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Drosophila Rumpelstiltskin alters Polycomb chromatin association and maintains proper 3D genome organization and barrier activity of the Homie insulator [ChIP-Seq]

ABSTRACT: Three-dimensional genome organization is maintained in part by chromatin insulators, DNA-protein complexes that create boundaries between active and inactive chromatin and regulate enhancer-promoter interactions. In Drosophila, the Homing insulator at eve (Homie) sequence prevents repressive Polycomb (PcG) chromatin at even-skipped (eve) from spreading into the neighboring essential gene, TER94. Use of an in vivo reporter assay identified the requirement of the hnRNP M homolog, Rumpelstiltskin (Rump), for Homie barrier activity. Interestingly, Rump depletion resulted in no changes to chromatin insulator protein binding at Homie but extensive chromatin association changes to the Polycomb response element (PRE)-associated protein Crooked legs (Crol) at Crol-bound PREs. Furthermore, global chromatin association changes were detected for a subset of Polycomb repressive complex 1 and 2 (PRC1 and PRC2) components. Finally, we observed increased cis-compaction within the eve PcG domain and increased distances between eve and other PcG domains in trans after Rump depletion. These data suggest a regulatory role of Rump for both cis and trans interactions of PcG proteins, likely promoting Homie barrier activity independently of chromatin insulator proteins.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE308569 | GEO | 2026/07/21

REPOSITORIES: GEO

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Drosophila Rumpelstiltskin alters Polycomb chromatin association and maintains proper 3D genome organization and barrier activity of the Homie insulator [RNA-Seq]

Project description:Three-dimensional genome organization is maintained in part by chromatin insulators, DNA-protein complexes that create boundaries between active and inactive chromatin and regulate enhancer-promoter interactions. In Drosophila, the Homing insulator at eve (Homie) sequence prevents repressive Polycomb (PcG) chromatin at even-skipped (eve) from spreading into the neighboring essential gene, TER94. Use of an in vivo reporter assay identified the requirement of the hnRNP M homolog, Rumpelstiltskin (Rump), for Homie barrier activity. Interestingly, Rump depletion resulted in no changes to chromatin insulator protein binding at Homie but extensive chromatin association changes to the Polycomb response element (PRE)-associated protein Crooked legs (Crol) at Crol-bound PREs. Furthermore, global chromatin association changes were detected for a subset of Polycomb repressive complex 1 and 2 (PRC1 and PRC2) components. Finally, we observed increased cis-compaction within the eve PcG domain and increased distances between eve and other PcG domains in trans after Rump depletion. These data suggest a regulatory role of Rump for both cis and trans interactions of PcG proteins, likely promoting Homie barrier activity independently of chromatin insulator proteins.

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