Interactions between pluripotency factors specify cis-regulation in embryonic stem cells

Area of Science:

• Molecular Biology
• Genetics
• Developmental Biology

Background:

• Pluripotency transcription factors (TFs) are crucial for maintaining embryonic stem cell (ES cell) identity.
• The precise mechanisms by which TF interactions regulate cis-regulatory elements (CREs) in ES cells are not fully understood.

Purpose of the Study:

• To investigate the impact of interactions between pluripotency TFs on the cis-regulatory activity.
• To develop and validate a model predicting CRE expression based on TF binding site combinations and interactions.

Main Methods:

• Creation of hundreds of synthetic CREs with varying combinations of pluripotency TF binding sites.
• Measurement of CRE expression levels in mouse embryonic stem cells.
• Development of a thermodynamic model incorporating TF-TF interactions to explain expression variance.

Main Results:

• A thermodynamic model accurately predicted 72% of the variance in CRE expression.
• Identified three favorable heterotypic TF interactions and one unfavorable homotypic TF interaction.
• Observed low expression from homotypic TF binding site chains, explained by the unfavorable interaction.
• KLF4 binding site chains showed unique regulatory contributions from KLF homologs.

Conclusions:

• Specific interactions between pluripotency TFs are major determinants of CRE expression levels in ES cells.
• TF-TF interactions, both favorable and unfavorable, are critical for fine-tuning gene regulation during pluripotency.