This PDF file includes:

• fig. S1. Mass spectrometry results.
• fig. S2. Western blot analysis of TAP-tagged proteins.
• fig. S3. Materials for in vitro RNA binding experiments.
• fig. S4. Loss of Jhd2 does not affect processing or polyA-dependent termination in vitro.
• fig. S5. RT-qPCR and Western blot analysis for Jhd2 mRNA and protein used in PMA1 studies.
• fig. S6. RT-qPCR and Western blot analysis for Jhd2 mRNA and protein used in KlCYC1 studies.
• fig. S7. Metagene plots of H3K4me3 levels.
• Legends for tables S1 to S3
• table S4. Plasmids used in this study.
• table S5. Yeast strains used in this study.
• table S6. Primers used in this study.

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Other Supplementary Material for this manuscript includes the following:

• table S1 (Microsoft Excel format). Jhd2 bound peaks identified using SICER.
• table S2 (Microsoft Excel format). Pcf11 bound peaks identified using SICER.
• table S3 (Microsoft Excel format). List of genes with APA after Jhd2 deletion.