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Sleeping Beauty transposon integrates into non-TA dinucleotides

BACKGROUND: Sleeping Beauty transposon (SB) has become an increasingly important genetic tool for generating mutations in vertebrate cells. It is widely thought that SB exclusively integrates into TA dinucleotides. However, this strict TA-preference has not been rigorously tested in large numbers of...

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Autores principales: Guo, Yabin, Zhang, Yin, Hu, Kaishun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5801840/
https://www.ncbi.nlm.nih.gov/pubmed/29445422
http://dx.doi.org/10.1186/s13100-018-0113-8
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author Guo, Yabin
Zhang, Yin
Hu, Kaishun
author_facet Guo, Yabin
Zhang, Yin
Hu, Kaishun
author_sort Guo, Yabin
collection PubMed
description BACKGROUND: Sleeping Beauty transposon (SB) has become an increasingly important genetic tool for generating mutations in vertebrate cells. It is widely thought that SB exclusively integrates into TA dinucleotides. However, this strict TA-preference has not been rigorously tested in large numbers of insertion sites that now can be detected with next generation sequencing. Li et al. found 71 SB insertions in non-TA dinucleotides in 2013, suggesting that TA dinucleotides are not the only sites of SB integration, yet further studies on this topic have not been carried out. RESULTS: In this study, we re-analyzed 600 million pairs of Illumina sequence reads from a high-throughput SB mutagenesis screen and identified 28 thousand SB insertions in non-TA sites. We recovered some of these non-TA sites using PCR and confirmed that at least a subset of the insertions at non-TA sites are real integrations. The consensus sequence of these non-TA sites shows an asymmetric pattern distinct from the symmetric pattern of the canonical TA sites. Perfect similarity between the downstream flanking sequence and SB transposon ends indicates there may be interaction between the transposon DNA binding domain of transposase and the target DNA. CONCLUSION: The TA-preference of SB transposon is not as strict as what people had thought. And the SB integrations at non-TA sites might be guided by the interaction between the transposon DNA binding domain of SB transposase and the target DNA. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13100-018-0113-8) contains supplementary material, which is available to authorized users.
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spelling pubmed-58018402018-02-14 Sleeping Beauty transposon integrates into non-TA dinucleotides Guo, Yabin Zhang, Yin Hu, Kaishun Mob DNA Research BACKGROUND: Sleeping Beauty transposon (SB) has become an increasingly important genetic tool for generating mutations in vertebrate cells. It is widely thought that SB exclusively integrates into TA dinucleotides. However, this strict TA-preference has not been rigorously tested in large numbers of insertion sites that now can be detected with next generation sequencing. Li et al. found 71 SB insertions in non-TA dinucleotides in 2013, suggesting that TA dinucleotides are not the only sites of SB integration, yet further studies on this topic have not been carried out. RESULTS: In this study, we re-analyzed 600 million pairs of Illumina sequence reads from a high-throughput SB mutagenesis screen and identified 28 thousand SB insertions in non-TA sites. We recovered some of these non-TA sites using PCR and confirmed that at least a subset of the insertions at non-TA sites are real integrations. The consensus sequence of these non-TA sites shows an asymmetric pattern distinct from the symmetric pattern of the canonical TA sites. Perfect similarity between the downstream flanking sequence and SB transposon ends indicates there may be interaction between the transposon DNA binding domain of transposase and the target DNA. CONCLUSION: The TA-preference of SB transposon is not as strict as what people had thought. And the SB integrations at non-TA sites might be guided by the interaction between the transposon DNA binding domain of SB transposase and the target DNA. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13100-018-0113-8) contains supplementary material, which is available to authorized users. BioMed Central 2018-02-07 /pmc/articles/PMC5801840/ /pubmed/29445422 http://dx.doi.org/10.1186/s13100-018-0113-8 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Guo, Yabin
Zhang, Yin
Hu, Kaishun
Sleeping Beauty transposon integrates into non-TA dinucleotides
title Sleeping Beauty transposon integrates into non-TA dinucleotides
title_full Sleeping Beauty transposon integrates into non-TA dinucleotides
title_fullStr Sleeping Beauty transposon integrates into non-TA dinucleotides
title_full_unstemmed Sleeping Beauty transposon integrates into non-TA dinucleotides
title_short Sleeping Beauty transposon integrates into non-TA dinucleotides
title_sort sleeping beauty transposon integrates into non-ta dinucleotides
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5801840/
https://www.ncbi.nlm.nih.gov/pubmed/29445422
http://dx.doi.org/10.1186/s13100-018-0113-8
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