Young Laboratory

The Richard Young Lab studies the transcriptional and epigenetic regulation of gene expression in mammalian cells. Genetic, biochemical, microscopic and computational methods are used to investigate gene control in healthy cells and to ascertain how these controls go awry in disease. Interests range from basic molecular mechanisms to drug discovery for cancer and other diseases caused by gene misregulation.

Transcriptional Condensates: We discovered that large clusters of enhancers, which we call super-enhancers, regulate genes that play the most prominent roles in cell identity.  Super-enhancers cooperatively assemble a high density of transcriptional apparatus to drive robust expression of genes. This high-density assembly at super-enhancers was found to exhibit sharp transitions of formation and dissolution, forming as the consequence of a single nucleation event and collapsing when concentrated factors are depleted from chromatin or when nucleation sites are deleted. These properties of super-enhancers led to our proposal that the high-density assembly of biomolecules at active super-enhancers is due to phase separation of enriched factors at these genetic elements. We recently provided experimental evidence that super-enhancers and their components do form phase-separated condensates, establishing a new framework to account for the diverse properties described for these regulatory elements. Furthermore, we found that phosphorylation of RNA polymerase II regulates a switch between transcriptional and splicing condensates during RNA synthesis. Current studies focus on the mechanisms that have evolved to regulate the behaviors of these nuclear condensates and on diseases associated with condensate dysregulation.

RNA-Mediated Control of Transcription: We have found that RNA transcribed from regulatory loci such as enhancers plays important roles in control of transcriptional processes. We showed that transcription factors interact not only with their specific DNA sites and protein partners, but also with RNA sequences produced from regulatory loci. Regulation of biological processes typically incorporate mechanisms that both initiate and terminate the process and, where understood, these mechanisms often involve feedback control. Regulation of transcription is a fundamental cellular process where the mechanisms involved in initiation have been studied extensively but those involved in arresting the process are poorly understood. We obtained evidence that RNAs produced during early steps in transcription initiation stimulate condensate formation whereas the burst of RNAs produced during elongation stimulate condensate dissolution, and propose that transcriptional regulation incorporates a feedback mechanism whereby transcribed RNAs initially stimulate but then ultimately arrest the process. Recent insights into the roles that RNA plays in gene regulation are reviewed in Henninger and Young (2024).

Protein Codes Promote Selective Compartmentalization in Condensates: Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. These include signal sequences that help guide proteins across membranes as well as interactions with other biomolecules that help retain proteins in specific compartments. We have found that proteins with shared functions also share amino acid sequence codes that guide them to compartment destinations. A protein language model, ProtGPS, was developed that predicts the compartment localization of human proteins. ProtGPS can also identify pathological mutations that change the compartment code and lead to altered subcellular localization of proteins. These results indicate that protein sequences contain not only a folding code, but also a previously unrecognized code governing their distribution to diverse subcellular compartments.

Drug Partitioning in Condensates: Studies of super-enhancers and their associated biomolecular condensates have led to new approaches to anti-cancer drugs. We found that tumor cells acquire large super-enhancers at driver oncogenes and that these can be unusually vulnerable to certain transcriptional inhibitors). These oncogenic super-enhancers can encompass exceptionally large domains, sometimes spanning more than 200 kb, and are highly vulnerable to transcriptional inhibitors that target BRD4 and CDK7. Normal cells appear to be relatively insensitive to inhibitors that target BRD4 and CDK7, suggesting that transcriptional inhibitors of this type may be useful for cancer therapy. The vulnerability of large oncogenic super-enhancers may be due to the selective concentration of drugs in super-enhancer condensates at oncogenes. We are now investigating how specific functional groups in small molecules provide drugs with the ability to concentrate within specific compartments in cells.

Protein Dysfunction in Chronic Disease: The pathogenic mechanisms of many diseases are well understood at the molecular level, but there are prevalent syndromes associated with pathogenic signaling, such as diabetes and chronic inflammation, where our understanding is more limited. We have found that pathogenic signaling suppresses the mobility of a spectrum of proteins that play essential roles in cellular functions known to be dysregulated in these chronic diseases. The reduced protein mobility, which we call proteolethargy, was linked to cysteine residues in the affected proteins and signaling-related increases in excess reactive oxygen species. Diverse pathogenic stimuli, including hyperglycemia, dyslipidemia, and inflammation, produce similar reduced protein mobility phenotypes. We propose that proteolethargy is an overlooked cellular mechanism that may account for various pathogenic features of diverse chronic diseases.

Chromosome Structure and Gene Regulation: Studies have revealed roles for specific chromosome structures in regulation of gene expression in healthy cells and in cancer. We found that DNA loops between the enhancers and core promoters of active genes are formed and maintained by Mediator and cohesin in mammalian cells.  Genome-wide maps of enhancer-promoter interactions in mammalian cells led to the discovery that super-enhancer driven genes occur in “insulated neighborhoods”, where large DNA loops that are co-bound by cohesin and CTCF serve to maintain proper expression of genes within and outside of the loop.  In cancer, disruption of these regulatory chromosome structures occurs at driver oncogenes and contributes to their dysregulation.  We also discovered that the transcription factor YY1 contributes to enhancer-promoter interactions by forming multimers analogous to the CTCF-CTCF interactions that contribute to chromosome neighborhoods.  These studies provide a foundation for our current studies of the relationships between chromosome structure and gene control in development and disease.