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Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
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Universal full-length nucleosome mapping sequence probe.

Vijay Tripathi1, Bilal Salih, Edward N Trifonov

  • 1a Genome Diversity Center, Institute of Evolution, University of Haifa , Mount Carmel, Haifa 31905 , Israel.

Journal of Biomolecular Structure & Dynamics
|March 11, 2014
PubMed
Summary

Researchers identified strong nucleosome (SN) DNA sequences, revealing a universal [R,Y] consensus pattern. This pattern aids in understanding DNA bendability for nucleosome positioning and computational mapping.

Keywords:
RR/YY probematrix of bendabilitynucleosome positioningnucleosome probestrong nucleosome

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Area of Science:

  • Genomics
  • Computational Biology
  • Biophysics

Background:

  • Nucleosome positioning is crucial for DNA regulation.
  • Existing methods using motifs and bendability matrices are insufficient for full DNA sequence reconstruction.
  • Strong nucleosome (SN) DNA sequences exhibit periodicity, enabling better pattern derivation.

Purpose of the Study:

  • To derive a full-length DNA bendability pattern for nucleosomes.
  • To establish a universal consensus sequence for nucleosome DNA.
  • To improve computational sequence-directed mapping of nucleosomes.

Main Methods:

  • Alignment of 512 SN sequences from A. thaliana, C. elegans, and H. sapiens.
  • Derivation of 115-dinucleotide long bendability matrices for each species.
  • Analysis of dinucleotide composition and periodicity within SN sequences.

Main Results:

  • Identified a common property in bendability matrices: alternation of purine-purine (RR) and pyrimidine-pyrimidine (YY) dinucleotide runs.
  • Determined an average period of 10.4 bases for these alternations.
  • Derived a universal [R,Y] consensus sequence for nucleosome DNA, pinpointing specific penta- and hexamers.

Conclusions:

  • The universal [R,Y] consensus sequence provides a refined model for nucleosome DNA.
  • This finding enhances the understanding of DNA bendability and sequence-directed nucleosome organization.
  • The derived consensus sequence can improve computational tools for nucleosome mapping.