A longstanding interest of the Chess lab is the study of unusual mechanisms involved in regulating gene expression. Recently we have been developing approaches to allow the study of epigenetic regulation at the scale of the entire human genome. Understanding of epigenetic mechanisms is essential to understanding normal development and disease. The Chess Lab website will have more information (http://research.mssm.edu/chesslab/ ).

 

DNA Methylation

 

DNA methylation stands out amongst epigenetic marks in that it is a covalent modification of the DNA molecule itself (albeit a modification that doesn’t change the DNA sequence). For DNA methylation (specifically methylation of cytosines within CpG dinucleotides) there is a known mechanism for replicating the mark. The DNA methyltransferase I encodes a protein which recognizes hemi-methylated DNA (arising from the replication of a double-stranded methylated DNA molecule) and methylates the other strand. Genome-scale analyses of DNA methylation have led to the first demonstration of methylation of the gene body (the entire transcribed region) of mammalian genes. This work also showed more methylation on the active X than the inactive X in female cells (Hellman and Chess, 2007). These observations resulted from our decision to consider all types of CpGs rather than earlier studies that focused on CpG islands. Gene body methylation, which is present in plant genomes as well as animal genomes, adds another layer of complexity to the role of DNA methylation in regulation of the genome.

 

Polymorphism in DNA sequence is well known, but until recently the potential for DNA methylation polymorphism was not explored. We and others have found evidence for such DNA methylation polymorphism. Our genome-scale analyses have revealed an interesting interplay between DNA sequence polymorphism and DNA methylation polymorphism (Hellman and Chess, 2010).

 

Random monoallelic expression

 

Monoallelic expression represents a good model system for studying epigenetics because it requires the differential treatment of two alleles (which are sometimes identical in sequence). Monoallelic expression with random choice between the maternal and paternal alleles defines an unusual class of genes comprising X-inactivated genes and a few autosomal gene-families. Using a genome-wide approach, a few years ago we assessed allele-specific transcription of ~4,000 human genes in clonal cell lines and found that over 300 were subject to random monoallelic expression (Gimelbrant et al., 2007). For a majority of monoallelic genes, they observed some clonal lines displaying biallelic expression. Clonal cell lines reflect an independent choice to express the maternal, the paternal, or both alleles for each of these genes. This can lead to differences in expressed protein sequence, and to differences in levels of gene expression.

 

Widespread monoallelic expression suggests a mechanism that generates diversity in individual human cells and their clonal descendants. We have extended these observations to the mouse genome (in preparation, 2011).

 

Some other highlights

 

Discovery of allelic exclusion of mouse odorant receptor genes (Chess et al., 1996).

 

Identification of the odorant receptor gene family in Drosophila, along with the demonstration that different olfactory neurons express different receptors and converge in their projections to the antennal lobe creating a spatial representation of olfactory space (Gao and Chess, 1999; Gao et al., 2000).

 

Elucidation of a role for asynchronous replication in immunoglobulin gene allelic exclusion (Mostoslavsky et al., 2001).

 

Demonstration of chromosome-level coordination of replication timing in mouse and human cells (Singh et al., 2003; Ensminger and Chess, 2004).

 

Cloning of a mouse from an olfactory neuron (Eggan et al., 2004).

 

Insights into the evolution of the odorant receptor gene family in humans (Gimelbrant et al., 2004).

 

Uncovering a role for alternative splicing in the specification of unique identity of neurons (Neves et al., 2004; Zhan et al., 2004).

 

Discovery of a non-coding RNAs associated with nuclear structures, and the demonstration that one of them, NEAT1, plays a structural role in the nuclear parapspeckle (Hutchinson et al., 2007; Clemson et al., 2009).