PCRD-seq: Proximity Crosslinking-induced RNA Depletion for Low-Input Chromatin-associated Transcriptome Profiling

Proximity labeling has emerged as a promising and versatile technique for profiling chromatin-associated RNAs with high spatiotemporal resolution. While being a powerful technique, traditional proximity labeling methods depend on complex, high-input enrichment protocols, which significantly limit their wide practical application.

Here, we developed a straightforward, enrichment-free chromatin-associated RNA profiling strategy: Proximity Crosslinking-induced RNA Depletion sequencing (PCRD-seq). This approach leverages the proximity crosslinking between chromatin and its surrounding RNAs induced by singlet oxygen generated by HoeDBF, a photosensitizer targeting chromatin region. The proximity crosslinking hinders the release of chromatin-associated RNAs during routine TRIzol extraction, consequently leading to a specific depletion of these RNAs.