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Research Interests

Epigenetic states are flexible yet persist through multiple cell divisions and exert powerful effects on normal and abnormal cellular phenotypes. We are interested in understanding the mechanistic basis for epigenetic regulation; both during normal development as well as in cancer. Our research focuses on two major topics: the role of epigenetics in the development of the immune system, and its involvement in stem cells and cancer.


Programming of allelic exclusion

Although mammals clearly benefit from the fact that they are diploid, over 10% of the genome is actually expressed monoallelically in a non-imprinted manner.  This includes olfactory receptor selection, X-inactivation in females, ribosomal RNA regulation, and allelic exclusion in the immune system. One of the cornerstones of immunology is that mature antigen receptors are only produced from a single allele in each cell, a phenomenon termed allelic exclusion. Very little is known about how this phenomenon is regulated and programmed during development. We have demonstrated that allelic choice takes place in a programmed manner. The main proof for this mode of action is based on the observation that the two immunoglobulin-kappa alleles can already be distinguished by a number of different epigenetic marks prior to the recombination reaction. These markings include; histone modification, nuclear localization, replication timing and DNA methylation (Mostoslavsky et al, Nature 2001; Goldmit et al., Nature Immunology, 2005; Fraenkel et al., Nature Immunology, 2006; Farago et al., Nature 2012). These findings form the basis for our current studies.


1. We are interested in deciphering the role of DNA methylation, histone modification, nuclear compartmentalization of chromatin domains, replication timing, long range interactions, and the B lineage specification and commitment transcriptional network in preserving allele-specific structure. In this way, we will understand how immunoglobulin kappa locus allelic exclusion is established during lymphoid development in a clonal manner, such that one allele in each cell has a closed structure while the other allele is in an epigenetically open conformation that allows it to undergo rearrangement.


2. Recently, we demonstrated for the first time that while individual hematopoietic stem cells are characterized by allelic plasticity, early lymphoid lineage cells become committed to the choice of a single allele and this decision is then stably maintained in a clonal manner that predetermines monoallelic rearrangement in B cells.  This is accompanied at the molecular level by underlying allelic changes in asynchronous replication timing patterns at the kappa locus, which outline a completely new concept as to how the production of antigen receptors is regulated in the immune cell (Farago et al., Nature 2012). Our aim is to study the molecular mechanisms that underlie allelic plasticity in embyonal and adult stem cells, a hallmark of stem cell biology.


The role of histone and DNA methylation in stem cells and cancer

Long-term repression plays an important part in the programming of gene expression profiles in the developing organism.  We have clearly demonstrated that the histone methylase G9a is a master structural regulator that plays an important role in early development by targeting a wide network of embryonic genes for post-implantation repression. This silencing process includes key genes, such as Oct-3/4, Nanog and Dnmt3L (Feldman et al., Nature Cell Biology, 2006; Epsztein-Litman et al., Nature Structural and Molecular Biology, 2008). Tumor properties are largely determined by the balance between the stem cell state, with its self-renewal capacity and phenotypic plasticity, and the inherent program that directs these cells to undergo differentiation. This balance is largely controlled by epigenetic regulators.


1. We are interested in studying the molecular mechanisms by which epigenetic regulators execute gene expression changes to control cancer cell differentiation state. Specifically, we will decipher how changes in the activity of chromatin regulators influence chromatin structure throughout the genome, and how these factors actually regulate the establishment of cancer specific methylation states.


2. Many studies have shown that cancer cells are subjected to abnormal de novo DNA methylation compared with their normal counterparts. Furthermore, it was shown that methylation occurs through a programmed mechanism that targets specific genes. Moreover recent findings show that chronic inflammation, which is now an established cancer risk factor, is associated with aberrant DNA methylation as well.  Our team is performing a comprehensive analysis that could help decipher the rules that govern this process of de novo methylation on a genome-wide basis, as well as understanding the molecular mechanisms that underlie this process. We will study how upstream signaling pathways regulate global de novo methylation in inflammation and cancer. Since this mechanism is characteristic of many types of tumors, it would potentially lead to a better understanding of cancer, and, hopefully, to a treatment across a wide spectrum of cancers.