Publication Information
Zheng et al., 2021
Abstract
Nucleic Acids Res. 2021 Jul 21;49(13):7347-7360. doi: 10.1093/nar/gkab536.
Functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation
in Arabidopsis under dark-induced starvation.
Zheng L(1)(2), Li C(1)(2), Ma X(1)(2), Zhou H(3), Liu Y(3), Wang P(4), Yang
H(4), Tamada Y(5), Huang J(6), Wang C(7), Hu Z(7), Wang X(8), Wang G(8), Li
H(1), Hu J(1), Liu X(4), Zhou C(3), Zhang Y(1)(2).
Author information:
(1)Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic
Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China.
(2)Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of
Bio-Medicine Research, Hubei University of Medicine, Shiyan 442000, China.
(3)Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm
Enhancement (CTGU) /Biotechnology Research Center, China Three Gorges
University, Yichang 443002, China.
(4)Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056,
China.
(5)School of Engineering, Utsunomiya University, Utsunomiya 321-8585, Japan.
(6)Center for Genomics and Systems Biology, Department of Biology, New York
University, New York 10003, USA.
(7)Center for Multi-Omics Research, Key Laboratory of Plant Stress Biology,
State Key Laboratory of Cotton Biology, School of Life Science, Henan
University, Kaifeng 475001, China.
(8)College of Life Sciences, Shaanxi Normal University, Xi'an Shaanxi 710119,
China.
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.
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic
Acids Research.
DOI: 10.1093/nar/gkab536
PMCID: PMC8287917
PMID: 34165567 [Indexed for MEDLINE]
