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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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2
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Gelléri M, Chen SY, Hübner B, Neumann J, Kröger O, Sadlo F, Imhoff J, Hendzel MJ, Cremer M, Cremer T, Strickfaden H, Cremer C. True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin. Cell Rep 2023; 42:112567. [PMID: 37243597 DOI: 10.1016/j.celrep.2023.112567] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 03/02/2023] [Accepted: 05/10/2023] [Indexed: 05/29/2023] Open
Abstract
Chromatin compaction differences may have a strong impact on accessibility of individual macromolecules and macromolecular assemblies to their DNA target sites. Estimates based on fluorescence microscopy with conventional resolution, however, suggest only modest compaction differences (∼2-10×) between the active nuclear compartment (ANC) and inactive nuclear compartment (INC). Here, we present maps of nuclear landscapes with true-to-scale DNA densities, ranging from <5 to >300 Mbp/μm3. Maps are generated from individual human and mouse cell nuclei with single-molecule localization microscopy at ∼20 nm lateral and ∼100 nm axial optical resolution and are supplemented by electron spectroscopic imaging. Microinjection of fluorescent nanobeads with sizes corresponding to macromolecular assemblies for transcription into nuclei of living cells demonstrates their localization and movements within the ANC and exclusion from the INC.
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Affiliation(s)
- Márton Gelléri
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany.
| | - Shih-Ya Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Barbara Hübner
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Jan Neumann
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Ole Kröger
- Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany
| | - Filip Sadlo
- Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany
| | - Jorg Imhoff
- Neuroconsult GmbH, 69120 Heidelberg, Germany
| | - Michael J Hendzel
- Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Marion Cremer
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Thomas Cremer
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Hilmar Strickfaden
- Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Max Planck Institute for Chemistry, 55128 Mainz, Germany; Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany; Kirchhoff Institute for Physics, University Heidelberg, 69120 Heidelberg, Germany.
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3
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Peña-Martínez EG, Rivera-Madera A, Pomales-Matos DA, Sanabria-Alberto L, Rosario-Cañuelas BM, Rodríguez-Ríos JM, Carrasquillo-Dones EA, Rodríguez-Martínez JA. Disease-associated non-coding variants alter NKX2-5 DNA-binding affinity. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194906. [PMID: 36690178 PMCID: PMC10013089 DOI: 10.1016/j.bbagrm.2023.194906] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/22/2023]
Abstract
Genome-wide association studies (GWAS) have mapped over 90 % of disease- or trait-associated variants within the non-coding genome, like cis-regulatory elements (CREs). Non-coding single nucleotide polymorphisms (SNPs) are genomic variants that can change how DNA-binding regulatory proteins, like transcription factors (TFs), interact with the genome and regulate gene expression. NKX2-5 is a TF essential for proper heart development, and mutations affecting its function have been associated with congenital heart diseases (CHDs). However, establishing a causal mechanism between non-coding genomic variants and human disease remains challenging. To address this challenge, we identified 8475 SNPs predicted to alter NKX2-5 DNA-binding using a position weight matrix (PWM)-based predictive model. Five variants were prioritized for in vitro validation; four of them are associated with traits and diseases that impact cardiovascular health. The impact of these variants on NKX2-5 binding was evaluated with electrophoretic mobility shift assay (EMSA) using purified recombinant NKX2-5 homeodomain. Binding curves were constructed to determine changes in binding between variant and reference alleles. Variants rs7350789, rs7719885, rs747334, and rs3892630 increased binding affinity, whereas rs61216514 decreased binding by NKX2-5 when compared to the reference genome. Our findings suggest that differential TF-DNA binding affinity can be key in establishing a causal mechanism of pathogenic variants.
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Mandahl N, Mitelman F. Giemsa-negative chromosome bands preferentially recombine in cancer-associated translocations and gene fusions. Genes Chromosomes Cancer 2023; 62:61-74. [PMID: 36116030 PMCID: PMC10092824 DOI: 10.1002/gcc.23095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 12/13/2022] Open
Abstract
Chromosome abnormalities, in particular translocations, and gene fusions are hallmarks of neoplasia. Although both have been recognized as important drivers of cancer for decades, our knowledge of the characterizing features of the cytobands involved in recombinations is poorly understood. The present study, based on a comparative analysis of 10 442 translocation breakpoints and 30 762 gene fusions comprising 13 864 protein-coding genes, is the most comprehensive evaluation of the interactions of cytobands participating in the formation of such rearrangements in cancer. The major conclusion is that although large G-negative, gene-rich bands are most frequently involved, the greatest impact was seen for staining properties. Thus, 60% of the recombinations leading to the formation of both translocations and fusion genes take place between two G-negative bands whereas only about 10% involve two G-positive bands. There is compelling evidence that G-negative bands contain more genes than dark staining bands and it has previously been shown that breakpoints involved in structural chromosome rearrangements and in gene fusions preferentially affect gene-rich bands. The present study not only corroborates these findings but in addition demonstrates that the recombination processes favor the joining of two G-negative cytobands and that this feature may be a stronger factor than gene content. It is reasonable to assume that the formation of translocations and fusion genes in cancer cells, irrespective of whether they have a pathogenetically significant impact or not, may be mediated by some underlying mechanisms that either favor the origin or provide a selective advantage for recombinations of G-negative cytobands.
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Affiliation(s)
- Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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5
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Matveevsky S, Bakloushinskaya I, Tambovtseva V, Atsaeva M, Grishaeva T, Bogdanov A, Kolomiets O. Nonhomologous Chromosome Interactions in Prophase I: Dynamics of Bizarre Meiotic Contacts in the Alay Mole Vole Ellobius alaicus (Mammalia, Rodentia). Genes (Basel) 2022; 13:genes13122196. [PMID: 36553461 PMCID: PMC9778597 DOI: 10.3390/genes13122196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Nonhomologous chromosome interactions take place in both somatic and meiotic cells. Prior to this study, we had discovered special contacts through the SYCP3 (synaptonemal complex protein 3) filament between the short arms of nonhomologous acrocentrics at the pachytene stage in the Alay mole vole, and these contacts demonstrate several patterns from proximity to the complete fusion stage. Here, we investigated the nonhomologous chromosome contacts in meiotic prophase I. It turned out that such contacts do not introduce changes into the classic distribution of DNA double-strand breaks. It is noteworthy that not all meiotic contacts were localized in the H3k9me3-positive heterochromatic environment. Both in the mid zygotene and in the early-mid diplotene, three types of contacts (proximity, touching, and anchoring/tethering) were observed, whereas fusion seems to be characteristic only for pachytene. The number of contacts in the mid pachytene is significantly higher than that in the zygotene, and the distance between centromeres in nonhomologous contacts is also the smallest in mid pachytene for all types of contacts. Thus, this work provides a new insight into the behavior of meiotic contacts during prophase I and points to avenues of further research.
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Affiliation(s)
- Sergey Matveevsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- Correspondence:
| | - Irina Bakloushinskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Valentina Tambovtseva
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Maret Atsaeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- Department of Cell Biology, Morphology and Microbiology, Chechen State University, 364024 Grozny, Russia
| | - Tatiana Grishaeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Aleksey Bogdanov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Oxana Kolomiets
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
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6
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Sun Y, Dotson GA, Muir LA, Ronquist S, Oravecz-Wilson K, Peltier D, Seike K, Li L, Meixner W, Rajapakse I, Reddy P. Rearrangement of T Cell genome architecture regulates GVHD. iScience 2022; 25:104846. [PMID: 36043052 PMCID: PMC9420521 DOI: 10.1016/j.isci.2022.104846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 05/10/2022] [Accepted: 07/22/2022] [Indexed: 11/19/2022] Open
Abstract
WAPL, cohesin's DNA release factor, regulates three-dimensional (3D) chromatin architecture. The 3D chromatin structure and its relevance to mature T cell functions is not well understood. We show that in vivo lymphopenic expansion, and alloantigen-driven proliferation, alters the 3D structure and function of the genome in mature T cells. Conditional deletion of WAPL, cohesin's DNA release factor, in T cells reduced long-range genomic interactions and altered chromatin A/B compartments and interactions within topologically associating domains (TADs) of the chromatin in T cells at baseline. WAPL deficiency in T cells reduced loop extensions, changed expression of cell cycling genes and reduced proliferation following in vitro and in vivo stimulation, and reduced severity of graft-versus-host disease (GVHD) following experimental allogeneic hematopoietic stem cell transplantation. These data collectively characterize 3D genomic architecture of T cells in vivo and demonstrate biological and clinical implications for its disruption by cohesin release factor WAPL.
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Affiliation(s)
- Yaping Sun
- 1Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Gabrielle A. Dotson
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lindsey A. Muir
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott Ronquist
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katherine Oravecz-Wilson
- 1Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Daniel Peltier
- 1Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Keisuke Seike
- 1Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Lu Li
- 1Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Walter Meixner
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Indika Rajapakse
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Mathematics, University of Michigan, Ann Arbor, MI, USA
| | - Pavan Reddy
- 1Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
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7
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Yadav M, Jalan M, Srivastava M. Enhancer dependent repositioning of TCRb locus with respect to the chromosome territory. J Mol Biol 2022; 434:167509. [PMID: 35202629 DOI: 10.1016/j.jmb.2022.167509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/19/2022]
Abstract
Intranuclear position of several genes is dynamically altered during development concordant with their activation. To understand this dynamic, but non-random, nuclear organization, it is important to identify the relevant regulatory elements and trans acting factors. Murine TCRb locus gets activated during thymic development. Enhancer Eb is important for VDJ recombination at TCRb locus as it is critically required establishment of recombination center. Our analysis revealed that TCRb locus gets located out of the chromosome territory specifically in developing thymocytes. Further, CRISPR/Cas9 based deletion mutagenesis established an unambiguous role of enhancer Eb in defining TCRb location relative to chromosome territory. The ability to reposition the target locus relative to chromosome territory highlights a novel aspect pertaining to activity of enhancers which may contribute to their ability to regulate gene expression. Additionally, our observations have implications for understanding the role of enhancers in three-dimensional genome organization and function.
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Affiliation(s)
- Monika Yadav
- National Institute of Immunology, Aruna Asaf Ali Road, New Delhi 110067, India
| | - Manisha Jalan
- National Institute of Immunology, Aruna Asaf Ali Road, New Delhi 110067, India
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8
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Razin SV, Gavrilov AA. Non-coding RNAs in chromatin folding and nuclear organization. Cell Mol Life Sci 2021; 78:5489-5504. [PMID: 34117518 PMCID: PMC11072467 DOI: 10.1007/s00018-021-03876-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/24/2021] [Accepted: 06/05/2021] [Indexed: 12/19/2022]
Abstract
One of the most intriguing questions facing modern biology concerns how the genome directs the construction of cells, tissues, and whole organisms. It is tempting to suggest that the part of the genome that does not encode proteins contains architectural plans. We are still far from understanding how these plans work at the level of building tissues and the body as a whole. However, the results of recent studies demonstrate that at the cellular level, special non-coding RNAs serve as scaffolds for the construction of various intracellular structures. The term "architectural RNAs" was proposed to designate this subset of non-coding RNAs. In this review, we discuss the role of architectural RNAs in the construction of the cell nucleus and maintenance of the three-dimensional organization of the genome.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia.
- Faculty of Biology, M. V. Lomonosov Moscow State University, 119234, Moscow, Russia.
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
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9
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Baroux C. Three-dimensional genome organization in epigenetic regulations: cause or consequence? CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102031. [PMID: 33819713 DOI: 10.1016/j.pbi.2021.102031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
The evolution of the nucleus is an evolutionary milestone. By enabling genome compartmentalization, it contributes to the fine-tuning of genome functions. The genome is partitioned into functional domains differing in spatial positioning and topological folding at different scales. The rise of '3D Genomics' embracing experimental, theoretical, and modeling approaches allowed the proposal of a multiscale model of the eukaryotic genome, capturing its organizing principles and functionalities. In these efforts, resolving causality remains an important objective. Are positioning and folding the cause or consequence of functional states? This minireview presents emerging answers to this question, borrowing examples from recent studies of the three-dimensional genome in both plants and animals.
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Affiliation(s)
- Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Switzerland.
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10
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Zhou Z, Yan R, Jiang W, Irudayaraj JMK. Chromatin hierarchical branching visualized at the nanoscale by electron microscopy. NANOSCALE ADVANCES 2021; 3:1019-1028. [PMID: 34381959 PMCID: PMC8323808 DOI: 10.1039/d0na00359j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/12/2020] [Indexed: 06/13/2023]
Abstract
Chromatin is spatially organized in a hierarchical manner by virtue of single nucleosomes condensing into higher order chromatin structures, conferring various mechanical properties and biochemical signals. These higher order chromatin structures regulate genomic function by organization of the heterochromatin and euchromatin landscape. Less is known about its transition state from higher order heterochromatin to the lower order nucleosome form, and there is no information on its physical properties. We have developed a facile method of electron microscopy visualization to reveal the interphase chromatin in eukaryotic cells and its organization into hierarchical branching structures. We note that chromatin hierarchical branching can be distinguished at four levels, clearly indicating the stepwise transition from heterochromatin to euchromatin. The protein-DNA density across the chromatin fibers decreases during the transition from compacted heterochromatin to dispersed euchromatin. Moreover, the thickness of the chromatin ranges between 10 to 270 nm, and the controversial 30 nm chromatin fiber exists as a prominent intermediate structure. This study provides important insights into higher order chromatin organization which plays a key role in diseases such as cancer.
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Affiliation(s)
- Zhongwu Zhou
- Bindley Bioscience Center, Department of Agricultural and Biological Engineering, Purdue University West Lafayette IN 47907 USA
- The University of Texas at Austin NHB 4.120, 100 E. 24th St. Austin TX 78712 USA
| | - Rui Yan
- Markey Center for Structural Biology, Department of Biological Science, Purdue University West Lafayette IN 47907 USA
- Howard Hughes Medical Institute, Janelia Research Campus 19700 Helix Drive Asburn Virginia 20147 USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Science, Purdue University West Lafayette IN 47907 USA
| | - Joseph M K Irudayaraj
- Bindley Bioscience Center, Department of Agricultural and Biological Engineering, Purdue University West Lafayette IN 47907 USA
- Cancer Center at Illinois, Department of Bioengineering, College of Engineering, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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11
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Abstract
Cancers and developmental disorders are associated with alterations in the 3D genome architecture in space and time (the fourth dimension). Mammalian 3D genome organization is complex and dynamic and plays an essential role in regulating gene expression and cellular function. To study the causal relationship between genome function and its spatio-temporal organization in the nucleus, new technologies for engineering and manipulating the 3D organization of the genome have been developed. In particular, CRISPR-Cas technologies allow programmable manipulation at specific genomic loci, enabling unparalleled opportunities in this emerging field of 3D genome engineering. We review advances in mammalian 3D genome engineering with a focus on recent manipulative technologies using CRISPR-Cas and related technologies.
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12
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Li Y, Eshein A, Virk RKA, Eid A, Wu W, Frederick J, VanDerway D, Gladstein S, Huang K, Shim AR, Anthony NM, Bauer GM, Zhou X, Agrawal V, Pujadas EM, Jain S, Esteve G, Chandler JE, Nguyen TQ, Bleher R, de Pablo JJ, Szleifer I, Dravid VP, Almassalha LM, Backman V. Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function. SCIENCE ADVANCES 2021; 7:eabe4310. [PMID: 33523864 PMCID: PMC7775763 DOI: 10.1126/sciadv.abe4310] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/09/2020] [Indexed: 05/10/2023]
Abstract
Extending across multiple length scales, dynamic chromatin structure is linked to transcription through the regulation of genome organization. However, no individual technique can fully elucidate this structure and its relation to molecular function at all length and time scales at both a single-cell level and a population level. Here, we present a multitechnique nanoscale chromatin imaging and analysis (nano-ChIA) platform that consolidates electron tomography of the primary chromatin fiber, optical super-resolution imaging of transcription processes, and label-free nano-sensing of chromatin packing and its dynamics in live cells. Using nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nanometers, sub-megabase genomic size, and an internal fractal structure. The chromatin packing behavior of these domains exhibits a complex bidirectional relationship with active gene transcription. Furthermore, we found that properties of PDs are correlated among progenitor and progeny cells across cell division.
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Affiliation(s)
- Yue Li
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Adam Eshein
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Ranya K A Virk
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Aya Eid
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Wenli Wu
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Jane Frederick
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - David VanDerway
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Scott Gladstein
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Kai Huang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Anne R Shim
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Nicholas M Anthony
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Greta M Bauer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Xiang Zhou
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Emily M Pujadas
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Surbhi Jain
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - George Esteve
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - John E Chandler
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - The-Quyen Nguyen
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Reiner Bleher
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Vinayak P Dravid
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA
| | - Luay M Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA.
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13
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Peng AYT, Kolhe JA, Behrens LD, Freeman BC. Genome organization: Tag it, move it, place it. Curr Opin Cell Biol 2020; 68:90-97. [PMID: 33166737 DOI: 10.1016/j.ceb.2020.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/28/2020] [Accepted: 10/08/2020] [Indexed: 12/14/2022]
Abstract
Chromosomes are selectively organized within the nuclei of interphase cells reflecting the current fate of each cell and are reorganized in response to various physiological cues to maintain homeostasis. Although substantial progress is being made to establish the various patterns of genome architecture, less is understood on how chromosome folding/positioning is achieved. Here, we discuss recent insights into the cellular mechanisms dictating chromatin movements including the use of epigenetic modifications and allosterically regulated transcription factors, as well as a nucleoskeleton system comprised of actin, myosin, and actin-binding proteins. Together, these nuclear factors help coordinate the positioning of both general and cell-specific genomic architectural features.
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Affiliation(s)
- Audrey Yi Tyan Peng
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, Urbana, IL, 61801, USA
| | - Janhavi A Kolhe
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, Urbana, IL, 61801, USA
| | - Lindsey D Behrens
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, Urbana, IL, 61801, USA
| | - Brian C Freeman
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, Urbana, IL, 61801, USA.
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14
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Cremer T, Cremer M, Hübner B, Silahtaroglu A, Hendzel M, Lanctôt C, Strickfaden H, Cremer C. The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus. Bioessays 2020; 42:e1900132. [PMID: 31994771 DOI: 10.1002/bies.201900132] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/24/2019] [Indexed: 12/11/2022]
Abstract
This article focuses on the role of the interchromatin compartment (IC) in shaping nuclear landscapes. The IC is connected with nuclear pore complexes (NPCs) and harbors splicing speckles and nuclear bodies. It is postulated that the IC provides routes for imported transcription factors to target sites, for export routes of mRNA as ribonucleoproteins toward NPCs, as well as for the intranuclear passage of regulatory RNAs from sites of transcription to remote functional sites (IC hypothesis). IC channels are lined by less-compacted euchromatin, called the perichromatin region (PR). The PR and IC together form the active nuclear compartment (ANC). The ANC is co-aligned with the inactive nuclear compartment (INC), comprising more compacted heterochromatin. It is postulated that the INC is accessible for individual transcription factors, but inaccessible for larger macromolecular aggregates (limited accessibility hypothesis). This functional nuclear organization depends on still unexplored movements of genes and regulatory sequences between the two compartments.
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Affiliation(s)
- Thomas Cremer
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Marion Cremer
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Barbara Hübner
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Asli Silahtaroglu
- Department of Cellular and Molecular Medicine Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Byg.18.03, 2200, Copenhagen N, Denmark
| | - Michael Hendzel
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Christian Lanctôt
- Integration Santé, 1250 Avenue de la Station local 2-304, Shawinigan, Québec, G9N 8K9, Canada
| | - Hilmar Strickfaden
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Christoph Cremer
- Institute of Molecular Biology (IMB) Ackermannweg 4, 55128 Mainz, Germany, and Institute of Pharmacy & Molecular Biotechnology (IPMB), University Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
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15
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Estève PO, Vishnu US, Chin HG, Pradhan S. Visualization and Sequencing of Accessible Chromatin Reveals Cell Cycle and Post-HDAC inhibitor Treatment Dynamics. J Mol Biol 2020; 432:5304-5321. [PMID: 32763232 DOI: 10.1016/j.jmb.2020.07.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/29/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022]
Abstract
Chromatin accessibility is a predictor of gene expression, cell division, and cell type specificity. NicE-viewSeq (Nicking Enzyme-assisted viewing and Sequencing) allows accessible chromatin visualization and sequencing with overall lower mitochondrial DNA and duplicated sequences interference relative to ATAC-see. Using NicE-viewSeq, we interrogated the accessibility of chromatin in a cell cycle (G1, S, and G2/M)-specific manner using mammalian cells. Despite DNA replication and subsequent condensation of chromatin to chromosomes, chromatin accessibility remained generally preserved with minimal subtle alterations. Genome-wide alteration of chromatin accessibility within TSS and enhancer elements gradually decreased as cells progressed from G1 to G2M, with distinct differential accessibility near consensus transcription factors sites. Inhibition of histone deacetylases promoted accessible chromatin within gene bodies, correlating with apoptotic gene expression. In addition, reduced chromatin accessibility for the MYC oncogene pathway correlated with downregulation of pertinent genes. Surprisingly, repetitive RNA loci expression remained unaltered following histone acetylation-mediated increased accessibility. Therefore, we suggest that subtle changes in chromatin accessibility are a prerequisite during the cell cycle and histone deacetylase inhibitor-mediated therapeutics.
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Affiliation(s)
| | | | - Hang Gyeong Chin
- Genome Biology Division, New England Biolabs, Inc., Ipswich, MA 01938, USA
| | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Inc., Ipswich, MA 01938, USA.
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16
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Heurteau A, Perrois C, Depierre D, Fosseprez O, Humbert J, Schaak S, Cuvier O. Insulator-based loops mediate the spreading of H3K27me3 over distant micro-domains repressing euchromatin genes. Genome Biol 2020; 21:193. [PMID: 32746892 PMCID: PMC7397589 DOI: 10.1186/s13059-020-02106-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 07/14/2020] [Indexed: 12/16/2022] Open
Abstract
Abstract
Background
Chromosomes are subdivided spatially to delimit long-range interactions into topologically associating domains (TADs). TADs are often flanked by chromatin insulators and transcription units that may participate in such demarcation. Remarkably, single-cell Drosophila TAD units correspond to dynamic heterochromatin nano-compartments that can self-assemble. The influence of insulators on such dynamic compartmentalization remains unclear. Moreover, to what extent heterochromatin domains are fully compartmentalized away from active genes remains unclear from Drosophila to human.
Results
Here, we identify H3K27me3 micro-domains genome-wide in Drosophila, which are attributed to the three-dimensional spreading of heterochromatin marks into euchromatin. Whereas depletion of insulator proteins increases H3K27me3 spreading locally, across heterochromatin borders, it concomitantly decreases H3K27me3 levels at distant micro-domains discrete sites. Quantifying long-range interactions suggests that random interactions between heterochromatin TADs and neighbor euchromatin cannot predict the presence of micro-domains, arguing against the hypothesis that they reflect defects in self-folding or in insulating repressive TADs. Rather, micro-domains are predicted by specific long-range interactions with the TAD borders bound by insulator proteins and co-factors required for looping. Accordingly, H3K27me3 spreading to distant sites is impaired by insulator mutants that compromise recruitment of looping co-factors. Both depletions and insulator mutants significantly reduce H3K27me3 micro-domains, deregulating the flanking genes.
Conclusions
Our data highlight a new regulatory mode of H3K27me3 by insulator-based long-range interactions controlling distant euchromatic genes.
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Affiliation(s)
- Alexandre Heurteau
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France
| | - Charlène Perrois
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France
| | - David Depierre
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France
| | - Olivier Fosseprez
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France
| | - Jonathan Humbert
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre Hospitalier Universitaire de Québec City, Quebec, QC, G1R 3S3, Canada
| | - Stéphane Schaak
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France
| | - Olivier Cuvier
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France.
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17
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Maeshima K, Tamura S, Hansen JC, Itoh Y. Fluid-like chromatin: Toward understanding the real chromatin organization present in the cell. Curr Opin Cell Biol 2020; 64:77-89. [PMID: 32283330 DOI: 10.1016/j.ceb.2020.02.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/16/2020] [Accepted: 02/22/2020] [Indexed: 12/23/2022]
Abstract
Eukaryotic chromatin is a negatively charged polymer consisting of genomic DNA, histones, and various nonhistone proteins. Because of its highly charged character, the structure of chromatin varies greatly depending on the surrounding environment (i.e. cations etc.): from an extended 10-nm fiber, to a folded 30-nm fiber, to chromatin condensates/liquid-droplets. Over the last ten years, newly developed technologies have drastically shifted our view on chromatin from a static regular structure to a more irregular and dynamic one, locally like a fluid. Since no single imaging (or genomics) method can tell us everything and beautiful images (or models) can fool our minds, comprehensive analyses based on many technical approaches are important to capture actual chromatin organization inside the cell. Here we critically discuss our current view on chromatin and methodology used to support the view.
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Affiliation(s)
- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, 411-8540, Japan.
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Yuji Itoh
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
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18
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Babokhov M, Hibino K, Itoh Y, Maeshima K. Local Chromatin Motion and Transcription. J Mol Biol 2020; 432:694-700. [DOI: 10.1016/j.jmb.2019.10.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 10/07/2019] [Accepted: 10/24/2019] [Indexed: 12/17/2022]
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19
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Birk UJ. Super-Resolution Microscopy of Chromatin. Genes (Basel) 2019; 10:E493. [PMID: 31261775 PMCID: PMC6678334 DOI: 10.3390/genes10070493] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/17/2019] [Accepted: 06/26/2019] [Indexed: 01/05/2023] Open
Abstract
Since the advent of super-resolution microscopy, countless approaches and studies have been published contributing significantly to our understanding of cellular processes. With the aid of chromatin-specific fluorescence labeling techniques, we are gaining increasing insight into gene regulation and chromatin organization. Combined with super-resolution imaging and data analysis, these labeling techniques enable direct assessment not only of chromatin interactions but also of the function of specific chromatin conformational states.
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Affiliation(s)
- Udo J Birk
- University of Applied Sciences HTW Chur, Pulvermühlestrasse 57, 7004 Chur, Switzerland.
- Institut für Physik, Universität Mainz, 55122 Mainz, Germany.
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20
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Dynamic chromatin organization in the cell. Essays Biochem 2019; 63:133-145. [PMID: 30967477 DOI: 10.1042/ebc20180054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/13/2019] [Accepted: 03/19/2019] [Indexed: 12/29/2022]
Abstract
The organization and regulation of genomic DNA as nuclear chromatin is necessary for proper DNA function inside living eukaryotic cells. While this has been extensively explored, no true consensus is currently reached regarding the exact mechanism of chromatin organization. The traditional view has assumed that the DNA is packaged into a hierarchy of structures inside the nucleus based on the regular 30-nm chromatin fiber. This is currently being challenged by the fluid-like model of the chromatin which views the chromatin as a dynamic structure based on the irregular 10-nm fiber. In this review, we focus on the recent progress in chromatin structure elucidation highlighting the paradigm shift in chromatin folding mechanism from the classical textbook perspective of the regularly folded chromatin to the more dynamic fluid-like perspective.
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21
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Mai S. Introduction to the special issue "3D nuclear architecture of the genome". Genes Chromosomes Cancer 2019; 58:405-406. [PMID: 30851140 DOI: 10.1002/gcc.22747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 12/17/2022] Open
Affiliation(s)
- Sabine Mai
- Department of Cell Biology, Research Institute of Oncology and Hematology, CancerCare Manitoba, University of Manitoba, Winnipeg, Canada
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22
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Mai S. The three-dimensional cancer nucleus. Genes Chromosomes Cancer 2019; 58:462-473. [PMID: 30536826 DOI: 10.1002/gcc.22720] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/11/2022] Open
Abstract
Research into the three-dimensional (3D) organization of the cancer cell genome started over 100 years ago. We follow an exciting avenue of research in this field, from Hansemann's early observations of aberrant mitoses and nuclei in cancer cells in the late 19th century to Boveri's theory of the cancer cell in the early 20th century, to current views of nuclear organization and its changes in cancer. Molecular and imaging methods go hand in hand with providing us with a better understanding of the spatial nature of the cancer cell genome. This has led to the concept that the structural order of the nucleus can be used as cancer cell biomarker.
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Affiliation(s)
- Sabine Mai
- Cell Biology, Research Institute for Oncology and Hematology, CancerCare Manitoba, The University of Manitoba, Winnipeg, Manitoba, Canada
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