Supporting data for “Chromatin-associated Transcriptome Profiling based on HoeDBF-assisted Proximity Labeling”

In eukaryotes, although RNAs are transcribed in nucleus, they can be transported and localized to various cell compartments. This process is termed RNA localization. The correct RNA subcellular localization is critical to proper cell functions. Therefore, multiple techniques have been developed to profile RNAs localized in various subcellular domains, including proximity labeling. Our group previously reported a small molecule HoeDBF, which is a proximity labeling system used for chromatin-associated biomolecule profiling. However, like other proximity labeling approaches, this system relies on a cumbersome, multi-step enrichment-based protocol. This not only imposes a significant burden on sample preparation but also introduces technical variability due to complex handling. Most critically, the enrichment-based method necessitates a large amount of total RNA as input to yield enough enriched RNA for downstream library preparation, posing a significant challenge in low-input scenarios. Therefore, in this work, we developed an enrichment-free chromatin-associated RNA profiling strategy, termed Proximity Crosslinking-induced RNA Depletion sequencing (PCRD-seq), based on our HoeDBF-mediated proximity labeling system. The uploaded dataset includes the fluorescence confocal imaging results that supports the sensitivity and specificity of HoeDBF labeling; the qRT-PCR results supporting proximity crosslinking-induced chromatin-associated RNA depletion; the RNA-seq results validating the capability of our PCRD-seq in profiling chromatin-associated RNAs.