scholarly journals The CTCF Anatomy of Topologically Associating Domains

2019 ◽  
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.

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

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.

scholarly journals The role of insulators and transcription in 3D chromatin organisation of flies

2021 ◽  
Author(s):  
Keerthi T Chathoth ◽  
Liudmila A Mikheeva ◽  
Gilles Crevel ◽  
Jareth C. Wolfe ◽  
Ioni Hunter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differentially Expressed Genes ◽  
Functional Role ◽  
Transcriptomic Data ◽  
Chromatin Loops ◽  
Topologically Associating Domains ◽  
Architectural Proteins ◽  
Chromatin Organisation

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.

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

2017 ◽  
Vol 36 (24) ◽  
pp. 3573-3599 ◽  
Author(s):  
Gordana Wutz ◽  
Csilla Várnai ◽  
Kota Nagasaka ◽  
David A Cisneros ◽  
Roman R Stocsits ◽  
...  
Keyword(s):  
Chromatin Loops ◽  
Topologically Associating Domains

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.

A few upstream bifurcations drive the spatial distribution of red blood cells in model microfluidic networks

Soft Matter ◽  
2022 ◽  
Author(s):  
Adlan Merlo ◽  
Maxime Berg ◽  
Paul Duru ◽  
Frédéric Risso ◽  
Yohan Davit ◽  
...  
Keyword(s):  
Blood Flow ◽  
Spatial Distribution ◽  
Blood Vessel ◽  
Red Blood Cells ◽  
Blood Cells ◽  
Small Vessel ◽  
Microfluidic Networks ◽  
Vessel Walls ◽  
Vessel Networks

The physics of blood flow in small vessel networks is dominated by the interactions between Red Blood Cells (RBCs), plasma and blood vessel walls. The resulting couplings between the microvessel...

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

2017 ◽  
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.

scholarly journals Topologically associated domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation

2016 ◽  
Author(s):  
Nathan Harmston ◽  
Elizabeth Ing-Simmons ◽  
Ge Tan ◽  
Malcolm Perry ◽  
Matthias Merkenschlager ◽  
...  
Keyword(s):  
Long Range ◽  
Close Correspondence ◽  
Developmental Genes ◽  
Regulatory Interactions ◽  
Topologically Associating Domains ◽  
Topologically Associated Domains ◽  
The Difference ◽  
Conserved Noncoding Elements ◽  
Extreme Conservation

AbstractIn vertebrates and other Metazoa, developmental genes are found surrounded by dense clusters of highly conserved noncoding elements (CNEs). CNEs exhibit extreme levels of sequence conservation of unexplained origin, with many acting as long-range enhancers during development. Clusters of CNEs, termed genomic regulatory blocks (GRBs), define the span of regulatory interactions for many important developmental regulators. The function and genomic distribution of these elements close to important regulatory genes raises the question of how they relate to the 3D conformation of these loci. We show that GRBs, defined using clusters of CNEs, coincide strongly with the patterns of topological organisation in metazoan genomes, predicting the boundaries of topologically associating domains (TADs) at hundreds of loci. The set of TADs that are associated with high levels of non-coding conservation exhibit distinct properties compared to TADs called in chromosomal regions devoid of extreme non-coding conservation. The correspondence between GRBs and TADs suggests that TADs around developmental genes are ancient, slowly evolving genomic structures, many of which have had conserved spans for hundreds of millions of years. This relationship also explains the difference in TAD numbers and sizes between genomes. While the close correspondence between extreme conservation and the boundaries of this subset of TADs does not reveal the mechanism leading to the conservation of these elements, it provides a functional framework for studying the role of TADs in long-range transcriptional regulation.

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

2017 ◽  
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.

Lithography below 100 nm

1983 ◽  
Vol 41 ◽  
pp. 96-99
Author(s):  
L. D. Jackel
Keyword(s):  
Spatial Distribution ◽  
Electron Beam ◽  
Electron Scattering ◽  
Electron Beam Lithography ◽  
Substrate Material ◽  
Local Electron ◽  
Electron Dose ◽  
Positive Resist ◽  
Exposure Process

Most production electron beam lithography systems can pattern minimum features a few tenths of a micron across. Linewidth in these systems is usually limited by the quality of the exposing beam and by electron scattering in the resist and substrate. By using a smaller spot along with exposure techniques that minimize scattering and its effects, laboratory e-beam lithography systems can now make features hundredths of a micron wide on standard substrate material. This talk will outline sane of these high- resolution e-beam lithography techniques.We first consider parameters of the exposure process that limit resolution in organic resists. For concreteness suppose that we have a “positive” resist in which exposing electrons break bonds in the resist molecules thus increasing the exposed resist's solubility in a developer. Ihe attainable resolution is obviously limited by the overall width of the exposing beam, but the spatial distribution of the beam intensity, the beam “profile” , also contributes to the resolution. Depending on the local electron dose, more or less resist bonds are broken resulting in slower or faster dissolution in the developer.

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