Ecdysone-Induced 3D Chromatin Reorganization Involves Active Enhancers Bound by Pipsqueak and Polycomb

Area of Science:

• Genomics
• Molecular Biology
• Developmental Biology

Background:

• Polycomb (Pc) proteins are implicated in chromatin loop anchors in Drosophila.
• Pipsqueak (Psq) is a GAGA binding factor involved in DNA recruitment.
• The psq gene has known roles in development and tumorigenesis.

Purpose of the Study:

• To investigate the role of distinct Psq isoforms in Drosophila genome 3D architecture.
• To understand how Psq variants interact with Polycomb and chromatin loop anchors.
• To elucidate the function of Psq in hormone-induced chromatin remodeling.

Main Methods:

• HiChIP in Drosophila cells to map genome-wide interactions.
• Analysis of Psq isoforms, including those with and without the BTB domain.
• Investigating chromatin changes upon ecdysone hormone stimulation.

Main Results:

• The BR-C, ttk, and bab domain (BTB)-containing Psq isoform (Psq^L) colocalizes with architectural proteins genome-wide.
• Psq lacking the BTB domain (Psq^S) localizes to Pc loop anchors and active enhancers.
• Ecdysone stimulation alters 3D genome organization, connecting promoters and enhancers bound by Psq^S.

Conclusions:

• Psq encodes distinct isoforms with novel roles in 3D genome organization.
• Psq^S variants are linked to Polycomb-bound active enhancers.
• These findings reveal Psq's molecular function in hormone-responsive chromatin dynamics.