Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

Area of Science:

• Genetics and Genomics
• Developmental Biology
• Molecular Biology

Background:

• Gene expression is regulated by transcription factors (TFs) binding to enhancer DNA regions.
• TF binding sites in vivo vary significantly depending on cellular or developmental context.
• The underlying cis-regulatory DNA sequence determinants for context-specific TF binding remain largely unknown.

Purpose of the Study:

• To computationally and experimentally investigate the sequence basis of context-specific transcription factor binding.
• To identify predictive cis-regulatory motif combinations that define individual TF binding sites and enhancers.
• To explore the evolutionary conservation of these sequence codes across different organisms.

Main Methods:

• Computational dissection of context-specific TF binding sites across multiple species (Drosophila, C. elegans, mouse, human).
• Identification and analysis of distinct combinations of sequence motifs for partner factors.
• Experimental validation of predicted motif requirements using Drosophila early embryos and the transcription factor Twist.

Main Results:

• Distinct combinations of sequence motifs for partner factors predict context-specific TF binding.
• Vielfaltig (Zelda) motifs were identified as critical for early Drosophila embryo transcription factor binding, including Twist.
• The motif content of cis-regulatory sequences can predict context-specific binding across different Drosophila species, indicating conserved motif codes.

Conclusions:

• Context-specific TF binding is encoded by characteristic combinations of sequence motifs, termed cis-regulatory signatures.
• These signatures are evolutionarily conserved and can be used to predict TF binding requirements.
• The developed approach offers a generalizable method to identify cis-regulatory sequence determinants and cognate TFs from binding data across diverse cell types and organisms.