scholarly journals Generation of dynamic three-dimensional genome structure through phase separation of chromatin

2021 ◽  
Author(s):  
Shin Fujishiro ◽  
Masaki Sasai
Keyword(s):  
Phase Separation ◽  
Genome Organization ◽  
Critical Role ◽  
Genome Structure ◽  
Three Dimensional ◽  
Human Cells ◽  
Polymer Model ◽  
Interphase Nuclei ◽  
Dynamic Genome ◽  
The Impact

Three-dimensional genome organization plays a critical role in DNA function. Flexible chromatin structure suggested that the genome is phase-separated to form A/B compartments in interphase nuclei. Here, we examined this hypothesis by developing a polymer model of the whole genome of human cells and assessing the impact of phase separation on genome structure. Upon entry to the G1 phase, the simulated genome expanded according to heterogeneous repulsion among chromatin chains, which moved chromatin heterogeneously, inducing phase separation. This repulsion-driven phase separation quantitatively reproduces the experimentally observed chromatin domains, A/B compartments, lamina-associated domains, and nucleolus-associated domains, consistently explaining nuclei of different human cells and predicting their dynamic fluctuations. We propose that phase separation induced by heterogeneous repulsive interactions among chromatin chains largely determines dynamic genome organization.

scholarly journals The three-dimensional genome organization of Drosophila melanogaster through data integration

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Qingjiao Li ◽  
Harianto Tjong ◽  
Xiao Li ◽  
Ke Gong ◽  
Xianghong Jasmine Zhou ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Data Integration ◽  
Genome Organization ◽  
Genome Structure ◽  
Three Dimensional ◽  
Structural Features ◽  
Embryonic Cells ◽  
Data Types ◽  
Chromosome Conformation ◽  
Topological Domains

Abstract Background Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome’s organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments. Results Our structures resolve the genome at the resolution of topological domains, and reproduce simultaneously both sets of experimental data. Importantly, this data deconvolution framework allows for structural heterogeneity between cells, and hence accounts for the expected plasticity of genome structures. As a case study we choose Drosophila melanogaster embryonic cells, for which both data types are available. Our three-dimensional genome structures have strong predictive power for structural features not directly visible in the initial data sets, and reproduce experimental hallmarks of the D. melanogaster genome organization from independent and our own imaging experiments. Also they reveal a number of new insights about genome organization and its functional relevance, including the preferred locations of heterochromatic satellites of different chromosomes, and observations about homologous pairing that cannot be directly observed in the original Hi-C or lamina-DamID data. Conclusions Our approach allows systematic integration of Hi-C and lamina-DamID data for complete three-dimensional genome structure calculation, while also explicitly considering genome structural variability.

EPCO-20. PEDIATRIC HIGH-GRADE GLIOMA EXHIBITS DISTINCT 3D GENOME STRUCTURE THAT IMPACTS TRANSCRIPTION REGULATION

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi6-vi6
Author(s):  
Tina Huang ◽  
Juan Wang ◽  
Ye Hu ◽  
Andrea Piunti ◽  
Elizabeth Bartom ◽  
...  
Keyword(s):  
Transcription Regulation ◽  
Cell Lines ◽  
Regulatory Networks ◽  
Critical Role ◽  
Genome Structure ◽  
High Grade Glioma ◽  
High Grade ◽  
Sequencing Data ◽  
Structural Variations ◽  
The Impact

Abstract INTRODUCTION Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are highly morbid brain tumors. Up to 80% of DIPGs harbor a somatic missense mutation in genes encoding Histone H3. To investigate whether the H3K27M mutant protein is associated with distinct chromatin structure affecting transcription regulation, we generated the first high-resolution Hi-C and ATAC-Seq maps of pHGG cell lines, and integrated these with tissue and cell genomic data. METHODS We generated sequencing data from patient-derived cell lines (DIPG n=6, GBM n=3, normal n=2) and frozen tissue specimens (DIPG n=1, normal brainstem n=1). Analyses included cell line RNA-Seq, ChIP-Seq (H3K27ac, H3K27me3, H3K27M) and genome-wide chromatin conformation capture (Hi-C), as well as tissue ATAC-Seq. Publicly available pediatric glioma tissue ChIP-Seq data was integrated with cell data. CRISPR knock-down of target enhancer regions was performed. RESULTS We identified tumor-specific enhancers and regulatory networks for known oncogenes in DIPG and GBM. In DIPG, FOX, SOX, STAT and SMAD families were among top H3K27Ac enriched motifs. Significant differences in Topologically Associating Domains (TADs) and DNA looping were observed at OLIG2 and MYCN in H3K27M mutant DIPG, relative to wild-type GBM and normal cells. Pharmacologic treatment targeting H3K27Ac (BET and Bromodomain inhibition) altered these 3D structures. Functional analysis of differentially enriched enhancers in DIPG implicated SOX2, SUZ12, and TRIM24 as top activated upstream regulators. Distinct genomic structural variations leading to enhancer hijacking and gene co-amplification were identified at A2M, JAG2, and FLRT1. CONCLUSION We show genome structural variations enhancer-promoter interactions that impact gene expression in pHGG in the presence and absence of the H3K27M mutation. Our results imply that tridimensional genome alterations may play a critical role in the pHGG epigenetic landscape and thereby contribute to pediatric gliomagenesis. Further studies examining the impact of the alterations is therefore underway.

scholarly journals Simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization

2020 ◽  
Author(s):  
Da-Inn Lee ◽  
Sushmita Roy
Keyword(s):  
High Throughput ◽  
Matrix Factorization ◽  
Genome Organization ◽  
Time Course ◽  
Critical Role ◽  
Chromatin Modification ◽  
Three Dimensional ◽  
Enrichment Analysis ◽  
Developmental Time ◽  
Chromosome Conformation

AbstractThe three-dimensional (3D) organization of the genome plays a critical role in gene regulation for diverse normal and disease processes. High-throughput chromosome conformation capture (3C) assays, such as Hi-C, SPRITE, GAM, and HiChIP, have revealed higher-order organizational units such as topologically associating domains (TADs), which can shape the regulatory landscape governing downstream phenotypes. Analysis of high-throughput 3C data depends on the sequencing depth, which directly affects the resolution and the sparsity of the generated 3D contact count map. Identification of TADs remains a significant challenge due to the sensitivity of existing methods to resolution and sparsity. Here we present GRiNCH, a novel matrix-factorization-based approach for simultaneous TAD discovery and smoothing of contact count matrices from high-throughput 3C data. GRiNCH TADs are enriched in known architectural proteins and chromatin modification signals and are stable to the resolution, and sparsity of the input data. GRiNCH smoothing improves the recovery of structure and significant interactions from low-depth datasets. Furthermore, enrichment analysis of 746 transcription factor motifs in GRiNCH TADs from developmental time-course and cell-line Hi-C datasets predicted transcription factors with potentially novel genome organization roles. GRiNCH is a broadly applicable tool for the analysis of high throughput 3C datasets from a variety of platforms including SPRITE and HiChIP to understand 3D genome organization in diverse biological contexts.

scholarly journals Chronic Loss of Stag2 Leads to Altered Chromatin Structure Contributing to De-Regulated Transcription in Aml.

2020 ◽  
Author(s):  
James Smith ◽  
Stephanie G Craig ◽  
Fabio G Liberante ◽  
Katrina M Lappin ◽  
Clare M Crean ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Structure ◽  
Three Dimensional ◽  
Cohesin Complex ◽  
Mapk Signalling Pathway ◽  
Altered Gene Expression ◽  
Increased Sensitivity ◽  
Altered Gene ◽  
Structure Lead ◽  
The Impact

Abstract Background The cohesin complex plays a major role in folding the human genome into 3D structural domains. Mutations in members of the cohesin complex are known early drivers of myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML), with STAG2 the most frequently mutated complex member.Methods Here we use functional genomics (RNA-seq, ChIP-seq and HiChiIP) to investigate the impact of chronic STAG2 loss on three-dimensional genome structure and transcriptional programming in a clinically relevant model of chronic STAG2 loss.Results The chronic loss of STAG2 led to loss of smaller loop domains and the maintenance/formation of large domains that in turn led to altered genome compartmentalisation. These changes in genome structure lead to altered gene expression, including deregulation of the HOXA locus and the MAPK signalling pathway resulting in increased sensitivity to MEK inhibition.Conclusions The altered genomic architecture driven by the chronic loss of STAG2 results in altered gene expression that may contribute to leukaemogenesis which may be therapeutically targeted.

scholarly journals Genome Compartmentalization with Nuclear Landmarks: Random yet Precise

2021 ◽  
Author(s):  
Kartik Kamat ◽  
Yifeng Qi ◽  
Yuchuan Wang ◽  
Jian Ma ◽  
Bin Zhang
Keyword(s):  
Phase Separation ◽  
Genome Organization ◽  
Large Scale ◽  
Three Dimensional ◽  
Nuclear Lamina ◽  
Spatial Arrangement ◽  
Nuclear Bodies ◽  
Chromatin Interaction ◽  
Nuclear Speckles ◽  
Heterogeneous Distribution

The three-dimensional (3D) organization of eukaryotic genomes plays an important role in genome function. While significant progress has been made in deciphering the folding mechanisms of individual chromosomes, the principles of the dynamic large-scale spatial arrangement of all chromosomes inside the nucleus are poorly understood. We use polymer simulations to model the diploid human genome compartmentalization relative to nuclear bodies such as nuclear lamina, nucleoli, and speckles. We show that a self-organization process based on a co-phase separation between chromosomes and nuclear bodies can capture various features of genome organization, including the formation of chromosome territories, phase separation of A/B compartments, and the liquid property of nuclear bodies. The simulated 3D structures quantitatively reproduce both sequencing-based genomic mapping and imaging assays that probe chromatin interaction with nuclear bodies. Importantly, our model captures the heterogeneous distribution of chromosome positioning across cells, while simultaneously producing well-defined distances between active chromatin and nuclear speckles. Such heterogeneity and preciseness of genome organization can coexist due to the non-specificity of phase separation and the slow chromosome dynamics. Together, our work reveals that the co-phase separation provides a robust mechanism for encoding functionally important 3D contacts without requiring thermodynamic equilibration that can be difficult to achieve.

scholarly journals Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages

2018 ◽  
Author(s):  
Evelien M. Bunnik ◽  
Kate B. Cook ◽  
Nelle Varoquaux ◽  
Gayani Batugedara ◽  
Jacques Prudhomme ◽  
...  
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Genome Organization ◽  
Genome Structure ◽  
Regulation Of Gene Expression ◽  
Three Dimensional ◽  
Gene Families ◽  
Specific Gene ◽  
Heterochromatin Protein 1 ◽  
Malaria Parasites

ABSTRACTThe development of malaria parasites throughout their various life cycle stages is controlled by coordinated changes in gene expression. We previously showed that the three-dimensional organization of the P. falciparum genome is strongly associated with gene expression during its replication cycle inside red blood cells. Here, we analyzed genome organization in the P. falciparum and P. vivax transmission stages. Major changes occurred in the localization and interactions of genes involved in pathogenesis and immune evasion, erythrocyte and liver cell invasion, sexual differentiation and master regulation of gene expression. In addition, we observed reorganization of subtelomeric heterochromatin around genes involved in host cell remodeling. Depletion of heterochromatin protein 1 (PfHP1) resulted in loss of interactions between virulence genes, confirming that PfHP1 is essential for maintenance of the repressive center. Overall, our results suggest that the three-dimensional genome structure is strongly connected with transcriptional activity of specific gene families throughout the life cycle of human malaria parasites.

scholarly journals Chronic Loss of STAG2 Leads to Altered Chromatin Structure Contributing to DE-Regulated Transcription in AML.

2020 ◽  
Author(s):  
James Smith ◽  
Katrina M Lappin ◽  
Stephanie G Craig ◽  
Fabio G Liberante ◽  
Clare M Crean ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Structure ◽  
Three Dimensional ◽  
Cohesin Complex ◽  
Mapk Signalling Pathway ◽  
Altered Gene Expression ◽  
Mapk Signalling ◽  
Increased Sensitivity ◽  
Altered Gene ◽  
The Impact

Abstract Background The cohesin complex plays a major role in folding the human genome into 3D structural domains. Mutations in members of the cohesin complex are known early drivers of myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML), with STAG2 the most frequently mutated complex member. Methods Here we use functional genomics (RNA-seq, ChIP-seq and HiChIP) to investigate the impact of chronic STAG2 loss on three-dimensional genome structure and transcriptional programming in a clinically relevant model of chronic STAG2 loss. Results The chronic loss of STAG2 led to loss of smaller loop domains and the maintenance/formation of large domains that, in turn, led to altered genome compartmentalisation. These changes in genome structure resulted in altered gene expression, including deregulation of the HOXA locus and the MAPK signalling pathway, resulting in increased sensitivity to MEK inhibition. Conclusions: The altered genomic architecture driven by the chronic loss of STAG2 results in altered gene expression that may contribute to leukaemogenesis and may be therapeutically targeted.

scholarly journals Epigenomic landscape and 3D genome structure in pediatric high-grade glioma

2021 ◽  
Vol 7 (23) ◽  
pp. eabg4126
Author(s):  
Juan Wang ◽  
Tina Yi-Ting Huang ◽  
Ye Hou ◽  
Elizabeth Bartom ◽  
Xinyan Lu ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Critical Role ◽  
Genome Structure ◽  
Three Dimensional ◽  
High Grade Glioma ◽  
Diffuse Intrinsic Pontine Glioma ◽  
Chromatin Accessibility ◽  
High Grade ◽  
Structural Variations ◽  
Type Specimens

Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are morbid brain tumors. Even with treatment survival is poor, making pHGG the number one cause of cancer death in children. Up to 80% of DIPGs harbor a somatic missense mutation in genes encoding histone H3. To investigate whether H3K27M is associated with distinct chromatin structure that alters transcription regulation, we generated the first high-resolution Hi-C maps of pHGG cell lines and tumor tissue. By integrating transcriptome (RNA-seq), enhancer landscape (ChIP-seq), genome structure (Hi-C), and chromatin accessibility (ATAC-seq) datasets from H3K27M and wild-type specimens, we identified tumor-specific enhancers and regulatory networks for known oncogenes. We identified genomic structural variations that lead to potential enhancer hijacking and gene coamplification, including A2M, JAG2, and FLRT1. Together, our results imply three-dimensional genome alterations may play a critical role in the pHGG epigenetic landscape and contribute to tumorigenesis.

scholarly journals MyoD is a 3D genome structure organizer for muscle cell identity

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Ruiting Wang ◽  
Fengling Chen ◽  
Qian Chen ◽  
Xin Wan ◽  
Minglei Shi ◽  
...  
Keyword(s):  
Muscle Cell ◽  
Genome Organization ◽  
Genome Structure ◽  
Three Dimensional ◽  
Cell Lineage ◽  
Muscle Cells ◽  
Cell Type ◽  
Cell Identity ◽  
3D Genome ◽  
A Genome

AbstractThe genome exists as an organized, three-dimensional (3D) dynamic architecture, and each cell type has a unique 3D genome organization that determines its cell identity. An unresolved question is how cell type-specific 3D genome structures are established during development. Here, we analyzed 3D genome structures in muscle cells from mice lacking the muscle lineage transcription factor (TF), MyoD, versus wild-type mice. We show that MyoD functions as a “genome organizer” that specifies 3D genome architecture unique to muscle cell development, and that H3K27ac is insufficient for the establishment of MyoD-induced chromatin loops in muscle cells. Moreover, we present evidence that other cell lineage-specific TFs might also exert functional roles in orchestrating lineage-specific 3D genome organization during development.

scholarly journals HGG-01. 3D GENOME STRUCTURE IMPACTS GENE EXPRESSION IN PEDIATRIC HIGH-GRADE GLIOMA

2021 ◽  
Vol 23 (Supplement_1) ◽  
pp. i17-i17
Author(s):  
Tina Huang ◽  
Juan Wang ◽  
Ye Hou ◽  
Andrea Piunti ◽  
Elizabeth Bartom ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Regulatory Networks ◽  
Critical Role ◽  
Genome Structure ◽  
High Grade Glioma ◽  
High Grade ◽  
Sequencing Data ◽  
Structural Variations ◽  
The Impact

Abstract Introduction Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are highly morbid brain tumors. Up to 80% of DIPGs harbor a somatic missense mutation in genes encoding Histone H3. To investigate whether the H3K27M mutant protein is associated with distinct chromatin structure affecting transcription regulation, we generated the first high-resolution Hi-C and ATAC-Seq maps of pHGG cell lines, and integrated these with tissue and cell genomic data. Methods We generated sequencing data from patient-derived cell lines (DIPG n=6, GBM n=3, normal n=2) and frozen tissue specimens (DIPG n=1, normal brainstem n=1). Analyses included cell line RNA-Seq, ChIP-Seq (H3K27ac, H3K27me3, H3K27M) and genome-wide chromatin conformation capture (Hi-C), as well as tissue ATAC-Seq. Publicly available pediatric glioma tissue ChIP-Seq data was integrated with cell data. Results We identified tumor-specific enhancers and regulatory networks for known oncogenes in DIPG and GBM. In DIPG, FOX, SOX, STAT and SMAD families were among top H3K27Ac enriched motifs. Significant differences in Topologically Associating Domains (TADs) and DNA looping were observed at OLIG2 and MYCN in H3K27M mutant DIPG, relative to wild-type GBM and normal cells. Pharmacologic treatment targeting H3K27Ac (BET and Bromodomain inhibition) altered these 3D structures. Functional analysis of differentially enriched enhancers in DIPG implicated SOX2, SUZ12, and TRIM24 as top activated upstream regulators. Distinct genomic structural variations leading to enhancer hijacking and gene co-amplification were identified at A2M, JAG2, and FLRT1. Conclusion We show genome structural variations enhancer-promoter interactions that impact gene expression in pHGG in the presence and absence of the H3K27M mutation. Our results imply that tridimensional genome alterations may play a critical role in the pHGG epigenetic landscape and thereby contribute to pediatric gliomagenesis. Further studies examining the impact of the alterations, including CRISPR knock-down of target enhancer regions, is therefore underway.

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