CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

Huang, Hui; Zhu, Quan; Jussila, Adam; Han, Yuanyuan; Bintu, Bogdan; Kern, Colin; Conte, Mattia; Zhang, Yanxiao; Bianco, Simona; Chiariello, Andrea M.; Yu, Miao; Hu, Rong; Tastemel, Melodi; Jurić, Ivan; Hu, Ming; Nicodemi, Mario; Zhuang, Xiaowei; Ren, Bing

doi:10.1038/s41588-021-00863-6

Cited by 129 publications

(174 citation statements)

References 74 publications

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“…We propose that this timebuffering model reconciles our observations with the unambiguous genetic evidence that CTCF and cohesin regulate some E-P interactions. This evidence includes the following: 1) Insertion of CTCF sites between an enhancer and a promoter can both reduce E-P interactions and strongly reduce gene expression [98][99][100] ; 2) CTCF binding site silencing 101,102 or genetic CTCF binding site loss 21,103,104 can cause aberrant E-P interactions and gene expression and drive disease; 3) Inversion or repositioning of CTCF sites can redirect E-P interactions that cause gene misexpression and diseases 105,106 . Two recent studies have also proposed variants of a time-buffering model based on mathematical modeling of E-P interactions and gene expression 100,107 .…”

Section: Discussionmentioning

confidence: 99%

Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1

Cattoglio

Slobodyanyuk³

et al. 2021

Preprint

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It remains unclear why acute depletion of CTCF and cohesin only marginally affects expression of most genes despite substantially perturbing 3D genome folding at the level of domains and structural loops. To address this conundrum, we used high-resolution Micro-C and nascent transcript profiling to find that enhancer-promoter (E-P) interactions are largely insensitive to acute (3-hour) depletion of CTCF, cohesin, and WAPL. YY1 has been proposed to be a structural regulator of E-P loops, but acute YY1 depletion also had minimal effects on E-P loops, transcription, and 3D genome folding. Strikingly, live-cell single-molecule imaging revealed that cohesin depletion reduced transcription factor binding to chromatin. Thus, although neither CTCF, cohesin, WAPL, nor YY1 are required for the short-term maintenance of most E-P interactions and gene expression, we propose that cohesin may serve as a "transcription factor binding platform" that facilitates transcription factor binding to chromatin.

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Section: Discussionmentioning

confidence: 99%

Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1

Cattoglio

Slobodyanyuk³

et al. 2021

Preprint

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“…For example, the deletion of some CTCF sites at the mouse Shh locus weakened the formation of large chromatin loops between the Shh gene and its ZRS enhancer (Paliou et al, 2019). Also, the importance of multiple CTCF sites for proper insulation at TAD borders through the formation of local chromatin domains has been assessed through mutagenesis of the Sox2 locus in ES cells (Huang et al, 2021), as well as their cooperative and redundant functions when disposed as arrays at the Pax3 locus (Anania et al, 2021). In this study, we genetically dissected a series of five CBSs all located on one side of the strong TAD boundary located within the HoxD gene cluster.…”

Section: Discussionmentioning

confidence: 99%

“…While several studies have revealed that the number of CBS was important for insulation at TAD boundaries, likely through a synergistic effect (Huang et al, 2021), particular CBS may be more important than others in achieving this task (Anania et al, 2021) and it appears that tandem distributions of CBS may provide robustness to the TAD border. In our allelic series, the global insulation capacity of the TAD border was increasingly affected along with more CTCF sites being mutated, as best seen in the case of the developing limbs.…”

Section: Cbss In the Making Of The Tad Boundary At The Hoxd Clustermentioning

confidence: 99%

“…Accordingly, the orientation and location of the CTCF binding sites (CBSs) play a critical role in DNA loop formation and high-order chromatin organization. In fact, TAD and sub-TADs boundaries are enriched in CBSs, with usually several CTCF motifs displaying the same orientation, facing those sites located at the other extremity of the TAD (Huang et al, 2021;Kentepozidou et al, 2020). Despite their prominent role in the establishment of TAD boundaries, most CBSs are found outside these regions and are associated with a wide range of functions including enhancer-promoter interaction, imprinting and recombination (Franco et al, 2014;Gosalia et al, 2014;Guo et al, 2011;Phillips-Cremins et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

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Sequential in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

Lhopitallier

Beccari

Lopez-Delisle

et al. 2021

Preprint

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Mammalian Hox gene clusters contain a range of CTCF binding sites. In addition to their importance in organizing a TAD border, which isolates the most posterior genes from the rest of the cluster, the positions and orientations of these sites suggest that CTCF may be instrumental in the selection of various subsets of contiguous genes, which are targets of distinct remote enhancers located in the flanking regulatory landscapes. We examined this possibility by producing an allelic series of cumulative in-cis mutations in these sites, up to the abrogation of CTCF binding in the five sites located on one side of the TAD border. In the most impactful alleles, the global chromatin architecture of the locus was modified, yet not drastically, illustrating that CTCF sites located on one side of a strong TAD border are sufficient to organize at least part of this insulation. Spatial colinearity in the expression of these genes along the major body axis was nevertheless maintained, despite abnormal expression boundaries. In contrast, strong effects were scored in the selection of target genes responding to particular enhancers, leading to the mis-regulation of Hoxd genes in specific structures. Altogether, while most enhancer-promoter interactions can occur in the absence of this series of CTCF sites, it seems that the binding of CTCF in the Hox cluster is required to properly transform a rather unprecise process into a highly discriminative mechanism of interactions, which is translated into various patterns of transcription accompanied by the distinctive chromatin topology found at this locus. Our allelic series also allowed us to reveal the distinct functional contributions for CTCF sites within this Hox cluster, some acting as insulator elements, others being necessary to anchor or stabilize enhancer-promoter interactions and some doing both, whereas all together contribute to the formation of a TAD border. This variety of tasks may explain the amazing evolutionary conservation in the distribution of these sites amongst paralogous Hox clusters or between various vertebrates.

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“…Accordingly, the orientation and location of the CTCF binding sites (CBSs) play a critical role in DNA loop formation and high-order chromatin organization. In fact, TAD and sub-TAD boundaries are enriched in CBSs, with usually several CTCF motifs displaying the same orientation, facing those sites located at the other extremity of the TAD (Kentepozidou et al 2020;Huang et al 2021). Despite their prominent role in the establishment of TAD boundaries, most CBSs are found outside these regions and are associated with a wide range of functions, including enhancer-promoter interaction, imprinting, and re-combination (Guo et al 2011;Phillips-Cremins et al 2013;Franco et al 2014;Gosalia et al 2014).…”

mentioning

confidence: 99%

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

et al. 2021

View full text Add to dashboard Cite

Mammalian Hox gene clusters contain a range of CTCF binding sites. In addition to their importance in organizing a TAD border, which isolates the most posterior genes from the rest of the cluster, the positions and orientations of these sites suggest that CTCF may be instrumental in the selection of various subsets of contiguous genes, which are targets of distinct remote enhancers located in the flanking regulatory landscapes. We examined this possibility by producing an allelic series of cumulative in cis mutations in these sites, up to the abrogation of CTCF binding in the five sites located on one side of the TAD border. In the most impactful alleles, the global chromatin architecture of the locus was modified, yet not drastically, illustrating that CTCF sites located on one side of a strong TAD border are sufficient to organize at least part of this insulation. Spatial colinearity in the expression of these genes along the major body axis was nevertheless maintained, despite abnormal expression boundaries. In contrast, strong effects were scored in the selection of target genes responding to particular enhancers, leading to the misregulation of Hoxd genes in specific structures. Altogether, while most enhancer–promoter interactions can occur in the absence of this series of CTCF sites, the binding of CTCF in the Hox cluster is required to properly transform a rather unprecise process into a highly discriminative mechanism of interactions, which is translated into various patterns of transcription accompanied by the distinctive chromatin topology found at this locus. Our allelic series also allowed us to reveal the distinct functional contributions for CTCF sites within this Hox cluster, some acting as insulator elements, others being necessary to anchor or stabilize enhancer–promoter interactions, and some doing both, whereas they all together contribute to the formation of a TAD border. This variety of tasks may explain the amazing evolutionary conservation in the distribution of these sites among paralogous Hox clusters or between various vertebrates.

show abstract

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

Cited by 129 publications

References 74 publications

Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1

Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1

Sequential in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

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