Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences

Abstract DNA strand asymmetries can have a major effect on several biological functions, including replication, transcription and transcription factor binding. As such, DNA strand asymmetries and mutational strand bias can provide information about biological function. However, a versatile tool to e...

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Published inNucleic acids research Vol. 49; no. 1; p. e4
Main Authors Georgakopoulos-Soares, Ilias, Mouratidis, Ioannis, Parada, Guillermo E, Matharu, Navneet, Hemberg, Martin, Ahituv, Nadav
Format Journal Article
LanguageEnglish
Published England Oxford University Press 11.01.2021
Subjects
A549 Cells
Algorithms
Cell Line, Transformed
Computational Biology - methods
DNA - chemistry
DNA - genetics
DNA - metabolism
DNA Replication - genetics
Hep G2 Cells
Humans
K562 Cells
MCF-7 Cells
Methods Online
Models, Genetic
Mutation
Protein Binding
Transcription Factors - genetics
Transcription Factors - metabolism
Transcription, Genetic - genetics
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Summary:Abstract DNA strand asymmetries can have a major effect on several biological functions, including replication, transcription and transcription factor binding. As such, DNA strand asymmetries and mutational strand bias can provide information about biological function. However, a versatile tool to explore this does not exist. Here, we present Asymmetron, a user-friendly computational tool that performs statistical analysis and visualizations for the evaluation of strand asymmetries. Asymmetron takes as input DNA features provided with strand annotation and outputs strand asymmetries for consecutive occurrences of a single DNA feature or between pairs of features. We illustrate the use of Asymmetron by identifying transcriptional and replicative strand asymmetries of germline structural variant breakpoints. We also show that the orientation of the binding sites of 45% of human transcription factors analyzed have a significant DNA strand bias in transcribed regions, that is also corroborated in ChIP-seq analyses, and is likely associated with transcription. In summary, we provide a novel tool to assess DNA strand asymmetries and show how it can be used to derive new insights across a variety of biological disciplines.
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ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkaa1052