Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements

Area of Science:

• Genomics
• Cancer Biology
• Molecular Endocrinology

Background:

• Three-dimensional (3D) genome interactions and regulatory elements are crucial for gene expression.
• Alterations in 3D genome structure are common in cancer, yet their functional impact on gene regulation is context-dependent.
• Estrogen receptor alpha (ER) signaling plays a key role in endometrial cancer.

Purpose of the Study:

• To investigate how estrogen treatment affects 3D genome interactions in endometrial cancer cells.
• To determine the relationship between altered 3D genome interactions, estrogen receptor binding sites, and gene expression changes.
• To functionally assess the role of specific regulatory regions in estrogen-mediated transcriptional responses.

Main Methods:

• HiChIP was employed to map 3D genome interactions in endometrial cancer cells upon estrogen treatment.
• Estrogen receptor alpha-bound sites (ERBSs) were identified and analyzed for their involvement in differential chromatin loops.
• CRISPR-based Enhancer-i technology was used to functionally perturb specific ERBSs.

Main Results:

• Estrogen treatment induced significant differential long-range interactions, enriched for ERBSs.
• ERBSs involved in differential chromatin loops showed a correlation with larger transcriptional responses to estrogen.
• Deactivation of ERBSs using Enhancer-i demonstrated varied effects on estrogen-induced transcription, with no significant enhancement for those in differential loops.
• Enrichment of 3D genome interactions between promoters of estrogen-upregulated genes was observed, suggesting cooperative promoter activity.

Conclusions:

• Estrogen treatment induces substantial changes in 3D genome architecture in endometrial cancer cells.
• While altered 3D genome interactions involving ERBSs correlate with gene expression changes, these structural modifications are not strictly required for regulatory regions to mediate estrogen responses.
• Cooperative interactions between looped promoters contribute to estrogen-driven gene expression.