Essential role of Cp190 in physical and regulatory boundary formation

Abstract

Boundaries in animal genomes delimit contact domains with enhanced internal contact frequencies and have debated functions in limiting regulatory cross-talk between domains and guiding enhancers to target promoters. Most mammalian boundaries form by stalling of chromosomal loop-extruding cohesin by CTCF, but most Drosophila boundaries form CTCF independently. However, how CTCF-independent boundaries form and function remains largely unexplored. Here, we assess genome folding and developmental gene expression in fly embryos lacking the ubiquitous boundary-associated factor Cp190. We find that sequence-specific DNA binding proteins such as CTCF and Su(Hw) directly interact with and recruit Cp190 to form most promoter-distal boundaries. Cp190 is essential for early development and prevents regulatory cross-talk between specific gene loci that pattern the embryo. Cp190 was, in contrast, dispensable for long-range enhancer-promoter communication at tested loci. Cp190 is thus currently the major player in fly boundary formation and function, revealing that diverse mechanisms evolved to partition genomes into independent regulatory domains.

CTCF, BEAF-32 and CP190 are not required for the initial establishment of TADs in early Drosophila embryos, but have locus specific roles

“…each boundary may rely on a specific combination of factors in addition to the surrounding genomic context to function. This is supported by the different sub-sets of boundaries that are more sensitive to depletion of different factors, as we observed here during ZGA and in recent studies at different stages ( 24, 29, 30, 39, 40, 72 ). For example, for the factors depleted here, most disrupted boundaries were genotype-specific.…”

“…Thus, both techniques indicate that removing any of the three insulators impacts btsz domain boundary function, even if these insulators (BEAF-32 and CTCF) are not directly binding at the central domain boundary. A recent study proposed that CP190 acts predominately to insulate the subset (∼20%) of Drosophila boundaries that do not contain an active promoter ( 29 ). At least in the context of ZGA, our data indicates that CP190 can influence insulation at a TAD boundary containing an active promoter, although it is not the only requirement.…”

“…Depletion of both CP190 and Chromator together in BG-3 cells impacted a subset of boundaries with repressive chromatin (H3K27me3), while it had little impact on active regions ( 40 ). Similarly, genetic deletion of CP190 impacted insulation on the subset of Drosophila boundaries (∼23% in Kc cells ( 24 )) that do not contain active promoters, and had little impact on others ( 29 ).…”

Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements

“…As clear from observations presented here and those by Kaushal and co-authors ( 66 ), at many sites co-bound by CTCF and Cp190, the former contributes to Cp190 recruitment to chromatin. Yet, ChIP-seq analysis of sites bound by multiple insulator proteins (e.g.…”

“…This argues that new models, which do not invoke chromatin loops formed by interacting insulator elements, are required to explain the mechanism of insulator action. Broadly similar conclusions were reached by the study of Kaushal and co-authors ( 66 ) who reported the analysis of genome folding in Drosophila embryos deficient for Cp190 and CTCF while this work being prepared for publication.…”