

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.

Chromatin Architecture in the Fly: Living without CTCF/Cohesin Loop Extrusion?

“…Whereas the lack of CTCF is embryonic lethal in mammals, in Drosophila CTCF null mutants (completely lacking both maternal and zygotic CTCF) survive past the larval stage and die as late pupae with visible defects associated with Hox gene misexpression . Although Drosophila CTCF is clearly linked to functional regulatory domains in the Hox complexes, it is generally only weakly enriched at TAD boundaries . A recent paper suggests that CTCF may have a specific role in certain differentiated cell types as this study found a stronger enrichment of CTCF at TAD borders in a cell line derived from larval central nervous system than in Kc167 cells originally derived from embryos .…”

“…A recent paper suggests that CTCF may have a specific role in certain differentiated cell types as this study found a stronger enrichment of CTCF at TAD borders in a cell line derived from larval central nervous system than in Kc167 cells originally derived from embryos . In addition to CTCF, Drosophila contains a number of less‐conserved insulator binding proteins, such as Chromator and boundary element associated factor of 32 kD (BEAF‐32), that are much more highly enriched at TAD boundaries and appear to serve a more general architectural function …”

“… Drosophila interaction domain profile. a) A 2 Mb region (chrom2L: 10 000 000–12 000 000) illustrating the correspondence between interaction profile and chromatin domain maps; D (green)/E (blue) domains, originally derived from primary spermatocyte data, A (green)/ B (blue) compartments from Kc167 cells, Kc167 cell Hi‐C interaction profile from Ramírez et al b) Portion of Drosophila polytene chromosome showing bands and interbands. Image reproduced with permission from Cell Image Library doi:10.7295/W9CIL25393.…”

“…This figure also illustrates different TAD hierarchies; the large TAD on the right, comprising an A compartment region, is further subdivided into minidomains (see Section and Figure ), whilst the large TAD on the left shows at least three levels of progressively larger domains, encompassing both A and B compartment regions. Hi‐C from Kc167 cells, A compartments from Kc167 cells, BEAF‐32 ChIP from Kc167 cells (ModENCODE GSM1535963), housekeeping genes from El‐Sharnouby et al and the FISH probe from Szabo et al ChIP, chromatin immunoprecipitation.…”

“…Insulators have long been proposed as major determinants of the regulatory architecture of the genome . Although binding profiles of architectural proteins such as Chromator, BEAF‐32, and Z4/Putzig show a strong correlation with domain architecture, only BEAF‐32 has been directly tested for a role in domain organization . Knockdown of BEAF‐32 by RNA interference in Drosophila S2 cells showed no change in the global Hi‐C interaction profile.…”