The structural basis for cohesin–CTCF-anchored loops

Li, Yan; Haarhuis, Judith H.I.; Cacciatore, Ángela Sedeño; Oldenkamp, Roel; Ruiten, Marjon S. van; Willems, Laureen; Teunissen, Hans; Muir, Kyle; Wit, Elzo de; Rowland, Benjamin D.; Panne, Daniel

doi:10.1038/s41586-019-1910-z

Cited by 340 publications

(411 citation statements)

References 79 publications

(102 reference statements)

Supporting

Mentioning

350

Contrasting

Unclassified

Order By: Relevance

“…To validate the specificity of the scC&T, we searched for enriched motifs in binding sites using MEME suite 24 in merged pseudo-bulk datasets of Rad21 and Olig2. We found the motif of chromatin architecture factor, CTCF as the highest enriched in the Rad21 dataset (Figure 5g), which is consistent with the cooperativeness between Ctcf and Cohesin 25 . We found several motifs enriched in the Olig2 scC&T, including motif CAGMTG, similar to the previously identified CAGMTG/CAGCTG motif specific for Olig2 (Figure 5h) in mouse 26 and rat 27 respectively.…”

Section: Single Cell Cutandtag Of Transcription Factorssupporting

confidence: 77%

Single-cell profiling of histone modifications in the mouse brain

Bartošovič

Kabbe

Castelo‐Branco

2020

Preprint

View full text Add to dashboard Cite

The development of the mouse central nervous system (CNS) involves coordinated execution of transcriptional and epigenetic programs. These programs have been extensively studied through single-cell technologies in a pursuit to characterize the underlying cell heterogeneity. However, histone modifications pose additional layers of both positive and negative regulation that defines cellular identity. Here we show that the Cut&Tag technology can be coupled with a droplet-based single cell library preparation platform to produce high quality chromatin modifications data at a single cell resolution in tens of thousands of cells. We apply single-cell Cut&Tag (scC&T) to probe histone modifications characteristic of active promoters (H3K4me3), active promoters and enhancers (H3K27ac), active gene bodies (H3K36me3) and inactive regions (H3K27me3) and generate scC&T profiles for almost 50,000 cells. scC&T profiles of each of these histone modifications were sufficient to determine cell identity and deconvolute at single cell level regulatory principles such as promoter bivalency, spreading of H3K4me3 and promoter-enhancer connectivity. Moreover, we used scC&T to investigate the single-cell chromatin occupancy of transcription factor Olig2 and the cohesin complex component Rad21. Our results indicate that analysis of histone modifications and transcription factor occupancy at a single cell resolution can provide unique insights of epigenomic landscapes in the CNS. We also provide an online resource that can be used to interactively explore the data at https://castelobranco.shinyapps.io/BrainCutAndTag2020/.

show abstract

Section: Single Cell Cutandtag Of Transcription Factorssupporting

confidence: 77%

Single-cell profiling of histone modifications in the mouse brain

Bartošovič

Kabbe

Castelo‐Branco

2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Orientation-biased CTCF binding has been proposed to play a role in initiating cohesin-mediated extrusion, which was inspired by the study of Pcdh gene loci 26, 33 . Recent findings from the structure analysis of the cohesin-CTCF complex 54 also provide an explanation for the orientation biased CTCF and cohesin binding at TAD borders. Together with our observation, these data strongly support a model in which the border plays a much more important role in initiating a cohesin-mediated directional extrusion process anchored at orientation-biased CTCF site (Figure 3M).…”

Section: Discussionmentioning

confidence: 95%

Systematic Chromatin Architecture Analysis inXenopus tropicalisReveals Conserved Three-Dimensional Folding Principles of Vertebrate Genomes

Niu

Shen

Shi

et al. 2020

Preprint

View full text Add to dashboard Cite

23Metazoan genomes are folded into 3D structures in interphase nuclei. 24 However, the molecular mechanism remains unknown. Here, we show that 25 topologically associating domains (TADs) form in two waves during Xenopus 26 tropicalis embryogenesis, first at zygotic genome activation and then as the 27 expression of CTCF and Rad21 is elevated. We also found TAD structures 28 continually change for at least three times during development. Surprisingly, 29 the directionality index is preferentially stronger on one side of TADs where 30 orientation-biased CTCF and Rad21 binding are observed, a conserved 31 pattern that is found in human cells as well. Depletion analysis revealed CTCF, 32 Rad21, and RPB1, a component of RNAPII, are required for the establishment 33 of TADs. Overall, our work shows that Xenopus is a powerful model for 34 chromosome architecture analysis. Furthermore, our findings indicate that 35 cohesin-mediated extrusion may anchor at orientation-biased CTCF binding 36 sites, supporting a CTCF-anchored extrusion model as the mechanism for 37 TAD establishment. 38 39 40 41 42 3 KEYWORDS 43 Hi-C, Topologically associating domain (TAD), CTCF, Orientation-biased 44 binding, Cohesin-mediated extrusion, Directionality, Zygotic genome activation 45 (ZGA), RNAPII, Xenopus tropicalis, Genome assembly 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 Interphase chromosomes are partitioned into topologically associating 65 domains (TADs) 1-4 which segregate into compartments of active or repressive 66 chromatins 5-7 . TAD structures are relatively stable and resilient to 67 environmental perturbations 8,9 . Chromosome architecture at the TAD level is 68 also evolutionarily conserved in eukaryotic species 4,10,11 . Disruption of TAD 69 borders leads to developmental disorders and even tumorigenesis, thus 70 underlining the importance of 3D genome organization in gene regulation 12-15 . 71 The establishment of chromatin architecture during embryogenesis provides 72 an initial spatial frame which may guide proper genome organization, 73 chromatin interaction and gene regulation in following development and 74 differentiation processes 16 . The timing of de novo TADs formation during 75 development has been examined in Drosophila, mouse, zebrafish, and 76 human 17-21 . TAD structures form at zygotic genome activation (ZGA) and 77 continually consolidate during early embryo development in fruit fly, mouse and 78 human 17,19-21 . However, in zebrafish, TADs already exist before ZGA and are 79 lost after ZGA before being reestablished in later developmental stages 18 . This 80 difference raises the question if the process of TAD formation is evolutionarily 81 conserved. 82 Cohesin complex-mediated DNA loop extrusion was recently reported in 83 several in vitro studies 22,23 and proposed as a functional mechanism 84 underlying TAD establishment 24-26 . In cultured cells, the deletion of cohesin 85 5 Rad21 alone is enough to abolish the establishment of TADs 27 . In addition, 86 CTCF, WAPL, and PDS5 proteins p...

show abstract

“…Cohesin-dependent loops occurred between more distal CTCF binding sites when the cohesin regulator WAPL was depleted, showing that WAPL restricts loop size. WAPL dissociates cohesin from chromosomes (Haarhuis et al, 2017), and by preventing WAPL binding to cohesin, CTCF is thought to protect the translocating cohesin (Li et al, 2020). The formation of specific loops by cohesin, CTCF, and WAPL has been proposed to contribute to the regulation of gene expression by controlling the interactions of enhancers with distal promoters (Schoenfelder and Fraser, 2019).…”

Section: Introductionmentioning

confidence: 99%

Cohesin residency determines chromatin loop patterns

Costantino

Lamothe

et al. 2020

Preprint

View full text Add to dashboard Cite

The organization of chromatin into higher-order structures is essential for chromosome segregation, the repair of DNA damage, and the regulation of gene expression. These structures are formed by the evolutionarily conserved SMC (structural maintenance of chromosomes) complexes. By analyzing synchronized populations of budding yeast with Micro-C, we observed that chromatin loops are formed genome-wide, and are dependent upon the SMC complex, cohesin. We correlated the loop signal with the position and intensity of cohesin binding to chromosomes in wild-type and cells depleted for the cohesin regulators Wpl1p and Pds5p. We generate a model to explain how the genomic distribution and frequency of loops are driven by cohesin residency on chromosomes. In this model a dynamic pool of cohesin with loop extrusion activity stops when encountering two regions occupied by stably bound cohesin, forming a loop. Different regions are occupied by cohesin in different cells, defining various patterns of chromatin loops.

show abstract

The structural basis for cohesin–CTCF-anchored loops

Cited by 340 publications

References 79 publications

Single-cell profiling of histone modifications in the mouse brain

Single-cell profiling of histone modifications in the mouse brain

Systematic Chromatin Architecture Analysis inXenopus tropicalisReveals Conserved Three-Dimensional Folding Principles of Vertebrate Genomes

Cohesin residency determines chromatin loop patterns

Contact Info

Product

Resources

About