Protocol for affordable and efficient profiling of nascent RNAs in bread wheat using GRO-seq

Exorbitant sequencing cost is one of the main obstacles limiting the widespread application of Global Run-On sequencing (GRO-seq) to detect transcriptional activity. Here, we describe a more efficient and affordable protocol for GRO-seq that incorporates an rRNA removal step after nuclear RNA isolat...

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Autores principales: Chen, Yan, Zhu, Jiafu, Xie, Yilin, Li, Zijuan, Zhang, Yijing, Liu, Min, Dong, Zhicheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9463444/
https://www.ncbi.nlm.nih.gov/pubmed/36097381
http://dx.doi.org/10.1016/j.xpro.2022.101657
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author Chen, Yan
Zhu, Jiafu
Xie, Yilin
Li, Zijuan
Zhang, Yijing
Liu, Min
Dong, Zhicheng
author_facet Chen, Yan
Zhu, Jiafu
Xie, Yilin
Li, Zijuan
Zhang, Yijing
Liu, Min
Dong, Zhicheng
author_sort Chen, Yan
collection PubMed
description Exorbitant sequencing cost is one of the main obstacles limiting the widespread application of Global Run-On sequencing (GRO-seq) to detect transcriptional activity. Here, we describe a more efficient and affordable protocol for GRO-seq that incorporates an rRNA removal step after nuclear RNA isolation and before nascent RNA immunoprecipitation. We have successfully applied this protocol to profile enhancer transcription in allohexaploid bread wheat and increased the proportion of valid data by 20 times. For complete details on the use and execution of this protocol, please refer to Xie et al. (2022).
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spelling pubmed-94634442022-09-11 Protocol for affordable and efficient profiling of nascent RNAs in bread wheat using GRO-seq Chen, Yan Zhu, Jiafu Xie, Yilin Li, Zijuan Zhang, Yijing Liu, Min Dong, Zhicheng STAR Protoc Protocol Exorbitant sequencing cost is one of the main obstacles limiting the widespread application of Global Run-On sequencing (GRO-seq) to detect transcriptional activity. Here, we describe a more efficient and affordable protocol for GRO-seq that incorporates an rRNA removal step after nuclear RNA isolation and before nascent RNA immunoprecipitation. We have successfully applied this protocol to profile enhancer transcription in allohexaploid bread wheat and increased the proportion of valid data by 20 times. For complete details on the use and execution of this protocol, please refer to Xie et al. (2022). Elsevier 2022-09-02 /pmc/articles/PMC9463444/ /pubmed/36097381 http://dx.doi.org/10.1016/j.xpro.2022.101657 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Chen, Yan
Zhu, Jiafu
Xie, Yilin
Li, Zijuan
Zhang, Yijing
Liu, Min
Dong, Zhicheng
Protocol for affordable and efficient profiling of nascent RNAs in bread wheat using GRO-seq
title Protocol for affordable and efficient profiling of nascent RNAs in bread wheat using GRO-seq
title_full Protocol for affordable and efficient profiling of nascent RNAs in bread wheat using GRO-seq
title_fullStr Protocol for affordable and efficient profiling of nascent RNAs in bread wheat using GRO-seq
title_full_unstemmed Protocol for affordable and efficient profiling of nascent RNAs in bread wheat using GRO-seq
title_short Protocol for affordable and efficient profiling of nascent RNAs in bread wheat using GRO-seq
title_sort protocol for affordable and efficient profiling of nascent rnas in bread wheat using gro-seq
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9463444/
https://www.ncbi.nlm.nih.gov/pubmed/36097381
http://dx.doi.org/10.1016/j.xpro.2022.101657
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