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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...

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Autores principales: Wang, Shoudong, Sun, Shuo, Guo, Runze, Liao, Wenying, Shou, Huixia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
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.
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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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