Genome access is transcription factor-specific and defined by nucleosome position

Area of Science:

• Molecular Biology
• Genetics
• Epigenetics

Background:

• Gene expression in mammals is regulated by transcription factors (TFs) binding specific DNA sequences.
• Nucleosomes, the basic units of chromatin, can limit TF access to DNA, but their precise impact on individual TFs is not fully understood.
• Understanding TF-nucleosome interactions is crucial for deciphering gene regulation in the context of a compacted genome.

Purpose of the Study:

• To systematically measure the DNA-binding capabilities of over one hundred transcription factor motifs within a chromatinized genome.
• To investigate how nucleosome positioning influences the binding affinity and accessibility of various transcription factors.
• To classify transcription factors based on their distinct strategies for engaging DNA motifs within or around nucleosomes.

Main Methods:

• Utilized a defined chromosomal locus in mouse embryonic stem cells to assay the recruitment of over one hundred transcription factor motifs.
• Quantified TF binding efficiency to motifs located in nucleosome-free, entry-exit, and internal nucleosomal sites.
• Employed nucleosome phasing techniques to precisely position nucleosomes relative to TF binding motifs.

Main Results:

• Identified a core set of transcription factors capable of binding DNA motifs within chromatin, exhibiting diverse tissue specificities, functions, and DNA-binding domains.
• Demonstrated that pluripotency factors OCT4-SOX2 preferentially bind to non-nucleosomal and nucleosome entry-exit sites, avoiding nucleosome-internal regions.
• Revealed that other factors, including BANP, REST, and CTCF, can bind to nucleosome-internal sites, often causing nucleosome displacement.

Conclusions:

• Transcription factor sensitivity to nucleosomes varies significantly, impacting their ability to access DNA motifs.
• Nucleosome position is a critical determinant of transcription factor binding and genome accessibility.
• TF-specific mechanisms for overcoming or utilizing nucleosome barriers contribute to the precise regulation of gene expression in the cell.