Surreal illustration of gene activation process within a cell nucleus.

Unlocking the Secrets of Gene Activation: How Our Cells Switch On

Kai Mendoza in Science & Nature July 2025 • 4 min read.

"Groundbreaking research reveals the complex process of transcription, offering new insights into gene regulation and cellular function"

Our genes, the blueprints of life, aren't always switched on. In fact, the regulation of gene expression is a highly controlled process, especially when it comes to transcribing our DNA. Think of it like a car idling at a stoplight – ready to go, but not quite in motion. This 'pause' in gene activity is a widespread phenomenon, particularly in metazoan protein-coding genes, and it's critical for proper cellular function.

For years, scientists have been working to understand the precise molecular mechanisms that govern this 'pause' and the subsequent 'release' into active transcription. The process involves a complex interplay of proteins, including key players like DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF), which essentially put the brakes on RNA polymerase II (Pol II), the enzyme responsible for transcribing DNA.

But what triggers the release of this pause, and how does Pol II transition into an active, elongating state? New research is providing unprecedented insights into these fundamental questions, revealing the critical roles of additional factors like P-TEFb, PAF, and SPT6 in the activation process.

The Activation Puzzle: A Step-by-Step Unveiling

Surreal illustration of gene activation process within a cell nucleus.

The new study, published in Nature, details the formation of an activated Pol II elongation complex in vitro, meticulously piecing together the steps required for this transition. Researchers discovered that the kinase function of positive transcription elongation factor b (P-TEFb) is absolutely essential. P-TEFb, comprising the kinase CDK9 and cyclin T1, is known to phosphorylate DSIF, NELF, and the C-terminal domain (CTD) of Pol II itself. However, the activation story doesn't end there.

The elongation factors PAF1 complex (PAF) and SPT6 also play critical roles. The study demonstrates that PAF is necessary to reverse the Pol II pausing effect, while SPT6 further stimulates elongation. To visualize this complex process, the team used cryo-electron microscopy (cryo-EM) to determine the structure of an activated elongation complex of Sus scrofa (pig) Pol II and Homo sapiens (human) DSIF, PAF, and SPT6 at a remarkable 3.1 Å resolution. By comparing this structure to that of the paused elongation complex (Pol II, DSIF, and NELF), they were able to map out the key changes that occur during activation.

The key findings of the study reveal a choreographed sequence of events:

PAF Displaces NELF: PAF physically knocks NELF off the Pol II funnel, the entry point for nucleotides, effectively removing the 'pause' signal.
P-TEFb Phosphorylates the CTD Linker: P-TEFb targets the linker region connecting the CTD to the Pol II body, modifying its structure.
SPT6 Binds and Opens the RNA Clamp: SPT6 latches onto the phosphorylated CTD linker and forces open the RNA clamp formed by DSIF, facilitating RNA exit.

This structural and functional dissection offers a clear picture of how paused Pol II is released and primed for productive RNA elongation. The study provides a molecular explanation for the combined action of PAF, SPT6, and P-TEFb, showcasing their coordinated roles in stimulating transcription. Moreover, it highlights how these factors can block the reassociation of initiation factors, ensuring Pol II commits to elongation rather than reverting to initiation.

Implications and Future Directions

This research not only clarifies a fundamental process in molecular biology but also opens new avenues for therapeutic interventions. Understanding the precise mechanisms that govern gene activation could be crucial in developing targeted therapies for diseases linked to transcriptional dysregulation, such as cancer, autoimmune disorders, and viral infections. By manipulating the activity of P-TEFb, PAF, or SPT6, it may be possible to selectively switch on or off specific genes, offering new strategies for disease treatment.

About this Article -

This article was crafted using a human-AI hybrid and collaborative approach. AI assisted our team with initial drafting, research insights, identifying key questions, and image generation. Our human editors guided topic selection, defined the angle, structured the content, ensured factual accuracy and relevance, refined the tone, and conducted thorough editing to deliver helpful, high-quality information.See our About page for more information.

This article is based on research published under:

DOI-LINK: 10.1038/s41586-018-0440-4, Alternate LINK

Title: Structure Of Activated Transcription Complex Pol Ii–Dsif–Paf–Spt6

Subject: Multidisciplinary

Journal: Nature

Publisher: Springer Science and Business Media LLC

Authors: Seychelle M. Vos, Lucas Farnung, Marc Boehning, Christoph Wigge, Andreas Linden, Henning Urlaub, Patrick Cramer

Published: 2018-08-01

Everything You Need To Know

What are the key proteins involved in the regulation of gene expression during transcription, and how do they interact to control the 'pause' and 'release' of RNA polymerase II?

The process of gene activation involves a complex interplay of proteins. Key players include DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF), which pause RNA polymerase II (Pol II). The release from this paused state requires additional factors like P-TEFb, PAF, and SPT6. P-TEFb phosphorylates DSIF, NELF, and the C-terminal domain (CTD) of Pol II. PAF reverses the Pol II pausing effect, and SPT6 further stimulates elongation. Cryo-electron microscopy reveals that PAF displaces NELF, P-TEFb phosphorylates the CTD linker, and SPT6 binds and opens the RNA clamp, facilitating RNA exit.

What specific role does P-TEFb play in gene activation, and what happens if its kinase function is impaired?

P-TEFb, which includes the kinase CDK9 and cyclin T1, is essential for gene activation. It phosphorylates DSIF, NELF, and the C-terminal domain (CTD) of Pol II. This phosphorylation is crucial for the transition of RNA polymerase II (Pol II) from a paused state to an actively elongating state during transcription. Without P-TEFb's kinase function, the activation process stalls, preventing the displacement of NELF and the subsequent progression of Pol II along the DNA.

How does the PAF1 complex (PAF) contribute to reversing the paused state of RNA polymerase II during transcription?

PAF, or PAF1 complex, plays a role in reversing the pausing effect on RNA polymerase II (Pol II). It achieves this by physically displacing NELF from the Pol II funnel, which is the entry point for nucleotides. By removing NELF, PAF effectively eliminates the 'pause' signal, allowing Pol II to proceed with transcription. This displacement is a critical step in transitioning from paused to active transcription.

Can you explain how SPT6 facilitates RNA elongation once RNA polymerase II is released from its paused state?

SPT6 stimulates elongation during gene activation. It latches onto the phosphorylated C-terminal domain (CTD) linker and forces open the RNA clamp formed by DSIF, facilitating RNA exit. This action ensures that RNA polymerase II (Pol II) can efficiently elongate the RNA transcript. SPT6's role is crucial for the productive synthesis of RNA and the completion of the transcription process.

What are the potential therapeutic implications of understanding the precise mechanisms of gene activation involving P-TEFb, PAF, and SPT6 in diseases related to transcriptional dysregulation?

Understanding the mechanisms that govern gene activation, particularly the roles of P-TEFb, PAF, and SPT6, could revolutionize the development of therapies for diseases linked to transcriptional dysregulation. By manipulating these factors, it may be possible to selectively switch genes on or off. This approach could be useful in treating diseases such as cancer, autoimmune disorders, and viral infections, offering more targeted and effective treatment strategies.