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Nickerson JA, Momen-Heravi F. Long non-coding RNAs: roles in cellular stress responses and epigenetic mechanisms regulating chromatin. Nucleus 2024; 15:2350180. [PMID: 38773934 PMCID: PMC11123517 DOI: 10.1080/19491034.2024.2350180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Most of the genome is transcribed into RNA but only 2% of the sequence codes for proteins. Non-coding RNA transcripts include a very large number of long noncoding RNAs (lncRNAs). A growing number of identified lncRNAs operate in cellular stress responses, for example in response to hypoxia, genotoxic stress, and oxidative stress. Additionally, lncRNA plays important roles in epigenetic mechanisms operating at chromatin and in maintaining chromatin architecture. Here, we address three lncRNA topics that have had significant recent advances. The first is an emerging role for many lncRNAs in cellular stress responses. The second is the development of high throughput screening assays to develop causal relationships between lncRNAs across the genome with cellular functions. Finally, we turn to recent advances in understanding the role of lncRNAs in regulating chromatin architecture and epigenetics, advances that build on some of the earliest work linking RNA to chromatin architecture.
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Affiliation(s)
- Jeffrey A Nickerson
- Division of Genes & Development, Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Fatemeh Momen-Heravi
- College of Dental Medicine, Columbia University Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
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2
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Deichmann U. Contrasting philosophical and scientific views in the long history of studying the generation of form in development. Biosystems 2024; 242:105260. [PMID: 38925338 DOI: 10.1016/j.biosystems.2024.105260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/23/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
Focusing on the opposing ways of thinking of philosophers and scientists to explain the generation of form in biological development, I show that today's controversies over explanations of early development bear fundamental similarities to the dichotomy of preformation theory versus epigenesis in Greek antiquity. They are related to the acceptance or rejection of the idea of a physical form of what today would be called information for the generating of the embryo as a necessary pre-requisite for specific development and heredity. As a recent example, I scrutinize the dichotomy of genomic causality versus self-organization in 20th and 21st century theories of the generation of form. On the one hand, the generation of patterns and form, as well as the constant outcome in development, are proposed to be causally related to something that is "preformed" in the germ cells, the nucleus of germ cells, or the genome. On the other hand, it is proposed that there is no pre-existing form or information, and development is seen as a process where genuinely new characters emerge from formless matter, either by immaterial "forces of life," or by physical-chemical processes of self-organization. I also argue that these different ways of thinking and the research practices associated with them are not equivalent, and maintain that it is impossible to explain the generation of form and constant outcome of development without the assumption of the transmission of pre-existing information in the form of DNA sequences in the genome. Only in this framework of "preformed" information can "epigenesis" in the form of physical and chemical processes of self-organization play an important role.
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Affiliation(s)
- Ute Deichmann
- Jacques Loeb Centre for the History and Philosophy of Science, Ben-Gurion University of the Negev, Beer Sheva, 8410500, Israel.
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3
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Stephens RK, Miroshnikova YA. Nuclear periphery and its mechanical regulation in cell fate transitions. Curr Opin Struct Biol 2024; 87:102867. [PMID: 38889500 DOI: 10.1016/j.sbi.2024.102867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024]
Abstract
Cell fate changes require rewiring of transcriptional programs to generate functionally specialized cell states. Reconfiguration of transcriptional networks requires overcoming epigenetic barriers imposed by silenced heterochromatin in order to activate lineage-specific genes. Further, cell fate decisions are made in a tissue-specific context, where cells are physically linked to each other as well as to the connective tissue environment. Here, cells are continuously exposed to a multitude of mechanical forces emanating from cellular dynamics in their local microenvironments, for example through cell movements, cell divisions, tissue contractions, or fluid flow. Through their ability to deform cellular structures and activate receptors, mechanical forces can be sensed at the plasma membrane, but also at the nuclear periphery through direct or cytoskeleton-mediated deformation of the nuclear envelope. This deformation and the associated signaling is capable of triggering changes in the mechanical state of the nuclear membranes, the organization and rigidity of the underlying nuclear lamina, compaction state of chromatin, and ultimately transcription. This review focuses on the role of nuclear architecture, particularly the nuclear lamina-chromatin interface, and its mechanical regulation in cell fate decisions as well as its physiological role in development and cellular reprogramming.
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Affiliation(s)
- Rebecca K Stephens
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA. https://twitter.com/BecKateStephens
| | - Yekaterina A Miroshnikova
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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4
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Rashid F, Kabbo SA, Wang N. Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force. Cell Rep 2024; 43:114462. [PMID: 39002538 PMCID: PMC11289711 DOI: 10.1016/j.celrep.2024.114462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/09/2024] [Accepted: 06/23/2024] [Indexed: 07/15/2024] Open
Abstract
Increasing evidence suggests that the mechanics of chromatin and nucleoplasm regulate gene transcription and nuclear function. However, how the chromatin and nucleoplasm sense and respond to forces remains elusive. Here, we employed a strategy of applying forces directly to the chromatin of a cell via a microinjected 200-nm anti-H2B-antibody-coated ferromagnetic nanoparticle (FMNP) and an anti-immunoglobulin G (IgG)-antibody-coated or an uncoated FMNP. The chromatin behaved as a viscoelastic gel-like structure and the nucleoplasm was a softer viscoelastic structure at loading frequencies of 0.1-5 Hz. Protein diffusivity of the chromatin, nucleoplasm, and RNA polymerase II (RNA Pol II) and RNA Pol II activity were upregulated in a chromatin-stretching-dependent manner and stayed upregulated for tens of minutes after force cessation. Chromatin stiffness increased, but the mechanomemory duration of chromatin diffusivity decreased, with substrate stiffness. These findings may provide a mechanomemory mechanism of transcription upregulation and have implications on cell and nuclear functions.
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Affiliation(s)
- Fazlur Rashid
- The Institute for Mechanobiology, Northeastern University, Boston, MA 02115, USA; Department of Bioengineering, College of Engineering, Northeastern University, Boston, MA 02115, USA; Department of Mechanical Science and Engineering, The Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sadia Amin Kabbo
- The Institute for Mechanobiology, Northeastern University, Boston, MA 02115, USA; Department of Bioengineering, College of Engineering, Northeastern University, Boston, MA 02115, USA
| | - Ning Wang
- The Institute for Mechanobiology, Northeastern University, Boston, MA 02115, USA; Department of Bioengineering, College of Engineering, Northeastern University, Boston, MA 02115, USA.
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5
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Munshi R. How Transcription Factor Clusters Shape the Transcriptional Landscape. Biomolecules 2024; 14:875. [PMID: 39062589 PMCID: PMC11274464 DOI: 10.3390/biom14070875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
In eukaryotic cells, gene transcription typically occurs in discrete periods of promoter activity, interspersed with intervals of inactivity. This pattern deviates from simple stochastic events and warrants a closer examination of the molecular interactions that activate the promoter. Recent studies have identified transcription factor (TF) clusters as key precursors to transcriptional bursting. Often, these TF clusters form at chromatin segments that are physically distant from the promoter, making changes in chromatin conformation crucial for promoter-TF cluster interactions. In this review, I explore the formation and constituents of TF clusters, examining how the dynamic interplay between chromatin architecture and TF clustering influences transcriptional bursting. Additionally, I discuss techniques for visualizing TF clusters and provide an outlook on understanding the remaining gaps in this field.
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Affiliation(s)
- Rahul Munshi
- Joseph Henry Laboratories of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
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6
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McCloskey NS, Mammedova A, Liberles DA. PEMPS: a phylogenetic software tool to model the evolution of metabolic pathways. BMC Bioinformatics 2024; 25:244. [PMID: 39026162 PMCID: PMC11264709 DOI: 10.1186/s12859-024-05867-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 07/11/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Metabolic pathways support the enzyme flux that converts input chemicals into energy and cellular building blocks. With a constant rate of input, steady-state flux is achieved when metabolite concentrations and reaction rates remain constant over time. Individual genes undergo mutation, while selection acts on higher level functions of the pathway, such as steady-state flux where applicable. Modeling the evolution of metabolic pathways through mechanistic sets of ordinary differential equations is a piece of the genotype-phenotype map model for interpreting genetic variation and inter-specific differences. Such models can generate distinct compensatory changes and adaptive changes from directional selection, indicating single nucleotide polymorphisms and fixed differences that could affect phenotype. If used for inference, this would ultimately enable detection of selection on metabolic pathways as well as inference of ancestral states for metabolic pathway function. RESULTS A software tool for simulating the evolution of metabolic pathways based upon underlying biochemistry, phylogenetics, and evolutionary considerations is presented. The Python program, Phylogenetic Evolution of Metabolic Pathway Simulator (PEMPS), implements a mutation-selection framework to simulate the evolution of the pathway over a phylogeny by interfacing with COPASI to calculate the steady-state flux of the metabolic network, introducing mutations as alterations in parameter values according to a model, and calculating a fitness score and corresponding probability of fixation based on the change in steady-state flux value(s). Results from simulations are consistent with a priori expectations of fixation probabilities and systematic change in model parameters. CONCLUSIONS The PEMPS program simulates the evolution of a metabolic pathway with a mutation-selection modeling framework based on criteria like steady-state flux that is designed to work with SBML-formatted kinetic models, and Newick-formatted phylogenetic trees. The Python software is run on the Linux command line and is available at https://github.com/nmccloskey/PEMPS .
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Affiliation(s)
- Nicholas S McCloskey
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Ayna Mammedova
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
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7
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Gholamalamdari O, van Schaik T, Wang Y, Kumar P, Zhang L, Zhang Y, Gonzalez GAH, Vouzas AE, Zhao PA, Gilbert DM, Ma J, van Steensel B, Belmont AS. Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590809. [PMID: 38712201 PMCID: PMC11071382 DOI: 10.1101/2024.04.23.590809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Models of nuclear genome organization often propose a binary division into active versus inactive compartments, yet they overlook nuclear bodies. Here we integrated analysis of sequencing and image-based data to compare genome organization in four human cell types relative to three different nuclear locales: the nuclear lamina, nuclear speckles, and nucleoli. Whereas gene expression correlates mostly with nuclear speckle proximity, DNA replication timing correlates with proximity to multiple nuclear locales. Speckle attachment regions emerge as DNA replication initiation zones whose replication timing and gene composition vary with their attachment frequency. Most facultative LADs retain a partially repressed state as iLADs, despite their positioning in the nuclear interior. Knock out of two lamina proteins, Lamin A and LBR, causes a shift of H3K9me3-enriched LADs from lamina to nucleolus, and a reciprocal relocation of H3K27me3-enriched partially repressed iLADs from nucleolus to lamina. Thus, these partially repressed iLADs appear to compete with LADs for nuclear lamina attachment with consequences for replication timing. The nuclear organization in adherent cells is polarized with nuclear bodies and genomic regions segregating both radially and relative to the equatorial plane. Together, our results underscore the importance of considering genome organization relative to nuclear locales for a more complete understanding of the spatial and functional organization of the human genome.
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8
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Uckelmann M, Levina V, Taveneau C, Ng XH, Pandey V, Martinez J, Mendiratta S, Houx J, Boudes M, Venugopal H, Trépout S, Zhang Q, Flanigan S, Li M, Sierecki E, Gambin Y, Das PP, Bell O, de Marco A, Davidovich C. Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.08.539931. [PMID: 38405976 PMCID: PMC10888862 DOI: 10.1101/2023.05.08.539931] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomography, we solved the three-dimensional structure of chromatin condensed by the Polycomb Repressive Complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilised through multivalent dynamic interactions of PRC1 with chromatin. Mechanistically, positively charged residues on the internally disordered regions (IDRs) of CBX8 mask negative charges on the DNA to stabilize the condensed state of chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provides a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.
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9
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Borghi F, Azevedo C, Johnson E, Burden JJ, Saiardi A. A mammalian model reveals inorganic polyphosphate channeling into the nucleolus and induction of a hyper-condensate state. CELL REPORTS METHODS 2024; 4:100814. [PMID: 38981472 PMCID: PMC11294840 DOI: 10.1016/j.crmeth.2024.100814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/23/2024] [Accepted: 06/13/2024] [Indexed: 07/11/2024]
Abstract
Inorganic polyphosphate (polyP) is a ubiquitous polymer that controls fundamental processes. To overcome the absence of a genetically tractable mammalian model, we developed an inducible mammalian cell line expressing Escherichia coli polyphosphate kinase 1 (EcPPK1). Inducing EcPPK1 expression prompted polyP synthesis, enabling validation of polyP analytical methods. Virtually all newly synthesized polyP accumulates within the nucleus, mainly in the nucleolus. The channeled polyP within the nucleolus results in the redistribution of its markers, leading to altered rRNA processing. Ultrastructural analysis reveals electron-dense polyP structures associated with a hyper-condensed nucleolus resulting from an exacerbation of the liquid-liquid phase separation (LLPS) phenomena controlling this membraneless organelle. The selective accumulation of polyP in the nucleoli could be interpreted as an amplification of polyP channeling to where its physiological function takes place. Indeed, quantitative analysis of several mammalian cell lines confirms that endogenous polyP accumulates within the nucleolus.
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Affiliation(s)
- Filipy Borghi
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Cristina Azevedo
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Errin Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Jemima J Burden
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Adolfo Saiardi
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
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10
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Lee J, Simpson L, Li Y, Becker S, Zou F, Zhang X, Bai L. Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579062. [PMID: 38370634 PMCID: PMC10871269 DOI: 10.1101/2024.02.06.579062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Some transcription factors (TFs) can form liquid-liquid phase separated (LLPS) condensates. However, the functions of these TF condensates in 3D genome organization and gene regulation remain elusive. In response to methionine (met) starvation, budding yeast TF Met4 and a few co-activators, including Met32, induce a set of genes involved in met biosynthesis. Here, we show that the endogenous Met4 and Met32 form co-localized puncta-like structures in yeast nuclei upon met depletion. Recombinant Met4 and Met32 form mixed droplets with LLPS properties in vitro. In relation to chromatin, Met4 puncta co-localize with target genes, and at least a subset of these target genes is clustered in 3D in a Met4-dependent manner. A MET3pr-GFP reporter inserted near several native Met4 binding sites becomes co-localized with Met4 puncta and displays enhanced transcriptional activity. A Met4 variant with a partial truncation of an intrinsically disordered region (IDR) shows less puncta formation, and this mutant selectively reduces the reporter activity near Met4 binding sites to the basal level. Overall, these results support a model where Met4 and co-activators form condensates to bring multiple target genes into a vicinity with higher local TF concentrations, which facilitates a strong response to methionine depletion.
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Affiliation(s)
- James Lee
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Leman Simpson
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Yi Li
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Samuel Becker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Fan Zou
- Department of Physics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Physics, The Pennsylvania State University, University Park, PA, 16802, USA
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11
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Cao Z, Wolynes PG. Motorized chain models of the ideal chromosome. Proc Natl Acad Sci U S A 2024; 121:e2407077121. [PMID: 38954553 PMCID: PMC11252987 DOI: 10.1073/pnas.2407077121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/06/2024] [Indexed: 07/04/2024] Open
Abstract
An array of motor proteins consumes chemical energy in setting up the architectures of chromosomes. Here, we explore how the structure of ideal polymer chains is influenced by two classes of motors. The first class which we call "swimming motors" acts to propel the chromatin fiber through three-dimensional space. They represent a caricature of motors such as RNA polymerases. Previously, they have often been described by adding a persistent flow onto Brownian diffusion of the chain. The second class of motors, which we call "grappling motors" caricatures the loop extrusion processes in which segments of chromatin fibers some distance apart are brought together. We analyze these models using a self-consistent variational phonon approximation to a many-body Master equation incorporating motor activities. We show that whether the swimming motors lead to contraction or expansion depends on the susceptibility of the motors, that is, how their activity depends on the forces they must exert. Grappling motors in contrast to swimming motors lead to long-ranged correlations that resemble those first suggested for fractal globules and that are consistent with the effective interactions inferred by energy landscape analyses of Hi-C data on the interphase chromosome.
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Affiliation(s)
- Zhiyu Cao
- Center for Theoretical Biological Physics, Rice University, Houston, TX77005
- Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui230026, China
| | - Peter G. Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX77005
- Department of Chemistry, Rice University, Houston, TX77005
- Department of Physics, Rice University, Houston, TX77005
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12
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Lucini F, Petrini C, Salviato E, Pal K, Rosti V, Gorini F, Santarelli P, Quadri R, Lembo G, Graziano G, Di Patrizio Soldateschi E, Tagliaferri I, Pinatel E, Sebestyén E, Rotta L, Gentile F, Vaira V, Lanzuolo C, Ferrari F. Biochemical properties of chromatin domains define genome compartmentalization. Nucleic Acids Res 2024; 52:e54. [PMID: 38808669 PMCID: PMC11229364 DOI: 10.1093/nar/gkae454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/22/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024] Open
Abstract
Chromatin three-dimensional (3D) organization inside the cell nucleus determines the separation of euchromatin and heterochromatin domains. Their segregation results in the definition of active and inactive chromatin compartments, whereby the local concentration of associated proteins, RNA and DNA results in the formation of distinct subnuclear structures. Thus, chromatin domains spatially confined in a specific 3D nuclear compartment are expected to share similar epigenetic features and biochemical properties, in terms of accessibility and solubility. Based on this rationale, we developed the 4f-SAMMY-seq to map euchromatin and heterochromatin based on their accessibility and solubility, starting from as little as 10 000 cells. Adopting a tailored bioinformatic data analysis approach we reconstruct also their 3D segregation in active and inactive chromatin compartments and sub-compartments, thus recapitulating the characteristic properties of distinct chromatin states. A key novelty of the new method is the capability to map both the linear segmentation of open and closed chromatin domains, as well as their compartmentalization in one single experiment.
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Affiliation(s)
- Federica Lucini
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
| | - Cristiano Petrini
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Elisa Salviato
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Koustav Pal
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Valentina Rosti
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
- ITB-CNR, Institute of Biomedical Technologies, National Research Council, Segrate 20054, Italy
| | - Francesca Gorini
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
| | - Philina Santarelli
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
| | - Roberto Quadri
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
| | - Giovanni Lembo
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Giulia Graziano
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Emanuele Di Patrizio Soldateschi
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
- ITB-CNR, Institute of Biomedical Technologies, National Research Council, Segrate 20054, Italy
| | | | - Eva Pinatel
- ITB-CNR, Institute of Biomedical Technologies, National Research Council, Segrate 20054, Italy
| | - Endre Sebestyén
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Luca Rotta
- IEO, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Francesco Gentile
- Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Valentina Vaira
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Chiara Lanzuolo
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
- ITB-CNR, Institute of Biomedical Technologies, National Research Council, Segrate 20054, Italy
| | - Francesco Ferrari
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
- IGM-CNR, Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, National Research Council, Pavia 27100, Italy
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13
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Gil J, Rosin LF, Navarrete E, Chowdhury N, Abraham S, Cornilleau G, Lei EP, Mozziconacci J, Mirny LA, Muller H, Drinnenberg IA. Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557757. [PMID: 37745315 PMCID: PMC10515926 DOI: 10.1101/2023.09.14.557757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The hallmarks of chromosome organization in multicellular eukaryotes are chromosome territories (CT), chromatin compartments, and insulated domains, including topologically associated domains (TADs). Yet, most of these elements of chromosome organization are derived from analyses of a limited set of model organisms, while large eukaryotic groups, including insects, remain mostly unexplored. Here we combine Hi-C, biophysical modeling, and microscopy to characterize the 3D genome architecture of the silkworm, Bombyx mori. In contrast to other eukaryotes, B. mori chromosomes form highly separated territories. Similar to other eukaryotes, B. mori chromosomes segregate into active A and inactive B compartments, yet unlike in vertebrate systems, contacts between euchromatic A regions appear to be a strong driver of compartmentalization. Remarkably, we also identify a third compartment, called secluded S, with a unique contact pattern. Each S region shows prominent short-range self-contacts and is remarkably devoid of contacts with the rest of the chromosome, including other S regions. Compartment S hosts a unique combination of genetic and epigenetic features, localizes towards the periphery of CTs, and shows developmental plasticity. Biophysical modeling reveals that the formation of such secluded domains requires highly localized loop extrusion within them, along with a low level of extrusion in A and B. Our Hi-C data supports predicted genome-wide and localized extrusion. Such a broad, non-uniform distribution of extruders has not been seen in other organisms. Overall, our analyses support loop extrusion in insects and highlight the evolutionary plasticity of 3D genome organization, driven by a new combination of known processes.
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14
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Li J, Zhang B, Wang ZY. Activity-induced stiffness, entanglement network and dynamic slowdown in unentangled semidilute polymer solutions. SOFT MATTER 2024; 20:5174-5182. [PMID: 38895794 DOI: 10.1039/d4sm00341a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Active polymers possess numerous unique properties that are quite different from those observed in the system of small active molecules due to the intricate interplay between their activity and topological constraints. This study focuses on the conformational changes induced by activity, impacting effective stiffness and crucially influencing entanglement and dynamics. When the two terminals of a linear chain undergo active modification through coupling to a high-temperature thermal bath, there is a substantial increase in chain size, indicating a notable enhancement in effective stiffness. Unlike in passive semiflexible chains where stiffness predominantly affects local bond angles, activity-induced stiffness manifests at the scale of tens of monomers. While activity raises the ambient temperature, it significantly decreases diffusion by over an order of magnitude. The slowdown of the dynamics observed can be attributed to increased entanglement due to chain elongation.
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Affiliation(s)
- Jing Li
- School of Physical Science and Technology, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Micro-Nano Structure Optoelectronics, Chongqing 400715, China
| | - Bokai Zhang
- School of Physical Science and Technology, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Micro-Nano Structure Optoelectronics, Chongqing 400715, China
| | - Zhi-Yong Wang
- School of Physical Science and Technology, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Micro-Nano Structure Optoelectronics, Chongqing 400715, China
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15
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Lakadamyali M. From feulgen to modern methods: marking a century of DNA imaging advances. Histochem Cell Biol 2024; 162:13-22. [PMID: 38753186 PMCID: PMC11227465 DOI: 10.1007/s00418-024-02291-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2024] [Indexed: 07/07/2024]
Abstract
The mystery of how human DNA is compactly packaged into a nucleus-a space a hundred thousand times smaller-while still allowing for the regulation of gene function, has long been one of the greatest enigmas in cell biology. This puzzle is gradually being solved, thanks in part to the advent of new technologies. Among these, innovative genome-labeling techniques combined with high-resolution imaging methods have been pivotal. These methods facilitate the visualization of DNA within intact nuclei and have significantly contributed to our current understanding of genome organization. This review will explore various labeling and imaging approaches that are revolutionizing our understanding of the three-dimensional organization of the genome, shedding light on the relationship between its structure and function.
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Affiliation(s)
- Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
- Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, USA.
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16
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Presman DM, Benítez B, Lafuente AL, Vázquez Lareu A. Chromatin structure and dynamics: one nucleosome at a time. Histochem Cell Biol 2024; 162:79-90. [PMID: 38607419 DOI: 10.1007/s00418-024-02281-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2024] [Indexed: 04/13/2024]
Abstract
Eukaryotic genomes store information on many levels, including their linear DNA sequence, the posttranslational modifications of its constituents (epigenetic modifications), and its three-dimensional folding. Understanding how this information is stored and read requires multidisciplinary collaborations from many branches of science beyond biology, including physics, chemistry, and computer science. Concurrent recent developments in all these areas have enabled researchers to image the genome with unprecedented spatial and temporal resolution. In this review, we focus on what single-molecule imaging and tracking of individual proteins in live cells have taught us about chromatin structure and dynamics. Starting with the basics of single-molecule tracking (SMT), we describe some advantages over in situ imaging techniques and its current limitations. Next, we focus on single-nucleosome studies and what they have added to our current understanding of the relationship between chromatin dynamics and transcription. In celebration of Robert Feulgen's ground-breaking discovery that allowed us to start seeing the genome, we discuss current models of chromatin structure and future challenges ahead.
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Affiliation(s)
- Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.
| | - Belén Benítez
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
- Instituto de Química Biológica (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Agustina L Lafuente
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Alejo Vázquez Lareu
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
- Instituto de Química Biológica (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
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17
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Misteli T. Seeing genomes. Histochem Cell Biol 2024; 162:1-2. [PMID: 38850309 DOI: 10.1007/s00418-024-02301-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2024]
Affiliation(s)
- Tom Misteli
- National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA.
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18
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Phan LMU, Yeo WH, Zhang HF, Huang S. Dynamic chromosome association with nuclear organelles in living cells. Histochem Cell Biol 2024; 162:149-159. [PMID: 38811432 DOI: 10.1007/s00418-024-02288-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2024] [Indexed: 05/31/2024]
Abstract
The development of progressively sophisticated tools complemented by the integration of live cell imaging enhances our understanding of the four-dimensional (4D) nucleome, revealing elaborate molecular interactions and chromatin states. Yet, the dynamics of chromosomes in relation to nuclear organelles or to each other across cell cycle in living cells are underexplored. We have developed photoconvertible GFP H3-Dendra2 stably expressing in PC3M cells. The nuclear lamina and perinucleolar associated heterochromatin or diffuse chromosome regions were photoconverted through a single-point activation using a confocal microscope. The results demonstrated a dynamic nature for both types of chromosomes in the same cell cycle and across mitosis. While some chromosome domains were heritably associated with either nuclear lamina or nucleoli, others changed alliance to different nuclear organelles postmitotically. In addition, co-photoconverted chromosome domains often do not stay together within the same cell cycle and across mitosis, suggesting a transient nature of chromosome neighborhoods. Long-range spreading and movement of chromosomes were also observed. Interestingly, when cells were treated with a low concentration of actinomycin D that inhibits Pol I transcription through intercalating GC-rich DNA, chromosome movement was significantly blocked. Treatment with another Pol I inhibitor, metarrestin, which does not impact DNA, had little effect on the movement, suggesting that the DNA structure itself plays a role in chromosome dynamics. Furthermore, inhibition of Pol II transcription with α-amanitin also reduced the chromosome movement, demonstrating that Pol II, but not Pol I transcription, is important for chromosome dynamics in the nucleus.
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Affiliation(s)
- Lam Minh Uyen Phan
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, USA
| | - Wei-Hong Yeo
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Hao F Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Sui Huang
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, USA.
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19
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Semeigazin A, Iida S, Minami K, Tamura S, Ide S, Higashi K, Toyoda A, Kurokawa K, Maeshima K. Behaviors of nucleosomes with mutant histone H4s in euchromatic domains of living human cells. Histochem Cell Biol 2024; 162:23-40. [PMID: 38743310 DOI: 10.1007/s00418-024-02293-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2024] [Indexed: 05/16/2024]
Abstract
Since Robert Feulgen first stained DNA in the cell, visualizing genome chromatin has been a central issue in cell biology to uncover how chromatin is organized and behaves in the cell. To approach this issue, we have developed single-molecule imaging of nucleosomes, a basic unit of chromatin, to unveil local nucleosome behavior in living cells. In this study, we investigated behaviors of nucleosomes with various histone H4 mutants in living HeLa cells to address the role of H4 tail acetylation, including H4K16Ac and others, which are generally associated with more transcriptionally active chromatin regions. We ectopically expressed wild-type (wt) or mutated H4s (H4K16 point; H4K5,8,12,16 quadruple; and H4 tail deletion) fused with HaloTag in HeLa cells. Cells that expressed wtH4-Halo, H4K16-Halo mutants, and multiple H4-Halo mutants had euchromatin-concentrated distribution. Consistently, the genomic regions of the wtH4-Halo nucleosomes corresponded to Hi-C contact domains (or topologically associating domains, TADs) with active chromatin marks (A-compartment). Utilizing single-nucleosome imaging, we found that none of the H4 deacetylation or acetylation mimicked H4 mutants altered the overall local nucleosome motion. This finding suggests that H4 mutant nucleosomes embedded in the condensed euchromatic domains with excess endogenous H4 nucleosomes cannot cause an observable change in the local motion. Interestingly, H4 with four lysine-to-arginine mutations displayed a substantial freely diffusing fraction in the nucleoplasm, whereas H4 with a truncated N-terminal tail was incorporated in heterochromatic regions as well as euchromatin. Our study indicates the power of single-nucleosome imaging to understand individual histone/nucleosome behavior reflecting chromatin environments in living cells.
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Affiliation(s)
- Adilgazy Semeigazin
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Koichi Higashi
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Ken Kurokawa
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan.
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20
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Almansour F, Keikhosravi A, Pegoraro G, Misteli T. Allele-level visualization of transcription and chromatin by high-throughput imaging. Histochem Cell Biol 2024; 162:65-77. [PMID: 38724854 PMCID: PMC11227451 DOI: 10.1007/s00418-024-02289-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2024] [Indexed: 05/21/2024]
Abstract
The spatial arrangement of the genome within the nucleus is a pivotal aspect of cellular organization and function with implications for gene expression and regulation. While all genome organization features, such as loops, domains, and radial positioning, are nonrandom, they are characterized by a high degree of single-cell variability. Imaging approaches are ideally suited to visualize, measure, and study single-cell heterogeneity in genome organization. Here, we describe two methods for the detection of DNA and RNA of individual gene alleles by fluorescence in situ hybridization (FISH) in a high-throughput format. We have optimized combined DNA/RNA FISH approaches either using simultaneous or sequential detection of DNA and nascent RNA. These optimized DNA and RNA FISH protocols were implemented in a 384-well plate format alongside automated image and data analysis and enable accurate detection of individual gene alleles and their gene expression status across a large cell population. We successfully visualized MYC and EGFR DNA and nascent RNA with allele-level resolution in multiple cell types, and we determined the radial position of active and inactive MYC and EGFR alleles. These optimized DNA/RNA detection approaches are versatile and sensitive tools for mapping of chromatin features and gene activity at the single-allele level and at high throughput.
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Affiliation(s)
- Faisal Almansour
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical School, Washington, DC, 20057, USA
| | - Adib Keikhosravi
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA.
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21
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Kotb NM, Ulukaya G, Chavan A, Nguyen SC, Proskauer L, Joyce EF, Hasson D, Jagannathan M, Rangan P. Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis. Genes Dev 2024; 38:436-454. [PMID: 38866556 PMCID: PMC11216175 DOI: 10.1101/gad.351402.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 05/21/2024] [Indexed: 06/14/2024]
Abstract
Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ cell genes during differentiation, and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. Surprisingly, we found that genome organization also contributes to NPC formation, mediated by the transcription factor Stonewall (Stwl). As GSCs differentiate, Stwl accumulates at boundaries between silenced and active gene compartments. Stwl at these boundaries plays a pivotal role in transitioning germ cell genes into a silenced state and activating a group of oocyte genes and nucleoporins (Nups). The upregulation of these Nups during differentiation is crucial for NPC formation and further genome organization. Thus, cross-talk between genome architecture and NPCs is essential for successful cell fate transitions.
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Affiliation(s)
- Noor M Kotb
- Department of Biomedical Sciences/Wadsworth Center, University at Albany State University of New York (SUNY), Albany, New York 12202, USA
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York 12202, USA
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
| | - Gulay Ulukaya
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
- Bioinformatics for Next-Generation Sequencing (BiNGS) Core, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Ankita Chavan
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8092 Zürich, Switzerland
| | - Son C Nguyen
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Lydia Proskauer
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York 12202, USA
| | - Eric F Joyce
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dan Hasson
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
- Bioinformatics for Next-Generation Sequencing (BiNGS) Core, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Madhav Jagannathan
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8092 Zürich, Switzerland
| | - Prashanth Rangan
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA;
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22
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Benchorin G, Cho RJ, Li MJ, Molotkova N, Kohwi M. Dan forms condensates in neuroblasts and regulates nuclear architecture and progenitor competence in vivo. Nat Commun 2024; 15:5097. [PMID: 38877037 PMCID: PMC11178893 DOI: 10.1038/s41467-024-49326-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/30/2024] [Indexed: 06/16/2024] Open
Abstract
Genome organization is thought to underlie cell type specific gene expression, yet how it is regulated in progenitors to produce cellular diversity is unknown. In Drosophila, a developmentally-timed genome reorganization in neural progenitors terminates competence to produce early-born neurons. These events require downregulation of Distal antenna (Dan), part of the conserved pipsqueak DNA-binding superfamily. Here we find that Dan forms liquid-like condensates with high protein mobility, and whose size and subnuclear distribution are balanced with its DNA-binding. Further, we identify a LARKS domain, a structural motif associated with condensate-forming proteins. Deleting just 13 amino acids from LARKS abrogates Dan's ability to retain the early-born neural fate gene, hunchback, in the neuroblast nuclear interior and maintain competence in vivo. Conversely, domain-swapping with LARKS from known phase-separating proteins rescues Dan's effects on competence. Together, we provide in vivo evidence for condensate formation and the regulation of progenitor nuclear architecture underlying neuronal diversification.
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Affiliation(s)
- Gillie Benchorin
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Richard Jangwon Cho
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Neuroscience, Columbia University, New York, NY, USA
| | - Maggie Jiaqi Li
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Neuroscience, Columbia University, New York, NY, USA
| | - Natalia Molotkova
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Neuroscience, Columbia University, New York, NY, USA
| | - Minoree Kohwi
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
- Department of Neuroscience, Columbia University, New York, NY, USA.
- Kavli Institute for Brain Science, Columbia University, New York, NY, USA.
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23
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Sun W, Xiong D, Ouyang J, Xiao X, Jiang Y, Wang Y, Li S, Xie Z, Wang J, Tang Z, Zhang Q. Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia. Nat Commun 2024; 15:5048. [PMID: 38871723 DOI: 10.1038/s41467-024-49376-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 06/04/2024] [Indexed: 06/15/2024] Open
Abstract
Despite the advent of genomic sequencing, molecular diagnosis remains unsolved in approximately half of patients with Mendelian disorders, largely due to unclarified functions of noncoding regions and the difficulty in identifying complex structural variations. In this study, we map a unique form of central iris hypoplasia in a large family to 6q15-q23.3 and 18p11.31-q12.1 using a genome-wide linkage scan. Long-read sequencing reveals a balanced translocation t(6;18)(q22.31;p11.22) with intergenic breakpoints. By performing Hi-C on induced pluripotent stem cells from a patient, we identify two chromatin topologically associating domains spanning across the breakpoints. These alterations lead the ectopic chromatin interactions between APCDD1 on chromosome 18 and enhancers on chromosome 6, resulting in upregulation of APCDD1. Notably, APCDD1 is specifically localized in the iris of human eyes. Our findings demonstrate that noncoding structural variations can lead to Mendelian diseases by disrupting the 3D genome structure and resulting in altered gene expression.
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Affiliation(s)
- Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Dan Xiong
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiamin Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yingwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Ziying Xie
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Zhonghui Tang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
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24
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Venu V, Roth C, Adikari SH, Small EM, Starkenburg SR, Sanbonmatsu KY, Steadman CR. Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection. Commun Biol 2024; 7:721. [PMID: 38862613 PMCID: PMC11166932 DOI: 10.1038/s42003-024-06389-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 05/27/2024] [Indexed: 06/13/2024] Open
Abstract
The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To unravel this interplay, here we provide a comprehensive investigation of simultaneous host chromatin structural (via Hi-C and ATAC-seq) and functional changes (via RNA-seq) in response to vaccinia virus infection. Over time, infection significantly impacts global and local chromatin structure by increasing long-range intra-chromosomal interactions and B compartmentalization and by decreasing chromatin accessibility and inter-chromosomal interactions. Local accessibility changes are independent of broad-scale chromatin compartment exchange (~12% of the genome), underscoring potential independent mechanisms for global and local chromatin reorganization. While infection structurally condenses the host genome, there is nearly equal bidirectional differential gene expression. Despite global weakening of intra-TAD interactions, functional changes including downregulated immunity genes are associated with alterations in local accessibility and loop domain restructuring. Therefore, chromatin accessibility and local structure profiling provide impactful predictions for host responses and may improve development of efficacious anti-viral counter measures including the optimization of vaccine design.
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Affiliation(s)
- Vrinda Venu
- Climate, Ecology & Environment Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Cullen Roth
- Genomics & Bioanalytics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Samantha H Adikari
- Biochemistry & Biotechnology Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Eric M Small
- Climate, Ecology & Environment Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Shawn R Starkenburg
- Genomics & Bioanalytics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Christina R Steadman
- Climate, Ecology & Environment Group, Los Alamos National Laboratory, Los Alamos, NM, USA.
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25
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Garate X, Gómez-García PA, Merino MF, Angles MC, Zhu C, Castells-García A, Ed-Daoui I, Martin L, Ochiai H, Neguembor MV, Cosma MP. The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition. Nucleic Acids Res 2024:gkae476. [PMID: 38850157 DOI: 10.1093/nar/gkae476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024] Open
Abstract
During early development, gene expression is tightly regulated. However, how genome organization controls gene expression during the transition from naïve embryonic stem cells to epiblast stem cells is still poorly understood. Using single-molecule microscopy approaches to reach nanoscale resolution, we show that genome remodeling affects gene transcription during pluripotency transition. Specifically, after exit from the naïve pluripotency state, chromatin becomes less compacted, and the OCT4 transcription factor has lower mobility and is more bound to its cognate sites. In epiblast cells, the active transcription hallmark, H3K9ac, decreases within the Oct4 locus, correlating with reduced accessibility of OCT4 and, in turn, with reduced expression of Oct4 nascent RNAs. Despite the high variability in the distances between active pluripotency genes, distances between Nodal and Oct4 decrease during epiblast specification. In particular, highly expressed Oct4 alleles are closer to nuclear speckles during all stages of the pluripotency transition, while only a distinct group of highly expressed Nodal alleles are in close proximity to Oct4 when associated with a nuclear speckle in epiblast cells. Overall, our results provide new insights into the role of the spatiotemporal genome remodeling during mouse pluripotency transition and its correlation with the expression of key pluripotency genes.
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Affiliation(s)
- Ximena Garate
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Pablo Aurelio Gómez-García
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Manuel Fernández Merino
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Marta Cadevall Angles
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Chenggan Zhu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Alvaro Castells-García
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 Zhongshan Er Road, Yuexiu district, 510080 Guangzhou, China
| | - Ilyas Ed-Daoui
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 Zhongshan Er Road, Yuexiu district, 510080 Guangzhou, China
| | - Laura Martin
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Hiroshi Ochiai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046, Japan
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 Zhongshan Er Road, Yuexiu district, 510080 Guangzhou, China
- ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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26
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Plante I, West DW, Weeks J, Risca VI. Simulation of Radiation-Induced DNA Damage and Protection by Histones Using the Code RITRACKS. BIOTECH 2024; 13:17. [PMID: 38921049 PMCID: PMC11201919 DOI: 10.3390/biotech13020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/10/2024] [Accepted: 05/31/2024] [Indexed: 06/27/2024] Open
Abstract
(1) Background: DNA damage is of great importance in the understanding of the effects of ionizing radiation. Various types of DNA damage can result from exposure to ionizing radiation, with clustered types considered the most important for radiobiological effects. (2) Methods: The code RITRACKS (Relativistic Ion Tracks), a program that simulates stochastic radiation track structures, was used to simulate DNA damage by photons and ions spanning a broad range of linear energy transfer (LET) values. To perform these simulations, the transport code was modified to include cross sections for the interactions of ions or electrons with DNA and amino acids for ionizations, dissociative electron attachment, and elastic collisions. The radiochemistry simulations were performed using a step-by-step algorithm that follows the evolution of all particles in time, including reactions between radicals and DNA structures and amino acids. Furthermore, detailed DNA damage events, such as base pair positions, DNA fragment lengths, and fragment yields, were recorded. (3) Results: We report simulation results using photons and the ions 1H+, 4He2+, 12C6+, 16O8+, and 56Fe26+ at various energies, covering LET values from 0.3 to 164 keV/µm, and performed a comparison with other codes and experimental results. The results show evidence of DNA protection from damage at its points of contacts with histone proteins. (4) Conclusions: RITRACKS can provide a framework for studying DNA damage from a variety of ionizing radiation sources with detailed representations of DNA at the atomic scale, DNA-associated proteins, and resulting DNA damage events and statistics, enabling a broader range of future comparisons with experiments such as those based on DNA sequencing.
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Affiliation(s)
| | - Devany W. West
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY 10065, USA; (D.W.W.); (V.I.R.)
| | - Jason Weeks
- NASA Johnson Space Center, Houston, TX 77058, USA;
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY 10065, USA; (D.W.W.); (V.I.R.)
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27
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Wang X, Yue F. Hijacked enhancer-promoter and silencer-promoter loops in cancer. Curr Opin Genet Dev 2024; 86:102199. [PMID: 38669773 DOI: 10.1016/j.gde.2024.102199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/19/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024]
Abstract
Recent work has shown that besides inducing fusion genes, structural variations (SVs) can also contribute to oncogenesis by disrupting the three-dimensional genome organization and dysregulating gene expression. At the chromatin-loop level, SVs can relocate enhancers or silencers from their original genomic loci to activate oncogenes or repress tumor suppressor genes. On a larger scale, different types of alterations in topologically associating domains (TADs) have been reported in cancer, such as TAD expansion, shuffling, and SV-induced neo-TADs. Furthermore, the transformation from normal cells to cancerous cells is usually coupled with active or repressive compartmental switches, and cancer-specific compartments have been proposed. This review discusses the sites, and the other latest advances in studying how SVs disrupt higher-order genome structure in cancer, which in turn leads to oncogene dysregulation. We also highlight the clinical implications of these changes and the challenges ahead in this field.
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Affiliation(s)
- Xiaotao Wang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China; Shanghai Key Laboratory of Reproduction and Development, Shanghai, China.
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, Illinois, USA; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois, USA.
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28
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Wu H, Zhang J, Jian F, Chen JP, Zheng Y, Tan L, Sunney Xie X. Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice. Nat Methods 2024; 21:974-982. [PMID: 38622459 PMCID: PMC11166570 DOI: 10.1038/s41592-024-02239-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/07/2024] [Indexed: 04/17/2024]
Abstract
The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding a genome's structure-function relationship, yet this is challenging for existing methods. Here we present 'Linking mRNA to Chromatin Architecture (LiMCA)', which jointly profiles the 3D genome and transcriptome with exceptional sensitivity and from low-input materials. Combining LiMCA and our high-resolution scATAC-seq assay, METATAC, we successfully characterized chromatin accessibility, as well as paired 3D genome structures and gene expression information, of individual developing olfactory sensory neurons. We expanded the repertoire of known olfactory receptor (OR) enhancers and discovered unexpected rules of their dynamics: OR genes and their enhancers are most accessible during early differentiation. Furthermore, we revealed the dynamic spatial relationship between ORs and enhancers behind stepwise OR expression. These findings offer valuable insights into how 3D connectivity of ORs and enhancers dynamically orchestrate the 'one neuron-one receptor' selection process.
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Affiliation(s)
- Honggui Wu
- Biomedical Pioneering Innovation Center (BIOPIC), and School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
| | - Jiankun Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), and School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
| | - Fanchong Jian
- Biomedical Pioneering Innovation Center (BIOPIC), and School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jinxin Phaedo Chen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Yinghui Zheng
- Biomedical Pioneering Innovation Center (BIOPIC), and School of Life Sciences, Peking University, Beijing, China
| | - Longzhi Tan
- Department of Neurobiology, Stanford University, Stanford, CA, USA.
| | - X Sunney Xie
- Biomedical Pioneering Innovation Center (BIOPIC), and School of Life Sciences, Peking University, Beijing, China.
- Changping Laboratory, Beijing, China.
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29
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Rudnizky S, Murray PJ, Wolfe CH, Ha T. Single-Macromolecule Studies of Eukaryotic Genomic Maintenance. Annu Rev Phys Chem 2024; 75:209-230. [PMID: 38382570 DOI: 10.1146/annurev-physchem-090722-010601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Genomes are self-organized and self-maintained as long, complex macromolecules of chromatin. The inherent heterogeneity, stochasticity, phase separation, and chromatin dynamics of genome operation make it challenging to study genomes using ensemble methods. Various single-molecule force-, fluorescent-, and sequencing-based techniques rooted in different disciplines have been developed to fill critical gaps in the capabilities of bulk measurements, each providing unique, otherwise inaccessible, insights into the structure and maintenance of the genome. Capable of capturing molecular-level details about the organization, conformational changes, and packaging of genetic material, as well as processive and stochastic movements of maintenance factors, a single-molecule toolbox provides an excellent opportunity for collaborative research to understand how genetic material functions in health and malfunctions in disease. In this review, we discuss novel insights brought to genomic sciences by single-molecule techniques and their potential to continue to revolutionize the field-one molecule at a time.
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Affiliation(s)
- Sergei Rudnizky
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Peter J Murray
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA;
| | - Clara H Wolfe
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
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30
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Vivo M, Rosti V, Cervone S, Lanzuolo C. Chromatin plasticity in mechanotransduction. Curr Opin Cell Biol 2024; 88:102376. [PMID: 38810318 DOI: 10.1016/j.ceb.2024.102376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 05/31/2024]
Abstract
Living organisms can detect and respond to physical forces at the cellular level. The pathways that transmit these forces to the nucleus allow cells to react quickly and consistently to environmental changes. Mechanobiology involves the interaction between physical forces and biological processes and is crucial for driving embryonic development and adapting to environmental cues during adulthood. Molecular studies have shown that cells can sense mechanical signals directly through membrane receptors linked to the cytoskeleton or indirectly through biochemical cascades that can influence gene expression for environmental adaptation. This review will explore the role of epigenetic modifications, emphasizing the 3D genome architecture and nuclear structures as responders to mechanical stimuli, which ensure cellular memory and adaptability. Understanding how mechanical cues are transduced and regulate cell functioning, governing processes such as cell programming and reprogramming, is essential for advancing our knowledge of human diseases.
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Affiliation(s)
- Maria Vivo
- Università degli Studi di Salerno, Fisciano, Italy.
| | - Valentina Rosti
- Institute of Biomedical Technologies, National Research Council (CNR), Milan, Italy; INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Sara Cervone
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Chiara Lanzuolo
- Institute of Biomedical Technologies, National Research Council (CNR), Milan, Italy; INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy.
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31
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Doležalová A, Beránková D, Koláčková V, Hřibová E. Insight into chromatin compaction and spatial organization in rice interphase nuclei. FRONTIERS IN PLANT SCIENCE 2024; 15:1358760. [PMID: 38863533 PMCID: PMC11165205 DOI: 10.3389/fpls.2024.1358760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Chromatin organization and its interactions are essential for biological processes, such as DNA repair, transcription, and DNA replication. Detailed cytogenetics data on chromatin conformation, and the arrangement and mutual positioning of chromosome territories in interphase nuclei are still widely missing in plants. In this study, level of chromatin condensation in interphase nuclei of rice (Oryza sativa) and the distribution of chromosome territories (CTs) were analyzed. Super-resolution, stimulated emission depletion (STED) microscopy showed different levels of chromatin condensation in leaf and root interphase nuclei. 3D immuno-FISH experiments with painting probes specific to chromosomes 9 and 2 were conducted to investigate their spatial distribution in root and leaf nuclei. Six different configurations of chromosome territories, including their complete association, weak association, and complete separation, were observed in root meristematic nuclei, and four configurations were observed in leaf nuclei. The volume of CTs and frequency of their association varied between the tissue types. The frequency of association of CTs specific to chromosome 9, containing NOR region, is also affected by the activity of the 45S rDNA locus. Our data suggested that the arrangement of chromosomes in the nucleus is connected with the position and the size of the nucleolus.
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Affiliation(s)
| | | | | | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Science, Centre of Plants Structural and Functional Genomics, Olomouc, Czechia
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32
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Xu J, Xu X, Huang D, Luo Y, Lin L, Bai X, Zheng Y, Yang Q, Cheng Y, Huang A, Shi J, Bo X, Gu J, Chen H. A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains. Nat Commun 2024; 15:4376. [PMID: 38782890 PMCID: PMC11116433 DOI: 10.1038/s41467-024-48593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the inner and smaller subTADs not only manifest cell-to-cell variability, but also precisely regulate transcription and differentiation. Although over 20 TAD callers are able to detect TAD, their usability in biomedicine is confined by a disagreement of outputs and a limit in understanding TAD hierarchy. We compare 13 computational tools across various conditions and develop a metric to evaluate the similarity of TAD hierarchy. Although outputs of TAD hierarchy at each level vary among callers, data resolutions, sequencing depths, and matrices normalization, they are more consistent when they have a higher similarity of larger TADs. We present comprehensive benchmarking of TAD hierarchy callers and operational guidance to researchers of life science researchers. Moreover, by simulating the mixing of different types of cells, we confirm that TAD hierarchy is generated not simply from stacking Hi-C heatmaps of heterogeneous cells. Finally, we propose an air conditioner model to decipher the role of TAD hierarchy in transcription.
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Affiliation(s)
- Jingxuan Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiang Xu
- Academy of Military Medical Science, Beijing, 100850, China
| | - Dandan Huang
- Department of Oncology, Peking University Shougang Hospital, Beijing, China
- Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Diseases, Peking University Health Science Center, Beijing, China
| | - Yawen Luo
- Academy of Military Medical Science, Beijing, 100850, China
| | - Lin Lin
- Academy of Military Medical Science, Beijing, 100850, China
- School of Computer Science and Information Technology& KLAS, Northeast Normal University, Changchun, China
| | - Xuemei Bai
- Academy of Military Medical Science, Beijing, 100850, China
| | - Yang Zheng
- Academy of Military Medical Science, Beijing, 100850, China
| | - Qian Yang
- Academy of Military Medical Science, Beijing, 100850, China
| | - Yu Cheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - An Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jingyi Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiaochen Bo
- Academy of Military Medical Science, Beijing, 100850, China.
| | - Jin Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
- Department of Oncology, Peking University Shougang Hospital, Beijing, China.
- Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Diseases, Peking University Health Science Center, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Peking University International Cancer Institute, Beijing, China.
| | - Hebing Chen
- Academy of Military Medical Science, Beijing, 100850, China.
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33
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Vorobyeva NE, Krasnov AN, Erokhin M, Chetverina D, Mazina M. Su(Hw) interacts with Combgap to establish long-range chromatin contacts. Epigenetics Chromatin 2024; 17:17. [PMID: 38773468 PMCID: PMC11106861 DOI: 10.1186/s13072-024-00541-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Insulator-binding proteins (IBPs) play a critical role in genome architecture by forming and maintaining contact domains. While the involvement of several IBPs in organising chromatin architecture in Drosophila has been described, the specific contribution of the Suppressor of Hairy wings (Su(Hw)) insulator-binding protein to genome topology remains unclear. RESULTS In this study, we provide evidence for the existence of long-range interactions between chromatin bound Su(Hw) and Combgap, which was first characterised as Polycomb response elements binding protein. Loss of Su(Hw) binding to chromatin results in the disappearance of Su(Hw)-Combgap long-range interactions and in a decrease in spatial self-interactions among a subset of Su(Hw)-bound genome sites. Our findings suggest that Su(Hw)-Combgap long-range interactions are associated with active chromatin rather than Polycomb-directed repression. Furthermore, we observe that the majority of transcription start sites that are down-regulated upon loss of Su(Hw) binding to chromatin are located within 2 kb of Combgap peaks and exhibit Su(Hw)-dependent changes in Combgap and transcriptional regulators' binding. CONCLUSIONS This study demonstrates that Su(Hw) insulator binding protein can form long-range interactions with Combgap, Polycomb response elements binding protein, and that these interactions are associated with active chromatin factors rather than with Polycomb dependent repression.
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Affiliation(s)
- Nadezhda E Vorobyeva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Alexey N Krasnov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Marina Mazina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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34
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Li Z, Sun L, Xu X, Liu Y, He H, Deng XW. Light control of three-dimensional chromatin organization in soybean. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38762905 DOI: 10.1111/pbi.14372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/24/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
Higher-order chromatin structure is critical for regulation of gene expression. In plants, light profoundly affects the morphogenesis of emerging seedlings as well as global gene expression to ensure optimal adaptation to environmental conditions. However, the changes and functional significance of chromatin organization in response to light during seedling development are not well documented. We constructed Hi-C contact maps for the cotyledon, apical hook and hypocotyl of soybean subjected to dark and light conditions. The resulting high-resolution Hi-C contact maps identified chromosome territories, A/B compartments, A/B sub-compartments, TADs (Topologically Associated Domains) and chromatin loops in each organ. We observed increased chromatin compaction under light and we found that domains that switched from B sub-compartments in darkness to A sub-compartments under light contained genes that were activated during photomorphogenesis. At the local scale, we identified a group of TADs constructed by gene clusters consisting of different numbers of Small Auxin-Upregulated RNAs (SAURs), which exhibited strict co-expression in the hook and hypocotyl in response to light stimulation. In the hypocotyl, RNA polymerase II (RNAPII) regulated the transcription of a SAURs cluster under light via TAD condensation. Our results suggest that the 3D genome is involved in the regulation of light-related gene expression in a tissue-specific manner.
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Affiliation(s)
- Zhu Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Linhua Sun
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Xiao Xu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
| | - Yutong Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
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35
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Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z, Ma J. GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Nat Genet 2024:10.1038/s41588-024-01745-3. [PMID: 38744973 DOI: 10.1038/s41588-024-01745-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 04/05/2024] [Indexed: 05/16/2024]
Abstract
The organization of mammalian genomes features a complex, multiscale three-dimensional (3D) architecture, whose functional significance remains elusive because of limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we introduce genome architecture and gene expression by sequencing (GAGE-seq), a scalable, robust single-cell co-assay measuring 3D genome structure and transcriptome simultaneously within the same cell. Applied to mouse brain cortex and human bone marrow CD34+ cells, GAGE-seq characterized the intricate relationships between 3D genome and gene expression, showing that multiscale 3D genome features inform cell-type-specific gene expression and link regulatory elements to target genes. Integration with spatial transcriptomic data revealed in situ 3D genome variations in mouse cortex. Observations in human hematopoiesis unveiled discordant changes between 3D genome organization and gene expression, underscoring a complex, temporal interplay at the single-cell level. GAGE-seq provides a powerful, cost-effective approach for exploring genome structure and gene expression relationships at the single-cell level across diverse biological contexts.
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Affiliation(s)
- Tianming Zhou
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ruochi Zhang
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deyong Jia
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Raymond T Doty
- Division of Hematology and Oncology, Department of Medicine/Fred Hutch Cancer Center, University of Washington, Seattle, WA, USA
| | - Adam D Munday
- Division of Hematology and Oncology, Department of Medicine/Fred Hutch Cancer Center, University of Washington, Seattle, WA, USA
| | - Daniel Gao
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Chemistry, Pomona College, Claremont, CA, USA
| | - Li Xin
- Department of Urology, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Janis L Abkowitz
- Division of Hematology and Oncology, Department of Medicine/Fred Hutch Cancer Center, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Zhijun Duan
- Division of Hematology and Oncology, Department of Medicine/Fred Hutch Cancer Center, University of Washington, Seattle, WA, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.
| | - Jian Ma
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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Chiariello AM, Abraham A, Bianco S, Esposito A, Fontana A, Vercellone F, Conte M, Nicodemi M. Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells. Nat Commun 2024; 15:4014. [PMID: 38740770 PMCID: PMC11091192 DOI: 10.1038/s41467-024-48370-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
SARS-CoV-2 can re-structure chromatin organization and alter the epigenomic landscape of the host genome, but the mechanisms that produce such changes remain unclear. Here, we use polymer physics to investigate how the chromatin of the host genome is re-organized upon infection with SARS-CoV-2. We show that re-structuring of A/B compartments can be explained by a re-modulation of intra-compartment homo-typic affinities, which leads to the weakening of A-A interactions and the enhancement of A-B mixing. At the TAD level, re-arrangements are physically described by a reduction in the loop extrusion activity coupled with an alteration of chromatin phase-separation properties, resulting in more intermingling between different TADs and a spread in space of the TADs themselves. In addition, the architecture of loci relevant to the antiviral interferon response, such as DDX58 or IFIT, becomes more variable within the 3D single-molecule population of the infected model, suggesting that viral infection leads to a loss of chromatin structural specificity. Analysing the time trajectories of pairwise gene-enhancer and higher-order contacts reveals that this variability derives from increased fluctuations in the chromatin dynamics of infected cells. This suggests that SARS-CoV-2 alters gene regulation by impacting the stability of the contact network in time.
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Affiliation(s)
- Andrea M Chiariello
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy.
| | - Alex Abraham
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy
| | - Simona Bianco
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy
| | - Andrea Esposito
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy
| | - Andrea Fontana
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy
| | - Francesca Vercellone
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell'Informazione - DIETI, Università degli Studi di Napoli Federico II, and INFN Napoli, Via Claudio 21, 80125, Naples, Italy
| | - Mattia Conte
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy
| | - Mario Nicodemi
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy.
- Berlin Institute for Medical Systems Biology at the Max Delbruck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
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Banerjee DS, Chigumira T, Lackner RM, Kratz JC, Chenoweth DM, Banerjee S, Zhang H. Interplay of condensate material properties and chromatin heterogeneity governs nuclear condensate ripening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.593010. [PMID: 38766065 PMCID: PMC11100695 DOI: 10.1101/2024.05.07.593010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Biomolecular condensates play pivotal roles in many cellular processes, yet predicting condensate growth dynamics within the complex intracellular environment is challenging. While chromatin mechanics are known to influence condensate coarsening in the nucleus, the effect of condensate properties remains unclear. Our study demonstrates that the interplay between condensate properties and chromatin mechanics dictates condensate growth dynamics. Through chemical dimerization, we induced condensates of various properties in the cell nuclei, revealing distinct growth mechanisms: diffusion-driven or ripening-dominated. To explain experimental observations, we developed a quantitative theory that uncovers the role of chromatin in modulating condensate growth via size-dependent pressure. We find that surface tension is a critical factor in determining whether condensates undergo elastic or Ostwald ripening. Our model predicts that different condensates are affected differently by chromatin heterogeneity, validated by experimentally perturbing chromatin organization. Taken together, our work elucidates how condensate surface tension and chromatin heterogeneity govern nuclear condensate ripening.
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Affiliation(s)
- Deb Sankar Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Present address: James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Tafadzwa Chigumira
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Rachel M Lackner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Josiah C Kratz
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Present address: Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - David M Chenoweth
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Huaiying Zhang
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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38
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Ames A, Seman M, Larkin A, Raiymbek G, Chen Z, Levashkevich A, Kim B, Biteen JS, Ragunathan K. Epigenetic memory is governed by an effector recruitment specificity toggle in Heterochromatin Protein 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.28.569027. [PMID: 38077059 PMCID: PMC10705379 DOI: 10.1101/2023.11.28.569027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
HP1 proteins are essential for establishing and maintaining transcriptionally silent heterochromatin. They dimerize, forming a binding interface to recruit diverse chromatin-associated factors. HP1 proteins are specialized and rapidly evolve, but the extent of variation required to achieve functional specialization is unknown. To investigate how changes in amino acid sequence impacts epigenetic inheritance, we performed a targeted mutagenesis screen of the S. pombe HP1 homolog, Swi6. Substitutions within an auxiliary surface adjacent to the HP1 dimerization interface produced Swi6 variants with divergent maintenance properties. Remarkably, substitutions at a single amino acid position led to the persistent gain or loss of epigenetic inheritance. These substitutions increased Swi6 chromatin occupancy in vivo and altered Swi6-protein interactions that reprogram H3K9me maintenance. We show that relatively minor changes in Swi6 amino acid composition can lead to profound changes in epigenetic inheritance which provides a redundant mechanism to evolve novel effector specificity. .
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Lerra L, Panatta M, Bär D, Zanini I, Tan JY, Pisano A, Mungo C, Baroux C, Panse VG, Marques AC, Santoro R. An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains. Mol Cell 2024; 84:1667-1683.e10. [PMID: 38599210 PMCID: PMC11065421 DOI: 10.1016/j.molcel.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/19/2023] [Accepted: 03/16/2024] [Indexed: 04/12/2024]
Abstract
The nucleus is composed of functionally distinct membraneless compartments that undergo phase separation (PS). However, whether different subnuclear compartments are connected remains elusive. We identified a type of nuclear body with PS features composed of BAZ2A that associates with active chromatin. BAZ2A bodies depend on RNA transcription and BAZ2A non-disordered RNA-binding TAM domain. Although BAZ2A and H3K27me3 occupancies anticorrelate in the linear genome, in the nuclear space, BAZ2A bodies contact H3K27me3 bodies. BAZ2A-body disruption promotes BAZ2A invasion into H3K27me3 domains, causing H3K27me3-body loss and gene upregulation. Weak BAZ2A-RNA interactions, such as with nascent transcripts, promote BAZ2A bodies, whereas the strong binder long non-coding RNA (lncRNA) Malat1 impairs them while mediating BAZ2A association to chromatin at nuclear speckles. In addition to unraveling a direct connection between nuclear active and repressive compartments through PS mechanisms, the results also showed that the strength of RNA-protein interactions regulates this process, contributing to nuclear organization and the regulation of chromatin and gene expression.
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Affiliation(s)
- Luigi Lerra
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Martina Panatta
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Dominik Bär
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland
| | - Isabella Zanini
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland
| | - Jennifer Yihong Tan
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Agnese Pisano
- Institute of Medical Microbiology, University of Zurich, Zurich 8057, Switzerland
| | - Chiara Mungo
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Célia Baroux
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8057, Switzerland
| | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich 8057, Switzerland
| | - Ana C Marques
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland.
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40
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Xiong K, Zhang R, Ma J. scGHOST: identifying single-cell 3D genome subcompartments. Nat Methods 2024; 21:814-822. [PMID: 38589516 PMCID: PMC11127718 DOI: 10.1038/s41592-024-02230-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 03/01/2024] [Indexed: 04/10/2024]
Abstract
Single-cell Hi-C (scHi-C) technologies allow for probing of genome-wide cell-to-cell variability in three-dimensional (3D) genome organization from individual cells. Computational methods have been developed to reveal single-cell 3D genome features based on scHi-C, including A/B compartments, topologically associating domains and chromatin loops. However, no method exists for annotating single-cell subcompartments, which is important for understanding chromosome spatial localization in single cells. Here we present scGHOST, a single-cell subcompartment annotation method using graph embedding with constrained random walk sampling. Applications of scGHOST to scHi-C data and contact maps derived from single-cell 3D genome imaging demonstrate reliable identification of single-cell subcompartments, offering insights into cell-to-cell variability of nuclear subcompartments. Using scHi-C data from complex tissues, scGHOST identifies cell-type-specific or allele-specific subcompartments linked to gene transcription across various cell types and developmental stages, suggesting functional implications of single-cell subcompartments. scGHOST is an effective method for annotating single-cell 3D genome subcompartments in a broad range of biological contexts.
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Affiliation(s)
- Kyle Xiong
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ruochi Zhang
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jian Ma
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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41
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Shi Z, Wu H. CTPredictor: A comprehensive and robust framework for predicting cell types by integrating multi-scale features from single-cell Hi-C data. Comput Biol Med 2024; 173:108336. [PMID: 38513390 DOI: 10.1016/j.compbiomed.2024.108336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/01/2024] [Accepted: 03/17/2024] [Indexed: 03/23/2024]
Abstract
Single-cell Hi-C (scHi-C) has emerged as a powerful technology for deciphering cell-to-cell variability in three-dimensional (3D) chromatin organization, providing insights into genome-wide chromatin interactions and their correlation with cellular functions. Nevertheless, the accurate identification of cell types across different datasets remains a formidable challenge, hindering comprehensive investigations into genome structure. In response, we introduce CTPredictor, an innovative computational method that integrates multi-scale features to accurately predict cell types in various datasets. CTPredictor strategically incorporates three distinct feature sets, namely, small intra-domain contact probability (SICP), smoothed small intra-domain contact probability (SSICP), and smoothed bin contact probability (SBCP). The resulting fusion classification model significantly enhances the accuracy of cell type prediction based on single-cell Hi-C data (scHi-C). Rigorous benchmarking against established methods and three conventional machine learning approaches demonstrates the robust performance of CTPredictor, positioning it as an advanced tool for cell type prediction within scHi-C data. Beyond its prediction capabilities, CTPredictor holds promise in illuminating 3D genome structures and their functional significance across a wide array of biological processes.
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Affiliation(s)
- Zhenqi Shi
- School of Software, Shandong University, 250100, Jinan, China
| | - Hao Wu
- School of Software, Shandong University, 250100, Jinan, China.
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42
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Guo J, Chen Y, Zhu H, Tong X, Cao L, Zhang Y, Xie W, Li C. Three-dimensional chromatin landscapes in somatotroph tumour. Clin Transl Med 2024; 14:e1682. [PMID: 38769659 PMCID: PMC11106515 DOI: 10.1002/ctm2.1682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/01/2024] [Accepted: 04/19/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND The three-dimensional (3D) genome architecture plays a critical role inregulating gene expression. However, the specific alterations in thisarchitecture within somatotroph tumors and their implications for gene expression remain largely unexplored. METHODS We employed Hi-C and RNA-seq analyses to compare the 3D genomic structures of somatotroph tumors with normal pituitary tissue. This comprehensive approachenabled the characterization of A/B compartments, topologically associateddomains (TADs), and chromatin loops, integrating these with gene expression patterns. RESULTS We observed a decrease in both the frequency of chromosomal interactions andthe size of TADs in tumor tissue compared to normal tissue. Conversely, the number of TADs and chromatin loops was found to be increased in tumors. Integrated analysis of Hi-C and RNA-seq data demonstrated that changes inhigher-order chromat in structure were associated with alterations in gene expression. Specifically, genes in A compartments showed higher density and increased expression relative to those in B compartments. Moreover, the weakand enhanced insulation boundaries were identified, and the associated genes were enriched in the Wnt/β-Catenin signaling pathway. We identified the gainedand lost loops in tumor and integrated these differences with transcriptional changes to examine the functional relevance of the identified loops. Notably, we observed an enhanced insulation boundary and a greater number of loops in the TCF7L2 gene region within tumors, which was accompanied by an upregulation of TCF7L2 expression. Subsequently, TCF7L2 expression was confirmed through qRT-PCR, and upregulated TCF7L2 prompted cell proliferation and growth hormone (GH) secretion in vitro. CONCLUSION Our results provide comprehensive 3D chromatin architecture maps of somatotroph tumors and offer a valuable resource for furthering the understanding of the underlying biology and mechanisms of gene expression regulation.
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Affiliation(s)
- Jing Guo
- Department of NeurosurgeryBeijing Tiantan Hospital affiliated to Capital Medical UniversityBeijingChina
- Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
| | - Yiyuan Chen
- Department of NeurosurgeryBeijing Tiantan Hospital affiliated to Capital Medical UniversityBeijingChina
- Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
| | - Haibo Zhu
- Department of NeurosurgeryBeijing Tiantan Hospital affiliated to Capital Medical UniversityBeijingChina
| | - Xinyu Tong
- Annoroad Gene Technology Co., LtdBeijingChina
| | - Lei Cao
- Department of NeurosurgeryBeijing Tiantan Hospital affiliated to Capital Medical UniversityBeijingChina
| | - Yazhuo Zhang
- Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Beijing Institute for Brain Disorders Brain Tumor CenterBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
| | - Weiyan Xie
- Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
| | - Chuzhong Li
- Department of NeurosurgeryBeijing Tiantan Hospital affiliated to Capital Medical UniversityBeijingChina
- Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Beijing Institute for Brain Disorders Brain Tumor CenterBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
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43
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Ocaña-Paredes B, Rivera-Orellana S, Ramírez-Sánchez D, Montalvo-Guerrero J, Freire MP, Espinoza-Ferrao S, Altamirano-Colina A, Echeverría-Espinoza P, Ramos-Medina MJ, Echeverría-Garcés G, Granda-Moncayo D, Jácome-Alvarado A, Andrade MG, López-Cortés A. The pharmacoepigenetic paradigm in cancer treatment. Front Pharmacol 2024; 15:1381168. [PMID: 38720770 PMCID: PMC11076712 DOI: 10.3389/fphar.2024.1381168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/11/2024] [Indexed: 05/12/2024] Open
Abstract
Epigenetic modifications, characterized by changes in gene expression without altering the DNA sequence, play a crucial role in the development and progression of cancer by significantly influencing gene activity and cellular function. This insight has led to the development of a novel class of therapeutic agents, known as epigenetic drugs. These drugs, including histone deacetylase inhibitors, histone acetyltransferase inhibitors, histone methyltransferase inhibitors, and DNA methyltransferase inhibitors, aim to modulate gene expression to curb cancer growth by uniquely altering the epigenetic landscape of cancer cells. Ongoing research and clinical trials are rigorously evaluating the efficacy of these drugs, particularly their ability to improve therapeutic outcomes when used in combination with other treatments. Such combination therapies may more effectively target cancer and potentially overcome the challenge of drug resistance, a significant hurdle in cancer therapy. Additionally, the importance of nutrition, inflammation control, and circadian rhythm regulation in modulating drug responses has been increasingly recognized, highlighting their role as critical modifiers of the epigenetic landscape and thereby influencing the effectiveness of pharmacological interventions and patient outcomes. Epigenetic drugs represent a paradigm shift in cancer treatment, offering targeted therapies that promise a more precise approach to treating a wide spectrum of tumors, potentially with fewer side effects compared to traditional chemotherapy. This progress marks a step towards more personalized and precise interventions, leveraging the unique epigenetic profiles of individual tumors to optimize treatment strategies.
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Affiliation(s)
- Belén Ocaña-Paredes
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | - David Ramírez-Sánchez
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | - María Paula Freire
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | | | | | - María José Ramos-Medina
- German Cancer Research Center (DKFZ), Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Gabriela Echeverría-Garcés
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática, Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
| | | | - Andrea Jácome-Alvarado
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - María Gabriela Andrade
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Andrés López-Cortés
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
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Banerjee A, Zhang S, Bahar I. Genome structural dynamics: insights from Gaussian network analysis of Hi-C data. Brief Funct Genomics 2024:elae014. [PMID: 38654598 DOI: 10.1093/bfgp/elae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/11/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
Characterization of the spatiotemporal properties of the chromatin is essential to gaining insights into the physical bases of gene co-expression, transcriptional regulation and epigenetic modifications. The Gaussian network model (GNM) has proven in recent work to serve as a useful tool for modeling chromatin structural dynamics, using as input high-throughput chromosome conformation capture data. We focus here on the exploration of the collective dynamics of chromosomal structures at hierarchical levels of resolution, from single gene loci to topologically associating domains or entire chromosomes. The GNM permits us to identify long-range interactions between gene loci, shedding light on the role of cross-correlations between distal regions of the chromosomes in regulating gene expression. Notably, GNM analysis performed across diverse cell lines highlights the conservation of the global/cooperative movements of the chromatin across different types of cells. Variations driven by localized couplings between genomic loci, on the other hand, underlie cell differentiation, underscoring the significance of the four-dimensional properties of the genome in defining cellular identity. Finally, we demonstrate the close relation between the cell type-dependent mobility profiles of gene loci and their gene expression patterns, providing a clear demonstration of the role of chromosomal 4D features in defining cell-specific differential expression of genes.
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Affiliation(s)
- Anupam Banerjee
- Laufer Center for Physical & Quantitative Biology, Stony Brook University, NY 11794, USA
| | - She Zhang
- OpenEye, Cadence Molecular Sciences, Santa Fe, NM 87508, USA
| | - Ivet Bahar
- Laufer Center for Physical & Quantitative Biology, Stony Brook University, NY 11794, USA
- Department of Biochemistry and Cell Biology, Renaissance School of Medicine, Stony Brook University, NY 11794, USA
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45
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Camerino M, Chang W, Cvekl A. Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers. Epigenetics Chromatin 2024; 17:10. [PMID: 38643244 PMCID: PMC11031936 DOI: 10.1186/s13072-024-00533-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/08/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Nuclear organization of interphase chromosomes involves individual chromosome territories, "open" and "closed" chromatin compartments, topologically associated domains (TADs) and chromatin loops. The DNA- and RNA-binding transcription factor CTCF together with the cohesin complex serve as major organizers of chromatin architecture. Cellular differentiation is driven by temporally and spatially coordinated gene expression that requires chromatin changes of individual loci of various complexities. Lens differentiation represents an advantageous system to probe transcriptional mechanisms underlying tissue-specific gene expression including high transcriptional outputs of individual crystallin genes until the mature lens fiber cells degrade their nuclei. RESULTS Chromatin organization between mouse embryonic stem (ES) cells, newborn (P0.5) lens epithelium and fiber cells were analyzed using Hi-C. Localization of CTCF in both lens chromatins was determined by ChIP-seq and compared with ES cells. Quantitative analyses show major differences between number and size of TADs and chromatin loop size between these three cell types. In depth analyses show similarities between lens samples exemplified by overlaps between compartments A and B. Lens epithelium-specific CTCF peaks are found in mostly methylated genomic regions while lens fiber-specific and shared peaks occur mostly within unmethylated DNA regions. Major differences in TADs and loops are illustrated at the ~ 500 kb Pax6 locus, encoding the critical lens regulatory transcription factor and within a larger ~ 15 Mb WAGR locus, containing Pax6 and other loci linked to human congenital diseases. Lens and ES cell Hi-C data (TADs and loops) together with ATAC-seq, CTCF, H3K27ac, H3K27me3 and ENCODE cis-regulatory sites are shown in detail for the Pax6, Sox1 and Hif1a loci, multiple crystallin genes and other important loci required for lens morphogenesis. The majority of crystallin loci are marked by unexpectedly high CTCF-binding across their transcribed regions. CONCLUSIONS Our study has generated the first data on 3-dimensional (3D) nuclear organization in lens epithelium and lens fibers and directly compared these data with ES cells. These findings generate novel insights into lens-specific transcriptional gene control, open new research avenues to study transcriptional condensates in lens fiber cells, and enable studies of non-coding genetic variants linked to cataract and other lens and ocular abnormalities.
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Affiliation(s)
- Michael Camerino
- The Departments Genetics, Albert Einstein College of Medicine, NY10461, Bronx, USA
| | - William Chang
- Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, NY10461, Bronx, USA
| | - Ales Cvekl
- The Departments Genetics, Albert Einstein College of Medicine, NY10461, Bronx, USA.
- Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, NY10461, Bronx, USA.
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46
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Chu Y, Jiang Z, Gong Z, Ji X, Zhu M, Shang Q, Gong P, Cao L, Chen Y, Li P, Shao C, Shi Y. PML-mediated nuclear loosening permits immunomodulation of mesenchymal stem/stromal cells under inflammatory conditions. Cell Prolif 2024; 57:e13566. [PMID: 37864298 PMCID: PMC10984101 DOI: 10.1111/cpr.13566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/16/2023] [Accepted: 10/10/2023] [Indexed: 10/22/2023] Open
Abstract
Nuclear configuration plays a critical role in the compartmentalization of euchromatin and heterochromatin and the epigenetic regulation of gene expression. Under stimulation by inflammatory cytokines IFN-γ and TNF-α, human mesenchymal stromal cells (hMSCs) acquire a potent immunomodulatory function enabled by drastic induction of various effector genes, with some upregulated several magnitudes. However, whether the transcriptional upregulation of the immunomodulatory genes in hMSCs exposed to inflammatory cytokines is associated with genome-wide nuclear reconfiguration has not been explored. Here, we demonstrate that hMSCs undergo remarkable nuclear reconfiguration characterized by an enlargement of the nucleus, downregulation of LMNB1 and LMNA/C, decondensation of heterochromatin, and derepression of repetitive DNA. Interestingly, promyelocytic leukaemia-nuclear bodies (PML-NBs) were found to mediate the nuclear reconfiguration of hMSCs triggered by the inflammatory cytokines. Significantly, when PML was depleted, the immunomodulatory function of hMSCs conferred by cytokines was compromised, as reflected by the attenuated expression of effector molecules in hMSCs and their failure to block infiltration of immune cells to lipopolysaccharide (LPS)-induced acute lung injury. Our results indicate that the immunomodulatory function of hMSCs conferred by inflammatory cytokines requires PML-mediated chromatin loosening.
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Affiliation(s)
- Yunpeng Chu
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational MedicineSoochow University Medical CollegeSuzhouChina
| | - Zishan Jiang
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational MedicineSoochow University Medical CollegeSuzhouChina
| | - Zheng Gong
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational MedicineSoochow University Medical CollegeSuzhouChina
| | - Xiaocao Ji
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational MedicineSoochow University Medical CollegeSuzhouChina
| | - Mengting Zhu
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational MedicineSoochow University Medical CollegeSuzhouChina
| | - Qianwen Shang
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational MedicineSoochow University Medical CollegeSuzhouChina
| | - Pixia Gong
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational MedicineSoochow University Medical CollegeSuzhouChina
| | - Lijuan Cao
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational MedicineSoochow University Medical CollegeSuzhouChina
| | - Yongjing Chen
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational MedicineSoochow University Medical CollegeSuzhouChina
| | - Peishan Li
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational MedicineSoochow University Medical CollegeSuzhouChina
| | - Changshun Shao
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational MedicineSoochow University Medical CollegeSuzhouChina
| | - Yufang Shi
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational MedicineSoochow University Medical CollegeSuzhouChina
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47
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Yoon I, Kim U, Song Y, Park T, Lee DS. 3C methods in cancer research: recent advances and future prospects. Exp Mol Med 2024; 56:788-798. [PMID: 38658701 PMCID: PMC11059347 DOI: 10.1038/s12276-024-01236-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
In recent years, Hi-C technology has revolutionized cancer research by elucidating the mystery of three-dimensional chromatin organization and its role in gene regulation. This paper explored the impact of Hi-C advancements on cancer research by delving into high-resolution techniques, such as chromatin loops, structural variants, haplotype phasing, and extrachromosomal DNA (ecDNA). Distant regulatory elements interact with their target genes through chromatin loops. Structural variants contribute to the development and progression of cancer. Haplotype phasing is crucial for understanding allele-specific genomic rearrangements and somatic clonal evolution in cancer. The role of ecDNA in driving oncogene amplification and drug resistance in cancer cells has also been revealed. These innovations offer a deeper understanding of cancer biology and the potential for personalized therapies. Despite these advancements, challenges, such as the accurate mapping of repetitive sequences and precise identification of structural variants, persist. Integrating Hi-C with multiomics data is key to overcoming these challenges and comprehensively understanding complex cancer genomes. Thus, Hi-C is a powerful tool for guiding precision medicine in cancer research and treatment.
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Affiliation(s)
- Insoo Yoon
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Uijin Kim
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Yousuk Song
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Taesoo Park
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Dong-Sung Lee
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea.
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48
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Ulanova A, Mansfeldt C. EcoGenoRisk: Developing a computational ecological risk assessment tool for synthetic biology. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123647. [PMID: 38402941 DOI: 10.1016/j.envpol.2024.123647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
The expanding field of synthetic biology (synbio) supports new opportunities in the design of targeted bioproducts or modified microorganisms. However, this rapid development of synbio products raises concerns surrounding the potential risks of modified microorganisms contaminating unintended environments. These potential invasion risks require new bioinformatic tools to inform the design phase. EcoGenoRisk is a newly constructed computational risk assessment tool for invasiveness that aims to predict where synbio microorganisms may establish a population by screening for habitats of genetically similar microorganisms. The first module of the tool identifies genetically similar microorganisms and potential ecological relationships such as competition, mutualism, and inhibition. In total, 520 archaeal and 32,828 bacterial complete assembly genomes were analyzed to test the specificity and accuracy of the tool as well as to characterize the enzymatic profiles of different taxonomic lineages. Additionally, ecological relationships were analyzed to determine which would result in the greatest potential overlap between shared functional profiles. Notably, competition displayed the significantly highest overlap of shared functions between compared genomes. Overall, EcoGenoRisk is a flexible software pipeline that assists environmental risk assessors to query large databases of known microorganisms and prioritize follow-up bench scale studies.
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Affiliation(s)
- Anna Ulanova
- University of Colorado Boulder, Department of Civil, Environmental, and Architectural Engineering, 1111 Engineering Drive, Boulder, CO, 80309, USA; University of Colorado Boulder, Environmental Engineering Program, 4001 Discovery Drive, Boulder, CO, 80303, USA
| | - Cresten Mansfeldt
- University of Colorado Boulder, Department of Civil, Environmental, and Architectural Engineering, 1111 Engineering Drive, Boulder, CO, 80309, USA; University of Colorado Boulder, Environmental Engineering Program, 4001 Discovery Drive, Boulder, CO, 80303, USA.
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49
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Eustermann S, Patel AB, Hopfner KP, He Y, Korber P. Energy-driven genome regulation by ATP-dependent chromatin remodellers. Nat Rev Mol Cell Biol 2024; 25:309-332. [PMID: 38081975 DOI: 10.1038/s41580-023-00683-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 03/28/2024]
Abstract
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re)arrange nucleosomes at the first level of chromatin organization. Their Snf2-type motor ATPases alter histone-DNA interactions through a common DNA translocation mechanism. Whether remodeller activities mainly catalyse nucleosome dynamics or accurately co-determine nucleosome organization remained unclear. In this Review, we discuss the emerging mechanisms of chromatin remodelling: dynamic remodeller architectures and their interactions, the inner workings of the ATPase cycle, allosteric regulation and pathological dysregulation. Recent mechanistic insights argue for a decisive role of remodellers in the energy-driven self-organization of chromatin, which enables both stability and plasticity of genome regulation - for example, during development and stress. Different remodellers, such as members of the SWI/SNF, ISWI, CHD and INO80 families, process (epi)genetic information through specific mechanisms into distinct functional outputs. Combinatorial assembly of remodellers and their interplay with histone modifications, histone variants, DNA sequence or DNA-bound transcription factors regulate nucleosome mobilization or eviction or histone exchange. Such input-output relationships determine specific nucleosome positions and compositions with distinct DNA accessibilities and mediate differential genome regulation. Finally, remodeller genes are often mutated in diseases characterized by genome dysregulation, notably in cancer, and we discuss their physiological relevance.
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Affiliation(s)
- Sebastian Eustermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Avinash B Patel
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Faculty of Chemistry and Pharmacy, LMU Munich, Munich, Germany
| | - Yuan He
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, LMU Munich, Martinsried, Germany.
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50
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Yuan T, Yan H, Bailey MLP, Williams JF, Surovtsev I, King MC, Mochrie SGJ. Effect of loops on the mean-square displacement of Rouse-model chromatin. Phys Rev E 2024; 109:044502. [PMID: 38755928 DOI: 10.1103/physreve.109.044502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/16/2024] [Indexed: 05/18/2024]
Abstract
Chromatin polymer dynamics are commonly described using the classical Rouse model. The subsequent discovery, however, of intermediate-scale chromatin organization known as topologically associating domains (TADs) in experimental Hi-C contact maps for chromosomes across the tree of life, together with the success of loop extrusion factor (LEF) model in explaining TAD formation, motivates efforts to understand the effect of loops and loop extrusion on chromatin dynamics. This paper seeks to fulfill this need by combining LEF-model simulations with extended Rouse-model polymer simulations to investigate the dynamics of chromatin with loops and dynamic loop extrusion. We show that loops significantly suppress the averaged mean-square displacement (MSD) of a gene locus, consistent with recent experiments that track fluorescently labeled chromatin loci. We also find that loops reduce the MSD's stretching exponent from the classical Rouse-model value of 1/2 to a loop-density-dependent value in the 0.45-0.40 range. Remarkably, stretching exponent values in this range have also been observed in recent experiments [Weber et al., Phys. Rev. Lett. 104, 238102 (2010)0031-900710.1103/PhysRevLett.104.238102; Bailey et al., Mol. Biol. Cell 34, ar78 (2023)1059-152410.1091/mbc.E23-04-0119]. We also show that the dynamics of loop extrusion itself negligibly affects chromatin mobility. By studying static "rosette" loop configurations, we also demonstrate that chromatin MSDs and stretching exponents depend on the location of the locus in question relative to the position of the loops and on the local friction environment.
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Affiliation(s)
- Tianyu Yuan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Hao Yan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Mary Lou P Bailey
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Jessica F Williams
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Ivan Surovtsev
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Megan C King
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Molecular, Cell and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Simon G J Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
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