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Biotinylated Tn5 transposase‐mediated CUT&Tag efficiently profiles transcription factor‐DNA interactions in plants

In contrast to CUT&Tag approaches for profiling bulk histone modifications, current CUT&Tag methods for analysing specific transcription factor (TF)‐DNA interactions remain technically challenging due to TFs having relatively low abundance. Moreover, an efficient CUT&Tag strategy for pla...

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Autores principales: Tao, Xiao‐Yuan, Guan, Xue‐Ying, Hong, Gao‐Jie, He, Yu‐Qing, Li, Su‐Juan, Feng, Shou‐Li, Wang, Jian, Chen, Guang, Xu, Fei, Wang, Jia‐Wei, Xu, Sheng‐Chun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10214755/
https://www.ncbi.nlm.nih.gov/pubmed/36786225
http://dx.doi.org/10.1111/pbi.14029
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author Tao, Xiao‐Yuan
Guan, Xue‐Ying
Hong, Gao‐Jie
He, Yu‐Qing
Li, Su‐Juan
Feng, Shou‐Li
Wang, Jian
Chen, Guang
Xu, Fei
Wang, Jia‐Wei
Xu, Sheng‐Chun
author_facet Tao, Xiao‐Yuan
Guan, Xue‐Ying
Hong, Gao‐Jie
He, Yu‐Qing
Li, Su‐Juan
Feng, Shou‐Li
Wang, Jian
Chen, Guang
Xu, Fei
Wang, Jia‐Wei
Xu, Sheng‐Chun
author_sort Tao, Xiao‐Yuan
collection PubMed
description In contrast to CUT&Tag approaches for profiling bulk histone modifications, current CUT&Tag methods for analysing specific transcription factor (TF)‐DNA interactions remain technically challenging due to TFs having relatively low abundance. Moreover, an efficient CUT&Tag strategy for plant TFs is not yet available. Here, we first applied biotinylated Tn5 transposase‐mediated CUT&Tag (B‐CUT&Tag) to produce high‐quality libraries for interrogating TF‐DNA interactions. B‐CUT&Tag combines streptavidin‐biotin‐based DNA purification with routine CUT&Tag, optimizing the removal of large amounts of intact chromatin not targeted by specific TFs. The biotinylated chromatin fragments are then purified for construction of deep sequencing libraries or qPCR analysis. We applied B‐CUT&Tag to probe genome‐wide DNA targets of Squamosa promoter‐binding‐like protein 9 (SPL9), a well‐established TF in Arabidopsis; the resulting profiles were efficient and consistent in demonstrating its well‐established target genes in juvenile‐adult transition/flowering, trichome development, flavonoid biosynthesis, wax synthesis and branching. Interestingly, our results indicate functions of AtSPL9 in modulating growth‐defence trade‐offs. In addition, we established a method for applying qPCR after CUT&Tag (B‐CUT&Tag‐qPCR) and successfully validated the binding of SPL9 in Arabidopsis and PHR2 in rice. Our study thus provides a convenient and highly efficient CUT&Tag strategy for profiling TF‐chromatin interactions that is widely applicable to the annotation of cis‐regulatory elements for crop improvement.
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spelling pubmed-102147552023-05-27 Biotinylated Tn5 transposase‐mediated CUT&Tag efficiently profiles transcription factor‐DNA interactions in plants Tao, Xiao‐Yuan Guan, Xue‐Ying Hong, Gao‐Jie He, Yu‐Qing Li, Su‐Juan Feng, Shou‐Li Wang, Jian Chen, Guang Xu, Fei Wang, Jia‐Wei Xu, Sheng‐Chun Plant Biotechnol J Research Articles In contrast to CUT&Tag approaches for profiling bulk histone modifications, current CUT&Tag methods for analysing specific transcription factor (TF)‐DNA interactions remain technically challenging due to TFs having relatively low abundance. Moreover, an efficient CUT&Tag strategy for plant TFs is not yet available. Here, we first applied biotinylated Tn5 transposase‐mediated CUT&Tag (B‐CUT&Tag) to produce high‐quality libraries for interrogating TF‐DNA interactions. B‐CUT&Tag combines streptavidin‐biotin‐based DNA purification with routine CUT&Tag, optimizing the removal of large amounts of intact chromatin not targeted by specific TFs. The biotinylated chromatin fragments are then purified for construction of deep sequencing libraries or qPCR analysis. We applied B‐CUT&Tag to probe genome‐wide DNA targets of Squamosa promoter‐binding‐like protein 9 (SPL9), a well‐established TF in Arabidopsis; the resulting profiles were efficient and consistent in demonstrating its well‐established target genes in juvenile‐adult transition/flowering, trichome development, flavonoid biosynthesis, wax synthesis and branching. Interestingly, our results indicate functions of AtSPL9 in modulating growth‐defence trade‐offs. In addition, we established a method for applying qPCR after CUT&Tag (B‐CUT&Tag‐qPCR) and successfully validated the binding of SPL9 in Arabidopsis and PHR2 in rice. Our study thus provides a convenient and highly efficient CUT&Tag strategy for profiling TF‐chromatin interactions that is widely applicable to the annotation of cis‐regulatory elements for crop improvement. John Wiley and Sons Inc. 2023-03-02 2023-06 /pmc/articles/PMC10214755/ /pubmed/36786225 http://dx.doi.org/10.1111/pbi.14029 Text en © 2023 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Articles
Tao, Xiao‐Yuan
Guan, Xue‐Ying
Hong, Gao‐Jie
He, Yu‐Qing
Li, Su‐Juan
Feng, Shou‐Li
Wang, Jian
Chen, Guang
Xu, Fei
Wang, Jia‐Wei
Xu, Sheng‐Chun
Biotinylated Tn5 transposase‐mediated CUT&Tag efficiently profiles transcription factor‐DNA interactions in plants
title Biotinylated Tn5 transposase‐mediated CUT&Tag efficiently profiles transcription factor‐DNA interactions in plants
title_full Biotinylated Tn5 transposase‐mediated CUT&Tag efficiently profiles transcription factor‐DNA interactions in plants
title_fullStr Biotinylated Tn5 transposase‐mediated CUT&Tag efficiently profiles transcription factor‐DNA interactions in plants
title_full_unstemmed Biotinylated Tn5 transposase‐mediated CUT&Tag efficiently profiles transcription factor‐DNA interactions in plants
title_short Biotinylated Tn5 transposase‐mediated CUT&Tag efficiently profiles transcription factor‐DNA interactions in plants
title_sort biotinylated tn5 transposase‐mediated cut&tag efficiently profiles transcription factor‐dna interactions in plants
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10214755/
https://www.ncbi.nlm.nih.gov/pubmed/36786225
http://dx.doi.org/10.1111/pbi.14029
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