Dynamic regulation of stress-responsive non-genomic CTCF complexes [ChIP-seq]

The nuclear protein CCCTC-binding factor (CTCF) has diverse roles in chromatin architecture and gene regulation. Functionally, CTCF associates with thousands of genomic sites and interacts with proteins, such as cohesin, or non-coding RNAs to facilitate specific transcriptional programming. In this study, we examined CTCF during the cellular stress response in human primary cells using immune-blotting, quantitative real time-PCR, chromatin immunoprecipitation-sequence analysis, mass spectrometry, RNA immunoprecipitation-sequence analysis, and Airyscan confocal microscopy. Unexpectedly, we found that CTCF is exquisitely sensitive to diverse forms of stress in normal patient-derived human mammary epithelial cells (HMECs). In HMECs, the majority of CTCF protein forms non-genomic complexes that localize to Serine/arginine-rich splicing factor (SC-35)-containing nuclear speckles, exclusive of its canonical association with chromatin. Upon stress, non-genomic CTCF protein is rapidly downregulated by changes in protein stability, resulting in loss of CTCF from SC-35 nuclear speckles and changes in CTCF-RNA interactions. CTCF complexes that associate with genomic DNA are resistant to stress-induced degradation and CTCF-DNA binding is largely unchanged. Restoration of cellular CTCF protein abundance and re-localization to nuclear speckles can be achieved by inhibition of proteasome-mediated degradation. Surprisingly, we observed the same characteristics of the stress response during neuronal differentiation of human pluripotent stem cells (hPSC). CTCF forms stress-sensitive complexes that localize to SC-35 nuclear speckles during a specific stage of neuronal commitment/development but not in differentiated neurons. We speculate that these non-canonical CTCF complexes serve a largely non-genomic role in RNA processing, potentially to maintain cells in a particular differentiation state, that is dynamically regulated by environmental signals. The non-canonical, stress-regulated activity of CTCF is uncoupled in persistently stressed, epigenetically re-programmed “variant” HMECs and certain cancer cell lines. These results reveal new insights into CTCF function in cell differentiation and the stress-response with implications for oxidative damage-induced cancer initiation and neuro-degenerative diseases. ChIP-Seq