Northwestern Medicine scientists have discovered new mechanisms underlying transcriptional initiation and elongation control for supporting proper gene expression, according to a recent study published in Molecular Cell.
The findings have the potential to inform more effective targeted therapeutic approaches for many diseases, including cancer, according to said Ali Shilatifard, PhD, the chair and Robert Francis Furchgott Professor of Biochemistry and Molecular Genetics, who was senior author of the study. Bin Zheng, PhD, a Feinberg fellow in the Department of Biochemistry and Molecular Genetics, was the lead author of the study.
“Dr. Bin Zheng has made a major discovery in turning the pharmacology of transcriptional regulation through the BET domain protein on its head and is really mechanistically defining what these pathways are to move the field forward,” said Shilatifard, who is also a member of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University.
Proteins in the bromodomain and extraterminal domain (BET) family, which include BRD2, BRD3, BRD4 and BRDT, play a crucial role in the transcription of RNA polymerase II, a multiprotein complex that travels along DNA and synthesizes RNA as the template.
Small-molecule inhibitors that block interactions between BET and acetylated histone proteins have recently been developed as potential targeted therapies for many diseases, including cancer, but have not been successful in clinic. Furthermore, mechanisms by which other BET proteins regulate RNA polymerase II function in transcription have remained poorly understood.
Previous work from the Shilatifard laboratory demonstrated that the BET protein BRD4 does not require bromodomains for its transcriptional elongation function — BET domains recognize and bind to acetylated lysine residues on histones to influence gene expression and DNA repair — to control transcription elongation.
“We found that the BRD4 BET domains are not required to perform the major function of pause release and elongation, and that says a lot for why these BET inhibitors don’t work as they’re supposed to,” Zheng said.
In the current study, the scientists used multiple high-throughput sequencing techniques to study human cells treated with BET inhibitors, finding that the BET protein BRD2 supports transcriptional initiation at both promoters (a region of DNA upstream of a gene where relevant proteins bind to initiate transcription) and enhancers (a short region of DNA that helps increase the likelihood of the transcription of a particular gene).
Additionally, the scientists found that BRD2 bromodomains preferentially bind to a specialized histone, called histone H4 harboring MOF-mediated H4K16ac, while the BRD2 C-terminal domain supports the recruitment of transcription factor II D (TFIID), one of several transcription factors that initiates gene transcription.
“Through these mechanistic and proteomics studies, we found that BRD2 recruits a major transcription factor, TFIID,” Zheng said. “It’s very interesting to see within the BET protein family that one helps initiate and another helps to release and elongate.”
The findings reveal new insights into the mechanistic roles of BRD2 and BRD4 in transcriptional initiation and elongation control for the regulation of gene expression.
“Now we know what these BET inhibitors are and their true targets in terms of transcription inhibition,” Zheng said. “This makes it more clear how this specific class of BET inhibitors function and as we gain more knowledge of the mechanisms behind these BET inhibitors, we can stratify those therapeutic strategies.”
This work was supported by the Outstanding Investigator Award from the National Cancer Institute (grant R35-CA197569).
