Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins

AbstractThe DNA in many organisms, including humans, is shown to be organised in topologically associating domains (TADs). InDrosophila, several architectural proteins are enriched at TAD borders, but it is still unclear whether these proteins play a functional role in the formation and maintenance of TADs. Here, we show that depletion of BEAF-32, Cp190, Chro and Dref leads to changes in TAD organisation and chromatin loops. Their depletion predominantly affects TAD borders located in heterochromatin, while TAD borders located in euchromatin are resilient to these mutants. Furthermore, transcriptomic data has revealed hundreds of genes displaying differential expression in these mutants and showed that the majority of differentially expressed genes are located within reorganised TADs. Our work identifies a novel and functional role for architectural proteins at TAD borders inDrosophilaand a link between TAD reorganisation and subsequent changes in gene expression.

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Molecular basis of CTCF binding polarity in genome folding

Nature Communications ◽

10.1038/s41467-020-19283-x ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 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.

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Molecular basis of CTCF binding polarity in genome folding

10.1101/2019.12.13.876177 ◽

2019 ◽

Cited By ~ 4

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.

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The CTCF Anatomy of Topologically Associating Domains

10.1101/746610 ◽

2019 ◽

Cited By ~ 1

Author(s):

Luca Nanni ◽

Cheng Wang ◽

Freek Manders ◽

Laszlo Groh ◽

Paula Haro ◽

...

Keyword(s):

Spatial Distribution ◽

Blood Cells ◽

Chromatin Loops ◽

Topologically Associating Domains ◽

Topologically Associated Domains ◽

Ctcf Site

AbstractTopologically associated domains (TADs) are defined as regions of self-interaction. To date, it is unclear how to reconcile TAD structure with CTCF site orientation, which is known to coordinate chromatin loops anchored by Cohesin rings at convergent CTCF site pairs. We first approached this problem by 4C analysis of the FKBP5 locus. This uncovered a CTCF loop encompassing FKBP5 but not its entire TAD. However, adjacent CTCF sites were able to form ‘back-up’ loops and these were located at TAD boundaries. We then analysed the spatial distribution of CTCF patterns along the genome together with a boundary identity conservation ‘gradient’ obtained from primary blood cells. This revealed that divergent CTCF sites are enriched at boundaries and that convergent CTCF sites mark the interior of TADs. This conciliation of CTCF site orientation and TAD structure has deep implications for the further study and engineering of TADs and their boundaries.

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Binless normalization of Hi-C data provides significant interaction and difference detection independently of resolution

10.1101/214403 ◽

2017 ◽

Cited By ~ 1

Author(s):

Yannick G. Spill ◽

David Castillo ◽

Marc A. Marti-Renom

Keyword(s):

Genome Organization ◽

Detection Method ◽

Gene Activation ◽

Chromatin Loops ◽

Interaction Detection ◽

Difference Detection ◽

Topologically Associating Domains ◽

Detailed Classification ◽

Dynamic Interplay

Abstract3C-like experiments, such as 4C or Hi-C, have been fundamental in understanding genome organization. Thanks to these technologies, it is now known, for example, that Topologically Associating Domains (TADs) and chromatin loops are implicated in the dynamic interplay of gene activation and repression, and their disruption can have dramatic effects on embryonic development. To make their detection easier, scientists have endeavored into deeper sequencing to mechanically increase the chances to detect weaker signals such as chromatin loops. Part of this mindset can be attributed to the limitations of existing software: the analysis of Hi-C experiments is both statistically and computationally demanding. Here, we devise a new way to represent Hi-C data, which leads to a more detailed classification of paired-end reads and, ultimately, to a new normalization and interaction detection method. Unlike any other, Binless is resolution-agnostic, and adapts to the quality and quantity of available data. We demonstrate its capacities to call interactions and differences and make the software freely available.

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CTCF, WAPL and PDS5 proteins control the formation of TADs and loops by cohesin

10.1101/177444 ◽

2017 ◽

Cited By ~ 7

Author(s):

Gordana Wutz ◽

Csilla Várnai ◽

Kota Nagasaka ◽

David A Cisneros ◽

Roman Stocsits ◽

...

Keyword(s):

Gene Regulation ◽

Long Range ◽

Direct Evidence ◽

Chromatin Loops ◽

Chromatin Interactions ◽

Binding Partners ◽

Topologically Associating Domains ◽

Genome Wide ◽

Mammalian Genomes

AbstractMammalian genomes are organized into compartments, topologically-associating domains (TADs) and loops to facilitate gene regulation and other chromosomal functions. Compartments are formed by nucleosomal interactions, but how TADs and loops are generated is unknown. It has been proposed that cohesin forms these structures by extruding loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here we show that cohesin suppresses compartments but is essential for TADs and loops, that CTCF defines their boundaries, and that WAPL and its PDS5 binding partners control the length of chromatin loops. In the absence of WAPL and PDS5 proteins, cohesin passes CTCF sites with increased frequency, forms extended chromatin loops, accumulates in axial chromosomal positions (vermicelli) and condenses chromosomes to an extent normally only seen in mitosis. These results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL.

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SuperTAD: robust detection of hierarchical topologically associated domains with optimized structural information

Genome Biology ◽

10.1186/s13059-020-02234-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yu Wei Zhang ◽

Meng Bo Wang ◽

Shuai Cheng Li

Keyword(s):

Structural Information ◽

Current Method ◽

Structural Proteins ◽

Robust Detection ◽

Topologically Associating Domains ◽

Topologically Associated Domains ◽

Significant Enrichment ◽

High Consistency ◽

Public Datasets ◽

State Of Art

AbstractTopologically associating domains (TADs) are the organizational units of chromosome structures. TADs can contain TADs, thus forming a hierarchy. TAD hierarchies can be inferred from Hi-C data through coding trees. However, the current method for computing coding trees is not optimal. In this paper, we propose optimal algorithms for this computation. In comparison with seven state-of-art methods using two public datasets, from GM12878 and IMR90 cells, SuperTAD shows a significant enrichment of structural proteins around detected boundaries and histone modifications within TADs and displays a high consistency between various resolutions of identical Hi-C matrices.

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Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency

Genome Biology ◽

10.1186/s13059-021-02424-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yongzheng Li ◽

Boxin Xue ◽

Mengling Zhang ◽

Liwei Zhang ◽

Yingping Hou ◽

...

Keyword(s):

Dna Replication ◽

Structural Dynamics ◽

Replication Origin ◽

High Efficiency ◽

S Phase ◽

Chromatin Domain ◽

Replication Origins ◽

Replication Efficiency ◽

Topologically Associating Domains ◽

Epigenetic Signatures

Abstract Background Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and epigenetic signatures have been linked to the replication efficiency of origins, there is no consensus on how the selection of origins is determined. Results We apply dual-color stochastic optical reconstruction microscopy (STORM) super-resolution imaging to map the spatial distribution of origins within individual topologically associating domains (TADs). We find that multiple replication origins initiate separately at the spatial boundary of a TAD at the beginning of the S phase. Intriguingly, while both high-efficiency and low-efficiency origins are distributed homogeneously in the TAD during the G1 phase, high-efficiency origins relocate to the TAD periphery before the S phase. Origin relocalization is dependent on both transcription and CTCF-mediated chromatin structure. Further, we observe that the replication machinery protein PCNA forms immobile clusters around TADs at the G1/S transition, explaining why origins at the TAD periphery are preferentially fired. Conclusion Our work reveals a new origin selection mechanism that the replication efficiency of origins is determined by their physical distribution in the chromatin domain, which undergoes a transcription-dependent structural re-organization process. Our model explains the complex links between replication origin efficiency and many genetic and epigenetic signatures that mark active transcription. The coordination between DNA replication, transcription, and chromatin organization inside individual TADs also provides new insights into the biological functions of sub-domain chromatin structural dynamics.

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Chromatin loop anchors contain core structural components of the gene expression machinery in maize

BMC Genomics ◽

10.1186/s12864-020-07324-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Stéphane Deschamps ◽

John A. Crow ◽

Nadia Chaidir ◽

Brooke Peterson-Burch ◽

Sunil Kumar ◽

...

Keyword(s):

Gene Expression ◽

High Resolution ◽

Transcriptional Activity ◽

Spatial Organization ◽

Regulatory Elements ◽

Open Chromatin ◽

Maize Genome ◽

Chromatin Loop ◽

Structural Components ◽

Chromatin Loops

Abstract Background Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. Results Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with hierarchical topologically-associating domains (TADs) and transcriptional activity. A majority of all anchors are shared between multiple loops from previous public maize high-resolution interactome datasets, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analyses indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Approximately 38% of all Hi-C chromatin loops are fully embedded within hierarchical TAD-like domains, while the remaining ones share anchors with domain boundaries or with distinct domains. Those various loop types exhibit specific patterns of overlap for open chromatin regions and expressed genes, but no apparent pattern of gene expression. In addition, up to 63% of all unique variants derived from a prior public maize eQTL dataset overlap with Hi-C loop anchors. Anchor annotation suggests that < 7% of all loops detected here are potentially devoid of any genes or regulatory elements. The overall organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. Conclusions Sets of conserved chromatin loop anchors mapping to hierarchical domains contains core structural components of the gene expression machinery in maize. The data presented here will be a useful reference to further investigate their function in regard to the formation of transcriptional complexes and the regulation of transcriptional activity in the maize genome.

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Large organized chromatin lysine domains help distinguish primitive from differentiated cell populations

Nature Communications ◽

10.1038/s41467-020-20830-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Seyed Ali Madani Tonekaboni ◽

Benjamin Haibe-Kains ◽

Mathieu Lupien

Keyword(s):

Transposable Elements ◽

Histone Modifications ◽

Cell Types ◽

Regulatory Elements ◽

Cell Populations ◽

Genomic Features ◽

Differentiated Cells ◽

Chromatin Interactions ◽

Topologically Associating Domains ◽

Highly Expressed Genes

AbstractThe human genome is partitioned into a collection of genomic features, inclusive of genes, transposable elements, lamina interacting regions, early replicating control elements and cis-regulatory elements, such as promoters, enhancers, and anchors of chromatin interactions. Uneven distribution of these features within chromosomes gives rise to clusters, such as topologically associating domains (TADs), lamina-associated domains, clusters of cis-regulatory elements or large organized chromatin lysine (K) domains (LOCKs). Here we show that LOCKs from diverse histone modifications discriminate primitive from differentiated cell types. Active LOCKs (H3K4me1, H3K4me3 and H3K27ac) cover a higher fraction of the genome in primitive compared to differentiated cell types while repressive LOCKs (H3K9me3, H3K27me3 and H3K36me3) do not. Active LOCKs in differentiated cells lie proximal to highly expressed genes while active LOCKs in primitive cells tend to be bivalent. Genes proximal to bivalent LOCKs are minimally expressed in primitive cells. Furthermore, bivalent LOCKs populate TAD boundaries and are preferentially bound by regulators of chromatin interactions, including CTCF, RAD21 and ZNF143. Together, our results argue that LOCKs discriminate primitive from differentiated cell populations.

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