Laboratory for Transcription Structural Biology

Transcription is a fundamental process that underpins virtually all biological activities. In cells, transcription machinery communicates with numerous biomolecules, forming multiple high-order complexes, which not only accomplish transcription, but also coordinate diverse cellular functions. In order to visualize these complexes and elucidate their action mechanisms, our team employs structural biology approach, in particular cryo-electron microscopy. Our research focus is on transcription regulation in chromatin and its crosstalk with essential biological phenomena and nuclear structures. In parallel, we also investigate viral-host interactions to provide structural foundations for drug development.

In metazoans, the early elongation complex of RNA polymerase II (RNAPII) generally stalls 20-60 bp downstream of the transcription start site. This regulatory step, known as promoter-proximal pausing, is critical for subsequent processive transcription elongation in the gene body. In addition to two pausing factors NELF and DSIF, chromatin structure plays a pivotal role in establishing and maintaining the pausing. To gain structural insights into the pausing, we performed cryo-EM analysis of arrested/paused elongation complexes yielded on a nucleosomal DNA template. These structures reveal dynamic interplay between RNAPII, pausing factors, elongation factors, and the +1 nucleosome, thereby establishing the promoter-proximal checkpoint.

Transcription is intricately coupled with chromatin modification. Trimethylation of Lys36 on the histone H3 tail domain (H3K36me3) is a hallmark of actively transcribed genes. H3K36me3 is catalyzed by a conserved methyltransferase enzyme Set2 in a transcription-dependent manner. To elucidate this mechanism, we investigated the structures of elongating RNAPII complexes transcribing nucleosomal templates in the presence of Set2. The structures reveal how transcription progression directs the deposition and spreading of active chromatin marks across gene bodies.