Distinct properties and functions of CTCF revealed by a rapidly inducible degron system

Luan, Jing; Xiang, Guanjue; Gómez-García, Pablo Aurelio; Tome, Jacob M.; Zhang, Zhe; Vermunt, Marit W.; Zhang, Haoyue; Huang, Anran; Keller, Cheryl A.; Giardine, Belinda; Zhang, Yu; Lan, Yemin; Lis, John T.; Lakadamyali, Melike; Hardison, R; Blobel, Gerd A.

doi:10.1016/j.celrep.2021.108783

Cited by 72 publications

(73 citation statements)

References 89 publications

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“…In agreement with this multifaceted role, CTCF depletion in the embryo resulted in the concomitant loss of TAD insulation and weakening of genes-enhancers interactions, sometimes with clearly documented effects upon gene transcription (e.g. (Paliou et al, 2019) whereas in other instances a more moderate and somewhat unpredictable impact was observed (Luan et al, 2021;Nora et al, 2017;Soshnikova et al, 2010). However, the potential importance of CTCF in helping tissue specific enhancers to select the right promoter(s) and thus activate a subset of genes located within the same TAD remains to be assessed with precision.…”

Section: Introductionmentioning

confidence: 58%

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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Section: Introductionmentioning

confidence: 58%

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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“…Additional external ChIP–seq data of histone modifications on asynchronous cells are available at: H3K27ac (GSE61349) 48 , H3K4me1 (GSM946535) 52 , H3K4me3 (GSM946533) 52 , H3K36me3 (GSM946529) 52 , H3K27me3 (GSM946531) 52 , H3K9me3 (GSM946542) 52 . Additional external data of CTCF and Rad21 before and after CTCF depletion in asynchronous G1E-ER4 cells are available at GSE150418 53 .…”

Section: Methodsmentioning

confidence: 99%

CTCF and transcription influence chromatin structure re-configuration after mitosis

Zhang

Lam

Zhang

et al. 2021

Preprint

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During mitosis, transcription is globally attenuated and chromatin architecture is dramatically reconfigured. Here we exploited the M- to G1-phase progression to interrogate the contributions of the architectural factor CTCF and the process of transcription to re-sculpting the genome in newborn nuclei. Depletion of CTCF specifically during the M- to G1-phase transition altered the re-establishment of local short-range compartmentalization after mitosis. Chromatin domain boundary reformation was impaired upon CTCF loss, but a subset (~27%) of boundaries, characterized by transitions in chromatin states, was established normally. Without CTCF, structural loops failed to form, leading to illegitimate contacts between cis-regulatory elements (CREs). Transient CRE contacts that are normally resolved after telophase persisted deeply into G1-phase in CTCF depleted cells. CTCF loss-associated gains in transcription were often linked to increased, normally illegitimate enhancer-promoter contacts. In contrast, at genes whose expression declined upon CTCF loss, CTCF seems to function as a conventional transcription activator, independent of its architectural role. CTCF-anchored structural loops facilitated formation CRE loops nested within them, especially those involving weak CREs. Transcription inhibition did not elicit global architectural changes and left transcription start site-associated boundaries intact. However, ongoing transcription contributed considerably to the formation of gene domains, regions of enriched contacts spanning the length of gene bodies. Notably, gene domains formed rapidly in ana/telophase prior to the completion of the first round of transcription, suggesting that epigenetic features in gene bodies contribute to genome reconfiguration prior to transcription. The focus on the de novo formation of nuclear architecture during G1 entry yielded novel insights into how CTCF and transcription contribute to the dynamic re-configuration of chromatin architecture during the mitosis to G1 phase progression.

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“…RAD21-mAID-eGFP cells were treated with auxin for 6 hr. Since complete depletion of CTCF takes longer to achieve 19,45 , CTCF-AID-eGFP cells were treated for 48 hr, with exchanging auxin-containing media after the first 24 hr. Alkaline phosphatase testing for the assessment of pluripotency before and after auxin treatment was performed using the Alkaline Phosphatase Detection Kit (EMD Millipore, SCR004).…”

Section: Depletion Of Rad21 and Ctcfmentioning

confidence: 99%

Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF

Aljahani

Hua

Karpinska

et al. 2021

Preprint

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Enhancers and promoters predominantly interact within large-scale topologically associating domains (TADs), which are formed by loop extrusion mediated by cohesin and CTCF. However, it is unclear whether complex chromatin structures exist at sub-kilobase-scale and to what extent fine-scale regulatory interactions depend on loop extrusion. To address these questions, we present an MNase-based chromosome conformation capture (3C) approach, which has enabled us to generate the most detailed local interaction data to date and precisely investigate the effects of cohesin and CTCF depletion on chromatin architecture. Our data reveal that cis-regulatory elements have distinct internal nano-scale structures, within which local insulation is dependent on CTCF, but which are independent of cohesin. In contrast, we find that depletion of cohesin causes a subtle reduction in longer-range enhancer-promoter interactions and that CTCF depletion can cause rewiring of regulatory contacts. Together, our data show that loop extrusion is not essential for enhancer-promoter interactions, but contributes to their robustness and specificity and to precise regulation of gene expression.

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Distinct properties and functions of CTCF revealed by a rapidly inducible degron system

Cited by 72 publications

References 89 publications

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

CTCF and transcription influence chromatin structure re-configuration after mitosis

Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF

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