scholarly journals The formation of chromatin domains: a new model

2018 ◽  
Author(s):  
Giorgio Bernardi
Keyword(s):  
Dna Sequences ◽  
Binding Sites ◽  
Ctcf Binding ◽  
Second Step ◽  
Essential Factor ◽  
Chromatin Domains ◽  
Topologically Associating Domains ◽  
Wavy Structure ◽  
Architectural Proteins ◽  
Nucleosome Density

In spite of the recent advances in the field of chromatin architecture1,2, the formation mechanism of chromatin domains, TADs, the topologically associating domains, and LADs, the lamina associated domains, is still an open problem. While previous models only dealt with TADs and essentially relied on the architectural proteins CTCF and cohesin, the model presented here concerns both TADs and LADs and is primarily based on the corresponding DNA sequences, the GC-rich and GC-poor isochores, more specifically on their newly discovered 3-D structures. Indeed, the compositionally homogeneous GC-poor isochores were shown to be locally stiff because of the presence of interspersed oligo- Adenines4,5, whereas the compositionally heterogeneous GC-rich isochores were found to be peak-shaped and characterized by increasing gradients of GC and of interspersed oligo- Guanines. In LADs, oligo-Adenines induce local nucleosome depletions4,5 that are responsible for a wavy structure well adapted for interaction with the lamina. In TADs, the increasing GC levels and increasing oligo-Guanines of the isochore peaks are responsible for a decreasing nucleosome density5,6, a decreasing supercoiling7 and an increasing accessibility8. These factors mould the loops of “primary TADs”, that lack self-interactions since they are CTCF/cohesin-free, yet transcriptionally functional structures9-11. This “moulding step” is followed by a second step, in which the cohesin rings bind to the tips of the “primary TADs” and slide down the loops. This process is very likely due to Scc2/Nipbl, an essential factor not only for loading cohesin, but also for stimulating its translocation12 and its ATPase activity13. This “sliding step” creates self-interactions in the loops and stops at the CTCF binding sites located at the base of the loops that are thus closed and insulated.

scholarly journals CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains

2020 ◽  
Author(s):  
Hui Huang ◽  
Quan Zhu ◽  
Adam Jussila ◽  
Yuanyuan Han ◽  
Bogdan Bintu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Binding Sites ◽  
Imaging Techniques ◽  
Critical Role ◽  
Embryonic Stem ◽  
Ctcf Binding ◽  
Chromatin Domain ◽  
Chromatin Domains ◽  
Binding Motifs ◽  
Binding Factor

AbstractInsulators play a critical role in spatiotemporal gene expression in metazoans by separating active and repressive chromatin domains and preventing inappropriate enhancer-promoter contacts. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here, we explore the sequence requirements of CTCF-mediated transcriptional insulation with the use of a sensitive insulator reporter assay in mouse embryonic stem cells. We find that insulation potency depends on the number of CTCF binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on DNA sequences flanking its core binding motifs, and CTCF binding sites at topologically associating domain(TAD) boundaries are more likely to function as insulators than those outside TAD boundaries, independent of binding strength. Using chromosomal conformation capture assays and high-resolution chromatin imaging techniques, we demonstrate that insulators form local chromatin domain boundaries and reduce enhancer-promoter contacts. Taken together, our results provide strong genetic, molecular, and structural evidence connecting chromatin topology to the action of insulators in the mammalian genome.

scholarly journals Systematic Chromatin Architecture Analysis in Xenopus tropicalis Reveals Conserved Three-Dimensional Folding Principles of Vertebrate Genomes

2020 ◽  
Author(s):  
Longjian Niu ◽  
Wei Shen ◽  
Zhaoying Shi ◽  
Na He ◽  
Jing Wan ◽  
...  
Keyword(s):  
Binding Sites ◽  
Three Dimensional ◽  
Xenopus Tropicalis ◽  
Ctcf Binding ◽  
Interphase Nuclei ◽  
Chromosome Architecture ◽  
Topologically Associating Domains ◽  
Genome Activation ◽  
Zygotic Genome ◽  
Architecture Analysis

ABSTRACTMetazoan genomes are folded into 3D structures in interphase nuclei. However, the molecular mechanism remains unknown. Here, we show that topologically associating domains (TADs) form in two waves during Xenopus tropicalis embryogenesis, first at zygotic genome activation and then as the expression of CTCF and Rad21 is elevated. We also found TAD structures continually change for at least three times during development. Surprisingly, the directionality index is preferentially stronger on one side of TADs where orientation-biased CTCF and Rad21 binding are observed, a conserved pattern that is found in human cells as well. Depletion analysis revealed CTCF, Rad21, and RPB1, a component of RNAPII, are required for the establishment of TADs. Overall, our work shows that Xenopus is a powerful model for chromosome architecture analysis. Furthermore, our findings indicate that cohesin-mediated extrusion may anchor at orientation-biased CTCF binding sites, supporting a CTCF-anchored extrusion model as the mechanism for TAD establishment.

scholarly journals Co-opted transposons help perpetuate conserved higher-order chromosomal structures

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Mayank NK Choudhary ◽  
Ryan Z. Friedman ◽  
Julia T. Wang ◽  
Hyo Sik Jang ◽  
Xiaoyu Zhuo ◽  
...  
Keyword(s):  
Binding Sites ◽  
Ctcf Binding ◽  
Ctcf Binding Site ◽  
Genome Architecture ◽  
Mutational Signatures ◽  
Domain Structures ◽  
Domain Boundaries ◽  
Architectural Proteins ◽  
Mammalian Genomes ◽  
Species Specific

Abstract Background Transposable elements (TEs) make up half of mammalian genomes and shape genome regulation by harboring binding sites for regulatory factors. These include binding sites for architectural proteins, such as CTCF, RAD21, and SMC3, that are involved in tethering chromatin loops and marking domain boundaries. The 3D organization of the mammalian genome is intimately linked to its function and is remarkably conserved. However, the mechanisms by which these structural intricacies emerge and evolve have not been thoroughly probed. Results Here, we show that TEs contribute extensively to both the formation of species-specific loops in humans and mice through deposition of novel anchoring motifs, as well as to the maintenance of conserved loops across both species through CTCF binding site turnover. The latter function demonstrates the ability of TEs to contribute to genome plasticity and reinforce conserved genome architecture as redundant loop anchors. Deleting such candidate TEs in human cells leads to the collapse of conserved loop and domain structures. These TEs are also marked by reduced DNA methylation and bear mutational signatures of hypomethylation through evolutionary time. Conclusions TEs have long been considered a source of genetic innovation. By examining their contribution to genome topology, we show that TEs can contribute to regulatory plasticity by inducing redundancy and potentiating genetic drift locally while conserving genome architecture globally, revealing a paradigm for defining regulatory conservation in the noncoding genome beyond classic sequence-level conservation.

scholarly journals Molecular basis of CTCF binding polarity in genome folding

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Elphège P. Nora ◽  
Laura Caccianini ◽  
Geoffrey Fudenberg ◽  
Kevin So ◽  
Vasumathi Kameswaran ◽  
...  
Keyword(s):  
Single Molecule ◽  
Binding Sites ◽  
Molecular Basis ◽  
Live Imaging ◽  
Ctcf Binding ◽  
Chromatin Loops ◽  
Topologically Associating Domains ◽  
N Terminus

Abstract Current models propose that boundaries of mammalian topologically associating domains (TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by cohesin. While the orientation of CTCF motifs determines which pairs of CTCF sites preferentially stabilize loops, the molecular basis of this polarity remains unclear. By combining ChIP-seq and single molecule live imaging we report that CTCF positions cohesin, but does not control its overall binding dynamics on chromatin. Using an inducible complementation system, we find that CTCF mutants lacking the N-terminus cannot insulate TADs properly. Cohesin remains at CTCF sites in this mutant, albeit with reduced enrichment. Given the orientation of CTCF motifs presents the N-terminus towards cohesin as it translocates from the interior of TADs, these observations explain how the orientation of CTCF binding sites translates into genome folding patterns.

scholarly journals Molecular basis of CTCF binding polarity in genome folding

2019 ◽  
Author(s):  
Elphège P. Nora ◽  
Laura Caccianini ◽  
Geoffrey Fudenberg ◽  
Vasumathi Kameswaran ◽  
Abigail Nagle ◽  
...  
Keyword(s):  
Single Molecule ◽  
Binding Sites ◽  
Molecular Basis ◽  
Live Imaging ◽  
Ctcf Binding ◽  
Dna Loops ◽  
Genomic Distribution ◽  
Chromatin Loops ◽  
Topologically Associating Domains ◽  
N Terminus

SummaryCurrent models propose that boundaries of mammalian topologically associating domains (TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by cohesin proteins (Merkenschlager & Nora, 2016; Fudenberg, Abdennur, Imakaev, Goloborodko, & Mirny, 2017). While the orientation of CTCF motifs determines which pairs of CTCF sites preferentially stabilize DNA loops (de Wit et al., 2015; Guo et al., 2015; Rao et al., 2014; Vietri Rudan et al., 2015), the molecular basis of this polarity remains mysterious. Here we report that CTCF positions cohesin but does not control its overall binding or dynamics on chromatin by single molecule live imaging. Using an inducible complementation system, we found that CTCF mutants lacking the N-terminus cannot insulate TADs properly, despite normal binding. Cohesin remained at CTCF sites in this mutant, albeit with reduced enrichment. Given that the orientation of the CTCF motif presents the CTCF N-terminus towards cohesin as it translocates from the interior of TADs, these observations provide a molecular explanation for how the polarity of CTCF binding sites determines the genomic distribution of chromatin loops.

scholarly journals Capturing the complexity of topologically associating domains through multi-feature optimization

2021 ◽  
Author(s):  
Natalie Sauerwald ◽  
Carl Kingsford
Keyword(s):  
Binding Sites ◽  
Three Dimensional ◽  
Replication Timing ◽  
Biological Properties ◽  
Ctcf Binding ◽  
Dimensional Structure ◽  
Biological Targets ◽  
Topologically Associating Domains ◽  
Contact Frequency ◽  
Algorithmic Framework

AbstractThe three-dimensional structure of human chromosomes is tied to gene regulation and replication timing, but there is still a lack of consensus on the computational and biological definitions for chromosomal substructures such as topologically associating domains (TADs). TADs are described and identified by various computational properties leading to different TAD sets with varying compatibility with biological properties such as boundary occupancy of structural proteins. We unify many of these computational and biological targets into one algorithmic framework that jointly maximizes several computational TAD definitions and optimizes TAD selection for a quantifiable biological property. Using this framework, we explore the variability of TAD sets optimized for six different desirable properties of TAD sets: high occupancy of CTCF, RAD21, and H3K36me3 at boundaries, reproducibility between replicates, high intra- vs inter-TAD difference in contact frequencies, and many CTCF binding sites at boundaries. The compatibility of these biological targets varies by cell type, and our results suggest that these properties are better reflected as subpopulations or families of TADs rather than a singular TAD set fitting all TAD definitions and properties. We explore the properties that produce similar TAD sets (reproducibility and inter- vs intra-TAD difference, for example) and those that lead to very different TADs (such as CTCF binding sites and inter- vs intra-TAD contact frequency difference).

scholarly journals A functional overlap between actively transcribed genes and chromatin boundary elements

2020 ◽  
Author(s):  
Caroline L Harrold ◽  
Matthew E Gosden ◽  
Lars L P Hanssen ◽  
Rosa J Stolper ◽  
Damien J Downes ◽  
...  
Keyword(s):  
Binding Sites ◽  
Globin Gene ◽  
Boundary Elements ◽  
Ctcf Binding ◽  
Chromatin Loop ◽  
Globin Genes ◽  
Topologically Associating Domains ◽  
Binding Factor ◽  
Mammalian Genomes ◽  
Chromatin Boundary

AbstractMammalian genomes are subdivided into large (50-2000 kb) regions of chromatin referred to as Topologically Associating Domains (TADs or sub-TADs). Chromatin within an individual TAD contacts itself more frequently than with regions in surrounding TADs thereby directing enhancer-promoter interactions. In many cases, the borders of TADs are defined by convergently orientated boundary elements associated with CCCTC-binding factor (CTCF), which stabilises the cohesin complex on chromatin and prevents its translocation. This delimits chromatin loop extrusion which is thought to underlie the formation of TADs. However, not all CTCF-bound sites act as boundaries and, importantly, not all TADs are flanked by convergent CTCF sites. Here, we examined the CTCF binding sites within a ∼70 kb sub-TAD containing the duplicated mouse α-like globin genes and their five enhancers (5’-R1-R2-R3-Rm-R4-α1-α2-3’). The 5’ border of this sub-TAD is defined by a pair of CTCF sites. Surprisingly, we show that deletion of the CTCF binding sites within and downstream of the α-globin locus leaves the sub-TAD largely intact. The predominant 3’ border of the sub-TAD is defined by a steep reduction in contacts: this corresponds to the transcribed α2-globin gene rather than the CTCF sites at the 3’-end of the sub-TAD. Of interest, the almost identical α1- and α2-globin genes interact differently with the enhancers, resulting in preferential expression of the proximal α1-globin gene which behaves as a partial boundary between the enhancers and the distal α2-globin gene. Together, these observations provide direct evidence that actively transcribed genes can behave as boundary elements.Significance StatementMammalian genomes are complex, organised 3D structures, partitioned into Topologically Associating Domains (TADs): chromatin regions that preferentially self-interact. These chromatin interactions are thought to be driven by a mechanism that continuously extrudes chromatin loops, forming structures delimited by chromatin boundary elements and reflecting the activity of enhancers and promoters. Boundary elements bind architectural proteins such as CCCTC-binding factor (CTCF). Previously, an overlap between the functional roles of enhancers and promoters has been shown. However, whether there is overlap between enhancers/promoters and boundary elements is not known. Here, we show that actively transcribed genes can also behave as boundary elements, similar to CTCF boundaries. In both cases, multi-protein complexes bound to these regions may stall the process of chromatin loop extrusion.

scholarly journals Chromatin topology and the timing of enhancer function at theHoxDlocus

2020 ◽  
Vol 117 (49) ◽  
pp. 31231-31241
Author(s):  
Eddie Rodríguez-Carballo ◽  
Lucille Lopez-Delisle ◽  
Andréa Willemin ◽  
Leonardo Beccari ◽  
Sandra Gitto ◽  
...  
Keyword(s):  
Binding Sites ◽  
Target Genes ◽  
Gene Activation ◽  
Ctcf Binding ◽  
Topologically Associating Domains ◽  
Regulatory Signal ◽  
Key Factor ◽  
Enhancer Function ◽  
Natural Target ◽  
Enhancer Sequences

TheHoxDgene cluster is critical for proper limb formation in tetrapods. In the emerging limb buds, different subgroups ofHoxdgenes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations are exclusive from one another and emanate from two distinct topologically associating domains (TADs) flankingHoxD, both containing a range of appropriate enhancer sequences. The telomeric TAD (T-DOM) contains several enhancers active in presumptive forearm cells and is divided into two sub-TADs separated by a CTCF-rich boundary, which defines two regulatory submodules. To understand the importance of this particular regulatory topology to controlHoxdgene transcription in time and space, we either deleted or inverted this sub-TAD boundary, eliminated the CTCF binding sites, or inverted the entire T-DOM to exchange the respective positions of the two sub-TADs. The effects of such perturbations on the transcriptional regulation ofHoxdgenes illustrate the requirement of this regulatory topology for the precise timing of gene activation. However, the spatial distribution of transcripts was eventually resumed, showing that the presence of enhancer sequences, rather than either their exact topology or a particular chromatin architecture, is the key factor. We also show that the affinity of enhancers to find their natural target genes can overcome the presence of both a strong TAD border and an unfavorable orientation of CTCF sites.

scholarly journals AN ISOCHORE FRAMEWORK UNDERLIES CHROMATIN ARCHITECTURE

2016 ◽  
Author(s):  
Kamel Jabbari ◽  
Giorgio Bernardi
Keyword(s):  
Dna Sequences ◽  
Evolutionary Conservation ◽  
Human Chromosomes ◽  
Chromatin Domains ◽  
Chromatin Architecture ◽  
Topologically Associating Domains ◽  
Architectural Features ◽  
New Information ◽  
Mammalian Genomes ◽  
Compositional Properties

AbstractA recent investigation showed the existence of correlations between the architectural features of mammalian interphase chromosomes and the compositional properties of isochores. This result prompted us to compare maps of the Topologically Associating Domains (TADs) and of the Lamina Associated Domains (LADs) with the corresponding isochore maps of mouse and human chromosomes. This approach revealed that: 1) TADs and LADs correspond to isochores, i.e., isochores are the genomic units that underlie chromatin domains; 2) the conservation of TADs and LADs in mammalian genomes is explained by the evolutionary conservation of isochores; 3) chromatin domains corresponding to GC-poor isochores (e.g., LADs) interact with other domains also corresponding to GC-poor isochores even if located far away on the chromosomes; in contrast, chromatin domains corresponding to GC-rich isochores (e.g., TADs) show more localized chromosomal interactions, many of which are inter-chromosomal. In conclusion, this investigation establishes a link between DNA sequences and chromatin architecture, explains the evolutionary conservation of TADs and LADs and provides new information on the spatial distribution of GC-poor/gene-poor and GC-rich/gene-rich chromosomal regions in the interphase nucleus.

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