The structure of chromatin is tightly regulated by the well choreographed actions of multiple elements. Disruption of the normal pattern of chromatin often leads to misregulation of gene expression, a common feature of cancer and other human diseases. Therefore, it is important to understand the detailed mechanism regulating chromatin dynamics.

The long-term objective of our laboratory is to understand how chromatin-related complexes help the transcription machinery overcome the nucleosomal barriers while still maintaining genome integrity. Recently, we and others discovered a novel signaling pathway through which RNA polymerase II (Pol II) maintains chromatin integrity while transcribing through nucleosomal templates. A histone methyltransferase Set2 binds the phosphorylated CTD of elongating Pol II and co-transcriptionally methylates histone H3K36, which is then recognized by a histone deacetylase complex, Rpd3S. Once targeted, Rpd3S deacetylates transcribed regions to preserve the accuracy of transcription initiation, thus restricting transcription to bonafide promoters but not cryptic transcription start sites.

We plan to take advantage of combinatorial tools including biochemistry, genetics, and genome-wide approaches to dissect the detailed mechanisms driving this crucial pathway.

The main directions include:

  1. Analysis of Rpd3S binding to K36 methylated nucleosomes and its implication in transcription elongation. We will test how multiple domains within Rpd3S coordinate to achieve synergistic binding.
  2. Dissecting the molecular mechanism by which Pol II exploits K36 methylation as a marker for short term transcription memory. We will examine if elongating Pol II can control the directionality of relevant histone modifications around the transcription fork.
  3. Identification of the temporal control mechanism of K36 methylation during transcription elongation. We will explore the roles of histone demethylases and the signals for removal of this reversible histone modification.
  4. A high throughput screen for the small molecules that can specifically modulates chromatin recognition both in-vitro and inside cells.

The pathway that we are currently investigating involves a histone methyltransferase, Set2, and the histone deacetylase complex Rpd3S. The human homolog of Set2 has been directly implicated in cancer as it is fused to the NUP98 gene in the t[5,11](q35:p15.5) translocation in acute myeloid leukemia.

More importantly, histone deacetylase inhibitors are currently used in clinical trials as anticancer drugs, and treatment of cells with histone deacetylase inhibitors such as TSA or oxamflatin promotes cellular differentiation, cell cycle arrest, and apoptosis. Interestingly, only the HDACs that are close to the Rpd3 family are sensitive to these drugs. Therefore, our research is highly relevant to the fundamental mechanism of tumorigenesis.