Inferring Chromosome Radial Organization from Hi-C Data

Das, Priyojit; Shen, Tongye; McCord, Rachel Patton

doi:10.1101/863803

Cited by 2 publications

(3 citation statements)

References 84 publications

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“…Chromosome 19 has few lamin associated domains (LADs) while chromosome 2 has many (Kind et al 2015). Correspondingly, chr19 tends to be located in the interior of the nucleus of GM12878 cells while chr2 is located at the periphery (Tanabe et al 2002;Das et al 2020). Indeed, when the changes in insulation profile are considered around boundaries in specific sub-compartments, we observe that chr19 B1 (polycomb-related) regions behave more like chr2 B compartment regions while chr19 B4 NAD regions match the insulation change seen in chr19 B compartment regions overall (Figure S5).…”

Section: Hi-c Experiments Reveal Remarkable Preservation Of Genome Contacts In Expanded Nucleimentioning

confidence: 99%

Loops, TADs, Compartments, and Territories are Elastic and Robust to Dramatic Nuclear Volume Swelling

Sanders

Golloshi

Terry

et al. 2021

Preprint

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Layers of genome organization are becoming increasingly better characterized, but less is known about how these structures respond to perturbation or shape changes. Low-salt swelling of isolated chromatin fibers or nuclei has been used for decades to investigate the structural properties of chromatin. But, visible changes in chromatin appearance have not been linked to known building blocks of genome structure or features along the genome sequence. We combine low-salt swelling of isolated nuclei with genome-wide chromosome conformation capture (Hi-C) and imaging approaches to probe the effects of chromatin extension genome-wide. Photoconverted patterns on nuclei during expansion and contraction indicate that global genome structure is preserved after dramatic nuclear volume swelling, suggesting a highly elastic chromosome topology. Hi-C experiments before, during, and after nuclear swelling show changes in average contact probabilities at short length scales, reflecting the extension of the local chromatin fiber. But, surprisingly, during this large increase in nuclear volume, there is a striking maintenance of loops, TADs, active and inactive compartments, and chromosome territories. Subtle differences after expansion are observed, suggesting that the local chromatin state, protein interactions, and location in the nucleus can affect how strongly a given structure is maintained under stress. From these observations, we propose that genome topology is robust to extension of the chromatin fiber and isotropic shape change, and that this elasticity may be beneficial in physiological circumstances of changes in nuclear size and volume.

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Section: Hi-c Experiments Reveal Remarkable Preservation Of Genome Contacts In Expanded Nucleimentioning

confidence: 99%

Loops, TADs, Compartments, and Territories are Elastic and Robust to Dramatic Nuclear Volume Swelling

Sanders

Golloshi

Terry

et al. 2021

Preprint

Self Cite

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“…Pure contact graphs were modelled by graph analysis as described by Das and co-workers 17 . The 2D modelling of graphs were performed by Gephi 29 .…”

Section: Multigraph Constructionmentioning

confidence: 99%

“…This approach represents a powerful tool to map simple, haploid genomes in 3D but appears more challenging when analysing complex, polyploid genomes. Chromatin capture sequencing cannot differentiate between the two parental genomes but chromosome representation can be interpreted as the average of the two homologous chromosomes 17 .…”

Section: Introductionmentioning

confidence: 99%

A Multigraph model of the 3D genome

Makai

Cseh

Sepsi

et al. 2021

Preprint

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Spatial organisation of the genome has a fundamental effect on its biological functions. Chromatin-chromatin interactions and 3D spatial structures are involved in transcriptional regulation and have a decisive role in DNA replication and repair. To understand how individual genes and their regulatory elements function within the larger genomic context, and how the genome reacts as a whole to environmental stimuli, the linear sequence information needs to be interpreted in 3-dimensional space. While recent advances in chromatin conformation capture technologies including Hi-C, considerably advanced our understanding of the genomes, defining the DNA, as it is organized in the cell nucleus is still a challenging task. 3D genome modelling needs to reflect the DNA as a flexible polymer, which can wind up to the fraction of its total length and greatly unwind and stretch to implement a multitude of functions. Here we propose a novel approach to model genomes as a multigraph based on Hi-C contact data. Multigraph-based 3D genome modelling of barley and rice revealed the well-known Rabl and Rosetta chromatin organizations, respectively, as well as other higher order structures. Our results shows that the well-established toolset of Graph theory is highly valuable in modelling large genomes in 3D.

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Inferring Chromosome Radial Organization from Hi-C Data

Cited by 2 publications

References 84 publications

Loops, TADs, Compartments, and Territories are Elastic and Robust to Dramatic Nuclear Volume Swelling

Loops, TADs, Compartments, and Territories are Elastic and Robust to Dramatic Nuclear Volume Swelling

A Multigraph model of the 3D genome

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