The Fan lab is interested in understanding the mechanisms of epigenetic regulation, focusing on two main directions: (1) the function and regulation of ATP-dependent chromatin remodelers, and (2) the mechanisms of mitotic transcription memory by the retention of sequence-specific transcription factors on mitotic chromatin. Results from these studies will shed light on fundamental mechanisms of epigenetic regulation and provide novel insights into the causes and mechanisms of disease.
The Fan lab is interested in understanding the mechanisms of epigenetic regulation, focusing on two main directions.
I. Functions and regulations of ATP-dependent chromatin remodelers
We are interested in understanding the mechanisms by which chromatin structure is regulated and how defects in chromatin structure regulation can lead to disease, including cancer. A major focus of our research has been aimed at understanding the mechanisms by which ATP-dependent chromatin remodelers regulate chromatin structure and how the biochemical activities of these enzymes are used to carry out diverse biological process, such as transcription regulation and DNA repair. ATP-dependent chromatin remodelers use energy from ATP hydrolysis to alter DNA-protein contacts, typically those between DNA and histones. Our work has made significant insights into remodeling mechanisms and regulation as well as the underlying causes of disease.
Mutations in the CSB remodeler lead to Cockayne syndrome: a devastating premature aging disorder associated with numerous developmental and neurological defects. There are more than 30 known and predicted ATP-dependent chromatin remodelers in humans; CSB, however, is the only remodeler that is essential for transcription-coupled DNA repair (TCR), a process that rapidly removes transcription-stalling DNA lesions. Moreover, CSB is critical for relieving oxidative stress. We have made significant advances in understanding how this chromatin remodeler is uniquely equipped to carry out its functions. (1) The association of CSB with chromatin is tightly regulated. In general, only 10% of CSB is chromatin bound, but upon UV irradiation or oxidative stress, more than 90% of CSB becomes chromatin associated; this is in stark contrast to other, well-studied remodelers such as SWI/SNF and ISWI that are constitutively bound to chromatin. (2) Using separation-of-function derivatives, we have demonstrated that the chromatin remodeling activity of CSB is essential for its function in transcription-coupled DNA repair (TCR). (3) The chromatin remodeling activity of CSB is tunable: CSB, on its own, displays weak remodeling activity (~20-fold less than SWI/SNF or ACF). Strikingly, together with NAP1-like histone chaperones, CSB remodels chromatin robustly, to a level similar to SWI/SNF or ACF. (4) CSB interacts with the CTCF protein and through this interaction becomes significantly enriched at CTCF binding sites upon oxidative stress. Given that CTCF is a key player in regulating higher- order chromatin-structure, CSB may collaborate with CTCF to reorganize chromatin structure in response to oxidative stress to facilitate coordinated gene expression or efficient DNA repair. We are exploiting these unique properties of CSB to understand how this ATP-dependent chromatin remodeler is uniquely equipped to protect cells from genotoxic stress. Moreover, this work may shed new light on the causes and mechanism of Cockayne syndrome.
II. Mechanisms of mitotic transcription memory by mitotic bookmarking factors.
We are also interested in unraveling the epigenetic mechanisms that maintain cell identity through mitosis. During the journey a zygote takes to become the greater than 200 specialized cell types that make up the human body, numerous cell divisions occur. Lineage commitment demands that specific transcription programs be maintained through these cell divisions with high fidelity to preserve cell identity. During mitosis, transcription ceases and the vast majority of the transcriptional regulatory machinery dissociates from the highly condensed chromatin. Intriguingly, specific transcription programs are propagated through mitosis and faithfully passed on to daughter cells. How then is the memory of a specific transcription program propagated through cell division? Accumulating evidence indicates that select transcription factors that are endowed with the capacity to remain associated with mitotic chromatin likely play critical roles in maintaining transcriptional memory through cell division. The unique properties that permit these transcription factors to remain associated with mitotic chromatin, their precise functions in transcriptional memory maintenance, and the mechanisms that regulate their occupancy sites during cell-fate specification remain poorly understood. Answers to these questions are essential to understand the underlying mechanisms that orchestrate the inheritance of transcription programs through mitosis and, thus, maintain cell identity, a fundamental question of developmental biology.
Notch signaling is central to development, and aberrant Notch signaling has been associated with developmental abnormalities and cancer. Little is known about the epigenetic mechanisms by which transcriptional programs established by Notch signaling are propagated through cell division to maintain cell identity. Our recent work has demonstrated that RBPJ, the major transcriptional effector of the Notch signaling pathway, can remain associated with mitotic chromatin. We also discovered that genes bound by RBPJ during mitosis exhibit an earlier requirement of RBPJ for their transcription reactivation upon mitotic exit. We are using Notch-signaling effector RBPJ as a model protein to investigate the epigenetic regulation of cell identity maintenance through the mitotic chromatin.