A CPF-like phosphatase module links transcription termination to chromatin silencing. Researchers identify APRF1, a homolog of Swd2/WDR82, as a key component of a CPF-like phosphatase module that links transcription termination to chromatin silencing in Arabidopsis. APRF1 interacts with TOPP4 (Glc7/PP1) and LD (Ref2/PNUTS), components of the CPF phosphatase module. Loss of APRF1 leads to transcriptional readthrough and RNA Pol II hyperphosphorylation, linking co-transcriptional processing with chromatin remodeling. The APRF1/LD-mediated polyadenylation/termination process influences subsequent rounds of transcription by changing the local chromatin environment at FLC. This work shows how the APRF1/LD-mediated polyadenylation/termination process influences subsequent rounds of transcription by changing the local chromatin environment at FLC. APRF1 is a structural component of a CPF-like phosphatase complex that directly links transcription termination with histone demethylase activity to alter the local chromatin environment and provide a mechanism resulting in graded repression of transcription. The study reveals that APRF1 functions downstream of FCA and is involved in the regulation of FLC transcription. APRF1 interacts with LD, the plant homolog of the phosphatase regulatory subunit Ref2/PNUTS. The APRF1-LD-TOPP4 complex forms a plant equivalent of the yeast (Swd2/Ref2/Glc7) and human (WDR82/PNUTS/PP1) CPF phosphatase modules. The study also shows that APRF1 affects RNA Pol II CTD Ser2/5 phosphorylation, which is crucial for transcription termination. The findings highlight the importance of transcription termination in defining chromatin domains around genes and preventing future transcriptional readthrough. The study provides insights into the molecular mechanisms underlying chromatin silencing and transcriptional regulation in plants.A CPF-like phosphatase module links transcription termination to chromatin silencing. Researchers identify APRF1, a homolog of Swd2/WDR82, as a key component of a CPF-like phosphatase module that links transcription termination to chromatin silencing in Arabidopsis. APRF1 interacts with TOPP4 (Glc7/PP1) and LD (Ref2/PNUTS), components of the CPF phosphatase module. Loss of APRF1 leads to transcriptional readthrough and RNA Pol II hyperphosphorylation, linking co-transcriptional processing with chromatin remodeling. The APRF1/LD-mediated polyadenylation/termination process influences subsequent rounds of transcription by changing the local chromatin environment at FLC. This work shows how the APRF1/LD-mediated polyadenylation/termination process influences subsequent rounds of transcription by changing the local chromatin environment at FLC. APRF1 is a structural component of a CPF-like phosphatase complex that directly links transcription termination with histone demethylase activity to alter the local chromatin environment and provide a mechanism resulting in graded repression of transcription. The study reveals that APRF1 functions downstream of FCA and is involved in the regulation of FLC transcription. APRF1 interacts with LD, the plant homolog of the phosphatase regulatory subunit Ref2/PNUTS. The APRF1-LD-TOPP4 complex forms a plant equivalent of the yeast (Swd2/Ref2/Glc7) and human (WDR82/PNUTS/PP1) CPF phosphatase modules. The study also shows that APRF1 affects RNA Pol II CTD Ser2/5 phosphorylation, which is crucial for transcription termination. The findings highlight the importance of transcription termination in defining chromatin domains around genes and preventing future transcriptional readthrough. The study provides insights into the molecular mechanisms underlying chromatin silencing and transcriptional regulation in plants.