Reduced non-CpG methylation is a potential epigenetic target after spinal cord injury

Zhourui Wu; Chen Li; Ran Zhu; Yiqiu Cao; Thomas C Chen; Liming Cheng

doi:10.4103/1673-5374.371399

Reduced non-CpG methylation is a potential epigenetic target after spinal cord injury

Neural Regen Res. 2023 Nov;18(11):2489-2496. doi: 10.4103/1673-5374.371399.

Authors

Zhourui Wu¹, Chen Li¹, Ran Zhu², Yiqiu Cao², Thomas C Chen³, Liming Cheng¹

Affiliations

¹ Key Laboratory of Spine and Spinal cord Injury Repair and Regeneration (Tongji University), Ministry of Education; Division of Spine, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine; Institute of Spinal and Spinal Cord Injury, Tongji University School of Medicine, Shanghai, China.
² Key Laboratory of Spine and Spinal cord Injury Repair and Regeneration (Tongji University), Ministry of Education; Institute of Spinal and Spinal Cord Injury, Tongji University School of Medicine, Shanghai, China.
³ Department of Neurosurgery, Keck School of Medical, University of Southern California, Los Angeles, CA, USA.

Abstract

DNA methylation is a critical epigenetic regulator in the occurrence and development of diseases and is closely related to various functional responses in relation to spinal cord injury. To investigate the role of DNA methylation in spinal cord injury, we constructed a library with reduced-representation bisulfite sequencing data obtained at various time points (day 0-42) after spinal cord injury in mice. Global DNA methylation levels, specifically non-CpG (CHG and CHH) methylation levels, decreased modestly following spinal cord injury. Stages post-spinal cord injury were classified as early (day 0-3), intermediate (day 7-14), and late (day 28-42) based on similarity and hierarchical clustering of global DNA methylation patterns. The non-CpG methylation level, which included CHG and CHH methylation levels, was markedly reduced despite accounting for a minor proportion of total methylation abundance. At multiple genomic sites, including the 5' untranslated regions, promoter, exon, intron, and 3' untranslated regions, the non-CpG methylation level was markedly decreased following spinal cord injury, whereas the CpG methylation level remained unchanged at these locations. Approximately one-half of the differentially methylated regions were located in intergenic areas; the other differentially methylated regions in both CpG and non-CpG regions were clustered in intron regions, where the DNA methylation level was highest. The function of genes associated with differentially methylated regions in promoter regions was also investigated. From Gene Ontology analysis results, DNA methylation was implicated in a number of essential functional responses to spinal cord injury, including neuronal synaptic connection creation and axon regeneration. Notably, neither CpG methylation nor non-CpG methylation was implicated in the functional response of glial or inflammatory cells. In summary, our work elucidated the dynamic pattern of DNA methylation in the spinal cord following injury and identified reduced non-CpG methylation as an epigenetic target after spinal cord injury in mice.

Keywords: CpG methylation; DNA methylation; DNA methyltransferases; Gene Ontology; cytosine fraction; differentially methylated regions; dynamic signatures; non-CpG methylation; single-cell RNA-Seq; spinal cord injury.