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. Overall design: Transient endogenous CTCF depletion coupled with genome wide CTCF binding site profiling (ChIP-seq) and nascent transcription quantification (PRO-seq)