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Functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation in Arabidopsis under dark-induced starvation

Lysine 2-hydroxyisobutyrylation (Khib) is a novel type of histone acylation whose prevalence and function in plants remain unclear. Here, we identified 41 Khib sites on histones in Arabidopsis thaliana, which did not overlap with frequently modified N-tail lysines (e.g. H3K4, H3K9 and H4K8). Chromat...

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Autores principales: Zheng, Lanlan, Li, Chen, Ma, Xueping, Zhou, Hanlin, Liu, Yuan, Wang, Ping, Yang, Huilan, Tamada, Yosuke, Huang, Ji, Wang, Chunfei, Hu, Zhubing, Wang, Xuening, Wang, Guodong, Li, Haihong, Hu, Juntao, Liu, Xiaoyun, Zhou, Chao, Zhang, Yonghong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8287917/
https://www.ncbi.nlm.nih.gov/pubmed/34165567
http://dx.doi.org/10.1093/nar/gkab536
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author Zheng, Lanlan
Li, Chen
Ma, Xueping
Zhou, Hanlin
Liu, Yuan
Wang, Ping
Yang, Huilan
Tamada, Yosuke
Huang, Ji
Wang, Chunfei
Hu, Zhubing
Wang, Xuening
Wang, Guodong
Li, Haihong
Hu, Juntao
Liu, Xiaoyun
Zhou, Chao
Zhang, Yonghong
author_facet Zheng, Lanlan
Li, Chen
Ma, Xueping
Zhou, Hanlin
Liu, Yuan
Wang, Ping
Yang, Huilan
Tamada, Yosuke
Huang, Ji
Wang, Chunfei
Hu, Zhubing
Wang, Xuening
Wang, Guodong
Li, Haihong
Hu, Juntao
Liu, Xiaoyun
Zhou, Chao
Zhang, Yonghong
author_sort Zheng, Lanlan
collection PubMed
description Lysine 2-hydroxyisobutyrylation (Khib) is a novel type of histone acylation whose prevalence and function in plants remain unclear. Here, we identified 41 Khib sites on histones in Arabidopsis thaliana, which did not overlap with frequently modified N-tail lysines (e.g. H3K4, H3K9 and H4K8). Chromatin immunoprecipitation-sequencing (ChIP-seq) assays revealed histone Khib in 35% of protein-coding genes. Most Khib peaks were located in genic regions, and they were highly enriched at the transcription start sites. Histone Khib is highly correlated with acetylation (ac), particularly H3K23ac, which it largely resembles in its genomic and genic distribution. Notably, co-enrichment of histone Khib and H3K23ac correlates with high gene expression levels. Metabolic profiling, transcriptome analyses, and ChIP-qPCR revealed that histone Khib and H3K23ac are co-enriched on genes involved in starch and sucrose metabolism, pentose and glucuronate interconversions, and phenylpropanoid biosynthesis, and help fine-tune plant response to dark-induced starvation. These findings suggest that Khib and H3K23ac may act in concert to promote high levels of gene transcription and regulate cellular metabolism to facilitate plant adaption to stress. Finally, HDA6 and HDA9 are involved in removing histone Khib. Our findings reveal Khib as a conserved yet unique plant histone mark acting with lysine acetylation in transcription-associated epigenomic processes.
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spelling pubmed-82879172021-07-19 Functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation in Arabidopsis under dark-induced starvation Zheng, Lanlan Li, Chen Ma, Xueping Zhou, Hanlin Liu, Yuan Wang, Ping Yang, Huilan Tamada, Yosuke Huang, Ji Wang, Chunfei Hu, Zhubing Wang, Xuening Wang, Guodong Li, Haihong Hu, Juntao Liu, Xiaoyun Zhou, Chao Zhang, Yonghong Nucleic Acids Res Data Resources and Analyses Lysine 2-hydroxyisobutyrylation (Khib) is a novel type of histone acylation whose prevalence and function in plants remain unclear. Here, we identified 41 Khib sites on histones in Arabidopsis thaliana, which did not overlap with frequently modified N-tail lysines (e.g. H3K4, H3K9 and H4K8). Chromatin immunoprecipitation-sequencing (ChIP-seq) assays revealed histone Khib in 35% of protein-coding genes. Most Khib peaks were located in genic regions, and they were highly enriched at the transcription start sites. Histone Khib is highly correlated with acetylation (ac), particularly H3K23ac, which it largely resembles in its genomic and genic distribution. Notably, co-enrichment of histone Khib and H3K23ac correlates with high gene expression levels. Metabolic profiling, transcriptome analyses, and ChIP-qPCR revealed that histone Khib and H3K23ac are co-enriched on genes involved in starch and sucrose metabolism, pentose and glucuronate interconversions, and phenylpropanoid biosynthesis, and help fine-tune plant response to dark-induced starvation. These findings suggest that Khib and H3K23ac may act in concert to promote high levels of gene transcription and regulate cellular metabolism to facilitate plant adaption to stress. Finally, HDA6 and HDA9 are involved in removing histone Khib. Our findings reveal Khib as a conserved yet unique plant histone mark acting with lysine acetylation in transcription-associated epigenomic processes. Oxford University Press 2021-06-24 /pmc/articles/PMC8287917/ /pubmed/34165567 http://dx.doi.org/10.1093/nar/gkab536 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Data Resources and Analyses
Zheng, Lanlan
Li, Chen
Ma, Xueping
Zhou, Hanlin
Liu, Yuan
Wang, Ping
Yang, Huilan
Tamada, Yosuke
Huang, Ji
Wang, Chunfei
Hu, Zhubing
Wang, Xuening
Wang, Guodong
Li, Haihong
Hu, Juntao
Liu, Xiaoyun
Zhou, Chao
Zhang, Yonghong
Functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation in Arabidopsis under dark-induced starvation
title Functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation in Arabidopsis under dark-induced starvation
title_full Functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation in Arabidopsis under dark-induced starvation
title_fullStr Functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation in Arabidopsis under dark-induced starvation
title_full_unstemmed Functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation in Arabidopsis under dark-induced starvation
title_short Functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation in Arabidopsis under dark-induced starvation
title_sort functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation in arabidopsis under dark-induced starvation
topic Data Resources and Analyses
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8287917/
https://www.ncbi.nlm.nih.gov/pubmed/34165567
http://dx.doi.org/10.1093/nar/gkab536
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