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Related Experiment Videos

Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences

I Ioshikhes1, A Bolshoy, K Derenshteyn

  • 1Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.

Journal of Molecular Biology
|September 20, 1996
PubMed
Summary

This study analyzed DNA sequences involved in nucleosome formation using five algorithms. AA and TT dinucleotide patterns show periodicity and symmetry, suggesting the central nucleosome DNA may not bend.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Nucleosome formation is crucial for DNA packaging in eukaryotes.
  • Understanding DNA sequence patterns involved in nucleosome formation can reveal insights into genome organization and regulation.
  • Previous studies have explored DNA sequence preferences for nucleosome binding, but detailed patterns remain under investigation.

Purpose of the Study:

  • To identify and characterize DNA sequence patterns, specifically AA and TT dinucleotide distributions, associated with nucleosome formation.
  • To refine these patterns by analyzing multiple algorithms and superimposing their results.
  • To investigate the implications of the identified patterns for nucleosome DNA structure, particularly regarding DNA bending.

Main Methods:

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  • Collected 204 DNA sequences experimentally linked to nucleosome formation.
  • Applied five distinct algorithms for multiple sequence alignment of these DNA sequences within a 145-nucleotide window.
  • Computed positional frequency distributions for AA and TT dinucleotides from the alignments.

    • Main Results:

    • Identified periodicity (10.3 ± 0.2 bases) in both AA and TT dinucleotide positional frequencies.
    • Observed symmetrical distribution of TT dinucleotides relative to AA dinucleotides, centered at the nucleosome core DNA midpoint.
    • Detected a novel absence of central peaks in AA and TT distributions, suggesting a lack of bending in the central 15 bp of nucleosome DNA around the dyad axis.

    Conclusions:

    • AA and TT dinucleotide patterns exhibit significant periodicity and symmetry within nucleosome core DNA.
    • The absence of central peaks in these patterns indicates that the DNA region around the nucleosome's dyad axis may be relatively straight.
    • These findings contribute to a refined understanding of DNA sequence determinants in nucleosome structure and function.