Selection for ancient periodic motifs that do not impart DNA bending

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• A ~10-11 base pair (bp) dinucleotide periodicity was hypothesized to aid DNA compaction, with variations linked to DNA supercoiling.
• This hypothesis is challenged by inconsistent period variations across different organism growth temperatures.

Purpose of the Study:

• To investigate the drivers of dinucleotide periodicity in genomes.
• To determine if dinucleotide periodicity is shaped by selection or mutational biases.
• To explore the evolutionary conservation and variation of dinucleotide periodicity across life.

Main Methods:

• Analysis of dinucleotide periodicity across diverse genomes using robust computational methods.
• Comparison of periodicity patterns with phylogenetic distance and growth temperatures.
• Identification of selected dinucleotides and core periodic motifs.

Main Results:

• Dinucleotide periodicity is under selection, not solely mutational bias.
• Period length and the specific periodic dinucleotides vary significantly between genomes.
• Period differences increase with phylogenetic distance, while a core set of periodic dinucleotides is conserved across all domains of life.
• The conserved periodic motifs are not involved in DNA bending.

Conclusions:

• Dinucleotide periodicity represents an ancient genomic architecture.
• This ancient architecture may play a significant role in shaping gene and genome evolution.
• The findings challenge previous hypotheses linking periodicity solely to DNA bending and compaction.