Coalescing into tiny liquid-like blobs and glomming onto specific DNA elements, transcription factors (TFs) boost the expression of nearby genes. The blobs are specialized droplets called phase-condensation condensates, and the DNA elements are called enhancers. Blobs and the enhancers manage to recognize and associate with each other. But how?
The question was taken up by MIT scientists who have been developing a blob-enhancer model of gene activation. In a 2017 Cell paper, the scientists described their computational studies of condensates, collections of molecules that form distinct cellular compartments but have no membrane separating them from the rest of the cell. These studies suggested that the blobby condensates, which are like oil droplets suspended in salad dressing, form at enhancers.
In a 2018 Science paper, the researchers took the next step. They showed that their dynamic blobs really do form at enhancer locations. Made of clusters of TFs and other molecules, the blobs attract enzymes such as RNA polymerases that are needed to copy DNA into messenger RNA, keeping gene transcription active at specific sites.
Finally, the scientists had positioned themselves to figure out how the dynamic blobs localize only at enhancer DNA, and not elsewhere on the genome. And soon, the scientists determined that blob-enhancer associations depend on a combination of specific and diffuse interactions.
Details about these interactions appeared August 8 in the journal Molecular Cell, in an article titled, “Enhancer Features that Drive Formation of Transcriptional Condensates.”
“We show that DNA sequences encoding TF binding site number, density, and affinity above sharply defined thresholds drive condensation of TFs and coactivators,” the article’s authors wrote. “A combination of specific structured (TF-DNA) and weak multivalent (TF-coactivator) interactions allows for condensates to form at particular genomic loci determined by the DNA sequence and the complement of expressed TFs.”
The MIT team, led by senior authors Richard Young, PhD, MIT professor of biology and member of the Whitehead Institute; Phillip Sharp, PhD, an MIT Institute professor and member of MIT’s Koch Institute for Integrative Cancer Research; and Arup K. Chakraborty, PhD, the Robert T. Haslam professor in chemical engineering, a professor of physics and chemistry, and a member of MIT’s Institute for Medical Engineering and Science and the Ragon Institute of MGH, MIT, and Harvard, also confirmed that DNA features found to drive condensation promote enhancer activity and transcription in cells. “Our study,” the article’s authors concluded, “provides a framework to understand how the genome can scaffold transcriptional condensates at specific loci and how the universal phenomenon of phase separation might regulate this process.”
Traditionally, biologists have focused on “lock and key” style interactions between rigidly structured protein segments to explain most cellular processes, but more recent evidence suggests that weak interactions between floppy protein regions also play an important role in cell activities. Aware of this evidence, the MIT scientists hypothesized that weak interactions between intrinsically disordered regions of TFs and other transcriptional molecules, along with specific interactions between TFs and particular DNA elements, might determine whether a condensate forms at a particular stretch of DNA.
To test their hypothesis, the MIT scientists used computational modeling and experimentation to reveal that weak interactions conspire with TF-DNA interactions to determine whether a condensate of TFs will form at a particular site on the genome. Different cell types produce different TFs, which bind to different enhancers. When many TFs cluster around the same enhancers, weak interactions between the proteins are more likely to occur. Once a critical threshold concentration is reached, condensates form.
“Creating these local high concentrations within the crowded environment of the cell enables the right material to be in the right place at the right time to carry out the multiple steps required to activate a gene,” noted Benjamin Sabari, a lead author of the current study and a postdoc in the Young laboratory. “[We’re beginning] to tease apart how certain regions of the genome are capable of pulling off this trick.”
The tiny, dynamic blobs form on a timescale of seconds to minutes, and they blink in and out of existence depending on a cell’s needs.
“It’s an on-demand biochemical factory that cells can form and dissolve, as and when they need it,” Chakraborty explained. “When certain signals happen at the right locus on a gene, the condensates form, which concentrates all of the transcription molecules. Transcription happens, and when the cells are done with that task, they get rid of them.”
The blob-enhancer model is opening a new view of gene control. In fact, this model suggests that weak cooperative interactions between proteins may play an important role not only in gene control, but also in evolution, as the MIT researchers proposed in a 2018 Proceedings of the National Academy of Sciences paper. There, the scientists speculated that sequences of intrinsically disordered regions of transcription factors need to change only a little to evolve new types of specific functionality. In contrast, evolving new specific functions via lock-and-key interactions requires much more significant changes.
“If you think about how biological systems have evolved,” said Sharp, you realize that “they have been able to respond to different conditions without creating new genes. We don’t have any more genes than a fruit fly, yet we’re much more complex in many of our functions. The incremental expanding and contracting of these intrinsically disordered domains could explain a large part of how that evolution happens.”
Similar condensates appear to play a variety of other roles in biological systems, offering a new way to look at how the interior of a cell is organized. Instead of floating through the cytoplasm and randomly bumping into other molecules, proteins involved in processes such as relaying molecular signals may transiently form droplets that help them interact with the right partners.
“This is a very exciting turn in the field of cell biology,” Sharp declared. “It is a whole new way of looking at biological systems that is richer and more meaningful.”
Some of the MIT researchers, led by Young, have helped form a company called Dewpoint Therapeutics to develop potential treatments for a wide variety of diseases by exploiting cellular condensates. There is emerging evidence that cancer cells use condensates to control sets of genes that promote cancer, and condensates have also been linked to neurodegenerative disorders such as amyotrophic lateral sclerosis and Huntington’s disease.