Comparative Analysis of RNA-Chromatin Interactome Data: Resolution, Completeness, and Specificity

Two types of experiments are used to study RNA-chromatin interactions: the interactome search for individual RNAs ("one-to-all" or OTA) and genome-wide contact mapping for all RNAs ("all-to-all" or ATA). Comparative analysis of ATA and OTA data revealed fundamental differences in resolution, completeness, and specificity. OTA data exhibit high resolution (~1000 bp) and reproducibility (>90%), serving as a "gold standard". ATA data, however, have lower resolution (~5000 bp), and their reproducibility (<10%) is critically dependent on the protocol, with two-step fixation using disuccinimidyl glutarate and formaldehyde (GRID-seq) showing a clear advantage over formaldehyde alone. The introduced "chromatin potential" metric and BaRDIC peak filtering effectively isolate the specific signal. This study proposes a strategy for reliable interactome analysis: combining RNA selection based on chromatin potential with the use of concordant contacts from peaks.