Chromosome Structure II: Stem-loops and circle-loops

Abstract

AbstractThe chromosomes in multicellular eukaryotes are organized into a series of topologically independent loops called TADs. In flies, TADs are formed by physical interactions between neighboring boundaries. Fly boundaries exhibit distinct partner preferences, and pairing interactions between boundaries are typically orientation dependent. Pairing can be head-to-tail or head-to-head. The former generates a stem-loop TAD, while the latter gives a circle-loop TAD. The TAD that encompasses theDrosophila even skipped(eve) gene is formed by the head-to-tail pairing of thenhomieandhomieboundaries. To explore the relationship between loop topology and the physical and regulatory landscape, we flanked thenhomieboundary region with two attP sites. The attP sites were then used to generate four boundary replacements:λ DNA, nhomie forward(WT orientation),nhomie reverse(opposite of WT), andhomie forward(same as WThomie). Thenhomie forwardreplacement restores the WT physical and regulatory landscape: In MicroC experiments, theeveTAD is a volcano triangle topped by a plume, and theevegene and its regulatory elements are sequestered from interactions with neighbors. Theλ DNAreplacement lacks boundary function: the endpoint of the “new”eveTAD on thenhomieside is ill-defined, andevestripe enhancers activate a nearby gene,eIF3j.Whilenhomie reverseandhomie forwardrestore theeveTAD, the topology is a circle-loop, and this changes the local physical and regulatory landscape. In MicroC experiments, theeveTAD interacts with its neighbors, and the plume at the top of theevevolcano triangle is replaced by a cloud of contacts with the next-door TADs. Consistent with the loss of isolation afforded by the stem-loop topology, theeveenhancers weakly activate genes in the neighboring TADs. Conversely,evefunction is partially disrupted.