Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts

AbstractThe sparseness of chromosomal contact information and the presence of homologous chromosomes with very similar nucleotide sequences make Hi-C analysis difficult. We propose a new algorithm using allele-specific single-nucleotide variations (SNVs) to reconstruct the three-dimensional (3D) chromosomal architectures from the Hi-C dataset of single diploid cells. Our algorithm has a function to discriminate SNVs specifically found between homologous chromosomes to our “recurrence plot”-based algorithm to estimate the 3D chromosome structure, which does not require imputation for ambiguous segment information. The new algorithm can efficiently reconstruct 3D chromosomal structures in single human diploid cells by employing only Hi-C segment pairs containing allele-specific SNVs. The datasets of the remaining pairs of segments without allele-specific SNVs are used to validate the estimated chromosome structure. This approach was used to reconstruct the 3D structures of human chromosomes in single diploid cells at a 1-Mb resolution. Introducing a subsequent mathematical measure further improved the resolution to 40-kb or 100-kb. The reconstruction data reveals that human chromosomes form chromosomal territories and take fractal structures where the mean dimension is a non-integer value. We also validate our approach by estimating 3D protein/polymer structures.

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The analysis of malignancy by cell fusion. VIII. Evidence for the intervention of an extra-chromosomal element

Journal of Cell Science ◽

10.1242/jcs.24.1.255 ◽

1977 ◽

Vol 24 (1) ◽

pp. 255-263

Author(s):

J. Jonasson ◽

H. Harris

Keyword(s):

Human Chromosome ◽

Gamma Radiation ◽

Cell Fusion ◽

Human Fibroblasts ◽

Melanoma Cells ◽

Human Chromosomes ◽

Mouse Melanoma ◽

Human Diploid Cells ◽

Diploid Cells ◽

Hybrid Clones

Diploid human fibroblasts and lymphocytes were fused with the cells of a malignant mouse melanoma and a range of hybrid clones selected for study. The ability of these clones to produce progressive tumours was assayed in nude mice. Although human chromosomes were preferentially eliminated in all the hybrid clones, the human diploid cells were as effective as mouse diploid cells in suppressing the malignancy of the mouse melanoma cells. The suppression produced by fibroblasts was again more profound than that produced by lymphocytes. Malignancy was also found to be suppressed in a hybrid clone in which a single X was the only human chromosome present; and this clone continued to give a very low take incidence even after the human X had been eliminated by back selection. Hybrids were made between the melanoma cells and diploid human fibroblasts that had been given 100 J kg-1 of gamma radiation before cell fusion. These hybrids contained no recognizable human chromosomes, but their ability to produce progressive tumours was greatly reduced compared to that of the melanoma parent cells. The take incidences given by the crosses between the melanoma cells and the irradiated human fibroblasts were, however, substantially higher than those given by the crosses between the melanoma cells and unirradiated fibroblasts. These findings suggest that the suppression of malignancy involves the activity of some extra-chromosomal element and that this element is radio-sensitive.

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COLLAGEN SUBSTRATA FOR STUDIES ON CELL BEHAVIOR

The Journal of Cell Biology ◽

10.1083/jcb.54.3.626 ◽

1972 ◽

Vol 54 (3) ◽

pp. 626-637 ◽

Cited By ~ 1055

Author(s):

Tom Elsdale ◽

Jonathan Bard

Keyword(s):

Soft Tissue ◽

Simple Technique ◽

Three Dimensional ◽

Capillary Forces ◽

Cell Behavior ◽

Malignant Cells ◽

Behavioral Studies ◽

Human Diploid Cells ◽

Diploid Cells ◽

Collagen Lattices

A simple technique is described for the preparation of collagen substrata containing 0 1% of collagen by weight, in the form of native bundles with a 640 A period, the substrata are similar in these respects to soft-tissue matrices These substrate are hydrated collagen lattices (HCLs) in which the watery milieu is held within a fibrous collagen net mainly by capillary forces. HCLs have been characterized in terms of the course of collagen precipitation and aggregation, ultrastructure, and their stability under various conditions. The ways in which HCLs can be employed as both two- and three-dimensional substrata in cell behavioral studies are illustrated with some preliminary observations on the form, motility, adhesion, and growth of human diploid cells and two lines of malignant cells.

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Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting

10.1101/386359 ◽

2018 ◽

Author(s):

Orsolya Symmons ◽

Marcello Chang ◽

Ian A. Mellis ◽

Jennifer M. Kalish ◽

Marisa S. Bartolomei ◽

...

Keyword(s):

Single Molecule ◽

Single Cells ◽

Gene Copy ◽

Specific Expression ◽

Rna Molecules ◽

Gene Copies ◽

Extensive Cell ◽

Allele Specific ◽

Transcriptional Bursting ◽

Diploid Cells

AbstractExtensive cell-to-cell variation exists even among putatively identical cells, and there is great interest in understanding how the properties of transcription relate to this heterogeneity. Differential expression from the two gene copies in diploid cells could potentially contribute, yet our ability to measure from which gene copy individual RNAs originated remains limited, particularly in the context of tissues. Here, we demonstrate quantitative, single molecule allele-specific RNA FISH adapted for use on tissue sections, allowing us to determine the chromosome of origin of individual RNA molecules in formaldehyde-fixed tissues. We used this method to visualize the allele-specific expression of Xist and multiple autosomal genes in mouse kidney. By combining these data with mathematical modeling, we evaluated models for allele-specific heterogeneity, in particular demonstrating that apparent expression from only one of the alleles in single cells can arise as a consequence of low-level mRNA abundance and transcriptional bursting.

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Principles of 3D Nucleus Organization and Epigenetic Regulation in Diploid Genome Revealed by Multi-omic Data from Hybrid Mouse

10.1101/783662 ◽

2019 ◽

Author(s):

Zhijun Han ◽

Cui Kairong ◽

Katarzyna Placek ◽

Ni Hong ◽

Chengqi Lin ◽

...

Keyword(s):

Epigenetic Regulation ◽

Specific Interaction ◽

Three Dimensional ◽

Nuclear Space ◽

Chromosome Territories ◽

Interaction Patterns ◽

Homologous Chromosomes ◽

Cellular Environment ◽

Allele Specific ◽

Hybrid Mice

AbstractMost mammalian genomes are diploid and previous studies have extensively investigated the average epigenetic profiles of homologous chromosomes. Here we use hybrid mice to distinguish the epigenetic status and three-dimensional organization of homologous chromosomes. We generated Hi-C, ChIP-seq and RNA-seq datasets from CD4 T cells of B6, Cast and hybrid mice, respectively, and systematically analyzed the 3D nucleus organization and epigenetic regulation. Our data indicate that the inter-chromosomal interaction patterns between homologous chromosomes are similar and the similarity is highly correlated with their allelic co-expression levels. Construction of 3D nucleus based on allele-specific interaction frequency revealed symmetric positioning of homologous chromosomes in the 3D nuclear space. The inter-chromosomal interactions at centromeres are significantly weaker than those at telomeres, indicating positioning of centromeres toward the inside of chromosome territories and telomeres toward the surface of chromosome territories. The majority A|B compartments or topologically associated domains (TADs) are consistent between B6 and Cast. We found 58% of the haploids in hybrids maintain their parental compartment status at B6/Cast divergent compartments due to cis-effect. About 95% of the trans-effected B6/Cast divergent compartments converge to same compartment status potentially due to a shared cellular environment. We found the differentially expressed genes between the two haploids in hybrid were associated with either genetic associated cis-effects or epigenetic associated trans-effects. The widespread epigenetic differences between B6 and Cast suggest that epigenetic changes may be major contributors to differences between B6 and Cast. Our data revealed symmetrical positioning of homologous chromosomes in 3D nucleus and enhanced our understanding of allele-specific epigenetic regulation.

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Three-dimensional chromatin architecture of early-stage mouse embryos reconstructed via recurrence plots

10.1101/2021.05.20.444916 ◽

2021 ◽

Author(s):

Yuki Kitanishi ◽

Hiroki Sugishita ◽

Yukiko Gotoh ◽

Yoshito Hirata

Keyword(s):

Time Series ◽

Single Cell ◽

Early Stage ◽

Three Dimensional ◽

Nuclear Architecture ◽

Recurrence Plot ◽

Cell Stage ◽

F1 Hybrid ◽

Chromatin Architecture ◽

Diploid Cells

The chromatin conformation capture-related methods such as Hi-C have improved our understanding of nuclear architecture and organization in recent years. However, reconstruction of nuclear architecture of individual cells from single cell Hi-C (scHi-C) data has been challenging due to limited information of DNA contacts owing to the low efficiency of DNA recovery from a single cell. We have previously developed an algorithm named as “recurrence plot- based reconstruction (RPR) method” for reconstructing three dimensional (3D) genomic structure from Hi-C data of single haploid cells and diploid cells. This mathematical method is based on a recurrence plot, a tool of nonlinear time series analysis for visualizing temporal patterns within a time series and enables the reconstruction of a unique 3D chromosome architecture even from sparse (low-coverage) DNA contact information. Here we applied the RPR method to analyzing published scHi-C data of diploid cells derived from early-stage F1 hybrid embryos. We found that paternal and maternal chromosomes become gradually intermingled from 1 cell to 64 cell stage and that discrete chromosome territories (CTs) are largely established between 8 cell and 64 cell stages. We also observed Rabl-like polarized distribution of chromosomes from 2 cell to 8 cell stage but this polarization becomes mostly dissolved by 64 cell stage. The formation of Rabl-like configuration precedes rod-like extension of the chromosomal shape and their parallel alignment, implicating a role of Rabl-like configuration in avoiding entanglement and promoting effective mixing of chromosomes before establishment of CTs. We also found a cell-to-cell variability in chromatin configuration. Combination of scHi-C and RPR analyses thus can characterize distinct 3D chromatin architecture of individual cells at different developmental stages during early embryogenesis.

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