Loss of IκBζ Drives Dentin Formation via Altered H3K4me3 Status

Abstract

Enforced enrichment of the active promoter marks trimethylation of histone H3 lysine 4 (H3K4me3) and acetylation of histone H3 lysine 27 (H3K27ac) by inhibiting histone demethylases and deacetylases is positively associated with hard tissue formation through the induction of osteo/odontogenic differentiation. However, the key endogenous epigenetic modulator of odontoblasts to regulate the expression of genes coding dentin extracellular matrix (ECM) proteins has not been identified. We focused on nuclear factor (NF)–κB inhibitor ζ (IκBζ), which was originally identified as the transcriptional regulator of NF-κB and recently regarded as the NF-κB–independent epigenetic modulator, and found that IκBζ null mice exhibit a thicker dentin width and narrower pulp chamber, with aged mice having more marked phenotypes. At 6 mo of age, dentin fluorescent labeling revealed significantly accelerated dentin synthesis in the incisors of IκBζ null mice. In the molars of IκBζ null mice, marked tertiary dentin formation adjacent to the pulp horn was observed. Mechanistically, the expression of COL1A2 and COL1A1 collagen genes increased more in the odontoblast-rich fraction of IκBζ null mice than in wild type in vivo, similar to human odontoblast-like cells transfected with small interfering RNA for IκBζ compared with cells transfected with control siRNA in vitro. Furthermore, the direct binding of IκBζ to the COL1A2 promoter suppressed COL1A2 expression and the local active chromatin status marked by H3K4me3. Based on whole-genome identification of H3K4me3 enrichment, ECM and ECM organization–related gene loci were selectively activated by the knockdown of IκBζ, which consistently resulted in the upregulation of these genes. Collectively, this study suggested that IκBζ is the key negative regulator of dentin formation in odontoblasts by inhibiting dentin ECM- and ECM organization–related gene expression through an altered local chromatin status marked by H3K4me3. Therefore, IκBζ is a potential target for epigenetically improving the clinical outcomes of dentin regeneration therapies such as pulp capping.

Pharmacological Activation of YAP/TAZ by Targeting LATS1/2 Enhances Periodontal Tissue Regeneration in a Murine Model

“…YAP/TAZ and the TEAD complex are known to directly associate with the gene regulatory domain and evoke osteogenic gene expression in osteoblasts and mesenchymal stem cells [ 32 ]. Epigenetic alteration of chromatin accessibility by genome-wide modulators, such as histone acetyltransferases and histone methyltransferase, and local modulators, such as NFkBiζ, are deeply linked with hard tissue formation and inflammation-induced alveolar bone destruction [ 33 , 34 , 35 ]. In contrast to osteogenic genes that were directly transcribed by YAP/TAZ transcriptional ability, YAP/TAZ involvement in cell proliferation is linked with metabolic reprogramming [ 36 ].…”

“…Micro-computed tomography (μCT) was conducted as described previously [ 33 ]. The hemimaxillae were dissected, fixed for 24 h in 4% paraformaldehyde, and stored in Dulbecco’s phosphate-buffered saline (DPBS) at 4 °C.…”

Tensor Decomposition and Principal Component Analysis-Based Unsupervised Feature Extraction Outperforms State-of-the-Art Methods When Applied to Histone Modification Profiles

“…This study consisted of four H3K27me3 ChIP-seq profiles (two controls and two treatments) and four H3K4me3 ChIP- seq profiles (two controls and two treatments) in addition to two input profiles that used cells as odontoblasts (treatment was siRNA: si-IKBz) [23]. Among them, four H3K27me3 ChIP-seq profiles were downloaded from the GEO Supplementary file.…”

The odontoblastic differentiation of dental mesenchymal stem cells: molecular regulation mechanism and related genetic syndromes

“…KDM5A negatively modulates the odontoblastic differentiation of hDPCs by deleting H3K4me3 from the promoters of target genes, and the inhibition of KDM5A increases H3K4me3 levels, as well as ALP activity and odontogenic markers ( Li et al, 2020 ). Inhibition of HDMs leads to the upregulation of H3K4me3 and promotes odontoblastic differentiation ( Yuan et al, 2022 ).…”