Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms

Klaus Harms; Asbjørn Lunnan; Nils Hülter; Tobias Mourier; Lasse Vinner; Cheryl P. Andam; Pekka Marttinen; Eva Marie Helena Fridholm; Anders Johannes Hansen; William P. Hanage; Kaare Magne Nielsen; Eske Willerslev; Pål Jarle Johnsen

doi:10.1073/pnas.1615819114

Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms

Klaus Harms, Asbjørn Lunnan, Nils Hülter, Tobias Mourier, Lasse Vinner, Cheryl P. Andam, Pekka Marttinen, Eva Marie Helena Fridholm, Anders Johannes Hansen, William P. Hanage, Kaare Magne Nielsen, Eske Willerslev, Pål Jarle Johnsen

5 Citations (Scopus)

Abstract

In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi. The source DNA is primarily intragenomic but can also be acquired through horizontal gene transfer. The DNA replacements are nonreciprocal and locus independent. Bioinformatic approaches reveal occurrence of SPDIR events in the gram-positive human pathogen Streptococcus pneumoniae and in the human genome.

Original language	English
Journal	National Academy of Sciences. Proceedings
Volume	113
Issue number	52
Pages (from-to)	15066-15071
Number of pages	6
ISSN	0027-8424
DOIs	https://doi.org/10.1073/pnas.1615819114
Publication status	Published - 27 Dec 2016

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Harms, K., Lunnan, A., Hülter, N., Mourier, T., Vinner, L., Andam, C. P., Marttinen, P., Fridholm, E. M. H., Hansen, A. J., Hanage, W. P., Nielsen, K. M., Willerslev, E., & Johnsen, P. J. (2016). Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms. National Academy of Sciences. Proceedings, 113(52), 15066-15071. https://doi.org/10.1073/pnas.1615819114

Harms, K, Lunnan, A, Hülter, N, Mourier, T, Vinner, L, Andam, CP, Marttinen, P, Fridholm, EMH, Hansen, AJ, Hanage, WP, Nielsen, KM, Willerslev, E & Johnsen, PJ 2016, 'Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms', National Academy of Sciences. Proceedings, vol. 113, no. 52, pp. 15066-15071. https://doi.org/10.1073/pnas.1615819114

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abstract = "In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi. The source DNA is primarily intragenomic but can also be acquired through horizontal gene transfer. The DNA replacements are nonreciprocal and locus independent. Bioinformatic approaches reveal occurrence of SPDIR events in the gram-positive human pathogen Streptococcus pneumoniae and in the human genome.",

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T1 - Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms

AU - Harms, Klaus

AU - Lunnan, Asbjørn

AU - Hülter, Nils

AU - Mourier, Tobias

AU - Vinner, Lasse

AU - Andam, Cheryl P.

AU - Marttinen, Pekka

AU - Fridholm, Eva Marie Helena

AU - Hansen, Anders Johannes

AU - Hanage, William P.

AU - Nielsen, Kaare Magne

AU - Willerslev, Eske

AU - Johnsen, Pål Jarle

PY - 2016/12/27

Y1 - 2016/12/27

N2 - In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi. The source DNA is primarily intragenomic but can also be acquired through horizontal gene transfer. The DNA replacements are nonreciprocal and locus independent. Bioinformatic approaches reveal occurrence of SPDIR events in the gram-positive human pathogen Streptococcus pneumoniae and in the human genome.

AB - In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi. The source DNA is primarily intragenomic but can also be acquired through horizontal gene transfer. The DNA replacements are nonreciprocal and locus independent. Bioinformatic approaches reveal occurrence of SPDIR events in the gram-positive human pathogen Streptococcus pneumoniae and in the human genome.

U2 - 10.1073/pnas.1615819114

DO - 10.1073/pnas.1615819114

M3 - Journal article

C2 - 27956618

SN - 0027-8424

VL - 113

SP - 15066

EP - 15071

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 52

ER -

Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms

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