Spatial Organization Of Chromatin Research Articles

ImAge quantitates aging and rejuvenation.

For efficient, cost-effective and personalized healthcare, biomarkers that capture aspects of functional, biological aging, thus predicting disease risk and lifespan more accurately and reliably than chronological age, are essential. We developed an imaging-based chromatin and epigenetic age (ImAge) that captures intrinsic age-related trajectories of the spatial organization of chromatin and epigenetic marks in single nuclei, in mice. We show that such trajectories readily emerge as principal changes in each individual dataset without regression on chronological age, and that ImAge can be computed using several epigenetic marks and DNA labeling. We find that interventions known to affect biological aging induce corresponding effects on ImAge, including increased ImAge upon chemotherapy treatment and decreased ImAge upon caloric restriction and partial reprogramming by transient OSKM expression in liver and skeletal muscle. Further, ImAge readouts from chronologically identical mice inversely correlated with their locomotor activity, suggesting that ImAge may capture elements of biological and functional age. In sum, we developed ImAge, an imaging-based biomarker of aging with single-cell resolution rooted in the analysis of spatial organization of epigenetic marks.

SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data

Chromatin spatial organization plays a crucial role in gene regulation. Recently developed and prospering multiplexed DNA FISH technologies enable direct visualization of chromatin conformation in the nucleus. However, incomplete data caused by limited detection efficiency can substantially complicate and impair downstream analysis. Here, we present SnapFISH-IMPUTE that imputes missing values in multiplexed DNA FISH data. Analysis on multiple published datasets shows that the proposed method preserves the distribution of pairwise distances between imaging loci, and the imputed chromatin conformations are indistinguishable from the observed conformations. Additionally, imputation greatly improves downstream analyses such as identifying enhancer-promoter loops and clustering cells into distinct cell types. SnapFISH-IMPUTE is freely available at https://github.com/hyuyu104/SnapFISH-IMPUTE.

Transcriptional Hubs Within Cliques in Ensemble Hi-C Chromatin Interaction Networks.

Chromatin conformation capture technologies permit the study of chromatin spatial organization on a genome-wide scale at a variety of resolutions. Despite the increasing precision and resolution of high-throughput chromatin conformation capture (Hi-C) methods, it remains challenging to conclusively link transcriptional activity to spatial organizational phenomena. We have developed a clique-based approach for analyzing Hi-C data that helps identify chromosomal hotspots that feature considerable enrichment of chromatin annotations for transcriptional start sites and, building on previously published work, show that these chromosomal hotspots are not only significantly enriched in RNA polymerase II binding sites as identified by the ENCODE project, but also identify a noticeable increase in FANTOM5 and GTEx transcription within our identified cliques across a variety of tissue types. From the obtained data, we surmise that our cliques are a suitable method for identifying transcription factories in Hi-C data, and outline further extensions to the method that may make it useful for locating regions of increased transcriptional activity in datasets where in-depth expression or polymerase data may not be available.

Bromodomain and Extraterminal Domain Protein 2 in Multiple Human Diseases.

Bromodomain and extraterminal domain protein 2 (BRD2), a member of the bromodomain and extraterminal domain (BET) protein family, is a crucial epigenetic regulator with significant function in various diseases and cellular processes. The central function of BRD2 is modulating gene transcription by binding to acetylated lysine residues on histones and transcription factors. This review highlights key findings on BRD2 in recent years, emphasizing its roles in maintaining genomic stability, influencing chromatin spatial organization, and participating in transcriptional regulation. BRD2's diverse functions are underscored by its involvement in diseases such as malignant tumors, neurologic disorders, inflammatory conditions, metabolic diseases, and virus infection. Notably, the potential role of BRD2 as a diagnostic marker and therapeutic target is discussed in the context of various diseases. Although pan inhibitors targeting the BET family have shown promise in preclinical studies, a critical need exists for the development of highly selective BRD2 inhibitors. In conclusion, this review offers insights into the multifaceted nature of BRD2 and calls for continued research to unravel its intricate mechanisms and harness its therapeutic potential. SIGNIFICANCE STATEMENT: BRD2 is involved in the occurrence and development of diseases through maintaining genomic stability, influencing chromatin spatial organization, and participating in transcriptional regulation. Targeting BRD2 through protein degradation-targeting complexes technology is emerging as a promising therapeutic approach for malignant cancer and inflammatory diseases.

Three-Dimensional Genomics: A New Perspective and Therapeutic Strategies in Prostate Cancer Research

Prostate cancer (PC) poses significant health risks to men globally. Enhancing our understanding of prostate cancer biology is crucial for facilitating early diagnosis and effective treatment strategies. A multitude of high-throughput sequencing studies, encompassing whole genome resequencing, transcriptome sequencing, and genome-wide association studies, have unearthed vital point mutations, structural variations, and epigenomic alterations linked to prostate cancer. These findings have significantly enriched our knowledge of the genomic framework for prostate cancer. Still, these investigations have predominantly centered on the one- or two-dimensional landscape of the genome. Research in three-dimensional genomics underscores the critical role of the genome's three-dimensional spatial structure in maintaining normal cellular functions. Additionally, it demonstrates that dysregulation of key genes in numerous cancers relates to the chromatin's spatial organization across various levels. This article explores the intricate three-dimensional architecture of chromosomes. It outlines the progressive development of techniques used in three-dimensional genomic research and synthesizes the application of these techniques in the study of prostate cancer biology. Furthermore, it proposes potential therapeutic strategies for prostate cancer.

Footprints of loop extrusion in statistics of intra-chromosomal distances: An analytically solvable model.

Active loop extrusion-the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes-is a firmly established mechanism responsible for chromatin spatial organization at different stages of a cell cycle in eukaryotes and bacteria. The theoretical insight into the effect of loop extrusion on the experimentally measured statistics of chromatin conformation can be gained with an appropriately chosen polymer model. Here, we consider the simplest analytically solvable model of an interphase chromosome, which is treated as an ideal chain with disorder of sufficiently sparse random loops whose conformations are sampled from the equilibrium ensemble. This framework allows us to arrive at the closed-form analytical expression for the mean-squared distance between pairs of genomic loci, which is valid beyond the one-loop approximation in diagrammatic representation. In addition, we analyze the loop-induced deviation of chain conformations from the Gaussian statistics by calculating kurtosis of probability density of the pairwise separation vector. The presented results suggest the possible ways of estimating the characteristics of the loop extrusion process based on the experimental data on the scale-dependent statistics of intra-chromosomal pair-wise distances.

Spatial organization of regulatory chromatin at transcription condensates

Spatial organization of regulatory chromatin at transcription condensates

Trisomies Reorganize Human 3D Genome.

Trisomy is the presence of one extra copy of an entire chromosome or its part in a cell nucleus. In humans, autosomal trisomies are associated with severe developmental abnormalities leading to embryonic lethality, miscarriage or pronounced deviations of various organs and systems at birth. Trisomies are characterized by alterations in gene expression level, not exclusively on the trisomic chromosome, but throughout the genome. Here, we applied the high-throughput chromosome conformation capture technique (Hi-C) to study chromatin 3D structure in human chorion cells carrying either additional chromosome 13 (Patau syndrome) or chromosome 16 and in cultured fibroblasts with extra chromosome 18 (Edwards syndrome). The presence of extra chromosomes results in systematic changes of contact frequencies between small and large chromosomes. Analyzing the behavior of individual chromosomes, we found that a limited number of chromosomes change their contact patterns stochastically in trisomic cells and that it could be associated with lamina-associated domains (LAD) and gene content. For trisomy 13 and 18, but not for trisomy 16, the proportion of compacted loci on a chromosome is correlated with LAD content. We also found that regions of the genome that become more compact in trisomic cells are enriched in housekeeping genes, indicating a possible decrease in chromatin accessibility and transcription level of these genes. These results provide a framework for understanding the mechanisms of pan-genome transcription dysregulation in trisomies in the context of chromatin spatial organization.

Hdac1 and Hdac2 positively regulate Notch1 gain-of-function pathogenic signaling in committed osteoblasts of male mice.

Skeletal development requires precise extrinsic and intrinsic signals to regulate processes that form and maintain bone and cartilage. Notch1 is a highly conserved signaling receptor that regulates cell fate decisions by controlling the duration of transcriptional bursts. Epigenetic molecular events reversibly modify DNA and histone tails by influencing the spatial organization of chromatin and can fine-tune the outcome of a Notch1 transcriptional response. Histone deacetylase 1 and 2 (HDAC1 and HDAC2) are chromatin modifying enzymes that mediate osteoblast differentiation. While an HDAC1-Notch interaction has been studied in vitro and in Drosophila, its role in mammalian skeletal development and disorders is unclear. Osteosclerosis is a bone disorder with an abnormal increase in the number of osteoblasts and excessive bone formation. Here, we tested whether Hdac1/2 contribute to the pathogenesis of osteosclerosis in a murine model of the disease owing to conditionally cre-activated expression of the Notch1 intracellular domain in immature osteoblasts. Importantly, selective homozygous deletions of Hdac1/2 in osteoblasts partially alleviate osteosclerotic phenotypes (Col2.3kb-Cre; TGRosaN1ICD/+ ; Hdac1flox/flox ; Hdac2flox/flox ) with a 40% decrease in bone volume and a 22% decrease in trabecular thickness in 4 weeks old when compared to male mice with heterozygous deletions of Hdac1/2 (Col2.3 kb-Cre; TGRosaN1ICD/+ ; Hdac1flox/+ ; Hdac2flox/+ ). Osteoblast-specific deletion of Hdac1/2 in male and female mice results in no overt bone phenotype in the absence of the Notch1 gain-of-function (GOF) allele. These results provide evidence that Hdac1/2 contribute to Notch1 pathogenic signaling in the mammalian skeleton. Our study on epigenetic regulation of Notch1 GOF-induced osteosclerosis may facilitate further mechanistic studies of skeletal birth defects caused by Notch-related GOF mutations in human patients, such as Adams-Oliver disease, congenital heart disease, and lateral meningocele syndrome.

SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data.

Single-cell high-throughput chromatin conformation capture technologies (scHi-C) has been used to map chromatin spatial organization in complex tissues. However, computational tools to detect differential chromatin contacts (DCCs) from scHi-C datasets in development and through disease pathogenesis are still lacking. Here, we present SnapHiC-D, a computational pipeline to identify DCCs between two scHi-C datasets. Compared to methods designed for bulk Hi-C data, SnapHiC-D detects DCCs with high sensitivity and accuracy. We used SnapHiC-D to identify cell-type-specific chromatin contacts at 10 Kb resolution in mouse hippocampal and human prefrontal cortical tissues, demonstrating that DCCs detected in the hippocampal and cortical cell types are generally associated with cell-type-specific gene expression patterns and epigenomic features. SnapHiC-D is freely available at https://github.com/HuMingLab/SnapHiC-D.

3D organization of regulatory elements for transcriptional regulation in Arabidopsis

BackgroundAlthough spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood in plants.ResultsHere we perform high-resolution chromatin interaction analysis using paired-end tag sequencing approach. We map chromatin interactions tethered with RNA polymerase II and associated with heterochromatic, transcriptionally active, and Polycomb-repressive histone modifications in Arabidopsis. Analysis of the regulatory repertoire shows that distal active cis-regulatory elements are linked to their target genes through long-range chromatin interactions with increased expression of the target genes, while poised cis-regulatory elements are linked to their target genes through long-range chromatin interactions with depressed expression of the target genes. Furthermore, we demonstrate that transcription factor MYC2 is critical for chromatin spatial organization, and propose that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. Analysis of functionally related gene-defined chromatin connectivity networks reveals that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or Polycomb-repressive mark-associated chromatin conformation to coordinated gene expression.ConclusionThe results reveal that the regulation of gene transcription in Arabidopsis is not only by linear juxtaposition, but also by long-range chromatin interactions. Our study uncovers the fine scale genome organization of Arabidopsis and the potential roles of such organization in orchestrating transcription and development.

Three-way contact analysis characterizes the higher order organization of the Tcra locus.

The generation of highly diverse antigen receptors in T and B lymphocytes relies on V(D)J recombination. The enhancer Eα has been implicated in regulating the accessibility of Vα and Jα genes through long-range interactions during rearrangements of the T-cell antigen receptor gene Tcra. However, direct evidence for Eα physically mediating the interaction of Vα and Jα genes is still lacking. In this study, we utilized the 3C-HTGTS assay, a chromatin interaction technique based on 3C, to analyze the higher order chromatin structure of the Tcra locus. Our analysis revealed the presence of sufficient information in the 3C-HTGTS data to detect multiway contacts. Three-way contact analysis of the Tcra locus demonstrated the co-occurrence of the proximal Jα genes, Vα genes and Eα in CD4+CD8+ double-positive thymocytes. Notably, the INT2-TEAp loop emerged as a prominent structure likely to be responsible for bringing the proximal Jα genes and the Vα genes into proximity. Moreover, the enhancer Eα utilizes this loop to establish physical proximity with the proximal Vα gene region. This study provides insights into the higher order chromatin structure of the Tcra locus, shedding light on the spatial organization of chromatin and its impact on V(D)J recombination.

MATR3-antisense LINE1 RNA meshwork scaffolds higher-order chromatin organization.

Long interspersed nuclear elements (LINEs) play essential roles in shaping chromatin states, while the factors that cooperate with LINEs and their roles in higher-order chromatin organization remain poorly understood. Here, we show that MATR3, a nuclear matrix protein, interplays with antisense LINE1 (AS L1) RNAs to form a meshwork via phase separation, providing a dynamic platform for chromatin spatial organization. MATR3 and AS L1 RNAs affect the nuclear localization of each other. After MATR3 depletion, the chromatin, particularly H3K27me3-modified chromatin, redistributes in the cell nuclei. Topologically associating domains (TADs) that highly transcribe MATR3-associated AS L1 RNAs show decreased intra-TAD interactions in both AML12 and ES cells. MATR3 depletion increases the accessibility of H3K27me3 domains adjacent to MATR3-associated AS L1, without affecting H3K27me3 modifications. Furthermore, amyotrophic lateral sclerosis (ALS)-associated MATR3 mutants alter biophysical features of the MATR3-AS L1 RNA meshwork and cause an abnormal H3K27me3 staining. Collectively, we reveal a role of the meshwork formed by MATR3 and AS L1 RNAs in gathering chromatin in the nucleus.

High-LET targeted microbeam irradiation induces local chromatin reorganization in living cells showing active basal mechanisms at highly complex DNA damage sites

DNA repair eukaryotic cells have additional protective mechanisms that avoid uncontrolled interaction of different parts of the chromatin and damaged regions. Key factors here are the regulation of chromatin density and mobility. The 4D (temporal and spatial) organization of chromatin is controlling this security barrier by regulating the accessibility of genes, flexibility of DNA, and its ability to move inside the nucleus. How this regulation mechanisms are involved in DNA repair upon radiation damage is until now rarely known but an important part to understand the enhanced effectiveness of high linear energy transfer (LET) particles. The damage recognition via PARP1 and the subsequent chromatin decondensation via PARylation is a crucial step in the DNA damage response (DDR). Upon We used the SNAKE microbeam with a beam spot size of <1 µm to induce highly localized DNA damage in living cells using 55 MeV Carbon ions to investigate the chromatin rearrangements in the early stage of DDR. The nuclei were irradiated with a cross pattern consisting of 1000 ions per spot and 25 spots per cell either with one (11 000 Gy), two (22 000 Gy), or three crosses (33 000 Gy). The chromatin rearrangement was imaged live for several minutes after irradiation at the beam using SiR chromatin stain. Upon 91% of the cells show a localized decondensation starting from a few seconds up to minutes after irradiation. The chromatin is decondensed by 6%-8% in the beam path with a local condensation at the edges of up to 8%. Our results suggest that chromatin decondensation is a fast process in the first few seconds after damage induction. Furthermore, decondensation status does not change over minutes, which gives evidence that this process and therefore DDR is paused or even stopped. In combination with the existing knowledge about early reactions to damage induction our data support the model of PARP induced chromatin decondensation. Furthermore, it is evident that also ultra-high doses of radiation are, in first place not able to inactivate initial basal mechanisms as response to damage induction.

Influence of human peripheral blood samples preprocessing on the quality of Hi-C libraries.

The genome-wide variant of the chromatin conformation capture technique (Hi-C) is a powerful tool for revealing patterns of genome spatial organization, as well as for understanding the effects of their disturbance on disease development. In addition, Hi-C can be used to detect chromosomal rearrangements, including balanced translocations and inversions. The use of the Hi-C method for the detection of chromosomal rearrangements is becoming more widespread. Modern high-throughput methods of genome analysis can effectively reveal point mutations and unbalanced chromosomal rearrangements. However, their sensitivity for determining translocations and inversions remains rather low. The storage of whole blood samples can affect the amount and integrity of genomic DNA, and it can distort the results of subsequent analyses if the storage was not under proper conditions. The Hi-C method is extremely demanding on the input material. The necessary condition for successfully applying Hi-C and obtaining high-quality data is the preservation of the spatial chromatin organization within the nucleus. The purpose of this study was to determine the optimal storage conditions of blood samples for subsequent Hi-C analysis. We selected 10 different conditions for blood storage and sample processing. For each condition, we prepared and sequenced Hi-C libraries. The quality of the obtained data was compared. As a result of the work, we formulated the requirements for the storage and processing of samples to obtain high-quality Hi-C data. We have established the minimum volume of blood sufficient for conducting Hi-C analysis. In addition, we have identified the most suitable methods for isolation of peripheral blood mononuclear cells and their long-term storage. The main requirement we have formulated is not to freeze whole blood.

Phase Separation: Direct and Indirect Driving Force for High-Order Chromatin Organization.

The multi-level spatial chromatin organization in the nucleus is closely related to chromatin activity. The mechanism of chromatin organization and remodeling attract much attention. Phase separation describes the biomolecular condensation which is the basis for membraneless compartments in cells. Recent research shows that phase separation is a key aspect to drive high-order chromatin structure and remodeling. In addition, chromatin functional compartmentalization in the nucleus which is formed by phase separation also plays an important role in overall chromatin structure. In this review, we summarized the latest work about the role of phase separation in spatial chromatin organization, focusing on direct and indirect effects of phase separation on 3D chromatin organization and its impact on transcription regulation.

Delivery and imaging of functionalized DNA origami in cells.

Human cells package over two meters of genetic information into the microscopic space of the nucleus in the form of chromatin (a complex between DNA and histone proteins). This packaging or “folding” of the genome is critical for the regulation of gene expression, maintenance of genomic stability, and defining cell fate during development. Change to the spatial organization of chromatin is implicated in a host of neurological disorders as well as in aging and cancer. Remodeling of chromatin via post-translational modifications allows for epigenetic regulation of transcription in healthy and diseased cells. Thus, tools to engineer chromatin epigenetics in a controlled manner are crucial to study the cause-consequence relationship between epigenetics, chromatin organization and gene expression. Previous approaches to chromatin engineering have significant limitations, namely the inability to perform multiple functions (visualize, modify, or detect downstream products) simultaneously. Our work seeks to develop and apply DNA origami nanodevices (DOs) as multi-functional platforms to probe and engineer chromatin epigenetics. We propose to leverage the versatility of DO and its potential as a platform for multiple functional elements to visualize, modify, and sense the transcriptional output of genomic regions in mammalian cell nuclei. We have taken an interdisciplinary approach to develop and test four different DNA origami structures (26-helix bundle, 14-helix bundle, 13-helix bundle, and 8-helix bundle) functionalized with fluorophores as well as an anti-RNA Polymerase II (Pol2) antibody. We show that electroporation enables delivery of these structures into cells and further, 8-helix bundle structures functionalized with RNA Pol2 antibodies are successfully piggybacked into the nucleus. Super-resolution imaging further demonstrates the delivery of single DNA origami structures into the cell nucleus. These results open the door for DNA origami as a multifunctional platform for targeting, modifying, and visualizing the genome.

High-content image-based CRISPR screening reveals regulators of 3D genome architectures.

The spatial organization of chromatin critically impacts many essential genomic functions, from the regulation of gene expression to the replication of the genome. Changes in chromatin organization are associated with aging and a wide range of diseases including cancer. Despite the fundamental importance of correct chromatin organization and its effects on cellular behavior, very little is known regarding the precise folding arrangement of chromatin in various cell states, nor the molecular mechanisms that control chromatin organization in the cell nucleus. Current approaches are severely limited by a lack of experimental tools to directly trace chromatin folding, and to efficiently screen for molecular regulators of chromatin organization in the genome. To address these needs, we previously developed an image-based 3D genomics technique termed chromatin tracing, which enables direct 3D tracing of chromatin folding along individual chromosomes in single cells. Recently, we further developed Multiplexed Imaging of Nucleome Architectures (MINA), which enables simultaneous measurements of multiscale chromatin folding, associations of genomic regions with nuclear lamina and nucleoli, and copy numbers of numerous RNA species in the same cells in mammalian tissue. Here we report our latest technology development - an image-based high-content CRISPR screening platform - to systematically uncover new regulators of 3D genome organization. We performed a pooled loss-of-function screen of hundreds of selected genes in human cells, identified target genes by inventing a cellular barcoding technique termed BARC-FISH, and visualized genome organization by chromatin tracing in the same single cells. Using 1.4 million imaged 3D-positions along chromosome traces, we identified tens of novel regulators of chromatin architectures at different length scales. Loss of the ATP-dependent helicase CHD7, which causes the congenital syndrome CHARGE, promotes multi-scale chromatin decompaction. This method enables scalable, high-throughput identification of chromatin topology regulators in diverse contexts.

Computational predictions of 3D chromatin many-body interactions reveal roles of chromatin hubs in gene expression.

Chromatin 3D organization plays important roles in the regulation of gene expression. Hi-C measurements provide a projection of 3D chromatin organization onto a 2D heatmap, which depicts the population-averaged pairwise contact frequencies between all genomic elements. These 2D heatmaps highlight structural units of chromatin organization such as TADs. As distal cis-regulatory elements such as enhancers interact with promoters to increase the transcriptional output of target genes in a tissue-specific manner, quantifying cell-type specific chromatin spatial organization is therefore critical. However, TADs have been found to be largely invariant across cell types, suggesting that features of 2D Hi-C heatmaps are insufficient to gain understanding of tissue-specific gene expression. Another challenge is when multiple genomic elements are involved: It is not possible to obtain higher-order many-body interactions from Hi-C data. In order to address these problems, we apply CHROMATIX, a computational method which reconstructs ensembles of single-cell chromatin conformations by deconvolving Hi-C data. We reconstructed large ensembles (2×104) of independent 3D single-cell chromatin conformations which reproduce imaging, Dip-C, and 3D FISH single cell measurements. The reconstructed ensembles of single-cell chromatin structures further enable us to uncover statistically significant 3D hubs of higher-order many-body interactions. We uncovered chromatin hubs of many-bodies across hundreds of loci in B-lymphocyte cells. We illustrate the functional roles of these 3D hubs of many-body interactions in regulating gene expression. Using the example of eQTL associated genes, we show that higher-order 3D hubs provide the physical basis of differential gene expression, with detailed examples of hubs of 1-gene-to-many-eQTLs and many-genes-to-1-eQTL. Overall, our results show 3D chromatin many-body hubs are important for regulating gene expression, and they can be discovered through CHROMATIX computational modeling single-cell 3D chromatin conformations using population Hi-C data.

Mesoscale chromatin organization is regulated by active transcription and epigenetic regulation.

Epigenetically regulated post-translational modifications of histone tails via acetylation or methylation have been established to play a role in determining the transcriptional status of genes. Beyond epigenetic regulation, chromatin loop extrusion through cohesin rings, driven by transcription-generated DNA supercoiling, can also alter spatial chromatin organization. Here, we present a mesoscale phase-field model to explain the underlying physics of chromatin reorganization in the presence of transcriptionally driven chromatin loop extrusion. The model incorporates energetic considerations of chromatin-chromatin and chromatin-lamina interactions leading to phase separation in the interior and periphery of the nucleus. We incorporate the kinetics of the diffusion of nucleoplasm and epigenetic marks. In addition, a non-conservative interconversion of euchromatin and heterochromatin is captured by incorporating first-order reaction kinetics of histone methylation and acetylation. Lastly, and vitally, the extrusion of genetically expressive chromatin enhancer-promoter loops is included via a kinetic conversion of heterochromatin into euchromatin in the presence of RNAPII-mediated transcriptional activity. Our theoretical analysis predicts that the size of the stable heterochromatin domains is determined solely by the kinetics of acetylation, methylation, and chromatin loop extrusion. Our numerical simulations, in conjunction with the super-resolution in-vitro nucleus imaging techniques, reveal that the absence of transcription increases chromatin compaction and heterochromatin domain sizes in the nucleus's interior and periphery. We also predict that enhanced chromatin loop extrusion would result in reduced sizes of heterochromatin domains - which is validated by super-resolution imaging of WAPL-deficient nuclei. Lastly, we reveal the synergistic effects of WAPL deficiency and transcriptional abrogation such that chromatin decompaction in WAPL-deficient nuclei is blocked by inhibiting transcription. By uncovering the physical mechanisms of mesoscale chromatin organization in the nucleus, our model presents a new step in understanding how cell fate is affected by its chemo-mechanical environment.