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Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [Capture-C]

ABSTRACT: While Drosophila has widespread contact domains, most domain boundaries are formed independently of CTCF by unclear mechanisms. We genetically ablate the ubiquitous boundary-associated factor Cp190 and examine impacts on genome folding and developmental gene regulation in Drosophila embryos. We find that Cp190 is widely required to form fly domain boundaries that are distal from transcribed gene promoters, while promoter proximal boundaries are unaffected by Cp190 loss.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE193530 | GEO | 2022/05/12

REPOSITORIES: GEO

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Essential role of Cp190 in physical and regulatory boundary formation in Drosophila

Project description:Animal genomes fold into contact domains defined by enhanced internal contact frequencies with debated functions in establishing independent gene regulatory domains. A large fraction of contact domains in mammals are formed by stalling of chromosomal loop-extruding cohesin by CTCF at domain boundaries. 90% of domain boundaries in Drosophila form CTCF-independently, and other proteins were proposed to form chromosomal loops with dual functions of segregating promoters from inappropriate regulatory elements and connecting distal regulatory elements to their correct targets. Here, we genetically ablate the ubiquitous boundary-associated factor Cp190 and assess impacts on genome folding and transcriptional regulation in embryos. Our results reveal that Cp190 is a major factor required for contact domain boundary formation and gene insulation in Drosophila.

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Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [HiC]

Project description:While Drosophila has widespread contact domains, most domain boundaries are formed independently of CTCF by unclear mechanisms. We genetically ablate the ubiquitous boundary-associated factor Cp190 and examine impacts on genome folding and developmental gene regulation in Drosophila embryos. We find that Cp190 is widely required to form fly domain boundaries that are distal from transcribed gene promoters, while promoter proximal boundaries are unaffected by Cp190 loss.

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Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [ChIP-seq]

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Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [Capture-C]

Project description:Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [Capture-C]

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Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogaster

Project description:The architectural protein Pita is critical for Drosophila embryogenesis and predominantly binds to gene promoters and insulators. In particular, Pita is involved in the organization of boundaries between regulatory domains, controlled by the expression of three hox genes in the Bithorax complex (BX-C). The best-characterized partner for Pita is the BTB/POZ-domain containing protein CP190. Here, we precisely mapped two unstructured regions of Pita that interact with the BTB domain of CP190. The deletion of the CP190-interacting regions did not significantly affect the binding of the mutant Pita protein to most chromatin sites. The expression of the mutant protein completely complemented the null pita mutation. However, the mutant Pita protein does not support the ability of multimerized Pita sites to prevent cross-talk between the iab-6 and iab-7 regulatory domains that activate the expression of Abdominal-B (Abd-B), one of the genes in the BX-C. The recruitment of the Pita region and the interaction with CP190 and the polytene chromosomes of larvae induces the formation of a new interband, which is a consequence of the formation of open chromatin in this region. These results suggested that the interaction with CP190 is required for the primary Pita activities, but other architectural proteins may also recruit CP190 in flies expressing only the mutant Pita protein.

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New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity [RNA-seq]

Project description:In Drosophila, a group of zinc finger architectural proteins recruits the CP190 protein to the chromatin, an interaction that is essential for the functional activity of promoters and insulators. In this study, we describe a new architectural C2H2 protein called Madf and Zinc-Finger Protein 1 (Mzfp1) that interacts with CP190. Mzfp1 has an unusual structure that includes six C2H2 domains organized in a C-terminal cluster and two tandem MADF domains. Mzfp1 predominantly binds to housekeeping gene promoters located in both euchromatin and heterochromatin genome regions. In vivo mutagenesis studies showed that Mzfp1 is an essential protein, and both MADF domains and the CP190 interaction region are required for its functional activity. The C2H2 cluster is sufficient for the specific binding of Mzfp1 to regulatory elements, while the second MADF domain is required for Mzfp1 recruitment to heterochromatin. Mzfp1 binds to the proximal part of the Fub boundary that separates regulatory domains of the Ubx and abd-A genes in the Bithorax complex. Mzfp1 participates in Fub functions in cooperation with the architectural proteins Pita and Su(Hw). Thus, Mzfp1 is a new architectural C2H2 protein involved in the organization of active promoters and insulators in Drosophila.

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