Paolo Sassone-Corsi (UCI) discussed how the cellular metabolism and the epigenome might communicate with each other in previously unsuspected ways. Specifically, he suggested that changes in the levels of cellular metabolites (which are partly controlled by the circadian clock) could influence the epigenome. Sassone-Corsi explained that because histone-modifying enzymes could “sense” the cellular metabolism, it is possible that they interpret the metabolic state of a cell at a given time by modifying chromatin in a specific cyclic manner.13
As an example, the oscillatory nature of NAD+ dictates oscillatory acetylation of Sirt1 targets, even though Sirt1 levels do not oscillate.14
An important fraction of the genome is transcriptionally controlled in a circadian manner; it is intriguing to now start to understand how the circadian clock could act through the epigenome to exert its regulatory function.
Histone modifications signal the recruitment or activity of downstream effectors. The interpretation of this epigenetic signal is mediated by the so-called “readers,” which are specialized proteins that are able to interpret the “epigenetic language.” Or Gozani’s lab (Stanford University) investigates the role of lysine methylation in disease. At this symposium he described a high-throughput peptide microarray assay designed to discover new “readers” containing chromatin-associated domains that could specifically recognize H4K20me2. Gozani and colleagues identified the BAH domain in Orc1 (the largest subunit of the origin recognition complex and previously implicated in primordial dwarfism) as the link between H4K20me2, Orc1 and primordial dwarfism. Binding of H4K20me2 appears to be required for efficient loading of ORC onto chromatin. Importantly, mutation in the BAH domain of Orc1 is implicated in the etiology of the Meier-Gorlin syndrome (a primordial dwarfism syndrome), due to the impairment of H4K20me2 recognition. There is therefore a potential role for H4K20me2 in determining organism size in mice. Remarkably, H4K20me2 depletion in zebrafish results in dwarfism.
RNA molecules are also important components of the dynamic epigenome. Axel Imhof (Ludwig-Maimilians Universität, München, Germany) discussed the role that RNA molecules play in chromatin. He explained that the binding of RNA to in vitro assembled chromatin appears to “open” chromatin, and the removal of RNA from chromatin leads to its compaction. This may be due to the removal of many (RNA-dependent) factors from chromatin, which he analyzed using an in vitro chromatin assembly system prepared from Drosophila embryos.15
In his talk, Imhof suggested that the formation of a chromatin associated RNP network may be responsible for maintaining an accessible chromatin structure.
The role of cohesin in the regulation of gene expression was the topic of Kyoko Yokomori’s (UCI) talk. In studies of the β-globin locus, she showed that cohesin, and the cohesin loading factor Nipbl, bind to the locus control region at the CTCF insulator region and distal enhancer, upon differentiation. Cohesin binding is critical for long-range chromatin interactions between the enhancer and the promoter and is important for β-globin gene expression in human cells. Nipbl haploinsufficiency affects cohesin binding, altering chromatin interactions and affecting gene expression.
Continuing the discussion on the mechanism by which the epigenome regulates transcriptional activation, Jean Marc Egly (IGBMC, INSERM, Strasbourg, France) talked about his studies of the intriguing role of nucleosome excision repair (NER) factors in transcription.16
Egly explained that, upon gene activation, the RNAP II transcription machinery associates with NER factors at the promoter. Egly and colleagues observed that, in patients with silenced NER factors, the changes necessary for transcription to initiate (such as, H3K4me, H2K9me, H3K9/K14ac and DNA demethylation) do not occur. Deficiencies in NER factors impede the recruitment of other necessary remodeling factors that modify chromatin. Specifically, XPG and XPF appear to have a role in the formation of the necessary chromatin loop between the promoter and terminator.