Three-dimensional genome structures of single diploid human cells

Three-dimensional genome structures play a key role in gene regulation and cell functions. Characterization of genome structures necessitates single-cell measurements. This has been achieved for haploid cells but has remained a challenge for diploid cells. We developed a single-cell chromatin conformation capture method, termed Dip-C, that combines a transposon-based whole-genome amplification method to detect many chromatin contacts, called META (multiplex end-tagging amplification), and an algorithm to impute the two chromosome haplotypes linked by each contact. We reconstructed the genome structures of single diploid human cells from a lymphoblastoid cell line and from primary blood cells with high spatial resolution, locating specific single-nucleotide and copy number variations in the nucleus. The two alleles of imprinted loci and the two X chromosomes were structurally different. Cells of different types displayed statistically distinct genome structures. Such structural cell typing is crucial for understanding cell functions.

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TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations

10.1101/2021.05.12.443887 ◽

2021 ◽

Author(s):

Yubao Cheng ◽

Miao Liu ◽

Mengwei Hu ◽

Siyuan Wang

Keyword(s):

Single Cell ◽

Single Cells ◽

Three Dimensional ◽

Population Level ◽

Building Blocks ◽

Genomic Region ◽

X Chromosomes ◽

Single Chromosome ◽

Domain Structures ◽

Distinct Cell

Background: Topologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs was shown to depend on cohesin in a loop-extrusion mechanism. Recently, advances in an image-based spatial genomics technique known as chromatin tracing led to the discovery of cohesin-independent TAD-like structures, also known as single-cell domains - highly variant self-interacting chromatin domains with boundaries that occasionally overlap with TAD boundaries but tend to differ among single cells and among single chromosome copies. Several recent computational modeling studies suggest that single-cell variations of epigenetic profiles may underlie the formation of the single-cell domains. Results: Here we use chromatin tracing to visualize in female human cells the fine-scale chromatin folding of inactive and active X chromosomes, which are known to have distinct global epigenetic landscapes and distinct population-averaged TAD profiles, with inactive X chromosomes largely devoid of TADs and cohesin. We show that both inactive and active X chromosomes possess highly variant single-cell domains across the same genomic region despite the fact that only active X chromosomes show clear TAD structures at the population level. These X chromosome single-cell domains exist in distinct cell lines. Perturbations of major epigenetic components did not significantly affect the frequency or strength of the single-cell domains. Increased chromatin compaction of inactive X chromosomes occurs at a length scale above that of the single-cell domains. Conclusions: In sum, this study suggests that single-cell domains are genome architecture building blocks independent of variations in major epigenetic landscapes.

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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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TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations

Genome Biology ◽

10.1186/s13059-021-02523-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yubao Cheng ◽

Miao Liu ◽

Mengwei Hu ◽

Siyuan Wang

Keyword(s):

Single Cell ◽

Single Cells ◽

Three Dimensional ◽

Population Level ◽

Building Blocks ◽

Genomic Region ◽

X Chromosomes ◽

Single Chromosome ◽

Domain Structures ◽

Distinct Cell

Abstract Background Topologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs has been shown to depend on cohesin in a loop-extrusion mechanism. Recently, advances in an image-based spatial genomics technique known as chromatin tracing lead to the discovery of cohesin-independent TAD-like structures, also known as single-cell domains, which are highly variant self-interacting chromatin domains with boundaries that occasionally overlap with TAD boundaries but tend to differ among single cells and among single chromosome copies. Recent computational modeling studies suggest that epigenetic interactions may underlie the formation of the single-cell domains. Results Here we use chromatin tracing to visualize in female human cells the fine-scale chromatin folding of inactive and active X chromosomes, which are known to have distinct global epigenetic landscapes and distinct population-averaged TAD profiles, with inactive X chromosomes largely devoid of TADs and cohesin. We show that both inactive and active X chromosomes possess highly variant single-cell domains across the same genomic region despite the fact that only active X chromosomes show clear TAD structures at the population level. These X chromosome single-cell domains exist in distinct cell lines. Perturbations of major epigenetic components and transcription mostly do not affect the frequency or strength of the single-cell domains. Increased chromatin compaction of inactive X chromosomes occurs at a length scale above that of the single-cell domains. Conclusions In sum, this study suggests that single-cell domains are genome architecture building blocks independent of the tested major epigenetic components.

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Single cell sequencing of the small and AT-skewed genome of malaria parasites

10.1101/2020.02.21.960039 ◽

2020 ◽

Author(s):

Shiwei Liu ◽

Adam C. Huckaby ◽

Audrey C. Brown ◽

Christopher C. Moore ◽

Ian Burbulis ◽

...

Keyword(s):

Single Cell ◽

Copy Number ◽

Mammalian Cells ◽

Copy Number Variations ◽

Single Cell Level ◽

Cell Level ◽

Single Cell Sequencing ◽

Base Content ◽

Amplification Method ◽

Adaptive Mechanisms

AbstractSingle cell genomics is a rapidly advancing field; however, most techniques are designed for mammalian cells. Here, we present a single cell sequencing pipeline for the intracellular parasite, Plasmodium falciparum, which harbors a relatively small genome with an extremely skewed base content. Through optimization of a quasi-linear genome amplification method, we achieve better targeting of the parasite genome over contaminants and generate coverage levels that allow detection of relatively small copy number variations on a single cell level. These improvements are important for expanding accessibility of single cell approaches to new organisms and for improving the study of adaptive mechanisms.

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Single-cell damagenome profiling unveils vulnerable genes and functional pathways in human genome toward DNA damage

Science Advances ◽

10.1126/sciadv.abf3329 ◽

2021 ◽

Vol 7 (27) ◽

pp. eabf3329

Author(s):

Qiangyuan Zhu ◽

Yichi Niu ◽

Michael Gundry ◽

Chenghang Zong

Keyword(s):

Dna Damage ◽

Single Cell ◽

Single Cells ◽

Three Dimensional ◽

Autism Spectrum ◽

Whole Genome ◽

Single Nucleotide Variants ◽

Amplification Method ◽

Human Neurons ◽

Cell Transcriptome

We report a novel single-cell whole-genome amplification method (LCS-WGA) that can efficiently capture spontaneous DNA damage existing in single cells. We refer to these damage-associated single-nucleotide variants as “damSNVs,” and the whole-genome distribution of damSNVs as the damagenome. We observed that in single human neurons, the damagenome distribution was significantly correlated with three-dimensional genome structures. This nonuniform distribution indicates different degrees of DNA damage effects on different genes. Next, we identified the functionals that were significantly enriched in the high-damage genes. Similar functionals were also enriched in the differentially expressed genes (DEGs) detected by single-cell transcriptome of both Alzheimer’s disease (AD) and autism spectrum disorder (ASD). This result can be explained by the significant enrichment of high-damage genes in the DEGs of neurons for both AD and ASD. The discovery of high-damage genes sheds new lights on the important roles of DNA damage in human diseases and disorders.

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