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 regulate gene expression and are frequently altered in cancer.
• The precise role of 3D genome interaction changes in differential gene expression is context-dependent.
• Estrogen signaling is a key driver in many endometrial cancers.

Purpose of the Study:

• To investigate how estrogen treatment remodels 3D genome interactions in endometrial cancer cells.
• To determine the relationship between altered 3D genome interactions, estrogen receptor binding, and gene expression changes.
• To functionally assess the necessity of differential 3D genome interactions for estrogen-mediated transcriptional regulation.

Main Methods:

• Utilized HiChIP to map genome-wide chromatin interactions in endometrial cancer cells.
• Analyzed differential long-range interactions enriched for estrogen receptor alpha (ER) bound sites (ERBS).
• Employed CRISPR-based Enhancer-i to deactivate specific ERBS and assess transcriptional effects.

Main Results:

• Identified significant differential long-range chromatin loops upon estrogen treatment, enriched for ERBS.
• ERBS involved in differential loops showed a correlation with larger estrogen-induced transcriptional changes.
• Deactivation of ERBS demonstrated varied impacts on estrogen response, with no significant enhancement for those in differential loops.
• Observed enrichment of 3D interactions between promoters of estrogen-upregulated genes, suggesting cooperative promoter activity.

Conclusions:

• Estrogen treatment induces substantial changes in the 3D genome structure of endometrial cancer cells.
• While altered 3D interactions are associated with ERBS, they are not strictly required for regulatory regions to mediate estrogen transcriptional responses.
• Cooperative interactions between looped promoters may contribute to estrogen-driven gene expression.