Epigenomic Regulation of Schwann Cell Reprogramming in Peripheral Nerve Injury

Abstract

The rapid and dynamic transcriptional changes of Schwann cells in response to injury are critical to peripheral nerve repair, yet the epigenomic reprograming that leads to the induction of injury-activated genes has not been characterized. Polycomb Repressive Complex 2 (PRC2) catalyzes the trimethylation of lysine 27 of histone H3 (H3K27me3), which produces a transcriptionally repressive chromatin environment. We find that many promoters and/or gene bodies of injury-activated genes of mature rat nerves are occupied with H3K27me3. In contrast, the majority of distal enhancers that gain H3K27 acetylation after injury are not repressed by H3K27 methylation before injury, which is normally observed in developmentally poised enhancers. Injury induces demethylation of H3K27 in many genes, such as Sonic hedgehog (Shh), which is silenced throughout Schwann cell development before injury. In addition, experiments using a Schwann cell-specific mouse knock-out of the Eed subunit of PRC2 indicate that demethylation is a rate-limiting step in the activation of such genes. We also show that some transcription start sites of H3K27me3-repressed injury genes of uninjured nerves are bound with a mark of active promoters H3K4me3, for example, Shh and Gdnf, and the reduction of H3K27me3 results in increased trimethylation of H3K4. Our findings identify reversal of polycomb repression as a key step in gene activation after injury.

Polycomb repression regulates Schwann cell proliferation and axon regeneration after nerve injury

“…Therefore, we decided to examine regulation of Neuregulin1 ( Nrg1 ) type I, which is induced in Schwann cells within 24 hours after injury, and increases remyelination efficiency (Ronchi et al 2016; Stassart et al 2013). Interestingly, the ChIP-seq mapping of H3K27me3 in mature nerve (Ma et al 2016) indicated that transcription start sites of Nrg1 type I and III are occupied by this repressive histone mark (Figure 3A), and ChIP-qPCR assays showed a decrease in H3K27me3 in the type I promoter after injury (Figure 3B), showing a correlation between methylation dynamics of H3K27 and Nrg1 type I gene activation. Gene expression analysis of Eed cKO nerves, which display a Schwann cell-specific loss of H3K27me3 (Ma et al 2015), revealed derepression of Nrg1 type I in Eed cKO nerves at 2 months of age in the absence of injury (Figure 3C).…”

“…Regenerating nerves initiate a program that includes myelin debris removal, axon regeneration and remyelination (Arthur-Farraj et al 2012; Jessen and Mirsky 2016). Since our previous studies showed precocious activation of injury genes in the Eed cKO (Ma et al 2016), we had anticipated that there may be accelerated regeneration. However, the ultrastructural analysis revealed that there were relatively fewer axons at the transverse sections 4 mm distal to the injury site in Eed cKO nerves compared to sections of control mice, which exhibited a substantial number of myelinated axons at 14 d after injury (Figure 1A, B).…”

“…Sciatic nerves were subjected to MNase-ChIP with an antibody targeting H3K27me3 as described previously (Ma et al 2016) with a few changes. Instead of washing with RIPA buffer after the immunoprecipitation, ChIP samples were washed with washing buffer 1 (WB1, 50 mM Tris–HCl, pH7.5; 10 mM EDTA; 125 mM NaCl) once, WB2 (50 mM Tris–HCl, pH7.5; 10 mM EDTA; 250 mM NaCl) once, and WB3 (50 mM Tris–HCl, pH7.5; 10 mM EDTA; 500 mM NaCl) twice.…”

“…Hypergeometric optimization of motif enrichment (HOMER, RRID:SCR_010881) (Heinz et al 2010) was used to determine enriched binding regions for H3K27me3-ChIP relative to sequencing of an input chromatin sample. H3K27me3-occupied genes were defined by the presence of the histone modification around the transcriptional start site (±7 Kb) with HOMER peak-score ≥ 10 (Ma et al 2016). The raw data files are deposited in National Center for Biotechnology Information Gene Expression Omnibus (GEO) under accession number GSE106994.…”

“…It has become clear that epigenomic changes are important for such reprogramming events, employing mechanisms of gene activation and derepression (Brügger et al 2017; He et al 2018; Hung et al 2015; Jacob 2017; Ma and Svaren 2018). Our previous studies identified the association of trimethylation at Lys27 of histone H3 tail (H3K27me3) at promoters of many genes that become activated after peripheral nerve injury, and we found that the demethylation is required for full activation of some repair genes (Ma et al 2016). H3K27 methylation is catalyzed by Polycomb Repressive Complex 2 (PRC2), comprising the lysine methyltransferase EZH1/2 and the nonredundant core subunits, suppressor of zeste 12 (SUZ12) and embryonic ectoderm development (EED).…”