3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription

Abstract

In mammals, insulators contribute to the regulation of loop extrusion to organize chromatin into topologically associating domains. In Drosophila the role of insulators in 3D genome organization is, however, under current debate. Here, we addressed this question by combining bioinformatics analysis and multiplexed chromatin imaging. We describe a class of Drosophila insulators enriched at regions forming preferential chromatin interactions genome-wide. Notably, most of these 3D interactions do not involve TAD borders. Multiplexed imaging shows that these interactions occur infrequently, and only rarely involve multiple genomic regions coalescing together in space in single cells. Finally, we show that non-border preferential 3D interactions enriched in this class of insulators are present before TADs and transcription during Drosophila development. Our results are inconsistent with insulators forming stable hubs in single cells, and instead suggest that they fine-tune existing 3D chromatin interactions, providing an additional regulatory layer for transcriptional regulation.

The N-Terminal Part of Drosophila CP190 Is a Platform for Interaction with Multiple Architectural Proteins

“…The binding of CP190/Z4/Chro to regulatory elements results in the attraction of transcriptional com-plexes and, as a result, in switching on of regulatory elements. There are also a number of experimental data indicating that CP190/Z4/Chro can also participate in the organization of TADs and distance interactions between regulatory elements [51,[98][99][100]. The CP190, Z4, and Chro proteins, by interacting with each other and homodimerizing, can support long-distance interactions between housekeeping gene clusters, which often form TAD boundaries [4].…”

PRE loops constitute a topological chromatin structure that restricts and specifies enhancer promoter communication

“…The procedure for oligopaint library amplification was previously described 22,29,41,42 . It consists Each barcode is unique and specific to an adapter oligo.…”