The insulating activity of the<i>Drosophila</i>BX-C chromatin boundary<i>Fub-1</i>is parasegmentally regulated by lncRNA read-through

Ibragimov, A. N.; Bing, Xin Yang; Shidlovskii, Yulii V.; Levine, Michael; Georgiev, Pavel; Schedl, Paul

doi:10.1101/2022.11.13.516321

Cited by 4 publications

(5 citation statements)

References 55 publications

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“…PRE pairing in cis typically takes place within the context of a larger chromosomal domain, or TAD. In contrast, boundary elements are responsible for defining the endpoints of these looped domains (Arzate-Mejía et al 2020;Batut et al 2022;Bing et al 2024;Chetverina et al 2017;Ibragimov et al 2023;Stadler et al 2017). While not much is known about the parameters governing PRE pairing, the pairing interactions of fly boundaries have been studied in some detail.…”

Section: Discussionmentioning

confidence: 99%

Chromosome Structure II: Stem-loops and circle-loops

Ke,

Fujioka,

Schedl

et al. 2024

Preprint

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The 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.

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Section: Discussionmentioning

confidence: 99%

Chromosome Structure II: Stem-loops and circle-loops

Ke,

Fujioka,

Schedl

et al. 2024

Preprint

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“…While our experimental paradigm is artificial, there are contexts in which transcriptional readthrough provides a mechanism for coordinating higher order chromosome organization with regulating gene activity. For example, the blocking activity of the Fub-1 boundary is turned off by readthrough of a lncRNA from a promoter that is activated by the Ubx regulatory domain bxd/pbx [62] in PS6/A1 and more posterior parasegments. Inactivation of the Fub-1 boundary enables enhancers in the bxd/pbx domain to regulate Ubx expression.…”

Section: Discussionmentioning

confidence: 99%

Transcriptional read through interrupts boundary function in Drosophila

Georgiev

Kyrchanova

Sokolov

et al. 2023

Preprint

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In higher eukaryotes enhancer-promoter interactions are known to be restricted by the chromatin insulators/boundaries that delimit topologically associated domains (TADs); however, there are instances in which enhancer-promoter interactions span one or more boundary elements/TADs. At present, the mechanisms that enable cross-TAD regulatory interaction are not known. In the studies reported here we have taken advantage of the well characterized Drosophila Bithorax complex (BX-C) to study one potential mechanism for controlling boundary function and TAD organization. The regulatory domains of BX-C are flanked by boundaries which function to block crosstalk with their neighboring domains and also to support long distance interactions between the regulatory domains and their target gene. As many lncRNAs have been found in BX-C, we asked whether transcriptional readthrough can impact boundary function. For this purpose, we took advantage of two BX-C boundary replacement platforms, Fab-7attP50 and F2attP, in which the Fab-7 and Fub boundaries, respectively, are deleted and replaced with an attP site. We introduced boundary elements, promoters and polyadenylation signals arranged in different combinations and then assayed for boundary function. Our results show that transcriptional readthrough can interfere with boundary activity. Since lncRNAs represent a significant fraction of Pol II transcripts in multicellular eukaryotes, it is possible that many of them may function in the regulation of TAD organization.

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“…While our experimental paradigm is artificial, there are contexts in which RT provides a mechanism for coordinating higher-order chromosome organization with regulating gene activity. For example, the blocking activity of the Fub-1 boundary is turned off by RT of a lncRNA from a promoter that is activated by the Ubx regulatory domain bxd/pbx [64] in PS6/A1 and more posterior parasegments. Inactivation of the Fub-1 boundary enables enhancers in the bxd/pbx domain to regulate Ubx expression.…”

Section: Discussionmentioning

confidence: 99%

Transcriptional Readthrough Interrupts Boundary Function in Drosophila

Kyrchanova

Sokolov

Tikhonov

et al. 2023

IJMS

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In higher eukaryotes, distance enhancer-promoter interactions are organized by topologically associated domains, tethering elements, and chromatin insulators/boundaries. While insulators/boundaries play a central role in chromosome organization, the mechanisms regulating their functions are largely unknown. In the studies reported here, we have taken advantage of the well-characterized Drosophila bithorax complex (BX-C) to study one potential mechanism for controlling boundary function. The regulatory domains of BX-C are flanked by boundaries, which block crosstalk with their neighboring domains and also support long-distance interactions between the regulatory domains and their target gene. As many lncRNAs have been found in BX-C, we asked whether readthrough transcription (RT) can impact boundary function. For this purpose, we took advantage of two BX-C boundary replacement platforms, Fab-7attP50 and F2attP, in which the Fab-7 and Fub boundaries, respectively, are deleted and replaced with an attP site. We introduced boundary elements, promoters, and polyadenylation signals arranged in different combinations and then assayed for boundary function. Our results show that RT can interfere with boundary activity. Since lncRNAs represent a significant fraction of Pol II transcripts in multicellular eukaryotes, it is therefore possible that RT may be a widely used mechanism to alter boundary function and regulation of gene expression.

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The insulating activity of theDrosophilaBX-C chromatin boundaryFub-1is parasegmentally regulated by lncRNA read-through

Cited by 4 publications

References 55 publications

Chromosome Structure II: Stem-loops and circle-loops

Chromosome Structure II: Stem-loops and circle-loops

Transcriptional read through interrupts boundary function in Drosophila

Transcriptional Readthrough Interrupts Boundary Function in Drosophila

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