Evidence of selection for an accessible nucleosomal array in human

Area of Science:

• Genomics
• Epigenetics
• Molecular Biology

Background:

• A physical model of DNA bending properties predicts nucleosome formation.
• Nucleosome-inhibiting energy barriers (NIEBs) are enriched near human replication origins.

Purpose of the Study:

• To predict the genomic distribution of NIEBs using a biophysical model.
• To investigate the in vivo and in vitro characteristics of NIEBs and their genomic impact.

Main Methods:

• Utilized a biophysical model of DNA sequence-dependent bending to predict NIEBs.
• Analyzed nucleosome occupancy, GC content, and mutation profiles in relation to NIEBs.
• Compared divergence rates to infer selection pressures.

Main Results:

• Predicted approximately 1.6 million NIEBs across human autosomes, corresponding to nucleosome-depleted regions (NDRs).
• Observed ordered nucleosome structures flanking NIEBs, correlating with GC content and mutation patterns.
• NIEBs and associated nucleosomes cover 37.5% of the genome, indicating stable sequence-encoded nucleosome positioning.

Conclusions:

• NIEBs and ordered nucleosomes represent a significant, sequence-encoded feature of the human genome.
• Selection pressures act on these regions, influencing mutation and divergence rates.
• These patterns may play a role in regulating chromatin condensation and epigenetic processes.