14 hours ago by Bendta Schroeder

Before DNA can be transcribed into RNA, an early step in turning the genetic template into protein, the nucleus must first assemble a molecular machine called the pre-initiation complex (PIC), capable of unzipping the double helix and loading the DNA onto the transcription enzyme.

The PIC's dozens of parts are scattered throughout a dense nucleus, packed with DNA, proteins, and other biomolecules. Transcription factors and enzymes must find their way to the transcription site, driven by weak and transient interactions, to be assembled into a living, working machine. The assembly can happen in a matter of seconds.

Weak and transient interactions are thought to propel, not just transcription, but the majority of vital cell processes. In these interactions, biomolecules join and disband easily, allowing them to act collectively and quickly in response to the needs of the cell. But exactly how these interactions work is a mystery.

Ibrahim Ciss, assistant professor of physics, wants to solve this mystery, molecule by molecule, in living cells, in real time.

"This is probably one of the most spectacular examples in nature where the interactions of individual biomolecules give rise to something we don't yet understandthe emergence of life," Ciss says.

Transcription, molecule by molecule

For Ciss to follow transcription as it unfolds, he would have to circumvent the limitations of conventional techniques for studying biomolecules. Biochemical techniques that isolate molecules in test tubes or label them in fixed cells destroy the conditions that make weak and transient interactions possible. Light microscopy can preserve those conditions, but most biomolecules are too small and interact too closely to be distinguished with the light diffraction limit of 200 nanometers.

Instead, Ciss uses tools from physics to illuminate the transcription process at high resolution. For example, he adapted a new fluorescent imaging technique called photoactivation localization microscopy (PALM). PALM activates fluorescent tagging proteins at random and then applies a statistical algorithm to determine the exact location of each protein with nanometer-accuracy within the pixel of light. When Ciss repeats the process at high speed and volume, he can map the precise location of tagged biomolecules as they cluster at a transcription site or trace the path of a single transcription factor as it moves across the nucleus. Furthermore, by developing a temporal correlation method coupled with PALM, called tcPALM, Ciss can get direct access to the clustering dynamics for the first time.

Recently, Ciss used tcPALM to show that the transcriptional enzyme RNA Polymerase II (Pol II) clusters for just a few seconds as transcription begins. The result is surprising, given that it takes several minutes for a full RNA sequence to be synthesized. When Ciss suppressed and then reactivated transcription just before imaging, he observed Pol II clustering at unusually high concentrations. When he blocked Pol II from escaping the promoter and transcribing the DNA, the cluster of Pol II around the promoter didn't dissipate.

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Unraveling the mystery of DNA transcription, one molecule at a time

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