Page 66 - ebook

[A. Biochemistry/Molecular Biology] A-33

CTCF-mediated chromatin looping provides a topological

framework for the formation of phase-separated

transcriptional condensates

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Bobae Yang³,⁴ , Ryanggeun Lee¹,² , Moo-Koo Kang³,⁴ , Yong-Jin Kim³,⁴ , Hwanyoung Shim¹ , Sugyung
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Kim³,⁴, Kyungwoo Kim³,⁴, Chul Min Yang³, Byeong-gyu Min¹, Woong-Jae Jung³, Eun-Chong Lee³, Jung-
Sik Joo³,⁴, Gunhee Park¹, Won-Ki Cho¹,⁵*, Hyoung-Pyo Kim³,⁴,⁶*
¹Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea, ²College of Natural Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,

Korea, ³Department of Environmental Medical Biology, Yonsei University College of Medicine, Seoul 03722, Korea,
⁴Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea, ⁵KI

for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), Daejeon
34141, Korea

CTCF is crucial to the organization of mammalian genomes into loop structures. According to recent studies, the
transcription apparatus is compartmentalized and concentrated at super-enhancers to form phase-separated
condensates and drive the expression of cell-identity genes. However, it remains unclear whether and how

transcriptional condensates are coupled to higher-order chromatin organization. Here, we show that CTCF is

essential for RNA polymerase II (Pol II)-mediated chromatin interactions, which occur as hyperconnected spatial
clusters at super-enhancers. We also demonstrate that CTCF clustering, unlike Pol II clustering, is independent of
liquid-liquid phase-separation and resistant to perturbation of transcription. Interestingly, clusters of Pol II, BRD4,

and MED1 were found to dissolve upon CTCF depletion, but were reinstated upon restoration of CTCF, suggesting

a potent instructive function for CTCF in the formation of transcriptional condensates. Overall, we provide the first
direct evidence showing that CTCF-mediated chromatin looping acts as an architectural prerequisite for the assembly
of phase-separated transcriptional condensates.