Extended Data Fig. 1: ChIP–exo targets within meta-assemblages.
From: A high-resolution protein architecture of the budding yeast genome
a, Simplified view of transcriptional regulation. A ssTF (TF; for example, Gal4) binds to its cognate motif (a UAS) within promoters in competition with chromatin/nucleosomes (red bar). The ssTF recruits (pink/green arrow) cofactors (for example, SAGA and Mediator) that assist in the assembly of a PIC (comprising TBP, TFIIB, and so on) and of Pol II at the transcript start site (TSS) of genes. Pol II then traverses the gene to the transcription end site (TES). b, Diagram showing the ChIP–exo assay. Protein targets are crosslinked to DNA, which is then fragmented. Specific proteins are captured through an engineered TAP tag that binds the common Fc region of any immobilized IgG. Near-base-pair resolution is achieved using a strand-specific λ exonuclease that digests each strand of DNA in the 5′–3′ direction up to the point of crosslinking. c, Pie chart showing assayed targets separated by broad GO-based classifications (inner ring), or by UMAP-based clustering of genome-wide binding locations (outer ring). Listed are the common names of ChIP–exo targets that generated significantly enriched locations (with ‘significance’ defined in the Methods section ‘ChExMix locations’), grouped by their UMAP/K-means-derived meta-assemblage abbreviations (along with membership count), which are further grouped by the simplified GO-related categories. See also Supplementary Data 2 (2H).
