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

Nucleic Acids Research
Ilias Georgakopoulos-SoaresNadav Ahituv

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.

References

Sep 15, 1991·Proceedings of the National Academy of Sciences of the United States of America·J CarcamoD Reinberg
Dec 1, 1993·Genes & Development·S Natesan, M Z Gilman
May 1, 1996·Molecular Biology and Evolution·J R Lobry
May 1, 1997·Nature Genetics·D M SassamanH H Kazazian
May 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·J Mrázek, S Karlin
Nov 26, 1999·Gene·T Kano-SueokaN Sueoka
Mar 4, 2003·Nature Genetics·Phil GreenEric D Green
Apr 19, 2003·Proceedings of the National Academy of Sciences of the United States of America·Brook BrouhaHaig H Kazazian
Aug 12, 2005·Cytogenetic and Genome Research·A M Roy-EngelP L Deininger
Oct 28, 2006·Genome Research·Eduardo P C RochaEdward J Feil
Jul 12, 2007·Genome Research·Maren KrullJürgen Schmitz
May 9, 2008·Genome Research·Paz Polak, Peter F Arndt
Jul 9, 2008·Annual Review of Genetics·Eduardo P C Rocha
Oct 7, 2008·Genome Research·E Andrew BennettScott E Devine
Nov 22, 2008·Nature Reviews. Molecular Cell Biology·Philip C Hanawalt, Graciela Spivak
Dec 18, 2009·Nature·Erin D PleasancePeter J Campbell
Feb 19, 2011·Bioinformatics·Charles E GrantWilliam Stafford Noble
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Nov 13, 2013·Nature Reviews. Genetics·Vicent Pelechano, Lars M Steinmetz
Jan 7, 2014·Human Genetics·Shira Weingarten-Gabbay, Eran Segal
Feb 26, 2015·Proceedings of the National Academy of Sciences of the United States of America·Samuel Million-WeaverHoura Merrikh
Jun 15, 2015·Genomics·Fumitaka Inoue, Nadav Ahituv
Oct 31, 2015·Science·Alla A SigovaRichard A Young
May 3, 2016·Nature Communications·Sandro MorganellaSerena Nik-Zainal
Sep 12, 2018·Genome Biology·Marketa TomkovaBenjamin Schuster-Böckler
Oct 26, 2018·Nucleic Acids Research·Adam FrankishPaul Flicek
Dec 6, 2018·Nucleic Acids Research·Marius GheorgheAnthony Mathelier
Feb 6, 2020·Nature Methods·Pauli VirtanenUNKNOWN SciPy 1.0 Contributors
Feb 7, 2020·Nature Genetics·Bernardo Rodriguez-MartinUNKNOWN PCAWG Consortium
Apr 15, 2020·Nature Communications·Zachariah E HolmesRobert T Batey
May 29, 2020·Nature·Konrad J KarczewskiDaniel G MacArthur

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Datasets Mentioned

BETA
GM12878

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
Repli-seq

Software Mentioned

py
Asymmetron
Python
ggplot2
RepeatMasker
pandas
mathop
scipy
numpy
orientation

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