RNA Pol III promoters—key players in precisely targeted plant genome editing

The clustered regularly interspaced short palindrome repeat (CRISPR)/CRISPR-associated protein Cas) system is a powerful and highly precise gene-editing tool in basic and applied research for crop improvement programs. CRISPR/Cas tool is being extensively used in plants to improve crop yield, qualit...

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Published in:Frontiers in genetics Vol. 13; p. 989199
Main Authors: Kor, Sakshi Dharmendra, Chowdhury, Naimisha, Keot, Ajay Kumar, Yogendra, Kalenahalli, Chikkaputtaiah, Channakeshavaiah, Sudhakar Reddy, Palakolanu
Format: Journal Article
Language:English
Published: Switzerland Frontiers Media S.A 04.01.2023
Subjects:
CRISPR/Cas9
Genetics
RNA pol III promoters
synthetic promoter
TATA-box
U6 and U3 snRNA promoters
USE
TATA-box
RNA pol III promoters
CRISPR/Cas9
synthetic promoter
USE
U6 and U3 snRNA promoters
ISSN:1664-8021, 1664-8021
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Abstract The clustered regularly interspaced short palindrome repeat (CRISPR)/CRISPR-associated protein Cas) system is a powerful and highly precise gene-editing tool in basic and applied research for crop improvement programs. CRISPR/Cas tool is being extensively used in plants to improve crop yield, quality, and nutritional value and make them tolerant to environmental stresses. CRISPR/Cas system consists of a Cas protein with DNA endonuclease activity and one CRISPR RNA transcript that is processed to form one or several short guide RNAs that direct Cas9 to the target DNA sequence. The expression levels of Cas proteins and gRNAs significantly influence the editing efficiency of CRISPR/Cas-mediated genome editing. This review focuses on insights into RNA Pol III promoters and their types that govern the expression levels of sgRNA in the CRISPR/Cas system. We discussed Pol III promoters structural and functional characteristics and their comparison with Pol II promoters. Further, the use of synthetic promoters to increase the targeting efficiency and overcome the structural, functional, and expressional limitations of RNA Pol III promoters has been discussed. Our review reports various studies that illustrate the use of endogenous U6/U3 promoters for improving editing efficiency in plants and the applicative approach of species-specific RNA pol III promoters for genome editing in model crops like Arabidopsis and tobacco, cereals, legumes, oilseed, and horticultural crops. We further highlight the significance of optimizing these species-specific promoters’ systematic identification and validation for crop improvement and biotic and abiotic stress tolerance through CRISPR/Cas mediated genome editing.
AbstractList The clustered regularly interspaced short palindrome repeat (CRISPR)/CRISPR-associated protein Cas) system is a powerful and highly precise gene-editing tool in basic and applied research for crop improvement programs. CRISPR/Cas tool is being extensively used in plants to improve crop yield, quality, and nutritional value and make them tolerant to environmental stresses. CRISPR/Cas system consists of a Cas protein with DNA endonuclease activity and one CRISPR RNA transcript that is processed to form one or several short guide RNAs that direct Cas9 to the target DNA sequence. The expression levels of Cas proteins and gRNAs significantly influence the editing efficiency of CRISPR/Cas-mediated genome editing. This review focuses on insights into RNA Pol III promoters and their types that govern the expression levels of sgRNA in the CRISPR/Cas system. We discussed Pol III promoters structural and functional characteristics and their comparison with Pol II promoters. Further, the use of synthetic promoters to increase the targeting efficiency and overcome the structural, functional, and expressional limitations of RNA Pol III promoters has been discussed. Our review reports various studies that illustrate the use of endogenous U6/U3 promoters for improving editing efficiency in plants and the applicative approach of species-specific RNA pol III promoters for genome editing in model crops like Arabidopsis and tobacco, cereals, legumes, oilseed, and horticultural crops. We further highlight the significance of optimizing these species-specific promoters' systematic identification and validation for crop improvement and biotic and abiotic stress tolerance through CRISPR/Cas mediated genome editing.The clustered regularly interspaced short palindrome repeat (CRISPR)/CRISPR-associated protein Cas) system is a powerful and highly precise gene-editing tool in basic and applied research for crop improvement programs. CRISPR/Cas tool is being extensively used in plants to improve crop yield, quality, and nutritional value and make them tolerant to environmental stresses. CRISPR/Cas system consists of a Cas protein with DNA endonuclease activity and one CRISPR RNA transcript that is processed to form one or several short guide RNAs that direct Cas9 to the target DNA sequence. The expression levels of Cas proteins and gRNAs significantly influence the editing efficiency of CRISPR/Cas-mediated genome editing. This review focuses on insights into RNA Pol III promoters and their types that govern the expression levels of sgRNA in the CRISPR/Cas system. We discussed Pol III promoters structural and functional characteristics and their comparison with Pol II promoters. Further, the use of synthetic promoters to increase the targeting efficiency and overcome the structural, functional, and expressional limitations of RNA Pol III promoters has been discussed. Our review reports various studies that illustrate the use of endogenous U6/U3 promoters for improving editing efficiency in plants and the applicative approach of species-specific RNA pol III promoters for genome editing in model crops like Arabidopsis and tobacco, cereals, legumes, oilseed, and horticultural crops. We further highlight the significance of optimizing these species-specific promoters' systematic identification and validation for crop improvement and biotic and abiotic stress tolerance through CRISPR/Cas mediated genome editing.
The clustered regularly interspaced short palindrome repeat (CRISPR)/CRISPR-associated protein Cas) system is a powerful and highly precise gene-editing tool in basic and applied research for crop improvement programs. CRISPR/Cas tool is being extensively used in plants to improve crop yield, quality, and nutritional value and make them tolerant to environmental stresses. CRISPR/Cas system consists of a Cas protein with DNA endonuclease activity and one CRISPR RNA transcript that is processed to form one or several short guide RNAs that direct Cas9 to the target DNA sequence. The expression levels of Cas proteins and gRNAs significantly influence the editing efficiency of CRISPR/Cas-mediated genome editing. This review focuses on insights into RNA Pol III promoters and their types that govern the expression levels of sgRNA in the CRISPR/Cas system. We discussed Pol III promoters structural and functional characteristics and their comparison with Pol II promoters. Further, the use of synthetic promoters to increase the targeting efficiency and overcome the structural, functional, and expressional limitations of RNA Pol III promoters has been discussed. Our review reports various studies that illustrate the use of endogenous U6/U3 promoters for improving editing efficiency in plants and the applicative approach of species-specific RNA pol III promoters for genome editing in model crops like Arabidopsis and tobacco, cereals, legumes, oilseed, and horticultural crops. We further highlight the significance of optimizing these species-specific promoters’ systematic identification and validation for crop improvement and biotic and abiotic stress tolerance through CRISPR/Cas mediated genome editing.
Author Yogendra, Kalenahalli
Chikkaputtaiah, Channakeshavaiah
Sudhakar Reddy, Palakolanu
Chowdhury, Naimisha
Kor, Sakshi Dharmendra
Keot, Ajay Kumar
AuthorAffiliation 2 Biological Sciences and Technology Division , CSIR-North East Institute of Science and Technology (CSIR-NEIST) , Jorhat , Assam , India
3 Academy of Scientific and Innovative Research (AcSIR) , Ghaziabad , India
1 International Crops Research Institute for the Semi-Arid Tropics , Hyderabad , Telangana , India
AuthorAffiliation_xml – name: 3 Academy of Scientific and Innovative Research (AcSIR) , Ghaziabad , India
– name: 1 International Crops Research Institute for the Semi-Arid Tropics , Hyderabad , Telangana , India
– name: 2 Biological Sciences and Technology Division , CSIR-North East Institute of Science and Technology (CSIR-NEIST) , Jorhat , Assam , India
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– sequence: 2
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  surname: Sudhakar Reddy
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/36685866$$D View this record in MEDLINE/PubMed
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Copyright Copyright © 2023 Kor, Chowdhury, Keot, Yogendra, Chikkaputtaiah and Sudhakar Reddy.
Copyright © 2023 Kor, Chowdhury, Keot, Yogendra, Chikkaputtaiah and Sudhakar Reddy. 2023 Kor, Chowdhury, Keot, Yogendra, Chikkaputtaiah and Sudhakar Reddy
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Keywords TATA-box
RNA pol III promoters
CRISPR/Cas9
synthetic promoter
USE
U6 and U3 snRNA promoters
Language English
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Edited by: Deepmala Sehgal, Syngenta, United Kingdom
These authors have contributed equally to this work and share first authorship
This article was submitted to Plant Genomics, a section of the journal Frontiers in Genetics
Rupesh Deshmukh, Plaksha University, India
Reviewed by: Muntazir Mushtaq, National Bureau of Plant Genetic Resources (ICAR), India
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Snippet The clustered regularly interspaced short palindrome repeat (CRISPR)/CRISPR-associated protein Cas) system is a powerful and highly precise gene-editing tool...
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SubjectTerms CRISPR/Cas9
Genetics
RNA pol III promoters
synthetic promoter
TATA-box
U6 and U3 snRNA promoters
USE
Title RNA Pol III promoters—key players in precisely targeted plant genome editing
URI https://www.ncbi.nlm.nih.gov/pubmed/36685866
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