Newswise — COLUMBUS, Ohio – The genetic information contained in DNA must be read by specific proteins that allow gene activation to begin – but in many cases these proteins cannot access their targets because of the DNA sequences are bundled to control what genes are used in a wide range of different cell types.
New research led by scientists at Ohio State University shows how one of these proteins, called a transcription factor, acts as a special «pioneer factor» by binding to a DNA fragment is blocked to initiate the opening and activation process. one gene.
The study was conducted on budding yeast, a single-celled organism, but the transcription factor under study, called Cbf1, belongs to a family of proteins with a long evolutionary history that has a helix-ring-helix configuration- basic helix – a structural feature similar to about 100 transcription factors known to exist in humans.
«In humans, mutations in this type of transcription factor play a central role in disease,» said Michael Poirier, lead author of the study and professor and chair of the Department of Physics at Ohio State University. cancer.
«This work tells us one of the main ways genes are activated,» Poirier said. «We’re trying to understand, at a fundamental level, how cells work with the idea that this will ultimately provide the information a person needs to understand disease and develop therapies.»
Benjamin Donovan, a graduate student in biophysics at Poirier’s lab, was the first author of the study. Song Tan and Lu Bai, professors in Penn State’s Department of Biochemistry and Molecular Biology, are co-authors of the paper, which was recently published in the journal Nature. molecular cells.
In plants, animals, and other organisms with nucleated cells, portions of the DNA coil surround a set of histone proteins to form chromosomes, similar to how a watering can be organized. function in the backyard. Once locked onto a nucleosome coil, most transcription factors cannot access portions of those DNA fragments.
But a special class of these binding proteins found in humans and recently discovered in plants, called pioneering factors, «can access unreachable sites,» Poirier said. «How they do it has been a complete mystery.»
In a previous paper, Poirier, Bai, Donovan and collaborators showed that the transcription factor Cbf1 can bind to its target site even though that site is embedded in a chromosome, essentially showed that Cbf1 is equivalent to the vanguard factor. The researchers also observed with single-molecule microscopy that this ability was related to the unexpected tendency of the protein to remain present in the spool for an unusually long time. Most transcription factors that manage to bind in chromosomes cannot stay connected for long – they quickly separate through a process called dissociation.
“We showed that this long-term Cbf1 retention induces very efficient occupancy in a chromosome even though the binding site is largely blocked so it has to wait for the chromosome to open. out to link. But that paper doesn’t provide details on how it works: How does the Cbf1 pioneer element last so long? And why?» said Poirier.
In this new study, the team tested their theory that Cbf1 was around using histone proteins around the forming chromosomes.
Using single molecular measurements, Donovan revealed that the helix-loop-helix structure of Cbf1, which resembles that of another well-studied yeast transcription factor, can play a role in its special abilities. A series of experiments confirmed this structure to be necessary for successful nucleosome binding.
Electron microscopy from Tan’s lab shows that the location of Cbf1 shows that the helix-loop-helix region of its structure interacts with histones, and the scientists confirmed the attachment site by transforming regions that interact with histones and observe the weakening of the binding.
These additional histone interactions facilitated the ability of Cbf1 to act as a vanguard factor by retaining, often for one minute, Cbf1 at its target DNA site in untagged chromosomes. partial separation. The researchers call this phenomenon the dissociation rate compensation mechanism.
Studies from the Bai laboratory on live budding yeast show that the chromosomes have been displaced by Cbf1 and that its histone interactions lead to the expected functional outcomes.
When vane elements bind to a nucleosome, other proteins and enzymes join the picture to move in a process that leads to gene expression and protein construction.
«We’ve explained in a mechanistic and molecular way how a vanguard might work, and shown where the dissociation ratio compensation mechanism comes from: in part, from histone interactions,» Poirier said. ,” said Poirier. «If they don’t bind, none of this can start – they’re the key to kick-starting gene expression.»
This work was supported by the National Institutes of Health, the National Science Foundation and the Estonian Research Council.
Other co-authors include Hengye Chen of Penn State, Priit Eek of Tallinn University of Technology, and Zhiyuan Meng and Caroline Jipa of Ohio State.
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