scholarly journals Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C

2020 ◽  
Author(s):  
Robert A. Beagrie ◽  
Christoph J. Thieme ◽  
Carlo Annunziatella ◽  
Catherine Baugher ◽  
Yingnan Zhang ◽  
...  
Keyword(s):  
Embryonic Stem ◽  
Active Regions ◽  
Detailed Comparison ◽  
Contact Mapping ◽  
3D Genome ◽  
Topologically Associating Domains ◽  
Genome Wide ◽  
Wide Contact ◽  
Genomic Regions ◽  
Mes Cells

Summary (Abstract)Technologies for measuring 3D genome topology are increasingly important for studying mechanisms of gene regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and other ligation-based methods have become routine but have specific biases. Here, we develop multiplex-GAM, a faster and more affordable version of Genome Architecture Mapping (GAM), a ligation-free technique to map chromatin contacts genomewide. We perform a detailed comparison of contacts obtained by multiplex-GAM and Hi-C using mouse embryonic stem (mES) cells. We find that both methods detect similar topologically associating domains (TADs). However, when examining the strongest contacts detected by either method, we find that only one third of these are shared. The strongest contacts specifically found in GAM often involve “active” regions, including many transcribed genes and super-enhancers, whereas in Hi-C they more often contain “inactive” regions. Our work shows that active genomic regions are involved in extensive complex contacts that currently go under-estimated in genome-wide ligation-based approaches, and highlights the need for orthogonal advances in genome-wide contact mapping technologies.

scholarly journals Functional correlation of H3K9me2 and nuclear compartment formation

2020 ◽  
Author(s):  
Kei Fukuda ◽  
Chikako Shimura ◽  
Hisashi Miura ◽  
Akie Tanigawa ◽  
Takehiro Suzuki ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Genome Organization ◽  
Mammalian Cells ◽  
Embryonic Stem ◽  
Epigenetic Mark ◽  
3 Dimensional ◽  
3D Genome ◽  
Functional Correlation ◽  
Genome Wide

AbstractBackgroundHistone H3 lysine 9 dimethylation (H3K9me2) is a highly conserved silencing epigenetic mark. Chromatin marked with H3K9me2 forms large domains in mammalian cells and correlates well with lamina-associated domains and the B compartment. However, the role of H3K9me2 in 3-dimensional (3D) genome organization remains unclear.ResultsWe investigated the genome-wide H3K9me2 distribution, the transcriptome and 3D genome organization in mouse embryonic stem cells (mESCs) upon the inhibition or depletion of H3K9 methyltransferases (MTases) G9a/GLP, SETDB1, and SUV39H1/2. We found that H3K9me2 is regulated by these five MTases; however, H3K9me2 and transcription in the A and B compartments were largely regulated by different sets of the MTases: H3K9me2 in the A compartments were mainly regulated by G9a/GLP and SETDB1, while H3K9me2 in the B compartments were regulated by all five H3K9 MTases. Furthermore, decreased H3K9me2 correlated with the changes to the more active compartmental state that accompanied transcriptional activation.ConclusionOur data showed that H3K9me2 domain formation is functionally linked to 3D genome organization.

scholarly journals Genome-wide stability of the DNA replication program in single mammalian cells

2017 ◽  
Author(s):  
Saori Takahashi ◽  
Hisashi Miura ◽  
Takahiro Shibata ◽  
Koji Nagao ◽  
Katsuzumi Okumura ◽  
...  
Keyword(s):  
Dna Replication ◽  
Mammalian Cells ◽  
Developmental Plasticity ◽  
Embryonic Stem ◽  
Replication Timing ◽  
Small Degree ◽  
3D Genome ◽  
Inactive X Chromosome ◽  
Genome Wide ◽  
Individual Mouse

ABSTRACTHere, we report the establishment of a single-cell DNA replication sequencing method, scRepli-seq, which is a simple genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct replication profiles, which were conserved from cell to cell. Haplotype-resolved scRepli-seq revealed similar replication timing profiles of homologous autosomes, while the inactive X chromosome was clearly replicated later than its active counterpart. However, a small degree of cell-to-cell replication timing heterogeneity was present, and we discovered that developmentally regulated domains are a source of such variability, suggesting a link between cell-to-cell heterogeneity and developmental plasticity. Together, our results form a foundation for single-cell-level understanding of DNA replication regulation and provide insights into 3D genome organization.

scholarly journals A supervised learning framework for chromatin loop detection in genome-wide contact maps

2019 ◽  
Author(s):  
Tarik J. Salameh ◽  
Xiaotao Wang ◽  
Fan Song ◽  
Bo Zhang ◽  
Sage M. Wright ◽  
...  
Keyword(s):  
Supervised Learning ◽  
Data Types ◽  
Random Forest Classification ◽  
Chromatin Loops ◽  
3D Genome ◽  
Contact Maps ◽  
Genome Wide ◽  
A Genome ◽  
Loop Detection ◽  
Wide Contact

ABSTRACTAccurately predicting chromatin loops from genome-wide interaction matrices such as Hi-C data is critical to deepen our understanding of proper gene regulation events. Current approaches are mainly focused on searching for statistically enriched dots on a genome-wide map. However, given the availability of a wide variety of orthogonal data types such as ChIA-PET, GAM, SPRITE, and high-throughput imaging, a supervised learning approach could facilitate the discovery of a comprehensive set of chromatin interactions. Here we present Peakachu, a Random Forest classification framework that predicts chromatin loops from genome-wide contact maps. Compared with current enrichment-based approaches, Peakachu identified more meaningful short-range interactions. We show that our models perform well in different platforms such as Hi-C, Micro-C, and DNA SPRITE, across different sequencing depths, and across different species. We applied this framework to systematically predict chromatin loops in 56 Hi-C datasets, and the results are available at the 3D Genome Browser (www.3dgenome.org).

scholarly journals Comparison of the 3D organization of sperm and fibroblast genomes using the Hi-C approach

2014 ◽  
Author(s):  
Nariman Battulin ◽  
Veniamin S Fishman ◽  
Alexander M Mazur ◽  
Mikhail Pomaznoy ◽  
Anna A Khabarova ◽  
...  
Keyword(s):  
Es Cells ◽  
3D Structure ◽  
Embryonic Stem ◽  
Cell Types ◽  
Chromatin Interaction ◽  
Sperm Cells ◽  
3D Genome ◽  
Genome Wide ◽  
Topologically Associated Domains ◽  
The Stability

The 3D organization of the genome is tightly connected to its biological function. The Hi-C approach was recently introduced as a method that can be used to identify higher-order chromatin interactions genome-wide. The aim of this study was to determine genome-wide chromatin interaction frequencies using the Hi-C approach in mouse sperm cells and embryonic fibroblasts. The obtained results demonstrated that the 3D genome organizations of sperm and fibroblast cells show a high degree of similarity both with each other and with the previously described mouse embryonic stem (ES) cells. Both A- and B-compartments and topologically associated domains (TADs) are present in spermatozoa and fibroblasts. Nevertheless, sperm cells and fibroblasts exhibited statistically significant differences between each other in the contact probabilities of defined loci. Tight packaging of the sperm genome resulted in an enrichment of long-range contacts compared with the fibroblasts. However, only 30% of the differences in the number of contacts are based on differences in the densities of their genome packages; the main source of the differences is the gain or loss of contacts that are specific for defined genome regions. An analysis of interchromosomal contacts in both cell types demonstrated that the large chromosomes showed a tendency to interact with each other more than with the small chromosomes and vice versa. We found that the dependence of the contact probability P(s) on genomic distance for sperm is in a good agreement with the fractal globular folding of chromatin. The similarity of the spatial DNA organization in sperm and somatic cell genomes suggests the stability of the 3D structure of genomes through generations.

scholarly journals Contribution of 3D genome topological domains to genetic risk of cancers

2021 ◽  
Author(s):  
Kim Philipp Jablonski ◽  
Leopold Carron ◽  
Julien Mozziconacci ◽  
Thierry Forné ◽  
Marc-Thorsten Hütt ◽  
...  
Keyword(s):  
Genetic Risk ◽  
Genome Organization ◽  
Association Studies ◽  
Embryonic Stem ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Entire Genome ◽  
Topological Domains ◽  
3D Genome ◽  
Genome Wide

Genome-wide association studies have identified statistical associations between various diseases, including cancers, and a large number of single-nucleotide polymorphisms (SNPs). However, they provide no direct explanation of the mechanisms underlying the association. Based on the recent discovery that changes in 3-dimensional genome organization may have functional consequences on gene regulation favoring diseases, we investigated systematically the genome-wide distribution of disease-associated SNPs with respect to a specific feature of 3D genome organization: topologically-associating domains (TADs) and their borders. For each of 449 diseases, we tested whether the associated SNPs are present in TAD borders more often than observed by chance, where chance (i.e. the null model in statistical terms) corresponds to the same number of pointwise loci drawn at random either in the entire genome, or in the entire set of disease-associated SNPs listed in the GWAS catalog. Our analysis shows that a fraction of diseases display such a preferential location of their risk loci. Moreover, cancers are relatively more frequent among these diseases, and this predominance is generally enhanced when considering only intergenic SNPs. The structure of SNP-based diseasome networks confirms that TAD border enrichment in risk loci differ between cancers and non-cancer diseases. Different TAD border enrichments are observed in embryonic stem cells and differentiated cells, which agrees with an evolution along embryogenesis of the 3D genome organization into topological domains. Our results suggest that, for certain diseases, part of the genetic risk lies in a local genetic variation affecting the genome partitioning in topologically-insulated domains. Investigating this possible contribution to genetic risk is particularly relevant in cancers. This study thus opens a way of interpreting genome-wide association studies, by distinguishing two types of disease-associated SNPs: one with a direct effect on an individual gene, the other acting in interplay with 3D genome organization.

scholarly journals Regulation of mammalian 3D genome organization and histone H3K9 dimethylation by H3K9 methyltransferases

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Kei Fukuda ◽  
Chikako Shimura ◽  
Hisashi Miura ◽  
Akie Tanigawa ◽  
Takehiro Suzuki ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Genome Organization ◽  
Mammalian Cells ◽  
Embryonic Stem ◽  
Epigenetic Mark ◽  
3 Dimensional ◽  
3D Genome ◽  
Genome Wide ◽  
H3k9 Dimethylation

AbstractHistone H3 lysine 9 dimethylation (H3K9me2) is a highly conserved silencing epigenetic mark. Chromatin marked with H3K9me2 forms large domains in mammalian cells and overlaps well with lamina-associated domains and the B compartment defined by Hi-C. However, the role of H3K9me2 in 3-dimensional (3D) genome organization remains unclear. Here, we investigated genome-wide H3K9me2 distribution, transcriptome, and 3D genome organization in mouse embryonic stem cells following the inhibition or depletion of H3K9 methyltransferases (MTases): G9a, GLP, SETDB1, SUV39H1, and SUV39H2. We show that H3K9me2 is regulated by all five MTases; however, H3K9me2 and transcription in the A and B compartments are regulated by different MTases. H3K9me2 in the A compartments is primarily regulated by G9a/GLP and SETDB1, while H3K9me2 in the B compartments is regulated by all five MTases. Furthermore, decreased H3K9me2 correlates with changes to more active compartmental state that accompanied transcriptional activation. Thus, H3K9me2 contributes to inactive compartment setting.

scholarly journals High resolution single-cell chromatin 3D modeling reveals coherent chromatin aggregation with varied structures in controlling genome function stability

2019 ◽  
Author(s):  
Luming Meng ◽  
Yi Shi ◽  
Chenxi Wang
Keyword(s):  
Single Cell ◽  
Gene Activation ◽  
Strongly Correlated ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Consistent Aggregation ◽  
3D Architecture ◽  
Genomic Regions

The genome 3D architecture is thought to be related to regulating gene expression levels in cells and can be explained by genome-wide chromatin interactions which have been explored by chromosome conformation capture based techniques, especially Hi-C. Based on single-cell Hi-C data, we developed a new method in constructing experimental consistent 3D intact genome structures for individual cells with a resolution of 10kb or higher. The modeled structures showed marked variations of 3D genome organization across different cells. However, chromosome loci marked by different proteins, such as CTCF and post-translationally modified histones, are consistently non-specifically aggregated in space. Interestingly, similar aggregations between active enhancers and active promoters were observed, especially for those separated by genomic regions of the scale of megabase or larger. Such long-range associations between active enhancers and promoters are strongly correlated with spatial aggregation of chromosome loci marked by different proteins. Through analyzing the 3D structures of intact genome, we proposed that coherent gene activation profiles among individual cells can be achieved by the consistent aggregation of protein marked loci instead of maintaining identical folded conformations.

scholarly journals Genomic and Proteomic Analyses of Prdm5 Reveal Interactions with Insulator Binding Proteins in Embryonic Stem Cells

2013 ◽  
Vol 33 (22) ◽  
pp. 4504-4516 ◽  
Author(s):  
Giorgio Giacomo Galli ◽  
Matteo Carrara ◽  
Chiara Francavilla ◽  
Kristian Honnens de Lichtenberg ◽  
Jesper Velgaard Olsen ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Molecular Mechanisms ◽  
Regulation Of Gene Expression ◽  
Embryonic Stem ◽  
Set Domain ◽  
Sequencing Technologies ◽  
Interaction Partners ◽  
Genomic Regions ◽  
Mes Cells

PRDM proteins belong to the SET domain protein family, which is involved in the regulation of gene expression. Although few PRDM members possess histone methyltransferase activity, the molecular mechanisms by which the other members exert transcriptional regulation remain to be delineated. In this study, we find that Prdm5 is highly expressed in mouse embryonic stem (mES) cells and exploit this cellular system to characterize molecular functions of Prdm5. By combining proteomics and next-generation sequencing technologies, we identify Prdm5 interaction partners and genomic occupancy. We demonstrate that although Prdm5 is dispensable for mES cell maintenance, it directly targets genomic regions involved in early embryonic development and affects the expression of a subset of developmental regulators during cell differentiation. Importantly, Prdm5 interacts with Ctcf, cohesin, and TFIIIC and cooccupies genomic loci. In summary, our data indicate how Prdm5 modulates transcription by interacting with factors involved in genome organization in mouse embryonic stem cells.

scholarly journals Global Genome Conformational Programming during Neuronal Development Is Associated with CTCF and Nuclear FGFR1—The Genome Archipelago Model

2020 ◽  
Vol 22 (1) ◽  
pp. 347
Author(s):  
Brandon Decker ◽  
Michal Liput ◽  
Hussam Abdellatif ◽  
Donald Yergeau ◽  
Yongho Bae ◽  
...  
Keyword(s):  
Neuronal Development ◽  
Embryonic Stem ◽  
Loop Formation ◽  
Hoxa Cluster ◽  
Chromatin Interactions ◽  
Topologically Associating Domains ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Genome Interactions

During the development of mouse embryonic stem cells (ESC) to neuronal committed cells (NCC), coordinated changes in the expression of 2851 genes take place, mediated by the nuclear form of FGFR1. In this paper, widespread differences are demonstrated in the ESC and NCC inter- and intra-chromosomal interactions, chromatin looping, the formation of CTCF- and nFGFR1-linked Topologically Associating Domains (TADs) on a genome-wide scale and in exemplary HoxA-D loci. The analysis centered on HoxA cluster shows that blocking FGFR1 disrupts the loop formation. FGFR1 binding and genome locales are predictive of the genome interactions; likewise, chromatin interactions along with nFGFR1 binding are predictive of the genome function and correlate with genome regulatory attributes and gene expression. This study advances a topologically integrated genome archipelago model that undergoes structural transformations through the formation of nFGFR1-associated TADs. The makeover of the TAD islands serves to recruit distinct ontogenic programs during the development of the ESC to NCC.

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