Distinct properties and functions of CTCF revealed by a rapidly inducible degron system [PRO-Seq]

We coupled an auxin-induced degron (AID) system with precision nuclear run-on (PRO-seq). Oriented CTCF motifs in gene bodies are associated with transcriptional stalling in a manner ostensibly independent of bound CTCF. CTCF binding sites display highly variable resistance to degradation, with persistent sites displaying architectural related features. Transient endogenous CTCF depletion coupled with genome wide CTCF binding site profiling (ChIP-seq) and nascent transcription quantification (PRO-seq)