Role of histone lysine methyltransferases and demethylases in axis patterning and regeneration of Hydra

Abstract

Hydra is a Cnidarian with the first polarized body axis in metazoans determined by the Wnt/β-catenin signalling pathway. It also possesses a remarkable ability to regenerate both from small tissue fragments and aggregates of dissociated cells. The processes of axis patterning and regeneration require the spatio-temporal regulation of gene expression, which is brought about by large-scale reprogramming of the chromatin. We focused on investigating the role of histone lysine methyltransferases (KMTs) and histone lysine demethylases (KDMs) during axis patterning and regeneration in Hydra. We first identified the complete repertoire of KMTs and KDMs present in Hydra. Hydra, multiple proteins harbour the relevant catalytic domains but do not have homologs in higher organisms indicating a putative taxon-specific function. The EZH2 and JMJD3/UTX enzymes that regulate the methylation of H3K27 residue play a critical role in the Wnt/β-catenin mediated axis patterning. Moreover, this study points towards a ‘methylation/acetylation’ switch at the H3K27 residue that regulates the head organizer genes via cis-regulatory elements. We also analysed the publicly available NGS data and integrated information from RNA sequencing, ChIP-sequencing and ATAC sequencing. This helped us find the crosstalk between different signalling pathways with the Wnt signalling pathway in Hydra. Further, abrogation of SETD8, EZH2, and JMJD3/UTX activity using pharmacological inhibitors revealed their role in regeneration. Inhibition of the catalytic activity of SETD8, which exclusively imparts the H4K20me1 mark on chromatin, delayed head and foot regeneration, both of which are dependent on the Wnt signalling pathway. Interestingly, SETD8 directly interacts with β-catenin and is also upregulated upon systemic activation of Wnt signalling in Hydra. We then performed ChIP-sequencing on the regenerating tips and studied the dynamics of H4K20me1 occupancy during the process. We observed that there is a negative correlation between the occupancy of this novel mark and the other activation associated histone marks. Collectively, these findings suggest that H4K20me1 might be dynamically orchestrated in a genome-wide manner to regulate the Wnt target genes during regeneration in Hydra. The unique H4K20me1 plays a dual role in the transcriptional regulation depending on a context and the unique physiology of Hydra has allowed the investigation of this phenomenon.