Identification of decondensed large-scale chromatin regions by TSA-seq and their localization to a subset of chromatin domain boundaries

AbstractLarge-scale chromatin compaction is nonuniform across the human genome and correlates with gene expression and genome organization. Current methodologies for assessing large-scale chromatin compaction are indirect and largely based on assays that probe lower levels of chromatin organization, primarily at the level of the nucleosome and/or the local compaction of nearby nucleosomes. These assays assume a one-to-one correlation between local nucleosomal compaction and large-scale compaction of chromosomes that may not exist. Here we describe a method to identify interphase chromosome regions with relatively high levels of large-scale chromatin decondensation using TSA-seq, which produces a signal proportional to microscopic-scale distances relative to a defined nuclear compartment. TSA-seq scores that change rapidly as a function of genomic distance, detected by their higher slope values, identify decondensed large-scale chromatin domains (DLCDs), as then validated by 3D DNA-FISH. DLCDs map near a subset of chromatin domain boundaries, defined by Hi-C, which separate active and repressed chromatin domains and correspond to compartment, subcompartment, and some TAD boundaries. Most DLCDs can also be detected by high slopes of their Hi-C compartment score. In addition to local enrichment in cohesin (RAD21, SMC3) and CTCF, DLCDs show the highest local enrichment to super-enhancers, but are also locally enriched in transcription factors, histone-modifying complexes, chromatin mark readers, and chromatin remodeling complexes. The localization of these DLCDs to a subset of Hi-C chromatin domain boundaries that separate active versus inactive chromatin regions, as measured by two orthogonal genomic methods, suggests a distinct role for DLCDs in genome organization.

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Erythrocytes 3D genome organization in vertebrates

Scientific Reports ◽

10.1038/s41598-021-83903-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Anastasia Ryzhkova ◽

Alena Taskina ◽

Anna Khabarova ◽

Veniamin Fishman ◽

Nariman Battulin

Keyword(s):

Blood Cells ◽

Genome Organization ◽

Large Scale ◽

Chromatin Condensation ◽

Erythroid Differentiation ◽

Interaction Patterns ◽

3D Interaction ◽

Interphase Chromosome ◽

3D Genome ◽

Contact Maps

AbstractGeneration of mature red blood cells, consisting mainly of hemoglobin, is a remarkable example of coordinated action of various signaling networks. Chromatin condensation is an essential step for terminal erythroid differentiation and subsequent nuclear expulsion in mammals. Here, we profiled 3D genome organization in the blood cells from ten species belonging to different vertebrate classes. Our analysis of contact maps revealed a striking absence of such 3D interaction patterns as loops or TADs in blood cells of all analyzed representatives. We also detect large-scale chromatin rearrangements in blood cells from mammals, birds, reptiles and amphibians: their contact maps display strong second diagonal pattern, representing an increased frequency of long-range contacts, unrelated to TADs or compartments. This pattern is completely atypical for interphase chromosome structure. We confirm that these principles of genome organization are conservative in vertebrate erythroid cells.

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Spatial Relationship between Transcription Sites and Chromosome Territories

The Journal of Cell Biology ◽

10.1083/jcb.147.1.13 ◽

1999 ◽

Vol 147 (1) ◽

pp. 13-24 ◽

Cited By ~ 162

Author(s):

Pernette J. Verschure ◽

Ineke van der Kraan ◽

Erik M.M. Manders ◽

Roel van Driel

Keyword(s):

X Chromosome ◽

Large Scale ◽

Fluorescent Protein ◽

Spatial Relationship ◽

Chromosome Territory ◽

Chromosome Territories ◽

Interphase Chromosome ◽

Chromatin Domains ◽

Transcription Sites ◽

Nascent Rna

We have investigated the spatial relationship between transcription sites and chromosome territories in the interphase nucleus of human female fibroblasts. Immunolabeling of nascent RNA was combined with visualization of chromosome territories by fluorescent in situ hybridization (FISH). Transcription sites were found scattered throughout the territory of one of the two X chromosomes, most likely the active X chromosome, and that of both territories of chromosome 19. The other X chromosome territory, probably the inactive X chromosome, was devoid of transcription sites. A distinct substructure was observed in interphase chromosome territories. Intensely labeled subchromosomal domains are surrounded by less strongly labeled areas. The intensely labeled domains had a diameter in the range of 300–450 nm and were sometimes interconnected, forming thread-like structures. Similar large scale chromatin structures were observed in HeLa cells expressing green fluorescent protein (GFP)-tagged histone H2B. Strikingly, nascent RNA was almost exclusively found in the interchromatin areas in chromosome territories and in between strongly GFP-labeled chromatin domains. These observations support a model in which transcriptionally active chromatin in chromosome territories is markedly compartmentalized. Active loci are located predominantly at or near the surface of compact chromatin domains, depositing newly synthesized RNA directly into the interchromatin space.

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Lamins organize the global three-dimensional genome from the nuclear periphery

10.1101/211656 ◽

2017 ◽

Cited By ~ 3

Author(s):

Xiaobin Zheng ◽

Jiabiao Hu ◽

Sibiao Yue ◽

Lidya Kristiani ◽

Miri Kim ◽

...

Keyword(s):

Genome Organization ◽

Es Cells ◽

Nuclear Periphery ◽

Three Dimensional ◽

Nuclear Lamina ◽

Chromatin Domain ◽

List Type ◽

Chromatin Domains ◽

Mouse Es Cells ◽

Domain Interactions

AbstractLamins are structural components of the nuclear lamina (NL) that regulate genome organization and gene expression, but the mechanism remains unclear. Using Hi-C, we show that lamins maintain proper interactions among the topologically associated chromatin domains (TADs) but not their overall architecture. Combining Hi-C with fluorescence in situ hybridization (FISH) and analyses of lamina-associated domains (LADs), we reveal that lamin loss causes expansion or detachment of specific LADs in mouse ES cells. The detached LADs disrupt 3D interactions of both LADs and interior chromatin. 4C and epigenome analyses further demonstrate that lamins maintain the active and repressive chromatin domains among different TADs. By combining these studies with transcriptome analyses, we found a significant correlation between transcription changes and the changes of active and inactive chromatin domain interactions. These findings provide a foundation to further study how the nuclear periphery impacts genome organization and transcription in development and NL-associated diseases.HighlightsLamin loss does not affect the overall TAD structure but alters TAD-TAD interactionsLamin null ES cells exhibit decondensation or detachment of specific LAD regionsExpansion and detachment of LADs can alter genome-wide 3D chromatin interactionsAltered chromatin domain interactions are correlated with altered transcription

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Acute condensin depletion causes genome decompaction without altering the level of global gene expression in Saccharomyces cerevisiae

10.1101/195487 ◽

2017 ◽

Cited By ~ 2

Author(s):

Matthew Robert Paul ◽

Tovah Elise Markowitz ◽

Andreas Hochwagen ◽

Sevinç Ercan

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Genome Organization ◽

Large Scale ◽

Global Gene Expression ◽

Higher Order ◽

Gene Clustering ◽

Global Changes ◽

Chromatin Compaction ◽

And Function

AbstractCondensins are broadly conserved chromosome organizers that function in chromatin compaction and transcriptional regulation, but to what extent these two functions are linked has remained unclear. Here, we analyzed the effect of condensin inactivation on genome compaction and global gene expression in the yeast Saccharomyces cerevisiae. Spike-in-controlled 3C-seq analysis revealed that acute condensin inactivation leads to a global decrease in close-range chromosomal interactions as well as more specific losses of homotypic tRNA gene clustering. In addition, a condensin-rich topologically associated domain between the ribosomal DNA and the centromere on chromosome XII is lost upon condensin inactivation. Unexpectedly, these large-scale changes in chromosome architecture are not associated with global changes in transcript levels as determined by spike-in-controlled mRNA-seq analysis. Our data suggest that the global transcriptional program of S. cerevisiae is resistant to condensin inactivation and the associated profound changes in genome organization.Significance StatementGene expression occurs in the context of higher-order chromatin organization, which helps compact the genome within the spatial constraints of the nucleus. To what extent higher-order chromatin compaction affects gene expression remains unknown. Here, we show that gene expression and genome compaction can be uncoupled in the single-celled model eukaryote Saccharomyces cerevisiae. Inactivation of the conserved condensin complex, which also organizes the human genome, leads to broad genome decompaction in this organism. Unexpectedly, this reorganization has no immediate effect on the transcriptome. These findings indicate that the global gene expression program is robust to large-scale changes in genome architecture in yeast, shedding important new light on the evolution and function of genome organization in gene regulation.

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ARID1A spatially partitions interphase chromosomes

Science Advances ◽

10.1126/sciadv.aaw5294 ◽

2019 ◽

Vol 5 (5) ◽

pp. eaaw5294 ◽

Cited By ~ 9

Author(s):

Shuai Wu ◽

Nail Fatkhutdinov ◽

Leah Rosin ◽

Jennifer M. Luppino ◽

Osamu Iwasaki ◽

...

Keyword(s):

Genome Organization ◽

Large Scale ◽

Three Dimensional ◽

Higher Order ◽

Interphase Chromosome ◽

Chromatin Remodeling Complex ◽

Chromosome Partitioning ◽

Topologically Associated Domains ◽

A Subunit

ARID1A, a subunit of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling complex, localizes to both promoters and enhancers to influence transcription. However, the role of ARID1A in higher-order spatial chromosome partitioning and genome organization is unknown. Here, we show that ARID1A spatially partitions interphase chromosomes and regulates higher-order genome organization. The SWI/SNF complex interacts with condensin II, and they display significant colocalizations at enhancers. ARID1A knockout drives the redistribution of condensin II preferentially at enhancers, which positively correlates with changes in transcription. ARID1A and condensin II contribute to transcriptionally inactive B-compartment formation, while ARID1A weakens the border strength of topologically associated domains. Condensin II redistribution induced by ARID1A knockout positively correlates with chromosome sizes, which negatively correlates with interchromosomal interactions. ARID1A loss increases the trans interactions of small chromosomes, which was validated by three-dimensional interphase chromosome painting. These results demonstrate that ARID1A is important for large-scale genome folding and spatially partitions interphase chromosomes.

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Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers

Genome Biology ◽

10.1186/s13059-021-02436-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Marie Zufferey ◽

Yuanlong Liu ◽

Daniele Tavernari ◽

Marco Mina ◽

Giovanni Ciriello

Keyword(s):

Complementary Information ◽

Chromatin Domains ◽

Algorithmic Approach ◽

Systematic Assessment ◽

Regulatory Interactions ◽

Human Cancers ◽

Domain Boundaries ◽

Gene Regulatory ◽

Systematic Identification ◽

The Relationship

Abstract Background Spatial interactions and insulation of chromatin regions are associated with transcriptional regulation. Domains of frequent chromatin contacts are proposed as functional units, favoring and delimiting gene regulatory interactions. However, contrasting evidence supports the association between chromatin domains and transcription. Result Here, we assess gene co-regulation in chromatin domains across multiple human cancers, which exhibit great transcriptional heterogeneity. Across all datasets, gene co-regulation is observed only within a small yet significant number of chromatin domains. We design an algorithmic approach to identify differentially active domains (DADo) between two conditions and show that these provide complementary information to differentially expressed genes. Domains comprising co-regulated genes are enriched in the less active B sub-compartments and for genes with similar function. Notably, differential activation of chromatin domains is not associated with major changes of domain boundaries, but rather with changes of sub-compartments and intra-domain contacts. Conclusion Overall, gene co-regulation is observed only in a minority of chromatin domains, whose systematic identification will help unravel the relationship between chromatin structure and transcription.

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Conformational Heterogeneity in Human Interphase Chromosome Organization Reconciles the FISH and Hi-C Paradox

10.1101/615120 ◽

2019 ◽

Author(s):

Guang Shi ◽

D. Thirumalai

Keyword(s):

Cell Population ◽

Genome Organization ◽

Large Cell ◽

Spatial Distance ◽

Chromosome Organization ◽

Conformational Heterogeneity ◽

Interphase Chromosome ◽

Length Scales ◽

Rouse Model ◽

Contact Probability

AbstractHi-C experiments are used to infer the contact probabilities between loci separated by varying genome lengths. Contact probability should decrease as the spatial distance between two loci increases. However, studies comparing Hi-C and FISH data show that in some cases the distance between one pair of loci, with larger Hi-C readout, is paradoxically larger compared to another pair with a smaller value of the contact probability. Here, we show that the FISH-Hi-C paradox can be resolved using a theory based on a Generalized Rouse Model for Chromosomes (GRMC). The FISH-Hi-C paradox arises because the cell population is highly heterogeneous, which means that a given contact is present in only a fraction of cells. Insights from the GRMC is used to construct a theory, without any adjustable parameters, to extract the distribution of subpopulations from the FISH data, which quantitatively reproduces the Hi-C data. Our results show that heterogeneity is pervasive in genome organization at all length scales, reflecting large cell-to-cell variations.

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A pitfall for machine learning methods aiming to predict across cell types

Genome Biology ◽

10.1186/s13059-020-02177-y ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Jacob Schreiber ◽

Ritambhara Singh ◽

Jeffrey Bilmes ◽

William Stafford Noble

Keyword(s):

Gene Expression ◽

Machine Learning ◽

Cell Types ◽

Chromatin Domain ◽

Learning Models ◽

Machine Learning Methods ◽

Domain Boundaries ◽

Average Activity ◽

Test Sets ◽

Machine Learning Models

AbstractMachine learning models that predict genomic activity are most useful when they make accurate predictions across cell types. Here, we show that when the training and test sets contain the same genomic loci, the resulting model may falsely appear to perform well by effectively memorizing the average activity associated with each locus across the training cell types. We demonstrate this phenomenon in the context of predicting gene expression and chromatin domain boundaries, and we suggest methods to diagnose and avoid the pitfall. We anticipate that, as more data becomes available, future projects will increasingly risk suffering from this issue.

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On the Time Evolution of Limited-Area Ensemble Variance: Case Studies with the Convection-Permitting Ensemble COSMO-E

Journal of the Atmospheric Sciences ◽

10.1175/jas-d-18-0013.1 ◽

2018 ◽

Vol 76 (1) ◽

pp. 11-26 ◽

Cited By ~ 4

Author(s):

Christina Klasa ◽

Marco Arpagaus ◽

André Walser ◽

Heini Wernli

Keyword(s):

Case Studies ◽

Time Evolution ◽

Large Scale ◽

Horizontal Wind ◽

Limited Area ◽

Convective Activity ◽

Moist Convection ◽

Domain Boundaries ◽

Large Scale Flow ◽

The Impact

Abstract Dynamical processes determining the time evolution of difference kinetic energy (DKE) in a limited-area domain are investigated with the convection-permitting ensemble model COSMO-E for a forecasting period of 4 days. DKE is quantified by means of ensemble variance of the irrotational and nondivergent horizontal wind. For three case studies characterized by contrasting predictability levels of precipitation, it is shown that DKE of the irrotational wind strongly increases during periods of solar-forced moist convective activity and decreases when the latter ceases. The response of DKE of the nondivergent wind is also clearly related to the convective activity, but delayed by a few hours, pointing to interactions between both wind components. Apart from the impact of moist convection, DKE of the nondivergent wind is primarily governed by large-scale advection, imposed at the lateral domain boundaries of the limited-area ensemble. This forcing may also sustain or increase DKE of the irrotational wind when moist convection is absent. Consequently, the large-scale flow and diurnal solar forcing, associated with higher spatiotemporal predictability, determines the overall evolution of the limited-area ensemble variance of the horizontal wind, which increases in the presence of moist convective activity or strong synoptic-scale forcing, and stagnates or decreases otherwise, rendering forecasts of convection-permitting ensembles valuable beyond the very short forecast range.

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