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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...

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Detalles Bibliográficos
Autores principales: Krispil, Ronen, Tannenbaum, Miriam, Sarusi-Portuguez, Avital, Loza, Olga, Raskina, Olga, Hakim, Ofir
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
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.
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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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