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. Author manuscript; available in PMC: 2024 Dec 7.
Published in final edited form as: Mol Cell. 2023 Nov 22;83(23):4205–4221.e9. doi: 10.1016/j.molcel.2023.10.037

Figure 1. Epi-Decoder reveals rewiring of the proteome of a tDNA locus in response to nutrient availability.

Figure 1.

(A) Schematic overview of Epi-Decoder. Using a DNA-barcode repair template library and CRISPR-Cas9 construct, a random DNA-barcode is inserted at the locus of interest. The library of barcoded transformants is arrayed, decoded, and crossed with an arrayed TAP-tag protein library. In the resulting Epi-Decoder library, each clone contains a unique barcode and a different protein tagged. After pooling the library, ChIP is performed and DNA barcodes from ChIP and input are amplified, sequenced, and counted to provide a binding score (ChIP/input) at the locus for all proteins in the library. (B) Epi-Decoder scores for 3707 proteins at the tDNA-Ty1 locus in glucose; arcsinh (fold change ChIP vs input) and FDR (p-value). Subunits that belong to RNAPIII, TFIIIB or TFIIIC are color-coded. Data describes three biological replicates (different DNA-barcode protein-TAG combinations) measured as three technical replicates (same DNA-barcode). Proteins classified as ‘binder’ are indicated with colored dots and significance thresholds with dashed lines (basemean ≥ 400, FDR ≤ 0.01 and log2 fold change ≥ 1). (C) Binding scores for the tDNA-Ty1 locus compared to the HO locus: log2 (fold change ChIPHO vs ChIPtDNA-Ty1) and FDR (p-value) for 154 factors that are ‘binder’ at either of the loci (also described in the Euler diagram). Data describes three biological replicates as described in (B). Colored dots show significant proteins and dashed lines show significance thresholds (FDR ≤ 0.25). (D) As in (C), fold change (log2 ChIPglucose vs ChIPglycerol) between glucose and glycerol 2h (37°C) and FDR (p-value) for 154 ‘binders’ at the tDNA-Ty1 locus in either growth condition (as described in the Euler diagram). (E) Heat maps with average fold change values (ChIP vs input, n = 3) for different protein complexes or families at the tDNA-Ty1 locus, each with a different color scale. Protein names are color-coded based on the Euler diagram in (D).