Chromatin-dependent motif syntax defines differentiation trajectories

Area of Science:

• Molecular Biology
• Developmental Biology
• Genomics

Background:

• Transcription factors (TFs) binding DNA motifs regulate cell identity.
• The precise mechanisms governing TF specificity remain incompletely understood.
• Neurogenin-2 (NGN2) and MyoD1 TFs bind similar E-box motifs but induce distinct neuronal and muscle cell fates, respectively.

Purpose of the Study:

• To investigate the factors governing the distinct cell fate choices driven by NGN2 and MyoD1.
• To elucidate the role of chromatin accessibility and DNA motif syntax in TF specificity.
• To develop and apply a machine learning approach for analyzing TF binding dynamics.

Main Methods:

• Monitoring TF binding dynamics during differentiation in mouse embryonic stem cells.
• Utilizing an interpretable machine learning model integrating DNA accessibility data.
• Validating binding predictions through cellular and in vitro assays.

Main Results:

• A chromatin-dependent motif syntax dictates both shared and factor-specific TF binding.
• Shared binding sites are located in open chromatin, influenced by local nucleosome positions.
• Factor-specific binding in closed chromatin involves pioneer factor activity, motif variants, spacing, and interaction partners.

Conclusions:

• TF specificity arises from a combination of opportunistic binding in accessible chromatin and context-specific chromatin opening.
• The interplay of chromatin state, DNA motif characteristics, and protein interactions determines cell differentiation trajectories.
• The developed methodology provides a framework for understanding TF specificity across various biological models.