The physiological template of our genome, called chromatin, is composed of DNA wrapped around histone proteins. In the process of development the genome is interpreted in a way that is dynamic, and yet, often heritable, to produce different specialized tissues and organs. A substantial portion of information that is required for proper interpretation of the genome is transmitted in a form of histone modifications. Specific combinations of chemical modifications of histones form a basis of epigenetic marking system, which helps to organize the genome into functional domains, some of which are active, while others are silenced. These marking patterns can be harnessed to discover genomic regulatory elements involved in human development and disease. Indeed, less than 2% of the human genome encodes protein-coding genes. But many trait-specific and disease specific mutations seem to map away from such coding sequences. This paradox is partially resolved by observation that some of the noncoding sequences are involved in regulation of when and where in the developing organism genes are to be turned on and off. One class of such regulatory sequences is called enhancers, since they have a property to greatly enhance gene expression.
In the last reporting period we showed that in human embryonic stem cells two different epigenetic signatures are associated with, and specifically distinguish, two classes of enhancer elements. One signature marks enhancers that are actively turned on in embryonic stem cells, and another marks class of enhancers that we dubbed “poised enhancers”, which are not active, but are kept in a state of anticipation that allows them to become rapidly activated when stem cells undergo a decision to differentiate. Discovery of poised enhancer signature in embryonic stem cells identified a set of over 2,000 putative early developmental enhancers in a single study, thereby creating an invaluable resource for generation of reporters for lineage tracking and isolation of transient cell populations representing early steps of human development.
In addition, with CIRM funding we also identified a new member of mouse embryonic stem cell transcriptional network, which protects stem cells from entering extraembryonic fates, and does so by functioning as a sequence-specific and context-dependent transcriptional regulator. During normal development, expression of this protein is restricted to pluripotent cells of the embryo, but interestingly it is also associated with human cancers.