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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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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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. |
format | Online Article Text |
id | pubmed-9182794 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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