Molecule of DNA forming inside the test tube equipment.3d rendering,conceptual image.
Molecule of DNA forming inside the test tube equipment. [undefined/Getty Images]

A new method by which cells turn genes on and off has been described by UT Southwestern Medical Center researchers. According to their work, biomolecular condensates with the intrinsically disordered region (IDR) of MED1 selectively partition RNA polymerase II with its positive allosteric regulators while excluding negative regulators. This compartmentalization allows transcription and is required for gene activation during a cell-state transition.

The team’s findings, reported in Cell, could lead to new ways of controlling gene regulation and possibly new treatments for a broad array of diseases.

“We think this is likely just the tip of the iceberg. Interactions among these disordered regions of proteins [IDRs] have largely been ignored because it was unclear how they worked. Now, they’re opening a new world of regulatory interactions that we previously didn’t know existed,” said Benjamin Sabari, PhD, assistant professor in the Departments of Molecular Biology and Obstetrics and Gynecology at UT Southwestern.

It’s established that certain proteins have IDRs—parts without a defined 3D structure— that are involved in forming condensates and that components of transcriptional machinery are selectively partitioned into specific condensates,Sabari said. However, it is largely unknown how interactions are mediated by these IDRs and whether this organization is functional.

Sabari and his colleagues focused on MED1, a protein that forms part of a complex involved in transcription. MED1, which has a large IDR, is composes part of some biomolecular condensates. It has also been linked to estrogen receptor-positive breast cancer.

To determine which other proteins join MED1 in condensates and which are excluded, the researchers opened human cells to expose their contents and reconstituted condensates in the presence of this extracted material by spiking in the IDR of MED1. They then isolated the MED1 condensates and used analytical techniques to determine the proteins present within the condensate and those left behind.

They found that the MED1/IDR protein forms condensates when added to a soluble nuclear extract. These condensates partition specific proteins from the nuclear extract and keep others out. Their results showed that the proteins in these MED1 condensates were enriched for positive regulators of transcription, while negative regulators were left out.
Further investigation showed that proteins present in the MED1 condensates contained IDRs with shared sequence features of having alternating blocks of positive and negative charge. When the researchers removed IDRs from some included proteins, they could no longer join the condensates. Conversely, when the researchers added IDRs to the excluded proteins, they became part of the condensates.

Which proteins were included in the condensates had functional consequences, Sabari said. When negative regulators joined the MED1 condensates or when positive regulators lost their access, the cells could no longer perform transcription necessary for specific cellular tasks.

Understanding how interactions among different IDRs within condensates are dysregulated in certain diseases and finding ways to alter their interactions could one day lead to a new class of treatments for these conditions.

“At UTSW, there are facilities and expert colleagues with whom to start screening for small molecules or peptides that can disrupt these IDR-mediated interactions occurring within condensates, which we plan to take advantage of,” Sabari said.

Also of Interest