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Genome-Wide Identification of m(6)A Writers, Erasers and Readers in Poplar 84K
N(6)-methyladenosine (m(6)A) RNA modification is a conserved mechanism to regulate gene expression that plays vital roles in the development of plants. However, the m(6)A RNA modification in forest trees remains limited. Here, we performed a complete analysis of m(6)A writers, erasers and readers 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/PMC9223284/ https://www.ncbi.nlm.nih.gov/pubmed/35741780 http://dx.doi.org/10.3390/genes13061018 |
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author | Sun, Xiaochen Wu, Wenli Yang, Yanfang Wilson, Iain Shao, Fenjuan Qiu, Deyou |
author_facet | Sun, Xiaochen Wu, Wenli Yang, Yanfang Wilson, Iain Shao, Fenjuan Qiu, Deyou |
author_sort | Sun, Xiaochen |
collection | PubMed |
description | N(6)-methyladenosine (m(6)A) RNA modification is a conserved mechanism to regulate gene expression that plays vital roles in the development of plants. However, the m(6)A RNA modification in forest trees remains limited. Here, we performed a complete analysis of m(6)A writers, erasers and readers in Poplar 84K, including gene location, gene structures, conserved motifs, phylogenetic relationships, promoter analysis, expression profiles and the homology modeling. We have identified 61 m(6)A pathway genes in Poplar 84K (Populus alba × Populus glandulosa), including 14 m(6)A writers, 14 m(6)A erasers and 33 m(6)A readers. Phylogenetic analysis indicated that the m(6)A writers and erasers were clustered into four groups and m(6)A readers were clustered into two groups. Promoter analysis showed that m(6)A pathway genes were mainly responsive to low oxygen followed by ABA and ethylene. The expression of the identified m(6)A pathway genes showed tissue-specific expression patterns in leaves, xylem, phloem and roots. Moreover, 17 genes were significantly up-regulated and 13 genes were significantly down-regulated in poplar overexpressing the transcription factor LBD15. Homology modeling and molecular docking results suggested that PagFIP37b was most likely to be regulated by LBD15, and the qPCRshowed that PagFIP37b were up-regulated in the LBD15-oe plants. The results provide insights that aid in the future elucidation of the functions of these m(6)A pathway genes and the epigenetic regulation mechanism of these genes in Poplar 84K. |
format | Online Article Text |
id | pubmed-9223284 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-92232842022-06-24 Genome-Wide Identification of m(6)A Writers, Erasers and Readers in Poplar 84K Sun, Xiaochen Wu, Wenli Yang, Yanfang Wilson, Iain Shao, Fenjuan Qiu, Deyou Genes (Basel) Article N(6)-methyladenosine (m(6)A) RNA modification is a conserved mechanism to regulate gene expression that plays vital roles in the development of plants. However, the m(6)A RNA modification in forest trees remains limited. Here, we performed a complete analysis of m(6)A writers, erasers and readers in Poplar 84K, including gene location, gene structures, conserved motifs, phylogenetic relationships, promoter analysis, expression profiles and the homology modeling. We have identified 61 m(6)A pathway genes in Poplar 84K (Populus alba × Populus glandulosa), including 14 m(6)A writers, 14 m(6)A erasers and 33 m(6)A readers. Phylogenetic analysis indicated that the m(6)A writers and erasers were clustered into four groups and m(6)A readers were clustered into two groups. Promoter analysis showed that m(6)A pathway genes were mainly responsive to low oxygen followed by ABA and ethylene. The expression of the identified m(6)A pathway genes showed tissue-specific expression patterns in leaves, xylem, phloem and roots. Moreover, 17 genes were significantly up-regulated and 13 genes were significantly down-regulated in poplar overexpressing the transcription factor LBD15. Homology modeling and molecular docking results suggested that PagFIP37b was most likely to be regulated by LBD15, and the qPCRshowed that PagFIP37b were up-regulated in the LBD15-oe plants. The results provide insights that aid in the future elucidation of the functions of these m(6)A pathway genes and the epigenetic regulation mechanism of these genes in Poplar 84K. MDPI 2022-06-05 /pmc/articles/PMC9223284/ /pubmed/35741780 http://dx.doi.org/10.3390/genes13061018 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 Sun, Xiaochen Wu, Wenli Yang, Yanfang Wilson, Iain Shao, Fenjuan Qiu, Deyou Genome-Wide Identification of m(6)A Writers, Erasers and Readers in Poplar 84K |
title | Genome-Wide Identification of m(6)A Writers, Erasers and Readers in Poplar 84K |
title_full | Genome-Wide Identification of m(6)A Writers, Erasers and Readers in Poplar 84K |
title_fullStr | Genome-Wide Identification of m(6)A Writers, Erasers and Readers in Poplar 84K |
title_full_unstemmed | Genome-Wide Identification of m(6)A Writers, Erasers and Readers in Poplar 84K |
title_short | Genome-Wide Identification of m(6)A Writers, Erasers and Readers in Poplar 84K |
title_sort | genome-wide identification of m(6)a writers, erasers and readers in poplar 84k |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9223284/ https://www.ncbi.nlm.nih.gov/pubmed/35741780 http://dx.doi.org/10.3390/genes13061018 |
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