PCMT1–BCLAF1/TET1-Related Regulatory Networks Involved in Chromatin Accessibility Remodeling and Epitranscriptional Regulation in Triple-Negative Breast Cancer

ATAC‑seq was employed to analyze genome‑wide chromatin accessibility changes between the sh‑PCMT1 and sh‑NC groups, and the results were integrated with previous RNA‑seq data from PCMT1 knockdown cells. Co‑immunoprecipitation coupled with mass spectrometry (Co‑IP/MS) was used to screen for potential PCMT1‑interacting proteins, and the possible involvement of BCLAF1 in the PCMT1 regulatory network was assessed by integrating BCLAF1 knockdown RNA‑seq data and BCLAF1 target gene sets.

Furthermore, TET1 CUT&Tag sequencing was performed to evaluate genome‑wide changes in TET1 chromatin occupancy following PCMT1 knockdown. Finally, ATAC‑seq, RNA‑seq, BCLAF1‑related datasets, and TET1 CUT&Tag data were jointly analyzed to identify potential downstream target genes, and the expression and prognostic significance of candidate genes in breast cancer were examined using the UALCAN and GEPIA2 databases.