biostudies-arrayexpressQian Yee WooHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15999ChIP-seq analysis was conducted to determine the genome-wide binding profiles of PRB, PRB-FFF, and PRB-QQQ cell lines following R5020 treatment compared to vehicle (ETOH). We propose a tripartite model in which transient and calibrated interactions among AF1, AF2, and coregulators are essential for productive enhancer function and dynamic cycling of the transcription complex. We hypothesize that the PRB-FFF mutation leads to more stable interactions, resulting in prolonged enhancer occupancy and a slower transcription rate.biostudies-arrayexpressLibrary Construction - The samples were submitted to Genome Institute of Singapore (Agency for Science, Technology and Research) for library preparation and paired-end sequencing using Illumina HiSeq4000 platform.Sequencing - The samples were submitted to Genome Institute of Singapore (Agency for Science, Technology and Research) for library preparation and paired-end sequencing using Illumina HiSeq4000 platform.Nucleic Acid Extraction - Chromatin immunoprecipitation was performed using anti-PR antibody H-190 (Santa Cruz Biotechnology Inc., Dallas, TX, USA, LOT number sc-7208). The lysate was incubated with 5 ug anti-PR antibody overnight at 4 °C. Protein-chromatin complex was captured using Pierce™ ChIP-grade Protein A/G Magnetic Beads (ThermoFisher Scientific, Cat. #26162). Chromatin was eluted, and crosslinks were reversed by treatment with RNase A and Proteinase K. Input samples and ChIP’ed DNA was purified using QIAquick PCR Purification Kit (Qiagen). DNA concentrations were quantified using Qubit Fluorometer (ThermoFisher Scientific).Sample Collection - After treatment, cells were crosslinked with formaldehyde at a final concentration of 1% for 10 minutes at room temperature. The cross-linking was quenched by the addition of glycine to a final concentration of 0.125 M. Cells were then harvested, lysed, and subjected to sonication using Diagenode Bioruptor Pico.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Model-based analysis of ChIP-seq version 2 (MACS2) was used to perform peak calling for ChIP-seq data, following default parameter. Integrative Genome Viewer (IGV) was used to create representative snapshot for the peaks called. Diffbind, a R Bioconductor package was used to identify the peaks with differential binding between cell lines and treatment. Binding sites were extended by 50 bp on both 5’ and 3’ ends, and the corresponding FASTA sequence were fetched using the Galaxy platform. The sequences were scanned for motif matches using MEME-ChIP suite. Motif analysis was also performed with the Seqpos motif tool.UnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 4000ChIP-seqHomo sapiensQian Yee WoofalseMethylation mimic mutations of progesterone receptor AF1 impair gene-specific regulation through stabilized chromatin interactionsChIP-seq analysis was conducted to determine the genome-wide binding profiles of PRB, PRB-FFF, and PRB-QQQ cell lines following R5020 treatment compared to vehicle (ETOH). We propose a tripartite model in which transient and calibrated interactions among AF1, AF2, and coregulators are essential for productive enhancer function and dynamic cycling of the transcription complex. We hypothesize that the PRB-FFF mutation leads to more stable interactions, resulting in prolonged enhancer occupancy and a slower transcription rate.2026-03-31T00:00:00Z2026-03-31T01:03:46.829Z2025-11-06T12:13:40.162ZE-MTAB-15999ERP183055ERP183804EFO_0002944EFO_0004170EFO_0002692EFO_0005518EFO_0003816EFO_0004184