Understanding the Molecular Mechanism of Chromatin Dynamics and Gene Expression
Long-term goals
We use biochemistry, cell biology and genomics approaches to study the mechanism of subnucleosomes and subnucleosome associated factors and help us to understand the gene regulation and other fundamental biological problems.
In the eukaryotic nucleus, chromatin is constantly reshaped to allow proper gene expression during development and homeostasis. The nucleosome, the repeat unit of chromatin, is also dynamic. A variety of regulatory cofactors, including chromatin remodeling factors, histone chaperones, post-translational modification writers and general transcription factors, actively change the position and composition of nucleosomes. The activities of these factors may result in the formation of different types of subnucleosomal species, such as the prenucleosome, which is a partially wrapped isomer of the nucleosome. Subnucleosomal species are often found in gene regulatory regions, such as promoters and enhancers, and their presence correlates well with the gene activity (Fig 1).
The formation of subnucleosomal particles likely increases the accessibility of the underlying DNA to the transcription machinery. Understanding these subnucleosomal species is therefore essential for uncovering the mechanisms of gene expression. This knowledge will have a broad impact on a diverse range of biological research, including development and cancer biology.
Immediate goal
We purified the nucleosome destabilization factor, termed NDF, from Drosophila embryo nuclear extracts and demonstrated that human NDF (hNDF) and Drosophila NDF can destabilize nucleosomes and facilitate transcription elongation through nucleosomes. NDF is recruited to transcribed regions of active genes and colocalizes with H3K36me3. Knockout of the hNDF gene leads to the transcription dysregulation of many genes. However, the molecular mechanism by which NDF destabilizes nucleosomes and facilitates transcription through nucleosomes remains to be determined. Some questions that we would like to address are as follows.
We use biochemistry, cell biology and genomics approaches to study the mechanism of subnucleosomes and subnucleosome associated factors and help us to understand the gene regulation and other fundamental biological problems.
In the eukaryotic nucleus, chromatin is constantly reshaped to allow proper gene expression during development and homeostasis. The nucleosome, the repeat unit of chromatin, is also dynamic. A variety of regulatory cofactors, including chromatin remodeling factors, histone chaperones, post-translational modification writers and general transcription factors, actively change the position and composition of nucleosomes. The activities of these factors may result in the formation of different types of subnucleosomal species, such as the prenucleosome, which is a partially wrapped isomer of the nucleosome. Subnucleosomal species are often found in gene regulatory regions, such as promoters and enhancers, and their presence correlates well with the gene activity (Fig 1).
The formation of subnucleosomal particles likely increases the accessibility of the underlying DNA to the transcription machinery. Understanding these subnucleosomal species is therefore essential for uncovering the mechanisms of gene expression. This knowledge will have a broad impact on a diverse range of biological research, including development and cancer biology.
Immediate goal
We purified the nucleosome destabilization factor, termed NDF, from Drosophila embryo nuclear extracts and demonstrated that human NDF (hNDF) and Drosophila NDF can destabilize nucleosomes and facilitate transcription elongation through nucleosomes. NDF is recruited to transcribed regions of active genes and colocalizes with H3K36me3. Knockout of the hNDF gene leads to the transcription dysregulation of many genes. However, the molecular mechanism by which NDF destabilizes nucleosomes and facilitates transcription through nucleosomes remains to be determined. Some questions that we would like to address are as follows.
- What factors work in conjunction with NDF? How does NDF function in context of other factors in cells?
- What is the mechanism by which NDF destabilizes nucleosomes? What is the structure of the NDF-nucleosome complex?
- What are roles of NDF in regulating gene expression in response to external stimuli during development and homeostasis?
- How is NDF recruited to specific genes? What determines whether DNA is recruited to a gene? Are there other factors with activities that are related to NDF?
Our research is currently supported by an R01 grant (GM145748) from NIGMS.