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The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE
The integration of T-DNA in plant genomes is widely used for basic research and agriculture. The high heterogeneity in the number of integration events per genome, their configuration, and their impact on genome integrity highlight the critical need to detect the genomic locations of T-DNA insertion...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7177604/ https://www.ncbi.nlm.nih.gov/pubmed/32235482 http://dx.doi.org/10.3390/ijms21072373 |
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author | Krispil, Ronen Tannenbaum, Miriam Sarusi-Portuguez, Avital Loza, Olga Raskina, Olga Hakim, Ofir |
author_facet | Krispil, Ronen Tannenbaum, Miriam Sarusi-Portuguez, Avital Loza, Olga Raskina, Olga Hakim, Ofir |
author_sort | Krispil, Ronen |
collection | PubMed |
description | The integration of T-DNA in plant genomes is widely used for basic research and agriculture. The high heterogeneity in the number of integration events per genome, their configuration, and their impact on genome integrity highlight the critical need to detect the genomic locations of T-DNA insertions and their associated chromosomal rearrangements, and the great challenge in doing so. Here, we present 4SEE, a circular chromosome conformation capture (4C)-based method for robust, rapid, and cost-efficient detection of the entire scope of T-DNA locations. Moreover, by measuring the chromosomal architecture of the plant genome flanking the T-DNA insertions, 4SEE outlines their associated complex chromosomal aberrations. Applying 4SEE to a collection of confirmed T-DNA lines revealed previously unmapped T-DNA insertions and chromosomal rearrangements such as inversions and translocations. Uncovering such events in a feasible, robust, and cost-effective manner by 4SEE in any plant of interest has implications for accurate annotation and phenotypic characterization of T-DNA insertion mutants and transgene expression in basic science applications as well as for plant biotechnology. |
format | Online Article Text |
id | pubmed-7177604 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-71776042020-04-28 The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE Krispil, Ronen Tannenbaum, Miriam Sarusi-Portuguez, Avital Loza, Olga Raskina, Olga Hakim, Ofir Int J Mol Sci Article The integration of T-DNA in plant genomes is widely used for basic research and agriculture. The high heterogeneity in the number of integration events per genome, their configuration, and their impact on genome integrity highlight the critical need to detect the genomic locations of T-DNA insertions and their associated chromosomal rearrangements, and the great challenge in doing so. Here, we present 4SEE, a circular chromosome conformation capture (4C)-based method for robust, rapid, and cost-efficient detection of the entire scope of T-DNA locations. Moreover, by measuring the chromosomal architecture of the plant genome flanking the T-DNA insertions, 4SEE outlines their associated complex chromosomal aberrations. Applying 4SEE to a collection of confirmed T-DNA lines revealed previously unmapped T-DNA insertions and chromosomal rearrangements such as inversions and translocations. Uncovering such events in a feasible, robust, and cost-effective manner by 4SEE in any plant of interest has implications for accurate annotation and phenotypic characterization of T-DNA insertion mutants and transgene expression in basic science applications as well as for plant biotechnology. MDPI 2020-03-30 /pmc/articles/PMC7177604/ /pubmed/32235482 http://dx.doi.org/10.3390/ijms21072373 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Krispil, Ronen Tannenbaum, Miriam Sarusi-Portuguez, Avital Loza, Olga Raskina, Olga Hakim, Ofir The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE |
title | The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE |
title_full | The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE |
title_fullStr | The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE |
title_full_unstemmed | The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE |
title_short | The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE |
title_sort | position and complex genomic architecture of plant t-dna insertions revealed by 4see |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7177604/ https://www.ncbi.nlm.nih.gov/pubmed/32235482 http://dx.doi.org/10.3390/ijms21072373 |
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