Extended Data Figure 9: Comparison of canonical enhancer-dependent and heterochromatin-dependent transcription activation pathways.

Schematic comparison of canonical enhancer-dependent transcription and transcription of small RNA source loci in Drosophila and Arabidopsis specified by chromatin marks. Canonical transcription initiation is driven by sequence-specific transcription factor binding to DNA motifs in accessible enhancer and promoter regions, which subsequently leads to positioning of TFIID/TBP onto core promoters (left). In contrast, while Moonshiner-mediated transcription also converges on recruitment of TFIID to DNA, this pathway exclusively utilizes the TBP paralogue TRF2. Furthermore, Moonshiner-mediated transcription gains locus specificity via recognition of heterochromatic histone marks through the HP1 protein Rhino, rather than through DNA motifs, thereby circumventing the transcriptional inhibition imposed by the compact state of heterochromatic DNA (middle). In plants, a conceptually similar pathway has evolved using an entirely different set of proteins (right). Here, the homeodomain protein SHH1 binds H3K9me histone marks and subsequently recruits the Pol IV variant RNA polymerase complex to transcribe small RNA precursors.