CCCTC-binding factor (CTCF) is a conserved zinc finger transcription factor implicated in a wide range of functions, including genome organization, transcription activation, and elongation. To explore the basis for CTCF functional diversity, we coupled an auxin-induced degron system with precision nuclear run-on. Unexpectedly, oriented CTCF motifs in gene bodies are associated with transcriptional stalling in a manner independent of bound CTCF. Moreover, CTCF at different binding sites (CBSs) displays highly variable resistance to degradation. Motif sequence does not significantly predict degradation behavior, but location at chromatin boundaries and chromatin loop anchors, as well as co-occupancy with cohesin, are associated with delayed degradation. Single-molecule tracking experiments link chromatin residence time to CTCF degradation kinetics, which has ramifications regarding architectural CTCF functions. Our study highlights the heterogeneity of CBSs, uncovers properties specific to architecturally important CBSs, and provides insights into the basic processes of genome organization and transcription regulation.

CCCTC 结合因子 (CTCF) 是一种保守的锌指转录因子，涉及多种功能，包括基因组组织、转录激活和延伸。为了探索 CTCF 功能多样性的基础，我们将生长素诱导的降解决定子系统与精确的核连续运行相结合。出乎意料的是，基因体中的定向 CTCF 基序以独立于结合的 CTCF 的方式与转录停​​滞相关。此外，不同结合位点 (CBS) 上的 CTCF 显示出高度可变的抗降解性。基序序列不能显着预测降解行为，但染色质边界和染色质环锚的位置以及与粘连蛋白的共占用与延迟降解相关。单分子追踪实验将染色质停留时间与 CTCF 降解动力学联系起来，这对 CTCF 的结构功能产生影响。我们的研究强调了 CBS 的异质性，揭示了结构上重要的 CBS 特有的特性，并提供了对基因组组织和转录调控的基本过程的见解。