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Updated: Jan 29, 2026

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Published on: May 26, 2013

Shortest paths through synonymous genomes.

Martijn Zuiddam¹, Helmut Schiessel¹

¹Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, the Netherlands.

Physical Review. E

|February 21, 2019

Summary

This summary is machine-generated.

DNA sequence elasticity influences nucleosome packaging, affecting gene regulation. Researchers used graph algorithms to map DNA bending, finding mechanical cues can position nucleosomes genome-wide in yeast.

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Area of Science:

Genomics
Biophysics
Computational Biology

Background:

DNA elasticity varies with base pair sequence.
DNA packaging into nucleosomes is crucial for biological processes like gene regulation.
Nucleosomes influence DNA packaging, affecting gene regulation, recombination, replication, and chromosome condensation.

Purpose of the Study:

To investigate how DNA sequence-derived mechanical cues influence nucleosome packaging.
To develop a method for predicting DNA bending within nucleosomes.
To explore the potential for mechanical information to guide nucleosome placement across a genome.

Main Methods:

Representing DNA sequences as graphs.
Applying shortest path algorithms to quantify DNA bending.
Analyzing graphs of synonymous codons to multiplex genetic and mechanical information.
Mapping nucleosome placement based on mechanical cues in Saccharomyces cerevisiae.

Main Results:

Identified specific DNA stretches that are easily or difficult to bend within nucleosomes.
Demonstrated the multiplexing of genetic and mechanical information through codon graphs.
Found that mechanical cues can direct nucleosome placement across most of the baker's yeast genome.

Conclusions:

DNA sequence-dependent elasticity provides mechanical cues for nucleosome positioning.
Computational methods, like graph theory and shortest path algorithms, can predict DNA bending and nucleosome placement.
Mechanical information plays a significant role in genome-wide nucleosome organization in Saccharomyces cerevisiae.