Molecular structure of elongation complex essential for DNA transcription determined

By using x-ray crystallography and cyro-electron microscopy data, an all-RIKEN team has elucidated the structure of a complex that plays a critical role in the copying of DNA into RNA¹. This structural information provides vital clues as to how the complex functions.

Before genes encoded in DNA can be expressed, the relevant section of DNA has to be transcribed into RNA. It is simple to transcribe DNA in a test tube—all you need are DNA, RNA polymerase and nucleotides—but the situation is more complex in a cell’s nucleus. “Many components, including transcription factors, associate with RNA polymerase II and form huge transcription complexes, many of which have not been structurally explored yet,” notes Shun-ichi Sekine from the RIKEN Center for Life Science Technologies.

His team is working on determining the structure of these large transcriptional complexes. In the current study, they focused on the elongation complex that forms in the early steps of transcription. It both ensures that transcription proceeds and regulates other essential processes linked to transcription, such as DNA repair. Sekine believes it is crucial to gain a full understanding of the complex’s mechanism in order to ascertain how this regulation can fail in diseases such as cancer.

His team focused on three proteins known to be essential for the elongation complex: the multidomain protein Spt5, its binding partner Spt4 and the elongation factor Elf1. They determined the domains that are important for the interaction between Spt5 and the RNA polymerase. The researchers then solved the crystal structure of one Spt5 domain, called KOW5, complexed with the polymerase and Elf1. They also obtained a model of the entire complex by merging this crystal structure with cryo-electron microscopy data of a complex that included Spt4, Spt5 and a transcription factor.

These results provide information on how the complex operates. “We found that the elongation factors Spt4/5 and Elf1 bind to functionally important parts of polymerase II,” says Sekine, adding that they act like subunits of the polymerase.

Sekine likens the polymerase’s structure to a needle, where DNA is a thread that can pass through the needle’s eye. Elf1 forms an entry tunnel that helps thread the DNA into the polymerase and keep it in place. Spt4 and 5 make up an exit tunnel that separates DNA from RNA and ensures efficient exit of DNA and nascent RNA from the complex (Fig. 1). This aspect is critical for avoiding DNA–RNA hybridization, which can prematurely terminate transcription.

“Our structure provides a firm foundation for further structural, molecular and cellular biology studies and research on disease mechanisms,” says Sekine.