Trithorax and Polycomb methyltransferase complexes in cell fate determination.

Trithorax and Polycomb methyltransferase complexes in cell fate determination.

Funding Type: 
New Faculty I
Grant Number: 
RN1-00579
Approved funds: 
$2,374,020
Stem Cell Use: 
Embryonic Stem Cell
Public Abstract: 
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 methylation of histones and associated DNA. Methylation marks are written by specific enzymatic activities, called methyltransferases. Different methyltransferases can activate or repress genes, and the right balance between the two is critical for proper execution of the developmental programs. Thus, not surprisingly, deregulation of methyltransferases leads to human disease, most notably cancer. Here we propose to address how the interplay between “activating” and “silencing” methylation signals regulates gene expression patterns in embryonic stem cells and during their differentiation along the neural lineage. These studies will advance our knowledge of the unique properties of chromatin in embryonic stem cells and will address the mechanisms of gene expression during neural commitment. This basic science foundation will be necessary for development of efficient protocols to direct the differentiation of stem cells into therapeutically useful neural tissues. In addition to advancing basic knowledge, our studies will lead to development of novel technology that takes advantage of the latest developments in bioengineering and proteomics. This technology will be broadly applicable in studies of stem and progenitor cells, human and from different model organisms and will push stem cell research forward.
Statement of Benefit to California: 
We believe the proposed research will benefit people of California in the following ways: It will result in development of novel technology that will be broadly applicable to study different stem and progenitor cells and will help position us and other Californian scientists at the forefront of stem cell research. It will help uncover unique biological properties of embryonic stem cells. It will generate wealth of information on novel molecules involved in embryonic stem cell pluripotency and differentiation. This information will provide a foundation for development of stem cell-based therapies. It will increase experience and knowledge of embryonic stem cells among residents of California. This project involves cooperation between three laboratories with complementary expertise. The interaction will facilitate skill exchange and staff training in cutting edge multidisciplinary approaches.
Progress Report: 

Year 1

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 methylation of histones. Histone methylation marks are written by specific enzymatic activities, called methyltransferases. Different methyltransferases can activate or repress genes, and the right balance between the two is critical for proper execution of the developmental programs. Thus, not surprisingly, deregulation of methyltransferases leads to human disease, including congenital malformation and cancer. Embryonic stem cells and other progenitor cells contain unique histone methylation signatures at genes that are dynamically activated or repressed in differentiation, depending on a specific cell type. With CIRM funding our research group made a significant progress in understanding how this unique methylation signatures are formed and properly maintained in embryonic and adult stem cells and resolved upon differentiation. We have identified novel chromatin proteins associated with methyltransferases in stem cells. We had shown that one of these proteins, called Jarid2, is responsible for directing the silencing methyltransferase to developmental genes and for regulating its activity. Depletion of Jarid2 affects developmental programs and leads to failure of differentiation. We have also made headways in understanding how methyltransferase complexes connect to the signaling pathways orchestrating stem cell self-renewal and differentiation. Our work contributes to the basic science foundation that furthers our understanding of what makes stem cell a stem cell and what processes are involved in transitions from stem cells to specific, differentiated cell types.

Year 2

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.

Year 3

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. With CIRM funding we characterized enhancer repertoires utilized by human embryonic cell types such as embryonic stem cells, neuroectoderm and neural crest. From these analyses we made interesting novel observations regarding gene regulation during human embryogenesis. We are now trying to understand how variation in regulatory elements and factors recognizing these elements contributes to developmental disorders.

Year 4

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. With CIRM funding we characterized enhancer repertoires utilized by human embryonic cell types such as embryonic stem cells, neuroectoderm and neural crest. From these analyses we made interesting novel observations regarding gene regulation during human embryogenesis. We are now trying to understand how variation in regulatory elements and factors recognizing these elements contributes to developmental disorders.

© 2013 California Institute for Regenerative Medicine