Low-affinity CTCF binding drives transcriptional regulation whereas high-affinity binding encompasses architectural functions

Marina-Zárate, Ester; Rodríguez-Ronchel, Ana; Gómez, Manuel J.; Sánchez-Cabo, Fátima; Ramiro, Almudena R.

doi:10.1016/j.isci.2023.106106

Cited by 10 publications

(9 citation statements)

References 65 publications

(147 reference statements)

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“…In the absence of RNA, CTCF is only stably bound to high-affinity binding sites, while RNA binding leads to stable binding also at low-affinity sites ( Figure S4A , C ). Correspondingly, in vivo , low-affinity CBSs flank regions of active chromatin and have been associated with transcriptional regulation, while high-affinity CBSs more often flank repressed chromatin and are associated with regulating genome architecture 19 . CTCF on high-affinity CBSs is highly stable 17,18 , and loop domains can persist for hours without energy input, requiring stable anchoring by CTCF 67 , in agreement with our observed long lifetimes on CBSs.…”

Section: Discussionmentioning

confidence: 99%

“…CTCF on high-affinity CBSs is highly stable 17,18 , and loop domains can persist for hours without energy input, requiring stable anchoring by CTCF 67 , in agreement with our observed long lifetimes on CBSs. Binding to low-affinity binding sites is less persistent 19 and disrupted by transcription inhibition or RNA-binding deficient mutants 29 . Our results therefore support a model where RNA transcripts are an important regulator of CTCF binding positions and stability.…”

Section: Discussionmentioning

confidence: 99%

“…CBSs can be further classified into high-and low-affinity binding sites, as certain CBSs have been shown to be more persistent in CTCF depletion experiments 17,18 . Low-affinity binding sites are often located within genes and at transcription start sites (TSSs), while high-affinity bindings sites can be found at TAD boundaries 19 . This implies that the sequence context modulates CTCF's activity on different target sites and defines its numerous tasks in genome organization and transcription regulation.…”

Section: Introductionmentioning

confidence: 99%

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Single-molecule imaging reveals a direct role of CTCF’s zinc fingers in SA interaction and cluster-dependent RNA recruitment

Huber,

Tanasie,

Zernia

et al. 2023

Preprint

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CTCF is a zinc finger protein associated with transcription regulation that also acts as a barrier factor for topologically associated domains (TADs) generated by cohesin via loop extrusion. These processes require different properties of CTCF-DNA interaction, and it is still unclear how CTCF’s structural features may modulate its diverse roles. Here, we employ single-molecule imaging to study both full-length CTCF and truncation mutants. We show that CTCF enriches at CTCF binding sites (CBSs), displaying a longer lifetime than observed previously. We demonstrate that the zinc finger domains mediate CTCF clustering and that clustering enables RNA recruitment, possibly creating a scaffold for interaction with RNA-binding proteins like cohesin’s subunit SA. We further reveal a direct recruitment and an increase of SA residence time by CTCF bound at CBSs, suggesting that CTCF-SA interactions are crucial for cohesin stability on chromatin at TAD borders. Furthermore, we establish a single-molecule transcription assay and show that although a transcribing polymerase can remove CTCF from CBSs, transcription is impaired. Our study shows that context-dependent nucleic acid binding determines the multifaceted CTCF roles in genome organization and transcription regulation.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Single-molecule imaging reveals a direct role of CTCF’s zinc fingers in SA interaction and cluster-dependent RNA recruitment

Huber,

Tanasie,

Zernia

et al. 2023

Preprint

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show abstract

“…CTCF binds tens of thousands of enhancers and promoters on mammalian chromosomes by the use of its 11 tandem zinc finger (ZF) DNA-binding domain and establishes interactions between distant enhancers and promoters by means of DNA loop extrusion ( 21 ). It is possible that high-affinity sites play structural roles in chromatin, while the lower-affinity sites are responsible for regulating transcription ( 22 ). A major question is how CTCF-bound enhancer and promoter elements find each other, stabilizing interactions between the two distant DNA elements and yielding associations with a long residence time [on the order of 22 min ( 23 )] that are detectable in heatmaps of Hi-C data.…”

Section: Introductionmentioning

confidence: 99%

Structures of CTCF–DNA complexes including all 11 zinc fingers

Yang

Horton

Liu

et al. 2023

Nucleic Acids Research

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The CCCTC-binding factor (CTCF) binds tens of thousands of enhancers and promoters on mammalian chromosomes by means of its 11 tandem zinc finger (ZF) DNA-binding domain. In addition to the 12–15-bp CORE sequence, some of the CTCF binding sites contain 5′ upstream and/or 3′ downstream motifs. Here, we describe two structures for overlapping portions of human CTCF, respectively, including ZF1–ZF7 and ZF3–ZF11 in complex with DNA that incorporates the CORE sequence together with either 3′ downstream or 5′ upstream motifs. Like conventional tandem ZF array proteins, ZF1–ZF7 follow the right-handed twist of the DNA, with each finger occupying and recognizing one triplet of three base pairs in the DNA major groove. ZF8 plays a unique role, acting as a spacer across the DNA minor groove and positioning ZF9–ZF11 to make cross-strand contacts with DNA. We ascribe the difference between the two subgroups of ZF1–ZF7 and ZF8–ZF11 to residues at the two positions −6 and −5 within each finger, with small residues for ZF1–ZF7 and bulkier and polar/charged residues for ZF8–ZF11. ZF8 is also uniquely rich in basic amino acids, which allows salt bridges to DNA phosphates in the minor groove. Highly specific arginine–guanine and glutamine–adenine interactions, used to recognize G:C or A:T base pairs at conventional base-interacting positions of ZFs, also apply to the cross-strand interactions adopted by ZF9–ZF11. The differences between ZF1–ZF7 and ZF8–ZF11 can be rationalized structurally and may contribute to recognition of high-affinity CTCF binding sites.

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“… 2 At a higher structural level, topologically associated domains (TADs) describe submegabase domains, while chromatin loops provide finer resolution contact information. 3 , 4 Incorrect chromosome structure misdirects the physical contacts between genomic loci, constituting pathogenic mechanisms that control various diseases, including cancer. 5 For instance, perturbations of insulated TAD boundaries are thought to be sufficient to activate oncogenes; 6 , 7 reprogramming of the multiscale 3D genome was found to control the transcriptome in prostate cancer 8 and pancreatic cancer.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive multiomics analyses reveal pervasive involvement of aberrant cohesin binding in transcriptional and chromosomal disorder of cancer cells

Wang

Nakato

2023

iScience

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Low-affinity CTCF binding drives transcriptional regulation whereas high-affinity binding encompasses architectural functions

Cited by 10 publications

References 65 publications

Single-molecule imaging reveals a direct role of CTCF’s zinc fingers in SA interaction and cluster-dependent RNA recruitment

Single-molecule imaging reveals a direct role of CTCF’s zinc fingers in SA interaction and cluster-dependent RNA recruitment

Structures of CTCF–DNA complexes including all 11 zinc fingers

Comprehensive multiomics analyses reveal pervasive involvement of aberrant cohesin binding in transcriptional and chromosomal disorder of cancer cells

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