The set of proteins synthesized by a cell in turn determines its structure and behaviour, and enables it to survive and reproduce. So it is crucial that the appropriate stretches of DNA are transcribed in each cell type. In today's issue of the journal Nature, a team of researchers at the Gene Center of Ludwig-Maximilians-Universität (LMU) in Munich, led by Professor Patrick Cramer, provides the first detailed description of how the RNA polymerase II initiates gene transcription.
"The findings led us to propose a model of the whole complicated process of transcription initiation," says Cramer. "This operation is of crucial importance in all organisms, because it determines which genes are expressed, and when. Our work thus represents a milestone in the quest to understand gene regulation."
Cell types such as liver cells and nerve cells differ from one another because they make distinct sets of proteins. Therefore, gene transcription and protein synthesis must be carried out with great precision. This requires the use of complicated assemblies made up of many different proteins, often referred to as molecular machines. The basic structure of RNA polymerase II, the protein complex that transcribes genes encoding proteins in multicellular organisms, was worked out some years ago, but this structure could not explain how the initial steps in transcription take place.
Signals encoded in the DNA sequence tell RNA polymerase II where to start and stop transcription. The regions in which transcription begins are called promoters. In many genes, the promoter region is marked by a short DNA sequence called the TATA box. The actual transcription start site (TSS) is located 30-40 nucleotides downstream. It was already known that the protein TBP recognizes and binds to the TATA box, producing a sharp kink in the DNA. TBP in turn binds TFIIB, to which the polymerase enzyme (comprising 12 different proteins) then attaches. So it is TFIIB that actually gives the start signal for transcription initiation.
What the LMU researchers in Cramer's group have now done is to determine the three-dimensional structure of the complex formed between RNA polymerase II and TFIIB from brewer's yeast. Analysis of this complex using X-ray diffraction gave them a map that could be compared with one obtained for the polymerase alone. The differences between the two enabled the scientists to localize the TFIIB with respect to both the polymerase and the DNA. On the basis of this structure they were able to deduce how the initiation of transcription occurs, how the TSS is selected and the first segment of RNA is synthesized and, finally, how the polymerase "shifts gear" from the initiation to the elongation mode, as it leaves the region of the promoter and proceeds on through the gene. In a fruitful collaboration with Professor Michael Thomm's lab at the University of Regensburg the researchers also confirmed important aspects of their model experimentally.
It turns out that TFIIB acts as a bridge between TBP and polymerase, so that the polymerase faces the DNA, in the so-called closed complex. This is converted into an open complex when part of the TFIIB (called the B-linker) inserts between the two DNA strands. One of the strands (the template strand) is displaced into a tunnel formed by TFIIB and the polymerase. The complex then searches the sequence in the tunnel for an initiator sequence that defines the TSS, "using a second element (the B-reader) in TFIIB, which functions rather like the reading head in a tape recorder", explains Cramer. When the TSS is located, the first two nucleotides of the new RNA transcript pair with their complementary partners on the DNA and are linked together by the polymerase. This marks the real initiation of transcription. After the addition of additional nucleotides, TFIIB is released from the complex.
The resulting elongation complex continues to synthesize an RNA sequence complementary to that of the template DNA strand, which later determines the structure of a specific protein. As Cramer points out, "The findings led us to propose a model of the whole complicated process of transcription initiation, an operation that is of crucial importance in all organisms, because it determines which genes are expressed, and when." The work of the LMU group thus represents a milestone in the quest to understand how genes are regulated. The results also provide the framework for investigating the mechanisms underlying the regulation of transcription initiation, which governs cellular gene expression. (PH)
Luise Dirscherl | EurekAlert!
Researchers identify potentially druggable mutant p53 proteins that promote cancer growth
09.12.2016 | Cold Spring Harbor Laboratory
Plant-based substance boosts eyelash growth
09.12.2016 | Fraunhofer-Institut für Angewandte Polymerforschung IAP
Physicists of the University of Würzburg have made an astonishing discovery in a specific type of topological insulators. The effect is due to the structure of the materials used. The researchers have now published their work in the journal Science.
Topological insulators are currently the hot topic in physics according to the newspaper Neue Zürcher Zeitung. Only a few weeks ago, their importance was...
In recent years, lasers with ultrashort pulses (USP) down to the femtosecond range have become established on an industrial scale. They could advance some applications with the much-lauded “cold ablation” – if that meant they would then achieve more throughput. A new generation of process engineering that will address this issue in particular will be discussed at the “4th UKP Workshop – Ultrafast Laser Technology” in April 2017.
Even back in the 1990s, scientists were comparing materials processing with nanosecond, picosecond and femtosesecond pulses. The result was surprising:...
Have you ever wondered how you see the world? Vision is about photons of light, which are packets of energy, interacting with the atoms or molecules in what...
A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.
Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...
In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.
“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...
16.11.2016 | Event News
01.11.2016 | Event News
14.10.2016 | Event News
09.12.2016 | Life Sciences
09.12.2016 | Ecology, The Environment and Conservation
09.12.2016 | Health and Medicine