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Genome-wide Analysis of Histone H3 Lysine 27 Trimethylation Profiles in Sciatic Nerve of Chronic Constriction Injury Rats

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Abstract

The histone H3 lysine 27 trimethylation (H3K27me3) is one of the most important chromatin modifications, which is associated with injury-activated gene expression in Schwann cells (SCs). However, the alteration of genome-wide H3K27me3 enrichments in the development of neuropathic pain is still unknown. Here, we applied the chromatin immunoprecipitation sequencing (ChIP-seq) approach to identify the alteration of differential enrichments of H3K27me3 in chronic constriction injury (CCI) sciatic nerve of rats and potential molecular mechanisms underlying the development of neuropathic pain. Our results indicated that CCI increased the numbers of SCs displaying H3K27 methyltransferase enhancer of zeste homolog 2 (EZH2) and H3K27me3 in the sciatic nerve. ChIP-seq data showed that CCI significantly changed H3K27me3 enrichments on gene promoters in the sciatic nerve. Bioinformatics analyses exhibited that genes gaining H3K27me3 were mostly associated with regulation of cell proliferation, response to stress and oxidation-reduction process. Genes losing this mark were enriched in neuronal generation, and MAPK, cAMP as well as ERBB signaling pathways. Importantly, IL1A, CCL2, NOS2, S100A8, BDNF, GDNF, ERBB3 and C3 were identified as key genes in neuropathic pain. CCI led to significant upregulation of key genes in the sciatic nerve. EZH2 inhibitor reversed CCI-induced increases of H3K27me3 and key gene protein levels, which were accompanied by relieved mechanical allodynia and thermal hyperalgesia in CCI rats. These results indicate that genes with differential enrichments of H3K27me3 in SCs function in various cellular processes and pathways, and many are linked to neuropathic pain after peripheral nerve injury.

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Abbreviations

BDNF:

Brain-derived neurotrophic factor

BP:

Biological processes

CCI:

Chronic constriction injury

CCL2:

C-C motif chemokine ligand 2

ChIP-seq:

Chromatin immunoprecipitation sequencing

EZH2:

Enhancer of zeste homolog-2

ERBB3:

Receptor tyrosine-protein kinase erbB-3

GDNF:

Glial cell-derived neurotrophic factor

GO:

Gene ontology

H3K27me3:

Histone H3 lysine 27 trimethylation

IL1A:

Interleukin-1α

KEGG:

Kyoto encyclopedia of genes and genomes

MAG:

Myelin-associated glycoprotein

MWT:

Mechanical withdrawal threshold

NOS2:

Nitric oxide synthase 2

PRC2:

Polycomb-repressive complex 2

SCs:

Schwann cells

TSSs:

Transcription start sites

TWL:

Thermal withdrawal latency

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Funding

The study was supported by National Natural Science Foundation of China (No. 3187125; No. 81371234) and Natural Science Foundation of Shandong Province, China (ZR2019MH027).

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  1. Shuhui Chen and Xinpei Gu have equally contributed to this work.

Authors and Affiliations

  1. Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, 2 Ying Sheng Dong Lu, Taian, 271000, China

    Shuhui Chen, Xinpei Gu, Ruidi Li, Shuhong An & Zhaojin Wang

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Contributions

SC and XG performed experiments, analyzed data, and wrote the manuscript. SA analyzed and interpreted data, and wrote the manuscript. RL conducted parts of the animal surgery and performed the experiments. ZW provided advice in the design of the study and in interpreting the data and revising the manuscript. All authors have read and approved the final version of the manuscript. The key data are included in figures, tables, and additional files. The full datasets that were analysed are available from the corresponding author on reasonable request. ChIP-seq experiments were performed by KangChen Bio-tech, Shanghai, China.

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Correspondence to Shuhong An or Zhaojin Wang.

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Chen, S., Gu, X., Li, R. et al. Genome-wide Analysis of Histone H3 Lysine 27 Trimethylation Profiles in Sciatic Nerve of Chronic Constriction Injury Rats. Neurochem Res 48, 1945–1957 (2023). https://doi.org/10.1007/s11064-023-03879-y

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