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Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulatory Mechanism in Rice
Iron (Fe) deficiency directly affects crop growth and development, ultimately resulting in reduced crop yield and quality. Recently, long non-coding RNAs (lncRNAs) have been demonstrated to play critical regulatory roles in a multitude of pathways across numerous species. However, systematic screeni...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8070830/ https://www.ncbi.nlm.nih.gov/pubmed/33919786 http://dx.doi.org/10.3390/genes12040567 |
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author | Wang, Shoudong Sun, Shuo Guo, Runze Liao, Wenying Shou, Huixia |
author_facet | Wang, Shoudong Sun, Shuo Guo, Runze Liao, Wenying Shou, Huixia |
author_sort | Wang, Shoudong |
collection | PubMed |
description | Iron (Fe) deficiency directly affects crop growth and development, ultimately resulting in reduced crop yield and quality. Recently, long non-coding RNAs (lncRNAs) have been demonstrated to play critical regulatory roles in a multitude of pathways across numerous species. However, systematic screening of lncRNAs responding to Fe deficiency and their regulatory mechanism in plants has not been reported. In this work, 171 differently expressed lncRNAs (DE-lncRNAs) were identified based on analysis of strand-specific RNA-seq data from rice shoots and roots under Fe-deficient conditions. We also found several lncRNAs, which could generate miRNAs or act as endogenous target mimics to regulate expression of Fe-related genes. Analysis of interaction networks and gene ontology enrichment revealed that a number of DE-lncRNAs were associated with iron transport and photosynthesis, indicating a possible role of lncRNAs in regulation of Fe homeostasis. Moreover, we identified 76 potential lncRNA targets of OsbHLH156, a key regulator for transcriptional response to Fe deficiency. This study provides insight into the potential functions and regulatory mechanism of Fe-responsive lncRNAs and would be an initial and reference for any further studies regarding lncRNAs involved in Fe deficiency in plants. |
format | Online Article Text |
id | pubmed-8070830 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-80708302021-04-26 Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulatory Mechanism in Rice Wang, Shoudong Sun, Shuo Guo, Runze Liao, Wenying Shou, Huixia Genes (Basel) Article Iron (Fe) deficiency directly affects crop growth and development, ultimately resulting in reduced crop yield and quality. Recently, long non-coding RNAs (lncRNAs) have been demonstrated to play critical regulatory roles in a multitude of pathways across numerous species. However, systematic screening of lncRNAs responding to Fe deficiency and their regulatory mechanism in plants has not been reported. In this work, 171 differently expressed lncRNAs (DE-lncRNAs) were identified based on analysis of strand-specific RNA-seq data from rice shoots and roots under Fe-deficient conditions. We also found several lncRNAs, which could generate miRNAs or act as endogenous target mimics to regulate expression of Fe-related genes. Analysis of interaction networks and gene ontology enrichment revealed that a number of DE-lncRNAs were associated with iron transport and photosynthesis, indicating a possible role of lncRNAs in regulation of Fe homeostasis. Moreover, we identified 76 potential lncRNA targets of OsbHLH156, a key regulator for transcriptional response to Fe deficiency. This study provides insight into the potential functions and regulatory mechanism of Fe-responsive lncRNAs and would be an initial and reference for any further studies regarding lncRNAs involved in Fe deficiency in plants. MDPI 2021-04-14 /pmc/articles/PMC8070830/ /pubmed/33919786 http://dx.doi.org/10.3390/genes12040567 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Wang, Shoudong Sun, Shuo Guo, Runze Liao, Wenying Shou, Huixia Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulatory Mechanism in Rice |
title | Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulatory Mechanism in Rice |
title_full | Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulatory Mechanism in Rice |
title_fullStr | Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulatory Mechanism in Rice |
title_full_unstemmed | Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulatory Mechanism in Rice |
title_short | Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulatory Mechanism in Rice |
title_sort | transcriptomic profiling of fe-responsive lncrnas and their regulatory mechanism in rice |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8070830/ https://www.ncbi.nlm.nih.gov/pubmed/33919786 http://dx.doi.org/10.3390/genes12040567 |
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