Cargando…
Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat
The precise spatiotemporal gene expression is orchestrated by enhancers that lack general sequence features and thus are difficult to be computationally identified. By nascent RNA sequencing combined with epigenome profiling, we detect active transcription of enhancers from the complex bread wheat g...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9063354/ https://www.ncbi.nlm.nih.gov/pubmed/35501845 http://dx.doi.org/10.1186/s13059-022-02675-1 |
_version_ | 1784699146916069376 |
---|---|
author | Xie, Yilin Chen, Yan Li, Zijuan Zhu, Jiafu Liu, Min Zhang, Yijing Dong, Zhicheng |
author_facet | Xie, Yilin Chen, Yan Li, Zijuan Zhu, Jiafu Liu, Min Zhang, Yijing Dong, Zhicheng |
author_sort | Xie, Yilin |
collection | PubMed |
description | The precise spatiotemporal gene expression is orchestrated by enhancers that lack general sequence features and thus are difficult to be computationally identified. By nascent RNA sequencing combined with epigenome profiling, we detect active transcription of enhancers from the complex bread wheat genome. We find that genes associated with transcriptional enhancers are expressed at significantly higher levels, and enhancer RNA is more precise and robust in predicting enhancer activity compared to chromatin features. We demonstrate that sub-genome-biased enhancer transcription could drive sub-genome-biased gene expression. This study highlights enhancer transcription as a hallmark in regulating gene expression in wheat. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02675-1. |
format | Online Article Text |
id | pubmed-9063354 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-90633542022-05-04 Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat Xie, Yilin Chen, Yan Li, Zijuan Zhu, Jiafu Liu, Min Zhang, Yijing Dong, Zhicheng Genome Biol Short Report The precise spatiotemporal gene expression is orchestrated by enhancers that lack general sequence features and thus are difficult to be computationally identified. By nascent RNA sequencing combined with epigenome profiling, we detect active transcription of enhancers from the complex bread wheat genome. We find that genes associated with transcriptional enhancers are expressed at significantly higher levels, and enhancer RNA is more precise and robust in predicting enhancer activity compared to chromatin features. We demonstrate that sub-genome-biased enhancer transcription could drive sub-genome-biased gene expression. This study highlights enhancer transcription as a hallmark in regulating gene expression in wheat. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02675-1. BioMed Central 2022-04-30 /pmc/articles/PMC9063354/ /pubmed/35501845 http://dx.doi.org/10.1186/s13059-022-02675-1 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Short Report Xie, Yilin Chen, Yan Li, Zijuan Zhu, Jiafu Liu, Min Zhang, Yijing Dong, Zhicheng Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat |
title | Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat |
title_full | Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat |
title_fullStr | Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat |
title_full_unstemmed | Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat |
title_short | Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat |
title_sort | enhancer transcription detected in the nascent transcriptomic landscape of bread wheat |
topic | Short Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9063354/ https://www.ncbi.nlm.nih.gov/pubmed/35501845 http://dx.doi.org/10.1186/s13059-022-02675-1 |
work_keys_str_mv | AT xieyilin enhancertranscriptiondetectedinthenascenttranscriptomiclandscapeofbreadwheat AT chenyan enhancertranscriptiondetectedinthenascenttranscriptomiclandscapeofbreadwheat AT lizijuan enhancertranscriptiondetectedinthenascenttranscriptomiclandscapeofbreadwheat AT zhujiafu enhancertranscriptiondetectedinthenascenttranscriptomiclandscapeofbreadwheat AT liumin enhancertranscriptiondetectedinthenascenttranscriptomiclandscapeofbreadwheat AT zhangyijing enhancertranscriptiondetectedinthenascenttranscriptomiclandscapeofbreadwheat AT dongzhicheng enhancertranscriptiondetectedinthenascenttranscriptomiclandscapeofbreadwheat |