Boundaries mediate long-distance interactions between enhancers and promoters in the Drosophila Bithorax complex

Postika, Nikolay; Metzler, Mario; Affolter, Markus; Müller, Martin; Schedl, Paul; Georgiev, Pavel; Kyrchanova, Olga

doi:10.1371/journal.pgen.1007702

Cited by 38 publications

(53 citation statements)

References 81 publications

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“…In this position, a boundary must be able to block cross-talk between iab-4 and iab-5 but does not need bypass activity. Consistent with this expectation, in Mcp replacement experiments, multimerized dCTCF sites have fully substituted for Mcp (48). In contrast, neither Fab-7 or Fab-8 functions appropriately in this genomic context.…”

Section: Resultsmentioning

confidence: 59%

“…While both block cross-talk between iab-4 and iab-5, they also actively promote productive interactions between enhancers in the abd-A regulatory domain iab-4 and the Abd-B gene. Consequently, Abd-B is ectopically activated in A4 (PS9), a segment in which it should remain silent (48).…”

Section: Resultsmentioning

confidence: 99%

“…the endogenous Fab-7 or Fab-8 boundaries, then it also should promote regulatory interactions between iab-4 and Abd-B when substituted for Mcp. To test this, we used a Mcp replacement platform, Mcp attP (48). In this platform, the 789 bp of the Mcp boundary was replaced with an eGFP reporter flanked by two attP sites for phiC31 recombination (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…However, subsequent studies showed that these elements are not required for bypassing either Fab-7 or Fab-8 (28). Instead, bypass activity in the context of the Abd-B regulatory region appears to be an intrinsic property of these two boundaries, a property not shared by boundaries from elsewhere in the fly genome, including the BX-C boundary Mcp (48).…”

Section: Discussionmentioning

confidence: 99%

“…While most of these boundaries blocked cross-talk between iab-6 and iab-7, only Fab-8 could support bypass. It was initially thought that Fab-7 and Fab-8 differed from other boundaries by being "permissive" for bypass; however, recent experiments in which Mcp was replaced by Fab-7 or Fab-8 indicate that both boundaries actively promote interactions between enhancers in distal regulatory domains and the Abd-B gene (48). Thus, these two BX-C boundaries are able to perform two seemingly opposite functions: blocking cross-talk between neighboring regulatory domains, while at the same time actively facilitating long-distance communication between these domains and their gene targets.…”

Section: Significancementioning

confidence: 99%

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Complete reconstitution of bypass and blocking functions in a minimal artificialFab-7insulator fromDrosophila bithoraxcomplex

Kyrchanova

Sabirov

Mogila

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Boundaries in the bithorax complex (BX-C) delimit autonomous regulatory domains that drive parasegment-specific expression of the Hox genes Ubx, abd-A, and Abd-B. The Fab-7 boundary is located between the iab-6 and iab-7 domains and has two key functions: blocking cross-talk between these domains and at the same time promoting communication (boundary bypass) between iab-6 and the Abd-B promoter. Using a replacement strategy, we found that multimerized binding sites for the architectural proteins Pita, Su(Hw), and dCTCF function as conventional insulators and block cross-talk between the iab-6 and iab-7 domains; however, they lack bypass activity, and iab-6 is unable to regulate Abd-B. Here we show that an ∼200-bp sequence of dHS1 from the Fab-7 boundary rescues the bypass defects of these multimerized binding sites. The dHS1 sequence is bound in embryos by a large multiprotein complex, Late Boundary Complex (LBC), that contains the zinc finger proteins CLAMP and GAF. Using deletions and mutations in critical GAGAG motifs, we show that bypass activity correlates with the efficiency of recruitment of LBC components CLAMP and GAF to the artificial boundary. These results indicate that LBC orchestrates long-distance communication between the iab-6 regulatory domain and the Abd-B gene, while the Pita, Su(Hw), and dCTCF proteins function to block local cross-talk between the neighboring regulatory domains iab-6 and iab-7.

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Section: Resultsmentioning

confidence: 59%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Significancementioning

confidence: 99%

See 3 more Smart Citations

Complete reconstitution of bypass and blocking functions in a minimal artificialFab-7insulator fromDrosophila bithoraxcomplex

Kyrchanova

Sabirov

Mogila

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Polycomb Repressive Complexes in Hox Gene Regulation: Silencing and Beyond

Gentile

Kmita

2020

BioEssays

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The coordinated expression of the Hox gene family encoding transcription factors is critical for proper embryonic development and patterning. Major efforts have thus been dedicated to understanding mechanisms controlling Hox expression. In addition to the temporal and spatial sequential activation of Hox genes, proper embryonic development requires that Hox genes get differentially silenced in a cell-type specific manner as development proceeds. Factors contributing to Hox silencing include the polycomb repressive complexes (PRCs), which control gene expression through epigenetic modifications. This review focuses on PRC-dependent regulation of the Hox genes and is aimed at integrating the growing complexity of PRC functional properties in the context of Hox regulation. In particular, mechanisms underlying PRC binding dynamics as well as a series of studies that have revealed the impact of PRC on the 3D organization of the genome is discussed, which has a significant role on Hox regulation during development.

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CRISPR/Cas9 and FLP-FRT mediated regulatory dissection of the BX-C of Drosophila melanogaster

2023

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The Homeotic genes or Hox de ne the anterior-posterior (AP) body axis formation in bilaterians and are often present on the chromosome in an order which is collinear to their function across the AP axis. However, there are many cases wherein the Hox are not collinear, but their expression pattern is conserved across the AP axis. The expression pattern of Hoxis attributed to the cis-regulatory modules (CRMs) consisting of enhancers, initiators, or repressor elements that together regulate the genes in a segment-speci c manner. In the Drosophila melanogaster Hoxcomplex, the bithorax complex (BX-C), even the CRMs are organized in an order that is collinear to their function in the thoracic and abdominal segments. In the present study, we performed in-silico analysis of the available ChIP data followed by systematic curation of experimentally validated regions of the BX-C gene, Abd-B, to generate functionally relevant map of the regulatory landscape. Next, the regulatorily inert regions were targeted using CRISPR/Cas9 to generate a series of transgenic lines with the insertion of FRT sequences. Further, these FRT lines are repurposed to shu e the CRMs associated with Abd-B to generate modular deletion, duplication, or inversion of multiple CRMs. The rearrangements yielded entirely novel phenotypes in the y suggesting the requirement of such complex manipulations to address the signi cance of higher order arrangement of the CRMs. The functional map and the transgenic ies generated in this study are important resource to decipher the collective ability of multiple regulatory elements in eukaryotic genome to function as complex modules.

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Boundaries mediate long-distance interactions between enhancers and promoters in the Drosophila Bithorax complex

Cited by 38 publications

References 81 publications

Complete reconstitution of bypass and blocking functions in a minimal artificialFab-7insulator fromDrosophila bithoraxcomplex

Complete reconstitution of bypass and blocking functions in a minimal artificialFab-7insulator fromDrosophila bithoraxcomplex

Polycomb Repressive Complexes in Hox Gene Regulation: Silencing and Beyond

CRISPR/Cas9 and FLP-FRT mediated regulatory dissection of the BX-C of Drosophila melanogaster

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