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Writing, reading and managing stress with H3K9me

Periodic Reporting for period 2 - Epiherigans (Writing, reading and managing stress with H3K9me)

Reporting period: 2018-12-01 to 2020-05-31

We continue to pursue our discovery of the epigenetic principles that control organismal development, somatic tissue differentiation, and germline immortality. These key phenomena depend on genome stability and the proper spatiotemporal regulation of gene expression. All higher eukaryotic genomes have a large fraction of repetitive DNA that must be kept in a transcriptionally silence mode to prevent R-loop – induced DNA damage (Zeller et al., 2016). Transcription is therefore tightly controlled by restricting the accessibility of transcription factors and RNA-polymerases to the DNA. In order to repress transcription across a large number of genes, the genome is organized into heterochromatin, a compact state of folding that prevents normal transcription. This heterochromatin depends on the methylation of histone H3 on lysine 9 (H3K9me), which functions as an essential platform for heterochromatin formation (Padeken et al., 2015). The correct segregation of inactive heterochromatin and active euchromatin is essential for healthy development and both the perturbation of H3K9me resulting in the aberrant expression of repetitive elements (Ting et al., 2011), as well as the mistargeting of H3K9me resulting in the silencing of tumor suppressor genes (Chen et al., 2010; Hua et al., 2014) has been described for a variety of cancers. Its role in restricting the expression of genes to individual tissues, and/or developmental stages and its role in constitutively repressing the transcription of repetitive elements requires that H3K9me can be selectively established, maintained and erased, both in time and in space. We have made a great deal of progress in understanding the mechanisms that target the enzymes that catalyze H3K9me during development, in face of stress such as heat shock, during tissue differentiation and in case of exogenous viral invasion. All these events are relevant to human health and the integrity of each tissue in a multicellular organism.
Our laboratory has shed light on the role of a specific ubiquitous histone modification – that of histone H3 lysine 9 methylation in the establishment and maintenance of heterochromatin in C. elegans. C elegans has only 2 histone methyltransferases involved in this key modification – and they represent conserved enzymes. Our work on C. elegans H3K9 methyltransferases (MET-2 and SET-25) has highlighted the essential function of MET-2 in ensuring genomic stability and the absolute dependence of H3K9me-mutants on factors ensuring replication fork stability (Padeken et al., 2019). Further molecular and biochemical studies of the MET-2 enzyme identified a novel interaction partner that ensures its proper nuclear localization and functional activity (Delaney et al., 2019). This work also highlighted a critical role for MET-2 during temperature stress, an observation we are following up on. An ongoing microscopy-based screen is also looking to identify additional factors that mediate MET-2 targeting to specific regions in chromatin. A similar screen was established to investigate SET-25 targeting and allowed us to connect the small RNA pathway to H3K9methyl-mediated silencing of specific regions of the genome. We then studied the role of spatial organization of heterochromatin in differentiated tissues – namely gut and muscle. We have shown that a lamin mutation causes deterioration of muscle in worms, recapitulating a human disease (Harr et al., 2020) and we have shown that in intestinal cells, the disruption of a strict sequestration of a euchromatic factor, CBP/p300, away from heterochromatin, leads to an activation of repressed tissue specific genes and loss of intestine-cell identity (Cabianca et al., Nature). Finally we have discovered a new principle of silencing that depends on selective nuclear degradation of transcripts. We showed that a complex called LSM2-8 – coupled with an RNA degrading machine (XRN-2) degrades specifically messages arising from genes repressed by the so-called Polycomb pathway, a system that maintains another histone mark on conditionally silent genes, histone H3K27me3. This mRNA degradation is the first proof that select mRNA turnover in the nucleus communicates to the compaction state of chromatin on genes. This has relevance, apparenetly, for the innate immunity genes in man.
Advances in medicine have contributed to people living longer than ever before. However, for a large proportion of the population these extra years are not spent as healthy disease-free years but are burdened with complex and often chronic diseases. Not only is an individual’s quality of life affected, but these conditions are a burden to European society and costly for healthcare systems. We understand now that almost all chronic and age-linked diseases – apart from those caused by infectious agents – are linked to a loss of cell type integrity. This occurs both on the level of genomic integrity, that is a loss of an intact, nonmutated genome, and on the level of proper transcription – the conversion of the genetic code into a given cell type. To understand and intervene effectively in disease, we must detect disease early and reverse degenerative events. Before we can do that we must understanding of the molecular events that establish and maintain cell fate, to be able to identify deviation from this at the very onset of disease. Our work addresses the molecular mechanisms that allow the physiological integrity of cells, tissues and organs to be lost. A deep understanding of these molecular processes at the level of specific tissues will provide informative biomarkers that will alert a physician when a cell or tissue enters a trajectory towards disease or other types of degeneration. Stratification of patients based on the underlying molecular mechanisms of disease will help a physician to select the most appropriate treatment or combination of treatments for an individual. Such targeted approaches, which aim to restore tissue and cell type integrity by steering deviant cells back to their healthy trajectory, will reduce detrimental side-effects and the threat of relapse. Such knowledge will also enable the systematic identification of new drug targets and therapeutic approaches based on a detailed understanding of a diseases’ molecular vulnerabilities. As a result, the success rates of therapy development, clinical trials and deployment in the clinic will be significantly increased. The outcome of which will be to further our understanding of human biology and transform medical practice over the next decade. In brief, understanding how euchromatin and heterochromatin identities are maintained and segregated not only contributes to our basic understanding of differentiation but is also relevant to the field of cell fate determination, maintenance and reprogramming. We believe that our work will have a profound impact on regenerative medicine and disease modelling approaches which will strongly shape medicine of the future.