Epigenetic regulation comprises numerous mechanisms providing regulatory information to the genome without altering its primary nucleotide sequence, information transferred heritably to offspring or from parent to daughter cells. Epigenetic mechanisms are implicated in various processes, including gene silencing and expression, apoptosis, maintenance of stem cell pluripotency, and X-chromosome inactivation. At the molecular level, epigenetic regulators include covalent modifications to the chromatin, which is composed of DNA in complex with proteins, mainly histones. This family of small proteins is usually represented by histones H1, H2A, H2B, H3 and H4, which in turn are composed of basic amino acids necessary for DNA binding. Post-translational modifications of histones (e.g. histone acetylation, methylation, and ubiquitination) or DNA (e.g. DNA methylation) locally modify the chromatin structure by altering the interaction between histones and DNA. The altered states can either facilitate or prevent gene transcription. Histone acetylation leads to chromatin relaxation and increased accessibility for transcription factors. On the contrary, deacetylation by histone deacetylases (HDACs) has a repressive impact on transcription. Among HDAC enzymes, class I comprises the constitutively expressed HDAC1-3 and HDAC8, having histones as their main substrates.
Given their nuclear localization, class I HDACs are among the key regulators responsible for epigenetic marks. Because several studies suggest that HDAC overexpression is linked to various diseases (such as cancer, cardiovascular, and neurodegenerative disorders), HDAC inhibition has emerged as an attractive therapeutic strategy to restore the histone acetylation balance. However, it is difficult to target drugs influencing histone-modifying enzymes to specific genomic loci. Moreover, HDAC inhibitors are known to have effects on the acetylation of other proteins. To have a direct effect on histone acetylation leading to transcriptional activation, HDAC inhibitors need to cross multiple cell membranes to reach the nucleus, avoid interaction with other lysine deacetylating enzymes, and avoid binding to HDAC isoforms located in the cytoplasm. Furthermore, the cellular effects of deacetylation inhibition on non-histone proteins need to be discriminated when trying to understand the effects of the HDAC inhibitors.
HDAC inhibitors are currently used in cancer therapy and have been considered as epigenetic drugs. However, whether the therapeutic effects of HDAC inhibitors are a direct consequence of changes in chromatin accessibility and transcription remains to be proven. Together with the drug localization issue, the specific mechanisms involved in therapeutic success/failure of HDAC inhibitors remain to be investigated. These mechanisms include i) the genome-wide transcriptional effects resulting from histone deacetylation in cells overexpressing specific HDAC isoforms; ii) the effects of isoform-dependent transcriptional regulation and their association with chromatin accessibility; and iii) the effects of HDAC inhibitory drugs that are a direct consequence of loci-related chromatin remodeling. This project aimed to address the issues mentioned above through an innovative approach, using HDAC-overexpressing cells, genome-wide studies, and a new epigenetic editing tool (CRISTONE) designed to bring an HDAC inhibitor to a specific locus using the guide-RNA-targeted CRISPR/dCas9 technology. This will be useful in the search for new cancer treatment, including epigenetic therapies.
