Genetic and epigenetic mechanisms of developmental gene regulation

项目总结/文摘

Project Summary/Abstract Nearly all cells in our bodies contain the same genome, and thus each of them has the capacity to adopt one of many cell identities. Normal development is characterized by progressive restriction in cell identity from multipotent progenitor cells toward terminally differentiated cells. Most cells choose a single identity and maintain it over time. However, defects in cell fate determination or maintenance can allow cells to escape the restrictions on cell identity, endowing them with new properties that cause disease. For this reason, the steps leading to disease have been described as development gone awry. More importantly, it suggests that cells proceed down the path to disease by inappropriately accessing genetic information controlling cell identity. Thus, studying the mechanisms controlling access to genetic information during normal development can inform how deregulation of these mechanisms contributes to disease. My lab studies two different regulatory layers controlling access to DNA-encoded information and their importance in controlling gene expression. Research during the term of this grant will interrogate the mechanisms underlying (1) how chromatin-based packaging of transcriptional enhancers determines where and when transcription factors bind DNA to switch genes on or off, and (2) how modifications of histone proteins contribute to chromatin organization and transcriptional control. DNA is wrapped around histone proteins to form nucleosomes, the repeating unit of chromatin. Nucleosomes are barriers to transcription factor binding, inhibiting early steps of gene activation. Thus, understanding how chromatin is made accessible to transcription factors is necessary for understanding gene control. More importantly, returning open chromatin to a closed state and reinstating this barrier is critical for preventing gene activation at the wrong time or place. However, the mechanisms controlling chromatin closing are uncharacterized. We have uncovered a temporal cascade of transcription factors, which we term “chromatin gatekeepers” due to their requirement for opening and closing access to enhancers, that we study to decipher these mechanisms. We will also investigate how information about decisions made earlier in development is propagated over time. A key to unlocking this question is a unique genetic resource we recently generated that enables us to directly test the function of histones. Histones are subject to a diverse array of post-translational modifications (PTMs) that are thought to carry epigenetic information to control DNA-templated processes, including transcription. However, evidence supporting the role of histone PTMs in animals is largely correlative due to the difficulty in creating mutant histone genotypes in animals. Drosophila is distinct among animal models in that the histone genes reside at a single locus in the genome. We can replace the endogenous histone genes with tailor-made versions, thereby providing us with the first opportunity to distinguish between regulatory information that is directly encoded in the DNA sequence and information that is epigenetically propagated. We will employ this approach to interrogate the role that histone PTMs play in transcriptional regulation and in control of 3D genome organization.