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In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy
Published on: September 6, 2024
"Anticipated" nucleosome positioning pattern in prokaryotes
Alexandra E Rapoport1, Edward N Trifonov
1Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel.
Gene
|September 3, 2011
Summary
Hidden DNA motifs in A+T rich prokaryotic genomes, identified using Shannon N-gram analysis, suggest ancient origins for nucleosome positioning patterns. These findings may indicate early DNA-protein binding mechanisms in prokaryotes.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Evolution
Background:
- Prokaryotic genomes are predominantly protein-coding.
- Hidden sequence motifs in DNA can reveal functional or structural patterns.
- Nucleosome positioning patterns are known in eukaryotes.
Purpose of the Study:
- To identify dominant hidden sequence motifs in A+T rich prokaryotic genomes.
- To explore the potential functional and evolutionary implications of these motifs.
Main Methods:
- Linguistic (word count) analysis of prokaryotic genome sequences.
- Shannon N-gram extension for motif discovery.
Main Results:
- Identified dominant hidden motifs T(A)(T)A and G(A)(T)C in A+T rich prokaryotic genomes.
- These motifs may correspond to amphipathic alpha-helices with specific amino acid patterns.
- Similar motifs are recognized as nucleosome positioning patterns in eukaryotes.
Conclusions:
- The presence of these motifs in prokaryotes suggests they may bind histone-like proteins.
- These patterns could represent "anticipated" nucleosome positioning patterns predating eukaryotic-prokaryotic divergence.
- This implies ancient origins for DNA-protein interactions related to genome organization.
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