In his book The Triple Helix, Richard Lewontin underscores the importance of integrating the contribution of genes, the organism, and the environment, if one intends to fully understand biological systems. The past few decades, and in particular the most recent years, have revealed that genetics alone is not sufficient to explain phenotypes. Epigenetics, defined as heritable changes in gene expression that do not involve alterations in the sequence of nucleotides, has assumed increasingly important roles.
Epigenetics promises to shed light on biological processes implicated in development and differentiation, the interface between organisms and environmental perturbations, and carcinogenesis.
One of the major questions during development is not only how the state of cell differentiation is achieved but, in addition, how it is maintained once it is established. “The main focus of our work is to understand how cells organize their specific regulatory landscapes,” says Gioacchino Natoli, M.D., group leader in the department of experimental oncology at the European Institute of Oncology, Milan.
While epigenetic mechanisms are required to establish a genomic landscape during differentiation, a more interesting question is to understand their involvement once cells become differentiated. “It is not sufficient to have epigenetic mechanisms, even though they are important, but the constant and continuous supervision by lineage-specific transcription factors is required for maintenance of lineage determination,” says Dr. Natoli.
This view is supported by several pieces of evidence, which reveal that the deletion of lineage-specific transcription factors from fully differentiated cells is followed by the loss of differentiation. Moreover, the constant action of environmental perturbations modifies the epigenome, which subsequently needs to revert to the initial stage from before the perturbation.
Transcription factors are constantly binding to the DNA and continually shape the chromatin landscape, and whenever they sense an environmental change, they may activate a different set of genes or identical genes at different times. An attractive possibility is that lineage determining transcription factors act mainly by organizing the repertoire of enhancers, which are known to be strongly cell type-specific, and an emerging concept is the involvement of a specific three-dimensional landscape, in which the spatial organization of the genome ensures that enhancers correctly activate only the right promoters. “This is the new idea that is coming out and requires additional work,” explains Dr. Natoli.
“We recently identified and characterized a new type of epigenetic control, a unique type of methylation that occurs on p53 and is quite instrumental in determining cell fate,” says Nicholas La Thangue, Ph.D., professor and chair of cancer biology at the University of Oxford.
At the “Oxford Symposium on Epigenetic Mechanisms in Health and Disease,” Dr. La Thangue talked about this modification, which occurs on an arginine residue located in the p53 tumor suppressor region and is mediated by an enzyme called protein arginine methyl transferase 5.
A second topic of interest in Dr. La Thangue’s lab is the retinoblastoma protein pRb, which acts as a gatekeeper by regulating the G1 to S phase transition during cell-cycle progression and is frequently mutated in tumors. We found that a lysine methyl transferase, Set7/9, targets pRb.”
In addition to unveiling this epigenetic modification, which is unlike the one in p53 where the methylated residue is an arginine, Dr. La Thangue and collaborators made another fundamental discovery when, after mapping this specific lysine residue that becomes methylated by Set7/9, they noticed that the same residue governs another level of control, which is pRb phosphorylation. However, pRb phosphorylation is mediated by cyclin-dependent kinases, which regulate cell-cycle progression, and by phosphorylating and inactivating pRb, they release its negative regulation of the cell cycle.
In its methylated state, pRb phosphorylation is switched off and cells enter a quiescent, nonproliferating state. “The provocative thing is the interplay that we observed between different modifications on pRb,” notes Dr. La Thangue. “This is a very nice example of interplay between different types of epigenetic marks that can occur on other proteins.”
This complex interplay between different types of epigenetic modification makes these proteins become promising leads in designing therapeutic targets, particularly when targeting one protein in a pathway can impact a global cellular event. “There are some truly superb drug targets to focus on.”