Structural basis of H3K36 trimethylation by SETD2 during chromatin transcription

During transcription, RNA polymerase II traverses through chromatin, and posttranslational modifications including histone methylations mark regions of active transcription. Histone protein H3 lysine 36 trimethylation (H3K36me3), which is established by the histone methyltransferase SET domain containing 2 (SETD2), suppresses cryptic transcription, regulates splicing, and serves as a binding site for transcription elongation factors. The mechanism by which the transcription machinery coordinates the deposition of H3K36me3 is not well understood. Here we provide cryo–electron microscopy structures of mammalian RNA polymerase II–DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome elongation complexes, revealing that the transcription machinery regulates H3K36me3 deposition by SETD2 on downstream and upstream nucleosomes. SPT6 binds the exposed H2A-H2B dimer during transcription, and the SPT6 death-like domain mediates an interaction with SETD2 bound to a nucleosome upstream of RNA polymerase II. Eukaryotic genomes are organized into chromatin, in which a strand of DNA is wrapped compactly around histone proteins to form nucleosomes. Nucleosomes can be chemically modified by epigenetic marks to regulate gene expression. Trimethylation of histone H3 at lysine 36 (H3K36me3) is critical for active transcription, splicing, and genomic stability. Using cryo–electron microscopy, Markert et al. determined the mechanism by which the enzyme SETD2 deposits H3K36me3 by recognizing and binding to nucleosomes partially unwrapped by the transcription machinery. This finding provides a structural basis for how some histone modifications are established co-transcriptionally. —Di Jiang