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Functional Characterization of the Lysine-Specific Histone Demethylases Family in Soybean

Histone modifications, such as methylation and demethylation, have crucial roles in regulating chromatin structure and gene expression. Lysine-specific histone demethylases (LSDs) belong to the amine oxidase family, which is an important family of histone lysine demethylases (KDMs), and functions in...

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Autores principales: Liu, Mengshi, Jiang, Jiacan, Han, Yapeng, Shi, Mengying, Li, Xianli, Wang, Yingxiang, Dong, Zhicheng, Yang, Cunyi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9182794/
https://www.ncbi.nlm.nih.gov/pubmed/35684171
http://dx.doi.org/10.3390/plants11111398
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author Liu, Mengshi
Jiang, Jiacan
Han, Yapeng
Shi, Mengying
Li, Xianli
Wang, Yingxiang
Dong, Zhicheng
Yang, Cunyi
author_facet Liu, Mengshi
Jiang, Jiacan
Han, Yapeng
Shi, Mengying
Li, Xianli
Wang, Yingxiang
Dong, Zhicheng
Yang, Cunyi
author_sort Liu, Mengshi
collection PubMed
description Histone modifications, such as methylation and demethylation, have crucial roles in regulating chromatin structure and gene expression. Lysine-specific histone demethylases (LSDs) belong to the amine oxidase family, which is an important family of histone lysine demethylases (KDMs), and functions in maintaining homeostasis of histone methylation. Here, we identified six LSD-like (LDL) genes from the important leguminous soybean. Phylogenetic analyses divided the six GmLDLs into four clusters with two highly conserved SWRIM and amine oxidase domains. Indeed, demethylase activity assay using recombinant GmLDL proteins in vitro demonstrated that GmLDLs have demethylase activity toward mono- and dimethylated Lys4 but not trimethylated histone 3, similar to their orthologs previously reported in animals. Using real-time PCR experiments in combination with public transcriptome data, we found that these six GmLDL genes exhibit comparable expressions in multiple tissues or in response to different abiotic stresses. Moreover, our genetic variation investigation of GmLDL genes among 761 resequenced soybean accessions indicates that GmLDLs are well conserved during soybean domestication and improvement. Taken together, these findings demonstrate that GmFLD, GmLDL1a, and GmLDL1b are bona fide H3K4 demethylases towards H4K4me1/2 and GmLDLs exist in various members with likely conserved and divergent roles in soybeans.
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spelling pubmed-91827942022-06-10 Functional Characterization of the Lysine-Specific Histone Demethylases Family in Soybean Liu, Mengshi Jiang, Jiacan Han, Yapeng Shi, Mengying Li, Xianli Wang, Yingxiang Dong, Zhicheng Yang, Cunyi Plants (Basel) Article Histone modifications, such as methylation and demethylation, have crucial roles in regulating chromatin structure and gene expression. Lysine-specific histone demethylases (LSDs) belong to the amine oxidase family, which is an important family of histone lysine demethylases (KDMs), and functions in maintaining homeostasis of histone methylation. Here, we identified six LSD-like (LDL) genes from the important leguminous soybean. Phylogenetic analyses divided the six GmLDLs into four clusters with two highly conserved SWRIM and amine oxidase domains. Indeed, demethylase activity assay using recombinant GmLDL proteins in vitro demonstrated that GmLDLs have demethylase activity toward mono- and dimethylated Lys4 but not trimethylated histone 3, similar to their orthologs previously reported in animals. Using real-time PCR experiments in combination with public transcriptome data, we found that these six GmLDL genes exhibit comparable expressions in multiple tissues or in response to different abiotic stresses. Moreover, our genetic variation investigation of GmLDL genes among 761 resequenced soybean accessions indicates that GmLDLs are well conserved during soybean domestication and improvement. Taken together, these findings demonstrate that GmFLD, GmLDL1a, and GmLDL1b are bona fide H3K4 demethylases towards H4K4me1/2 and GmLDLs exist in various members with likely conserved and divergent roles in soybeans. MDPI 2022-05-25 /pmc/articles/PMC9182794/ /pubmed/35684171 http://dx.doi.org/10.3390/plants11111398 Text en © 2022 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
Liu, Mengshi
Jiang, Jiacan
Han, Yapeng
Shi, Mengying
Li, Xianli
Wang, Yingxiang
Dong, Zhicheng
Yang, Cunyi
Functional Characterization of the Lysine-Specific Histone Demethylases Family in Soybean
title Functional Characterization of the Lysine-Specific Histone Demethylases Family in Soybean
title_full Functional Characterization of the Lysine-Specific Histone Demethylases Family in Soybean
title_fullStr Functional Characterization of the Lysine-Specific Histone Demethylases Family in Soybean
title_full_unstemmed Functional Characterization of the Lysine-Specific Histone Demethylases Family in Soybean
title_short Functional Characterization of the Lysine-Specific Histone Demethylases Family in Soybean
title_sort functional characterization of the lysine-specific histone demethylases family in soybean
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9182794/
https://www.ncbi.nlm.nih.gov/pubmed/35684171
http://dx.doi.org/10.3390/plants11111398
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