Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice

The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest rem...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Eudald Illa-Berenguer [verfasserIn] Peter R. LaFayette [verfasserIn] Wayne A. Parrott [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	genome editing cas proteins editing efficiency specificity temperature heat treatment

Übergeordnetes Werk:	In: Frontiers in Genome Editing - Frontiers Media S.A., 2020, 5(2023)
Übergeordnetes Werk:	volume:5 ; year:2023

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fgeed.2023.1074641

Katalog-ID:	DOAJ087589699

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520			\|a The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest remains challenging in many cases. To assess target site flexibility, we tested five different Cas9/Cas12a endonucleases (SpCas9, SaCas9, St1Cas9, Mb3Cas12a, and AsCas12a) in embryogenic rice calli from Taipei 309 at 37°C (optimal temperature for most Cas9/Cas12a proteins) and 27°C (optimal temperature for tissue culture) and measured their editing rates under regular tissue culture conditions using Illumina sequencing. StCas9 and AsCas12 were not functional as tested, regardless of the temperature used. SpCas9 was the most efficient endonuclease at either temperature, regardless of whether monoallelic or biallelic edits were considered. Mb3Cas12a at 37°C was the next most efficient endonuclease. Monoallelic edits prevailed for both SaCas9 and Mb3Cas12a at 27°C, but biallelic edits prevailed at 37°C. Overall, the use of other Cas9 orthologs, the use of Cas12a endonucleases, and the optimal temperature can expand the range of targetable sequences.
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allfields	10.3389/fgeed.2023.1074641 doi (DE-627)DOAJ087589699 (DE-599)DOAJ7d9863c8bebd4c52a6a97a55364fc327 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Eudald Illa-Berenguer verfasserin aut Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest remains challenging in many cases. To assess target site flexibility, we tested five different Cas9/Cas12a endonucleases (SpCas9, SaCas9, St1Cas9, Mb3Cas12a, and AsCas12a) in embryogenic rice calli from Taipei 309 at 37°C (optimal temperature for most Cas9/Cas12a proteins) and 27°C (optimal temperature for tissue culture) and measured their editing rates under regular tissue culture conditions using Illumina sequencing. StCas9 and AsCas12 were not functional as tested, regardless of the temperature used. SpCas9 was the most efficient endonuclease at either temperature, regardless of whether monoallelic or biallelic edits were considered. Mb3Cas12a at 37°C was the next most efficient endonuclease. Monoallelic edits prevailed for both SaCas9 and Mb3Cas12a at 27°C, but biallelic edits prevailed at 37°C. Overall, the use of other Cas9 orthologs, the use of Cas12a endonucleases, and the optimal temperature can expand the range of targetable sequences. genome editing cas proteins editing efficiency specificity temperature heat treatment Biotechnology Genetics Peter R. LaFayette verfasserin aut Wayne A. Parrott verfasserin aut Wayne A. Parrott verfasserin aut Wayne A. Parrott verfasserin aut In Frontiers in Genome Editing Frontiers Media S.A., 2020 5(2023) (DE-627)1695605101 (DE-600)3017800-9 26733439 nnns volume:5 year:2023 https://doi.org/10.3389/fgeed.2023.1074641 kostenfrei https://doaj.org/article/7d9863c8bebd4c52a6a97a55364fc327 kostenfrei https://www.frontiersin.org/articles/10.3389/fgeed.2023.1074641/full kostenfrei https://doaj.org/toc/2673-3439 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 5 2023
spelling	10.3389/fgeed.2023.1074641 doi (DE-627)DOAJ087589699 (DE-599)DOAJ7d9863c8bebd4c52a6a97a55364fc327 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Eudald Illa-Berenguer verfasserin aut Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest remains challenging in many cases. To assess target site flexibility, we tested five different Cas9/Cas12a endonucleases (SpCas9, SaCas9, St1Cas9, Mb3Cas12a, and AsCas12a) in embryogenic rice calli from Taipei 309 at 37°C (optimal temperature for most Cas9/Cas12a proteins) and 27°C (optimal temperature for tissue culture) and measured their editing rates under regular tissue culture conditions using Illumina sequencing. StCas9 and AsCas12 were not functional as tested, regardless of the temperature used. SpCas9 was the most efficient endonuclease at either temperature, regardless of whether monoallelic or biallelic edits were considered. Mb3Cas12a at 37°C was the next most efficient endonuclease. Monoallelic edits prevailed for both SaCas9 and Mb3Cas12a at 27°C, but biallelic edits prevailed at 37°C. Overall, the use of other Cas9 orthologs, the use of Cas12a endonucleases, and the optimal temperature can expand the range of targetable sequences. genome editing cas proteins editing efficiency specificity temperature heat treatment Biotechnology Genetics Peter R. LaFayette verfasserin aut Wayne A. Parrott verfasserin aut Wayne A. Parrott verfasserin aut Wayne A. Parrott verfasserin aut In Frontiers in Genome Editing Frontiers Media S.A., 2020 5(2023) (DE-627)1695605101 (DE-600)3017800-9 26733439 nnns volume:5 year:2023 https://doi.org/10.3389/fgeed.2023.1074641 kostenfrei https://doaj.org/article/7d9863c8bebd4c52a6a97a55364fc327 kostenfrei https://www.frontiersin.org/articles/10.3389/fgeed.2023.1074641/full kostenfrei https://doaj.org/toc/2673-3439 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 5 2023
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allfieldsGer	10.3389/fgeed.2023.1074641 doi (DE-627)DOAJ087589699 (DE-599)DOAJ7d9863c8bebd4c52a6a97a55364fc327 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Eudald Illa-Berenguer verfasserin aut Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest remains challenging in many cases. To assess target site flexibility, we tested five different Cas9/Cas12a endonucleases (SpCas9, SaCas9, St1Cas9, Mb3Cas12a, and AsCas12a) in embryogenic rice calli from Taipei 309 at 37°C (optimal temperature for most Cas9/Cas12a proteins) and 27°C (optimal temperature for tissue culture) and measured their editing rates under regular tissue culture conditions using Illumina sequencing. StCas9 and AsCas12 were not functional as tested, regardless of the temperature used. SpCas9 was the most efficient endonuclease at either temperature, regardless of whether monoallelic or biallelic edits were considered. Mb3Cas12a at 37°C was the next most efficient endonuclease. Monoallelic edits prevailed for both SaCas9 and Mb3Cas12a at 27°C, but biallelic edits prevailed at 37°C. Overall, the use of other Cas9 orthologs, the use of Cas12a endonucleases, and the optimal temperature can expand the range of targetable sequences. genome editing cas proteins editing efficiency specificity temperature heat treatment Biotechnology Genetics Peter R. LaFayette verfasserin aut Wayne A. Parrott verfasserin aut Wayne A. Parrott verfasserin aut Wayne A. Parrott verfasserin aut In Frontiers in Genome Editing Frontiers Media S.A., 2020 5(2023) (DE-627)1695605101 (DE-600)3017800-9 26733439 nnns volume:5 year:2023 https://doi.org/10.3389/fgeed.2023.1074641 kostenfrei https://doaj.org/article/7d9863c8bebd4c52a6a97a55364fc327 kostenfrei https://www.frontiersin.org/articles/10.3389/fgeed.2023.1074641/full kostenfrei https://doaj.org/toc/2673-3439 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 5 2023
allfieldsSound	10.3389/fgeed.2023.1074641 doi (DE-627)DOAJ087589699 (DE-599)DOAJ7d9863c8bebd4c52a6a97a55364fc327 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Eudald Illa-Berenguer verfasserin aut Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest remains challenging in many cases. To assess target site flexibility, we tested five different Cas9/Cas12a endonucleases (SpCas9, SaCas9, St1Cas9, Mb3Cas12a, and AsCas12a) in embryogenic rice calli from Taipei 309 at 37°C (optimal temperature for most Cas9/Cas12a proteins) and 27°C (optimal temperature for tissue culture) and measured their editing rates under regular tissue culture conditions using Illumina sequencing. StCas9 and AsCas12 were not functional as tested, regardless of the temperature used. SpCas9 was the most efficient endonuclease at either temperature, regardless of whether monoallelic or biallelic edits were considered. Mb3Cas12a at 37°C was the next most efficient endonuclease. Monoallelic edits prevailed for both SaCas9 and Mb3Cas12a at 27°C, but biallelic edits prevailed at 37°C. Overall, the use of other Cas9 orthologs, the use of Cas12a endonucleases, and the optimal temperature can expand the range of targetable sequences. genome editing cas proteins editing efficiency specificity temperature heat treatment Biotechnology Genetics Peter R. LaFayette verfasserin aut Wayne A. Parrott verfasserin aut Wayne A. Parrott verfasserin aut Wayne A. Parrott verfasserin aut In Frontiers in Genome Editing Frontiers Media S.A., 2020 5(2023) (DE-627)1695605101 (DE-600)3017800-9 26733439 nnns volume:5 year:2023 https://doi.org/10.3389/fgeed.2023.1074641 kostenfrei https://doaj.org/article/7d9863c8bebd4c52a6a97a55364fc327 kostenfrei https://www.frontiersin.org/articles/10.3389/fgeed.2023.1074641/full kostenfrei https://doaj.org/toc/2673-3439 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 5 2023
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authorswithroles_txt_mv	Eudald Illa-Berenguer @@aut@@ Peter R. LaFayette @@aut@@ Wayne A. Parrott @@aut@@
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callnumber-first	T - Technology
author	Eudald Illa-Berenguer
spellingShingle	Eudald Illa-Berenguer misc TP248.13-248.65 misc QH426-470 misc genome editing misc cas proteins misc editing efficiency misc specificity misc temperature misc heat treatment misc Biotechnology misc Genetics Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice
authorStr	Eudald Illa-Berenguer
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topic_title	TP248.13-248.65 QH426-470 Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice genome editing cas proteins editing efficiency specificity temperature heat treatment
topic	misc TP248.13-248.65 misc QH426-470 misc genome editing misc cas proteins misc editing efficiency misc specificity misc temperature misc heat treatment misc Biotechnology misc Genetics
topic_unstemmed	misc TP248.13-248.65 misc QH426-470 misc genome editing misc cas proteins misc editing efficiency misc specificity misc temperature misc heat treatment misc Biotechnology misc Genetics
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title	Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice
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title_full	Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice
author_sort	Eudald Illa-Berenguer
journal	Frontiers in Genome Editing
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author_browse	Eudald Illa-Berenguer Peter R. LaFayette Wayne A. Parrott
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title_sort	editing efficiencies with cas9 orthologs, cas12a endonucleases, and temperature in rice
callnumber	TP248.13-248.65
title_auth	Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice
abstract	The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest remains challenging in many cases. To assess target site flexibility, we tested five different Cas9/Cas12a endonucleases (SpCas9, SaCas9, St1Cas9, Mb3Cas12a, and AsCas12a) in embryogenic rice calli from Taipei 309 at 37°C (optimal temperature for most Cas9/Cas12a proteins) and 27°C (optimal temperature for tissue culture) and measured their editing rates under regular tissue culture conditions using Illumina sequencing. StCas9 and AsCas12 were not functional as tested, regardless of the temperature used. SpCas9 was the most efficient endonuclease at either temperature, regardless of whether monoallelic or biallelic edits were considered. Mb3Cas12a at 37°C was the next most efficient endonuclease. Monoallelic edits prevailed for both SaCas9 and Mb3Cas12a at 27°C, but biallelic edits prevailed at 37°C. Overall, the use of other Cas9 orthologs, the use of Cas12a endonucleases, and the optimal temperature can expand the range of targetable sequences.
abstractGer	The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest remains challenging in many cases. To assess target site flexibility, we tested five different Cas9/Cas12a endonucleases (SpCas9, SaCas9, St1Cas9, Mb3Cas12a, and AsCas12a) in embryogenic rice calli from Taipei 309 at 37°C (optimal temperature for most Cas9/Cas12a proteins) and 27°C (optimal temperature for tissue culture) and measured their editing rates under regular tissue culture conditions using Illumina sequencing. StCas9 and AsCas12 were not functional as tested, regardless of the temperature used. SpCas9 was the most efficient endonuclease at either temperature, regardless of whether monoallelic or biallelic edits were considered. Mb3Cas12a at 37°C was the next most efficient endonuclease. Monoallelic edits prevailed for both SaCas9 and Mb3Cas12a at 27°C, but biallelic edits prevailed at 37°C. Overall, the use of other Cas9 orthologs, the use of Cas12a endonucleases, and the optimal temperature can expand the range of targetable sequences.
abstract_unstemmed	The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest remains challenging in many cases. To assess target site flexibility, we tested five different Cas9/Cas12a endonucleases (SpCas9, SaCas9, St1Cas9, Mb3Cas12a, and AsCas12a) in embryogenic rice calli from Taipei 309 at 37°C (optimal temperature for most Cas9/Cas12a proteins) and 27°C (optimal temperature for tissue culture) and measured their editing rates under regular tissue culture conditions using Illumina sequencing. StCas9 and AsCas12 were not functional as tested, regardless of the temperature used. SpCas9 was the most efficient endonuclease at either temperature, regardless of whether monoallelic or biallelic edits were considered. Mb3Cas12a at 37°C was the next most efficient endonuclease. Monoallelic edits prevailed for both SaCas9 and Mb3Cas12a at 27°C, but biallelic edits prevailed at 37°C. Overall, the use of other Cas9 orthologs, the use of Cas12a endonucleases, and the optimal temperature can expand the range of targetable sequences.
collection_details	GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700
title_short	Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice
url	https://doi.org/10.3389/fgeed.2023.1074641 https://doaj.org/article/7d9863c8bebd4c52a6a97a55364fc327 https://www.frontiersin.org/articles/10.3389/fgeed.2023.1074641/full https://doaj.org/toc/2673-3439
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author2	Peter R. LaFayette Wayne A. Parrott
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doi_str	10.3389/fgeed.2023.1074641
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up_date	2024-07-04T02:16:58.793Z
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Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice

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