1
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Moindrot B, Imaizumi Y, Feil R. Differential 3D genome architecture and imprinted gene expression: cause or consequence? Biochem Soc Trans 2024; 52:973-986. [PMID: 38775198 DOI: 10.1042/bst20230143] [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: 02/12/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 06/27/2024]
Abstract
Imprinted genes provide an attractive paradigm to unravel links between transcription and genome architecture. The parental allele-specific expression of these essential genes - which are clustered in chromosomal domains - is mediated by parental methylation imprints at key regulatory DNA sequences. Recent chromatin conformation capture (3C)-based studies show differential organization of topologically associating domains between the parental chromosomes at imprinted domains, in embryonic stem and differentiated cells. At several imprinted domains, differentially methylated regions show allelic binding of the insulator protein CTCF, and linked focal retention of cohesin, at the non-methylated allele only. This generates differential patterns of chromatin looping between the parental chromosomes, already in the early embryo, and thereby facilitates the allelic gene expression. Recent research evokes also the opposite scenario, in which allelic transcription contributes to the differential genome organization, similarly as reported for imprinted X chromosome inactivation. This may occur through epigenetic effects on CTCF binding, through structural effects of RNA Polymerase II, or through imprinted long non-coding RNAs that have chromatin repressive functions. The emerging picture is that epigenetically-controlled differential genome architecture precedes and facilitates imprinted gene expression during development, and that at some domains, conversely, the mono-allelic gene expression also influences genome architecture.
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Affiliation(s)
- Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yui Imaizumi
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
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2
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Xie T, Danieli-Mackay A, Buccarelli M, Barbieri M, Papadionysiou I, D'Alessandris QG, Robens C, Übelmesser N, Vinchure OS, Lauretti L, Fotia G, Schwarz RF, Wang X, Ricci-Vitiani L, Gopalakrishnan J, Pallini R, Papantonis A. Pervasive structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs. Nat Commun 2024; 15:3905. [PMID: 38724522 PMCID: PMC11082206 DOI: 10.1038/s41467-024-48053-2] [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: 11/24/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Glioblastoma multiforme (GBM) encompasses brain malignancies marked by phenotypic and transcriptional heterogeneity thought to render these tumors aggressive, resistant to therapy, and inevitably recurrent. However, little is known about how the spatial organization of GBM genomes underlies this heterogeneity and its effects. Here, we compile a cohort of 28 patient-derived glioblastoma stem cell-like lines (GSCs) known to reflect the properties of their tumor-of-origin; six of these were primary-relapse tumor pairs from the same patient. We generate and analyze 5 kbp-resolution chromosome conformation capture (Hi-C) data from all GSCs to systematically map thousands of standalone and complex structural variants (SVs) and the multitude of neoloops arising as a result. By combining Hi-C, histone modification, and gene expression data with chromatin folding simulations, we explain how the pervasive, uneven, and idiosyncratic occurrence of neoloops sustains tumor-specific transcriptional programs via the formation of new enhancer-promoter contacts. We also show how even moderately recurrent neoloops can relate to patient-specific vulnerabilities. Together, our data provide a resource for dissecting GBM biology and heterogeneity, as well as for informing therapeutic approaches.
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Affiliation(s)
- Ting Xie
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Adi Danieli-Mackay
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Mariachiara Buccarelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Mariano Barbieri
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Q Giorgio D'Alessandris
- Department of Neuroscience, Catholic University School of Medicine, Rome, Italy
- Department of Neuroscience, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Claudia Robens
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), University of Cologne, Cologne, Germany
| | - Nadine Übelmesser
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Omkar Suhas Vinchure
- Institute of Human Genetics, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Liverana Lauretti
- Department of Neuroscience, Catholic University School of Medicine, Rome, Italy
| | - Giorgio Fotia
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy
| | - Roland F Schwarz
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), University of Cologne, Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data (BIFOLD), Berlin, Germany
| | - Xiaotao Wang
- Institute of Reproduction and Development, Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Lucia Ricci-Vitiani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Jay Gopalakrishnan
- Institute of Human Genetics, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Institute of Human Genetics, Jena University Hospital and Friedrich Schiller University of Jena, Jena, Germany
| | - Roberto Pallini
- Department of Neuroscience, Catholic University School of Medicine, Rome, Italy.
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany.
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3
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Afanasyev AY, Kim Y, Tolokh IS, Sharakhov IV, Onufriev AV. The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies. Epigenetics Chromatin 2024; 17:13. [PMID: 38705995 PMCID: PMC11071202 DOI: 10.1186/s13072-024-00528-8] [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] [Received: 12/08/2023] [Accepted: 02/08/2024] [Indexed: 05/07/2024] Open
Abstract
BACKGROUND Multiple studies have demonstrated a negative correlation between gene expression and positioning of genes at the nuclear envelope (NE) lined by nuclear lamina, but the exact relationship remains unclear, especially in light of the highly stochastic, transient nature of the gene association with the NE. RESULTS In this paper, we ask whether there is a causal, systematic, genome-wide relationship between the expression levels of the groups of genes in topologically associating domains (TADs) of Drosophila nuclei and the probabilities of TADs to be found at the NE. To investigate the nature of this possible relationship, we combine a coarse-grained dynamic model of the entire Drosophila nucleus with genome-wide gene expression data; we analyze the TAD averaged transcription levels of genes against the probabilities of individual TADs to be in contact with the NE in the control and lamins-depleted nuclei. Our findings demonstrate that, within the statistical error margin, the stochastic positioning of Drosophila melanogaster TADs at the NE does not, by itself, systematically affect the mean level of gene expression in these TADs, while the expected negative correlation is confirmed. The correlation is weak and disappears completely for TADs not containing lamina-associated domains (LADs) or TADs containing LADs, considered separately. Verifiable hypotheses regarding the underlying mechanism for the presence of the correlation without causality are discussed. These include the possibility that the epigenetic marks and affinity to the NE of a TAD are determined by various non-mutually exclusive mechanisms and remain relatively stable during interphase. CONCLUSIONS At the level of TADs, the probability of chromatin being in contact with the nuclear envelope has no systematic, causal effect on the transcription level in Drosophila. The conclusion is reached by combining model-derived time-evolution of TAD locations within the nucleus with their experimental gene expression levels.
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Affiliation(s)
- Alexander Y Afanasyev
- Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Yoonjin Kim
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Igor S Tolokh
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
| | - Alexey V Onufriev
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- Center for Soft Matter and Biological Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
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4
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Oberbeckmann E, Oudelaar AM. Genome organization across scales: mechanistic insights from in vitro reconstitution studies. Biochem Soc Trans 2024; 52:793-802. [PMID: 38451192 PMCID: PMC11088924 DOI: 10.1042/bst20230883] [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: 01/12/2024] [Revised: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Eukaryotic genomes are compacted and organized into distinct three-dimensional (3D) structures, which range from small-scale nucleosome arrays to large-scale chromatin domains. These chromatin structures play an important role in the regulation of transcription and other nuclear processes. The molecular mechanisms that drive the formation of chromatin structures across scales and the relationship between chromatin structure and function remain incompletely understood. Because the processes involved are complex and interconnected, it is often challenging to dissect the underlying principles in the nuclear environment. Therefore, in vitro reconstitution systems provide a valuable approach to gain insight into the molecular mechanisms by which chromatin structures are formed and to determine the cause-consequence relationships between the processes involved. In this review, we give an overview of in vitro approaches that have been used to study chromatin structures across scales and how they have increased our understanding of the formation and function of these structures. We start by discussing in vitro studies that have given insight into the mechanisms of nucleosome positioning. Next, we discuss recent efforts to reconstitute larger-scale chromatin domains and loops and the resulting insights into the principles of genome organization. We conclude with an outlook on potential future applications of chromatin reconstitution systems and how they may contribute to answering open questions concerning chromatin architecture.
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Affiliation(s)
- Elisa Oberbeckmann
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - A. Marieke Oudelaar
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
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5
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Daniel B, Chen AY, Sandor K, Zhang W, Miao Z, Lareau CA, Yost KE, Chang HY, Satpathy AT. Regulation of immune signal integration and memory by inflammation-induced chromosome conformation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582872. [PMID: 38496446 PMCID: PMC10942375 DOI: 10.1101/2024.02.29.582872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
3-dimensional (3D) genome conformation is central to gene expression regulation, yet our understanding of its contribution to rapid transcriptional responses, signal integration, and memory in immune cells is limited. Here, we study the molecular regulation of the inflammatory response in primary macrophages using integrated transcriptomic, epigenomic, and chromosome conformation data, including base pair-resolution Micro-Capture C. We demonstrate that interleukin-4 (IL-4) primes the inflammatory response in macrophages by stably rewiring 3D genome conformation, juxtaposing endotoxin-, interferon-gamma-, and dexamethasone-responsive enhancers in close proximity to their cognate gene promoters. CRISPR-based perturbations of enhancer-promoter contacts or CCCTC-binding factor (CTCF) boundary elements demonstrated that IL-4-driven conformation changes are indispensable for enhanced and synergistic endotoxin-induced transcriptional responses, as well as transcriptional memory following stimulus removal. Moreover, transcriptional memory mediated by changes in chromosome conformation often occurred in the absence of changes in chromatin accessibility or histone modifications. Collectively, these findings demonstrate that rapid and memory transcriptional responses to immunological stimuli are encoded in the 3D genome.
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Affiliation(s)
- Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
- Present address: Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA, USA
| | - Andy Y. Chen
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
| | - Wenxi Zhang
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Zhuang Miao
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Caleb A. Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Present address: Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn E. Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Present address: Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Ansuman T. Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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6
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Oberbeckmann E, Quililan K, Cramer P, Oudelaar AM. In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization. Nat Genet 2024; 56:483-492. [PMID: 38291333 PMCID: PMC10937381 DOI: 10.1038/s41588-023-01649-8] [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] [Received: 03/30/2023] [Accepted: 12/15/2023] [Indexed: 02/01/2024]
Abstract
Eukaryotic genomes are organized into chromatin domains. The molecular mechanisms driving the formation of these domains are difficult to dissect in vivo and remain poorly understood. Here we reconstitute Saccharomyces cerevisiae chromatin in vitro and determine its 3D organization at subnucleosome resolution by micrococcal nuclease-based chromosome conformation capture and molecular dynamics simulations. We show that regularly spaced and phased nucleosome arrays form chromatin domains in vitro that resemble domains in vivo. This demonstrates that neither loop extrusion nor transcription is required for basic domain formation in yeast. In addition, we find that the boundaries of reconstituted domains correspond to nucleosome-free regions and that insulation strength scales with their width. Finally, we show that domain compaction depends on nucleosome linker length, with longer linkers forming more compact structures. Together, our results demonstrate that regular nucleosome positioning is important for the formation of chromatin domains and provide a proof-of-principle for bottom-up 3D genome studies.
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Affiliation(s)
- Elisa Oberbeckmann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany.
| | - Kimberly Quililan
- Max Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany
- The Francis Crick Institute, London, UK
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - A Marieke Oudelaar
- Max Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany.
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7
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Kocanova S, Raynal F, Goiffon I, Oksuz BA, Baú D, Kamgoué A, Cantaloube S, Zhan Y, Lajoie B, Marti-Renom MA, Dekker J, Bystricky K. Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells. Life Sci Alliance 2024; 7:e202302154. [PMID: 37989525 PMCID: PMC10663337 DOI: 10.26508/lsa.202302154] [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: 05/12/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023] Open
Abstract
The genome is organized in functional compartments and structural domains at the sub-megabase scale. How within these domains interactions between numerous cis-acting enhancers and promoters regulate transcription remains an open question. Here, we determined chromatin folding and composition over several hundred kb around estrogen-responsive genes in human breast cancer cell lines after hormone stimulation. Modeling of 5C data at 1.8 kb resolution was combined with quantitative 3D analysis of multicolor FISH measurements at 100 nm resolution and integrated with ChIP-seq data on transcription factor binding and histone modifications. We found that rapid estradiol induction of the progesterone gene expression occurs in the context of preexisting, cell type-specific chromosomal architectures encompassing the 90 kb progesterone gene coding region and an enhancer-spiked 5' 300 kb upstream genomic region. In response to estradiol, interactions between estrogen receptor α (ERα) bound regulatory elements are reinforced. Whereas initial enhancer-gene contacts coincide with RNA Pol 2 binding and transcription initiation, sustained hormone stimulation promotes ERα accumulation creating a regulatory hub stimulating transcript synthesis. In addition to implications for estrogen receptor signaling, we uncover that preestablished chromatin architectures efficiently regulate gene expression upon stimulation without the need for de novo extensive rewiring of long-range chromatin interactions.
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Affiliation(s)
- Silvia Kocanova
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Flavien Raynal
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Isabelle Goiffon
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Betul Akgol Oksuz
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Davide Baú
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
| | - Alain Kamgoué
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Sylvain Cantaloube
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Ye Zhan
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Bryan Lajoie
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Marc A Marti-Renom
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
- Genome Biology Program, Centre de Regulació Genòmica (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Job Dekker
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Kerstin Bystricky
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
- Institut Universitaire de France (IUF), Paris, France
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8
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Tourdot E, Grob S. Three-dimensional chromatin architecture in plants - General features and novelties. Eur J Cell Biol 2023; 102:151344. [PMID: 37562220 DOI: 10.1016/j.ejcb.2023.151344] [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: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Research on the three-dimensional (3D) structure of the genome and its distribution within the nuclear space has made a big leap in the last two decades. Work in the animal field has led to significant advances in our general understanding on eukaryotic genome organization. This did not only bring along insights into how the 3D genome interacts with the epigenetic landscape and the transcriptional machinery but also how 3D genome architecture is relevant for fundamental developmental processes, such as cell differentiation. In parallel, the 3D organization of plant genomes have been extensively studied, which resulted in both congruent and novel findings, contributing to a more complete view on how eukaryotic genomes are organized in multiple dimensions. Plant genomes are remarkably diverse in size, composition, and ploidy. Furthermore, as intrinsically sessile organisms without the possibility to relocate to more favorable environments, plants have evolved an elaborate epigenetic repertoire to rapidly respond to environmental challenges. The diversity in genome organization and the complex epigenetic programs make plants ideal study subjects to acquire a better understanding on universal features and inherent constraints of genome organization. Furthermore, considering a wide range of species allows us to study the evolutionary crosstalk between the various levels of genome architecture. In this article, we aim at summarizing important findings on 3D genome architecture obtained in various plant species. These findings cover many aspects of 3D genome organization on a wide range of levels, from gene loops to topologically associated domains and to global 3D chromosome configurations. We present an overview on plant 3D genome organizational features that resemble those in animals and highlight facets that have only been observed in plants to date.
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Affiliation(s)
- Edouard Tourdot
- Department of Plant and Microbial Biology, University of Zurich, Switzerland.
| | - Stefan Grob
- Department of Plant and Microbial Biology, University of Zurich, Switzerland.
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9
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Gunsalus LM, Keiser MJ, Pollard KS. In silico discovery of repetitive elements as key sequence determinants of 3D genome folding. CELL GENOMICS 2023; 3:100410. [PMID: 37868032 PMCID: PMC10589630 DOI: 10.1016/j.xgen.2023.100410] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/08/2022] [Accepted: 08/31/2023] [Indexed: 10/24/2023]
Abstract
Natural and experimental genetic variants can modify DNA loops and insulating boundaries to tune transcription, but it is unknown how sequence perturbations affect chromatin organization genome wide. We developed a deep-learning strategy to quantify the effect of any insertion, deletion, or substitution on chromatin contacts and systematically scored millions of synthetic variants. While most genetic manipulations have little impact, regions with CTCF motifs and active transcription are highly sensitive, as expected. Our unbiased screen and subsequent targeted experiments also point to noncoding RNA genes and several families of repetitive elements as CTCF-motif-free DNA sequences with particularly large effects on nearby chromatin interactions, sometimes exceeding the effects of CTCF sites and explaining interactions that lack CTCF. We anticipate that our disruption tracks may be of broad interest and utility as a measure of 3D genome sensitivity, and our computational strategies may serve as a template for biological inquiry with deep learning.
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Affiliation(s)
- Laura M. Gunsalus
- Gladstone Institutes, San Francisco, CA, USA
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Michael J. Keiser
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA
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10
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Crump NT, Smith AL, Godfrey L, Dopico-Fernandez AM, Denny N, Harman JR, Hamley JC, Jackson NE, Chahrour C, Riva S, Rice S, Kim J, Basrur V, Fermin D, Elenitoba-Johnson K, Roeder RG, Allis CD, Roberts I, Roy A, Geng H, Davies JOJ, Milne TA. MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia. Nat Commun 2023; 14:5208. [PMID: 37626123 PMCID: PMC10457349 DOI: 10.1038/s41467-023-40981-9] [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: 12/08/2022] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Aberrant enhancer activation is a key mechanism driving oncogene expression in many cancers. While much is known about the regulation of larger chromosome domains in eukaryotes, the details of enhancer-promoter interactions remain poorly understood. Recent work suggests co-activators like BRD4 and Mediator have little impact on enhancer-promoter interactions. In leukemias controlled by the MLL-AF4 fusion protein, we use the ultra-high resolution technique Micro-Capture-C (MCC) to show that MLL-AF4 binding promotes broad, high-density regions of enhancer-promoter interactions at a subset of key targets. These enhancers are enriched for transcription elongation factors like PAF1C and FACT, and the loss of these factors abolishes enhancer-promoter contact. This work not only provides an additional model for how MLL-AF4 is able to drive high levels of transcription at key genes in leukemia but also suggests a more general model linking enhancer-promoter crosstalk and transcription elongation.
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, W12 0NN, UK.
| | - Alastair L Smith
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana M Dopico-Fernandez
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Nicholas Denny
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Joe R Harman
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Joseph C Hamley
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Nicole E Jackson
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Catherine Chahrour
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Simone Riva
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Siobhan Rice
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Damian Fermin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kojo Elenitoba-Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Paediatrics, University of Oxford, Oxford, OX3 9DU, UK
| | - Anindita Roy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Paediatrics, University of Oxford, Oxford, OX3 9DU, UK
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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11
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Penagos-Puig A, Claudio-Galeana S, Stephenson-Gussinye A, Jácome-López K, Aguilar-Lomas A, Chen X, Pérez-Molina R, Furlan-Magaril M. RNA polymerase II pausing regulates chromatin organization in erythrocytes. Nat Struct Mol Biol 2023; 30:1092-1104. [PMID: 37500929 DOI: 10.1038/s41594-023-01037-0] [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: 06/14/2022] [Accepted: 06/16/2023] [Indexed: 07/29/2023]
Abstract
Chicken erythrocytes are nucleated cells often considered to be transcriptionally inactive, although the epigenetic changes and chromatin remodeling that would mediate transcriptional repression and the extent of gene silencing during avian terminal erythroid differentiation are not fully understood. Here, we characterize the changes in gene expression, chromatin accessibility, genome organization and chromatin nuclear disposition during the terminal stages of erythropoiesis in chicken and uncover complex chromatin reorganization at different genomic scales. We observe a robust decrease in transcription in erythrocytes, but a set of genes maintains their expression, including genes involved in RNA polymerase II (Pol II) promoter-proximal pausing. Erythrocytes exhibit a reoriented nuclear architecture, with accessible chromatin positioned towards the nuclear periphery together with the paused RNA Pol II. In erythrocytes, chromatin domains are partially lost genome-wide, except at minidomains retained around paused promoters. Our results suggest that promoter-proximal pausing of RNA Pol II contributes to the transcriptional regulation of the erythroid genome and highlight the role of RNA polymerase in the maintenance of local chromatin organization.
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Affiliation(s)
- Andrés Penagos-Puig
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sherlyn Claudio-Galeana
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Aura Stephenson-Gussinye
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Karina Jácome-López
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Amaury Aguilar-Lomas
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Rosario Pérez-Molina
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mayra Furlan-Magaril
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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12
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Liu M, Jin S, Agabiti SS, Jensen TB, Yang T, Radda JSD, Ruiz CF, Baldissera G, Muzumdar MD, Wang S. A genome-wide single-cell 3D genome atlas of lung cancer progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.23.550157. [PMID: 37546882 PMCID: PMC10401964 DOI: 10.1101/2023.07.23.550157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Alterations in three-dimensional (3D) genome structures are associated with cancer1-5. However, how genome folding evolves and diversifies during subclonal cancer progression in the native tissue environment remains unknown. Here, we leveraged a genome-wide chromatin tracing technology to directly visualize 3D genome folding in situ in a faithful Kras-driven mouse model of lung adenocarcinoma (LUAD)6, generating the first single-cell 3D genome atlas of any cancer. We discovered stereotypical 3D genome alterations during cancer development, including a striking structural bottleneck in preinvasive adenomas prior to progression to LUAD, indicating a stringent selection on the 3D genome early in cancer progression. We further showed that the 3D genome precisely encodes cancer states in single cells, despite considerable cell-to-cell heterogeneity. Finally, evolutionary changes in 3D genome compartmentalization - partially regulated by polycomb group protein Rnf2 through its ubiquitin ligase-independent activity - reveal novel genetic drivers and suppressors of LUAD progression. Our results demonstrate the importance of mapping the single-cell cancer 3D genome and the potential to identify new diagnostic and therapeutic biomarkers from 3D genomic architectures.
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Affiliation(s)
- Miao Liu
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Shengyan Jin
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Sherry S. Agabiti
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Yale Cancer Biology Institute, Yale University; West Haven, CT 06516, USA
| | - Tyler B. Jensen
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- M.D.-Ph.D. Program, Yale University; New Haven, CT 06510, USA
| | - Tianqi Yang
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Jonathan S. D. Radda
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Christian F. Ruiz
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Yale Cancer Biology Institute, Yale University; West Haven, CT 06516, USA
| | - Gabriel Baldissera
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Mandar Deepak Muzumdar
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Yale Cancer Biology Institute, Yale University; West Haven, CT 06516, USA
- M.D.-Ph.D. Program, Yale University; New Haven, CT 06510, USA
- Department of Internal Medicine, Section of Medical Oncology, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Yale Cancer Center, Smilow Cancer Hospital, New Haven, CT 06510, USA
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University; New Haven, CT 06510, USA
- Molecular Cell Biology, Genetics and Development Program, Yale University; New Haven, CT 06510, USA
| | - Siyuan Wang
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- M.D.-Ph.D. Program, Yale University; New Haven, CT 06510, USA
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University; New Haven, CT 06510, USA
- Molecular Cell Biology, Genetics and Development Program, Yale University; New Haven, CT 06510, USA
- Department of Cell Biology, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Biochemistry, Quantitative Biology, Biophysics, and Structural Biology Program, Yale University; New Haven, CT 06510, USA
- Yale Center for RNA Science and Medicine, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Liver Center, Yale University School of Medicine; New Haven, CT 06510, USA
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13
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Brückner DB, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science 2023; 380:1357-1362. [PMID: 37384691 PMCID: PMC10439308 DOI: 10.1126/science.adf5568] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression.
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Affiliation(s)
- David B. Brückner
- Institute of Science and Technology, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Hongtao Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Lev Barinov
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Benjamin Zoller
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France
| | - Thomas Gregor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France
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14
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Ohira T, Yoshimura K, Kugoh H. Human artificial chromosome carrying 3p21.3-p22.2 region suppresses hTERT transcription in oral cancer cells. Chromosome Res 2023; 31:17. [PMID: 37353691 PMCID: PMC10289923 DOI: 10.1007/s10577-023-09726-8] [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] [Received: 03/10/2023] [Revised: 04/24/2023] [Accepted: 06/06/2023] [Indexed: 06/25/2023]
Abstract
Telomerase is a ribonucleoprotein ribonucleic enzyme that elongates telomere repeat sequences at the ends of chromosomes and contributes to cellular immortalization. The catalytic component of telomerase, human telomerase reverse transcriptase (hTERT), has been observed to be reactivated in immortalized cells. Notably, most cancer cells have been found to have active hTERT mRNA transcription, resulting in continuous cell division, which is crucial for malignant transformation. Therefore, discovering mechanisms underlying the regulation of hTERT transcription is an attractive target for cancer-specific treatments.Loss of heterozygosity (LOH) of chromosome 3p21.3 has been frequently observed in human oral squamous cell carcinoma (OSCC). Moreover, we previously reported that HSC3 OSCC microcell hybrid clones with an introduced human chromosome 3 (HSC3#3) showed inhibition of hTERT transcription compared with the parental HSC3 cells. This study examined whether hTERT transcription regulators are present in the 3p21.3 region. We constructed a human artificial chromosome (HAC) vector (3p21.3-HAC) with only the 3p21.3-p22.2 region and performed functional analysis using the 3p21.3-HAC. HSC3 microcell hybrid clones with an introduced 3p21.3-HAC exhibited significant suppression of hTERT transcription, similar to the microcell hybrid clones with an intact chromosome 3. In contrast, HSC3 clones with truncated chromosome 3 with deletion of the 3p21.3 region (3delp21.3) showed no effect on hTERT expression levels. These results provide direct evidence that hTERT suppressor gene(s) were retained in the 3p21.3 region, suggesting that the presence of regulatory factors that control telomerase enzyme activity may be involved in the development of OSCC.
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Affiliation(s)
- Takahito Ohira
- Department of Chromosome Biomedical Engineering, Tottori University, 86 Nishi-Cho, Yonago, Tottori, 683-8503, Japan
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-Cho, Yonago, Tottori, 683-8503, Japan
| | - Kaho Yoshimura
- Department of Chromosome Biomedical Engineering, Tottori University, 86 Nishi-Cho, Yonago, Tottori, 683-8503, Japan
| | - Hiroyuki Kugoh
- Department of Chromosome Biomedical Engineering, Tottori University, 86 Nishi-Cho, Yonago, Tottori, 683-8503, Japan.
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-Cho, Yonago, Tottori, 683-8503, Japan.
- Division of Genome and Cellular Function, Department of Molecular and Cellular Biology, Tottori University, 86 Nishi-Cho, Yonago, Tottori, 683-8503, Japan.
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15
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Krasikova A, Kulikova T, Rodriguez Ramos JS, Maslova A. Assignment of the somatic A/B compartments to chromatin domains in giant transcriptionally active lampbrush chromosomes. Epigenetics Chromatin 2023; 16:24. [PMID: 37322523 DOI: 10.1186/s13072-023-00499-2] [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: 04/07/2023] [Accepted: 06/04/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND The three-dimensional configuration of the eukaryotic genome is an emerging area of research. Chromosome conformation capture outlined genome segregation into large scale A and B compartments corresponding mainly to transcriptionally active and repressive chromatin. It remains unknown how the compartmentalization of the genome changes in growing oocytes of animals with hypertranscriptional type of oogenesis. Such oocytes are characterized by highly elongated chromosomes, called lampbrush chromosomes, which acquire a typical chromomere-loop appearance, representing one of the classical model systems for exploring the structural and functional organization of chromatin domains. RESULTS Here, we compared the distribution of A/B compartments in chicken somatic cells with chromatin domains in lampbrush chromosomes. We found that in lampbrush chromosomes, the extended chromatin domains, restricted by compartment boundaries in somatic cells, disintegrate into individual chromomeres. Next, we performed FISH-mapping of the genomic loci, which belong to A or B chromatin compartments as well as to A/B compartment transition regions in embryonic fibroblasts on isolated lampbrush chromosomes. We found, that in chicken lampbrush chromosomes, clusters of dense compact chromomeres bearing short lateral loops and enriched with repressive epigenetic modifications generally correspond to constitutive B compartments in somatic cells. A compartments align with lampbrush chromosome segments with smaller, less compact chromomeres, longer lateral loops, and a higher transcriptional status. Clusters of small loose chromomeres with relatively long lateral loops show no obvious correspondence with either A or B compartment identity. Some genes belonging to facultative B (sub-) compartments can be tissue-specifically transcribed during oogenesis, forming distinct lateral loops. CONCLUSIONS Here, we established a correspondence between the A/B compartments in somatic interphase nucleus and chromatin segments in giant lampbrush chromosomes from diplotene stage oocytes. The chromomere-loop structure of the genomic regions corresponding to interphase A and B compartments reveals the difference in how they are organized at the level of chromatin domains. The results obtained also suggest that gene-poor regions tend to be packed into chromomeres.
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Affiliation(s)
- Alla Krasikova
- Saint-Petersburg State University, Saint-Petersburg, Russia.
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16
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Kyrchanova O, Ibragimov A, Postika N, Georgiev P, Schedl P. Boundary Bypass Activity in the Abdominal-B Region of the Drosophila Bithorax Complex is Position Dependent and Regulated. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543971. [PMID: 37333165 PMCID: PMC10274778 DOI: 10.1101/2023.06.06.543971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Expression of Abdominal-B ( Abd-B ) in abdominal segments A5 - A8 is controlled by four regulatory domains, iab-5 - iab-8 . Each domain has an initiator element (which sets the activity state), elements that maintain this state and tissue-specific enhancers. To ensure their functional autonomy, each domain is bracketed by boundary elements ( Mcp , Fab-7 , Fab-7 and Fab-8 ). In addition to blocking crosstalk between adjacent regulatory domains, the Fab boundaries must also have bypass activity so the relevant regulatory domains can "jump over" intervening boundaries and activate the Abd-B promoter. In the studies reported here we have investigated the parameters governing bypass activity. We find that the bypass elements in the Fab-7 and Fab-8 boundaries must be located in the regulatory domain that is responsible for driving Abd-B expression. We suggest that bypass activity may also be subject to regulation. Summary Statement Boundaries separating Abd-B regulatory domains block crosstalk between domains and mediate their interactions with Abd-B . The latter function is location but not orientation dependent.
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Affiliation(s)
- Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Airat Ibragimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Nikolay Postika
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Paul Schedl
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
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17
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Jia X, Lin W, Wang W. Regulation of chromatin organization during animal regeneration. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:19. [PMID: 37259007 DOI: 10.1186/s13619-023-00162-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/21/2023] [Indexed: 06/02/2023]
Abstract
Activation of regeneration upon tissue damages requires the activation of many developmental genes responsible for cell proliferation, migration, differentiation, and tissue patterning. Ample evidence revealed that the regulation of chromatin organization functions as a crucial mechanism for establishing and maintaining cellular identity through precise control of gene transcription. The alteration of chromatin organization can lead to changes in chromatin accessibility and/or enhancer-promoter interactions. Like embryogenesis, each stage of tissue regeneration is accompanied by dynamic changes of chromatin organization in regeneration-responsive cells. In the past decade, many studies have been conducted to investigate the contribution of chromatin organization during regeneration in various tissues, organs, and organisms. A collection of chromatin regulators were demonstrated to play critical roles in regeneration. In this review, we will summarize the progress in the understanding of chromatin organization during regeneration in different research organisms and discuss potential common mechanisms responsible for the activation of regeneration response program.
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Affiliation(s)
- Xiaohui Jia
- National Institute of Biological Sciences, Beijing, 102206, China
- China Agricultural University, Beijing, 100083, China
| | - Weifeng Lin
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
| | - Wei Wang
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China.
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18
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Goychuk A, Kannan D, Chakraborty AK, Kardar M. Polymer folding through active processes recreates features of genome organization. Proc Natl Acad Sci U S A 2023; 120:e2221726120. [PMID: 37155885 PMCID: PMC10194017 DOI: 10.1073/pnas.2221726120] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 04/02/2023] [Indexed: 05/10/2023] Open
Abstract
From proteins to chromosomes, polymers fold into specific conformations that control their biological function. Polymer folding has long been studied with equilibrium thermodynamics, yet intracellular organization and regulation involve energy-consuming, active processes. Signatures of activity have been measured in the context of chromatin motion, which shows spatial correlations and enhanced subdiffusion only in the presence of adenosine triphosphate. Moreover, chromatin motion varies with genomic coordinate, pointing toward a heterogeneous pattern of active processes along the sequence. How do such patterns of activity affect the conformation of a polymer such as chromatin? We address this question by combining analytical theory and simulations to study a polymer subjected to sequence-dependent correlated active forces. Our analysis shows that a local increase in activity (larger active forces) can cause the polymer backbone to bend and expand, while less active segments straighten out and condense. Our simulations further predict that modest activity differences can drive compartmentalization of the polymer consistent with the patterns observed in chromosome conformation capture experiments. Moreover, segments of the polymer that show correlated active (sub)diffusion attract each other through effective long-ranged harmonic interactions, whereas anticorrelations lead to effective repulsions. Thus, our theory offers nonequilibrium mechanisms for forming genomic compartments, which cannot be distinguished from affinity-based folding using structural data alone. As a first step toward exploring whether active mechanisms contribute to shaping genome conformations, we discuss a data-driven approach.
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Affiliation(s)
- Andriy Goychuk
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Deepti Kannan
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Arup K. Chakraborty
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Mehran Kardar
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
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19
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Fragoso-Luna A, Askjaer P. The Nuclear Envelope in Ageing and Progeria. Subcell Biochem 2023; 102:53-75. [PMID: 36600129 DOI: 10.1007/978-3-031-21410-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Development from embryo to adult, organismal homeostasis and ageing are consecutive processes that rely on several functions of the nuclear envelope (NE). The NE compartmentalises the eukaryotic cells and provides physical stability to the genetic material in the nucleus. It provides spatiotemporal regulation of gene expression by controlling nuclear import and hence access of transcription factors to target genes as well as organisation of the genome into open and closed compartments. In addition, positioning of chromatin relative to the NE is important for DNA replication and repair and thereby also for genome stability. We discuss here the relevance of the NE in two classes of age-related human diseases. Firstly, we focus on the progeria syndromes Hutchinson-Gilford (HGPS) and Nestor-Guillermo (NGPS), which are caused by mutations in the LMNA and BANF1 genes, respectively. Both genes encode ubiquitously expressed components of the nuclear lamina that underlines the nuclear membranes. HGPS and NGPS patients manifest symptoms of accelerated ageing and cells from affected individuals show similar defects as cells from healthy old donors, including signs of increased DNA damage and epigenetic alternations. Secondly, we describe how several age-related neurodegenerative diseases, such as amyotrophic lateral sclerosis and Huntington's disease, are related with defects in nucleocytoplasmic transport. A common feature of this class of diseases is the accumulation of nuclear pore proteins and other transport factors in inclusions. Importantly, genetic manipulations of the nucleocytoplasmic transport machinery can alleviate disease-related phenotypes in cell and animal models, paving the way for potential therapeutic interventions.
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Affiliation(s)
- Adrián Fragoso-Luna
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Pablo de Olavide, Sevilla, Spain
| | - Peter Askjaer
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Pablo de Olavide, Sevilla, Spain.
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20
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Cai Z, Han X, Li R, Yu T, Chen L, Wu X, Jin J. Research Progress of Long Non-coding RNAs in Spinal Cord Injury. Neurochem Res 2023; 48:1-12. [PMID: 35974214 PMCID: PMC9823062 DOI: 10.1007/s11064-022-03720-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/24/2022] [Accepted: 08/01/2022] [Indexed: 01/11/2023]
Abstract
Spinal cord injury (SCI) can result in a partial or complete loss of motor and sensory function below the injured segment, which has a significant impact on patients' quality of life and places a significant social burden on them. Long non-coding RNA (LncRNA) is a 200-1000 bp non-coding RNA that has been shown to have a key regulatory role in the progression of a variety of neurological illnesses. Many studies have demonstrated that differentially expressed LncRNAs following spinal cord injury can participate in inflammatory damage, apoptosis, and nerve healing by functioning as competitive endogenous RNA (ceRNA); at the same time, it has a significant regulatory effect on sequelae such neuropathic pain. As a result, we believe that LncRNAs could be useful as a molecular regulatory target in the diagnosis, treatment, and prognosis of spinal cord injury.
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Affiliation(s)
- Zongyan Cai
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Xue Han
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Ruizhe Li
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Tianci Yu
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Lei Chen
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - XueXue Wu
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Jiaxin Jin
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China.
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, 730000, People's Republic of China.
- Department of Orthopaedics, The Second Hospital of Lanzhou University, Lanzhou, 730000, People's Republic of China.
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21
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Kołat D, Zhao LY, Kciuk M, Płuciennik E, Kałuzińska-Kołat Ż. AP-2δ Is the Most Relevant Target of AP-2 Family-Focused Cancer Therapy and Affects Genome Organization. Cells 2022; 11:cells11244124. [PMID: 36552887 PMCID: PMC9776946 DOI: 10.3390/cells11244124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/26/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Formerly hailed as "undruggable" proteins, transcription factors (TFs) are now under investigation for targeted therapy. In cancer, this may alter, inter alia, immune evasion or replicative immortality, which are implicated in genome organization, a process that accompanies multi-step tumorigenesis and which frequently develops in a non-random manner. Still, targeting-related research on some TFs is scarce, e.g., among AP-2 proteins, which are known for their altered functionality in cancer and prognostic importance. Using public repositories, bioinformatics tools, and RNA-seq data, the present study examined the ligandability of all AP-2 members, selecting the best one, which was investigated in terms of mutations, targets, co-activators, correlated genes, and impact on genome organization. AP-2 proteins were found to have the conserved "TF_AP-2" domain, but manifested different binding characteristics and evolution. Among them, AP-2δ has not only the highest number of post-translational modifications and extended strands but also contains a specific histidine-rich region and cleft that can receive a ligand. Uterine, colon, lung, and stomach tumors are most susceptible to AP-2δ mutations, which also co-depend with cancer hallmark genes and drug targets. Considering AP-2δ targets, some of them were located proximally in the spatial genome or served as co-factors of the genes regulated by AP-2δ. Correlation and functional analyses suggested that AP-2δ affects various processes, including genome organization, via its targets; this has been eventually verified in lung adenocarcinoma using expression and immunohistochemistry data of chromosomal conformation-related genes. In conclusion, AP-2δ affects chromosomal conformation and is the most appropriate target for cancer therapy focused on the AP-2 family.
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Affiliation(s)
- Damian Kołat
- Department of Experimental Surgery, Medical University of Lodz, 90-136 Lodz, Poland
- Correspondence:
| | - Lin-Yong Zhao
- Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Centre for Biotherapy, Chengdu 610041, China
| | - Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, 90-237 Lodz, Poland
- Doctoral School of Exact and Natural Sciences, University of Lodz, 90-237 Lodz, Poland
| | - Elżbieta Płuciennik
- Department of Functional Genomics, Medical University of Lodz, 90-752 Lodz, Poland
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22
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Zhu X, Qi C, Wang R, Lee JH, Shao J, Bei L, Xiong F, Nguyen PT, Li G, Krakowiak J, Koh SP, Simon LM, Han L, Moore TI, Li W. Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization. Cell Rep 2022; 41:111576. [PMID: 36323253 PMCID: PMC9744245 DOI: 10.1016/j.celrep.2022.111576] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/26/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
The nuclear pore complex (NPC) comprises more than 30 nucleoporins (NUPs) and is a hallmark of eukaryotes. NUPs have been suggested to be important in regulating gene transcription and 3D genome organization. However, evidence in support of their direct roles remains limited. Here, by Cut&Run, we find that core NUPs display broad but also cell-type-specific association with active promoters and enhancers in human cells. Auxin-mediated rapid depletion of two NUPs demonstrates that NUP93, but not NUP35, directly and specifically controls gene transcription. NUP93 directly activates genes with high levels of RNA polymerase II loading and transcriptional elongation by facilitating full BRD4 recruitment to their active enhancers. dCas9-based tethering confirms a direct and causal role of NUP93 in gene transcriptional activation. Unexpectedly, in situ Hi-C and H3K27ac or H3K4me1 HiChIP results upon acute NUP93 depletion show negligible changesS2211-1247(22)01437-1 of 3D genome organization ranging from A/B compartments and topologically associating domains (TADs) to enhancer-promoter contacts.
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Affiliation(s)
- Xiaoyu Zhu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA,These authors contributed equally
| | - Chuangye Qi
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA,These authors contributed equally
| | - Ruoyu Wang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA,The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA,These authors contributed equally
| | - Joo-Hyung Lee
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jiaofang Shao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lanxin Bei
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA,The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Phuoc T. Nguyen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA,The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Guojie Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Joanna Krakowiak
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Su-Pin Koh
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lukas M. Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Travis I. Moore
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA,The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA,Lead contact,Correspondence:
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23
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Episomes and Transposases-Utilities to Maintain Transgene Expression from Nonviral Vectors. Genes (Basel) 2022; 13:genes13101872. [PMID: 36292757 PMCID: PMC9601623 DOI: 10.3390/genes13101872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/04/2022] Open
Abstract
The efficient delivery and stable transgene expression are critical for applications in gene therapy. While carefully selected and engineered viral vectors allowed for remarkable clinical successes, they still bear significant safety risks. Thus, nonviral vectors are a sound alternative and avoid genotoxicity and adverse immunological reactions. Nonviral vector systems have been extensively studied and refined during the last decades. Emerging knowledge of the epigenetic regulation of replication and spatial chromatin organisation, as well as new technologies, such as Crispr/Cas, were employed to enhance the performance of different nonviral vector systems. Thus, nonviral vectors are in focus and hold some promising perspectives for future applications in gene therapy. This review addresses three prominent nonviral vector systems: the Sleeping Beauty transposase, S/MAR-based episomes, and viral plasmid replicon-based EBV vectors. Exemplarily, we review different utilities, modifications, and new concepts that were pursued to overcome limitations regarding stable transgene expression and mitotic stability. New insights into the nuclear localisation of nonviral vector molecules and the potential consequences thereof are highlighted. Finally, we discuss the remaining limitations and provide an outlook on possible future developments in nonviral vector technology.
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24
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Marchal C, Singh N, Batz Z, Advani J, Jaeger C, Corso-Díaz X, Swaroop A. High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci. Nat Commun 2022; 13:5827. [PMID: 36207300 PMCID: PMC9547065 DOI: 10.1038/s41467-022-33427-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022] Open
Abstract
Chromatin organization and enhancer-promoter contacts establish unique spatiotemporal gene expression patterns in distinct cell types. Non-coding genetic variants can influence cellular phenotypes by modifying higher-order transcriptional hubs and consequently gene expression. To elucidate genomic regulation in human retina, we mapped chromatin contacts at high resolution and integrated with super-enhancers (SEs), histone marks, binding of CTCF and select transcription factors. We show that topologically associated domains (TADs) with central SEs exhibit stronger insulation and augmented contact with retinal genes relative to TADs with edge SEs. Merging genome-wide expression quantitative trait loci (eQTLs) with topology map reveals physical links between 100 eQTLs and corresponding eGenes associated with retinal neurodegeneration. Additionally, we uncover candidate genes for susceptibility variants linked to age-related macular degeneration and glaucoma. Our study of high-resolution genomic architecture of human retina provides insights into genetic control of tissue-specific functions, suggests paradigms for missing heritability, and enables the dissection of common blinding disease phenotypes.
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Affiliation(s)
- Claire Marchal
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
- In silichrom Ltd, First Floor, Angel Court, 81 St Clements St, Oxford, OX4 1AW, UK
| | - Nivedita Singh
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Zachary Batz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Catherine Jaeger
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Ximena Corso-Díaz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA.
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25
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Wang H, Li B, Zuo L, Wang B, Yan Y, Tian K, Zhou R, Wang C, Chen X, Jiang Y, Zheng H, Qin F, Zhang B, Yu Y, Liu CP, Xu Y, Gao J, Qi Z, Deng W, Ji X. The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors. Nat Commun 2022; 13:5703. [PMID: 36171202 PMCID: PMC9519968 DOI: 10.1038/s41467-022-33433-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 09/16/2022] [Indexed: 11/10/2022] Open
Abstract
RNA polymerase II (Pol II) apparatuses are compartmentalized into transcriptional clusters. Whether protein factors control these clusters remains unknown. In this study, we find that the ATPase-associated with diverse cellular activities (AAA + ) ATPase RUVBL2 co-occupies promoters with Pol II and various transcription factors. RUVBL2 interacts with unphosphorylated Pol II in chromatin to promote RPB1 carboxy-terminal domain (CTD) clustering and transcription initiation. Rapid depletion of RUVBL2 leads to a decrease in the number of Pol II clusters and inhibits nascent RNA synthesis, and tethering RUVBL2 to an active promoter enhances Pol II clustering at the promoter. We also identify target genes that are directly linked to the RUVBL2-Pol II axis. Many of these genes are hallmarks of cancers and encode proteins with diverse cellular functions. Our results demonstrate an emerging activity for RUVBL2 in regulating Pol II cluster formation in the nucleus. RNA polymerase II (Pol II) transcription factories play a central role in gene expression and 3D chromatin organization. Here, the authors demonstrate that RUVBL2 directly regulates Pol II clustering at active gene promoters.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.,Department of Pathogenic Biology, Chengdu Medical College, Chengdu, 610500, China
| | - Boyuan Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Linyu Zuo
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Bo Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences (CLS), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yan Yan
- Institute for TCM-X; MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist (Beijing National Research Center for Information Science and Technology); Department of Automation, Tsinghua University, Beijing, 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Rong Zhou
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Chenlu Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Haonan Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Fangfei Qin
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Bin Zhang
- Departments of Pathology and Laboratory Medicine, and Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA
| | - Yang Yu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chao-Pei Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Juntao Gao
- Institute for TCM-X; MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist (Beijing National Research Center for Information Science and Technology); Department of Automation, Tsinghua University, Beijing, 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Zhi Qi
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Wulan Deng
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences (CLS), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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26
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Fleck K, Raj R, Erceg J. The 3D genome landscape: Diverse chromosomal interactions and their functional implications. Front Cell Dev Biol 2022; 10:968145. [PMID: 36036013 PMCID: PMC9402908 DOI: 10.3389/fcell.2022.968145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Genome organization includes contacts both within a single chromosome and between distinct chromosomes. Thus, regulatory organization in the nucleus may include interplay of these two types of chromosomal interactions with genome activity. Emerging advances in omics and single-cell imaging technologies have allowed new insights into chromosomal contacts, including those of homologs and sister chromatids, and their significance to genome function. In this review, we highlight recent studies in this field and discuss their impact on understanding the principles of chromosome organization and associated functional implications in diverse cellular processes. Specifically, we describe the contributions of intra-chromosomal, inter-homolog, and inter-sister chromatid contacts to genome organization and gene expression.
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Affiliation(s)
- Katherine Fleck
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Romir Raj
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Jelena Erceg
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, United States
- *Correspondence: Jelena Erceg,
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27
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Jiang Z, Qi Y, Kamat K, Zhang B. Phase Separation and Correlated Motions in Motorized Genome. J Phys Chem B 2022; 126:5619-5628. [PMID: 35858189 PMCID: PMC9899348 DOI: 10.1021/acs.jpcb.2c03238] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The human genome is arranged in the cell nucleus nonrandomly, and phase separation has been proposed as an important driving force for genome organization. However, the cell nucleus is an active system, and the contribution of nonequilibrium activities to phase separation and genome structure and dynamics remains to be explored. We simulated the genome using an energy function parametrized with chromosome conformation capture (Hi-C) data with the presence of active, nondirectional forces that break the detailed balance. We found that active forces that may arise from transcription and chromatin remodeling can dramatically impact the spatial localization of heterochromatin. When applied to euchromatin, active forces can drive heterochromatin to the nuclear envelope and compete with passive interactions among heterochromatin that tend to pull them in opposite directions. Furthermore, active forces induce long-range spatial correlations among genomic loci beyond single chromosome territories. We further showed that the impact of active forces could be understood from the effective temperature defined as the fluctuation-dissipation ratio. Our study suggests that nonequilibrium activities can significantly impact genome structure and dynamics, producing unexpected collective phenomena.
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Affiliation(s)
- Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Yifeng Qi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Kartik Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
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28
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Stefanucci L, Frontini M. Non-coding genetic variation in regulatory elements determines thrombosis and hemostasis phenotypes. J Thromb Haemost 2022; 20:1759-1765. [PMID: 35514262 PMCID: PMC9540108 DOI: 10.1111/jth.15754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 11/26/2022]
Abstract
Since the early inception of genome-wide association studies (GWAS), it became clear that, in all diseases or traits studied, most genetic variants are likely to exert their effect on gene expression mainly by altering the function of regulatory elements. At the same time, the regulation of the gene expression field broadened its boundaries, from the univocal relationship between regulatory elements and genes to include genome organization, long-range DNA interactions, and epigenetics. Next-generation sequencing has introduced genome-wide approaches that have greatly improved our understanding of the general principles of gene expression. However, elucidating how these apply in every single genomic locus still requires painstaking experimental work, in which several independent lines of evidence are required, and often this is helped by rare genetic variants in individuals with rare diseases. This review will focus on the non-coding features of the genome involved in transcriptional regulation, that when altered, leads to known cases of inherited (familial) thrombotic and hemostatic phenotypes, emphasizing the role of enhancers and super-enhancers.
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Affiliation(s)
- Luca Stefanucci
- Department of HaematologyUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
- National Health Service (NHS) Blood and TransplantCambridge Biomedical CampusCambridgeUK
- British Heart Foundation, Cambridge Centre for Research ExcellenceUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
| | - Mattia Frontini
- Department of HaematologyUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
- National Health Service (NHS) Blood and TransplantCambridge Biomedical CampusCambridgeUK
- British Heart Foundation, Cambridge Centre for Research ExcellenceUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
- Institute of Biomedical & Clinical Science, College of Medicine and HealthUniversity of Exeter Medical SchoolExeterUK
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29
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Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery. Nat Commun 2022; 13:4199. [PMID: 35859152 PMCID: PMC9300685 DOI: 10.1038/s41467-022-31857-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/06/2022] [Indexed: 11/08/2022] Open
Abstract
The genome can be divided into two spatially segregated compartments, A and B, which partition active and inactive chromatin states. While constitutive heterochromatin is predominantly located within the B compartment near the nuclear lamina, facultative heterochromatin marked by H3K27me3 spans both compartments. How epigenetic modifications, compartmentalization, and lamina association collectively maintain heterochromatin architecture remains unclear. Here we develop Lamina-Inducible Methylation and Hi-C (LIMe-Hi-C) to jointly measure chromosome conformation, DNA methylation, and lamina positioning. Through LIMe-Hi-C, we identify topologically distinct sub-compartments with high levels of H3K27me3 and differing degrees of lamina association. Inhibition of Polycomb repressive complex 2 (PRC2) reveals that H3K27me3 is essential for sub-compartment segregation. Unexpectedly, PRC2 inhibition promotes lamina association and constitutive heterochromatin spreading into H3K27me3-marked B sub-compartment regions. Consistent with this repositioning, genes originally marked with H3K27me3 in the B compartment, but not the A compartment, remain largely repressed, suggesting that constitutive heterochromatin spreading can compensate for H3K27me3 loss at a transcriptional level. These findings demonstrate that Polycomb sub-compartments and their antagonism with lamina association are fundamental features of genome structure. More broadly, by jointly measuring nuclear position and Hi-C contacts, our study demonstrates how compartmentalization and lamina association represent distinct but interdependent modes of heterochromatin regulation.
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30
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Jeppsson K, Sakata T, Nakato R, Milanova S, Shirahige K, Björkegren C. Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks. SCIENCE ADVANCES 2022; 8:eabn7063. [PMID: 35687682 PMCID: PMC9187231 DOI: 10.1126/sciadv.abn7063] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 12/15/2021] [Accepted: 04/27/2022] [Indexed: 05/31/2023]
Abstract
Genome function depends on regulated chromosome folding, and loop extrusion by the protein complex cohesin is essential for this multilayered organization. The chromosomal positioning of cohesin is controlled by transcription, and the complex also localizes to stalled replication forks. However, the role of transcription and replication in chromosome looping remains unclear. Here, we show that reduction of chromosome-bound RNA polymerase weakens normal cohesin loop extrusion boundaries, allowing cohesin to form new long-range chromosome cis interactions. Stress response genes induced by transcription inhibition are also shown to act as new loop extrusion boundaries. Furthermore, cohesin loop extrusion during early S phase is jointly controlled by transcription and replication units. Together, the results reveal that replication and transcription machineries are chromosome-folding regulators that block the progression of loop-extruding cohesin, opening for new perspectives on cohesin's roles in genome function and stability.
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Affiliation(s)
- Kristian Jeppsson
- Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden
- Institute for Quantitative Bioscience, Tokyo University, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Toyonori Sakata
- Institute for Quantitative Bioscience, Tokyo University, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Bioscience, Tokyo University, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Stefina Milanova
- Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden
| | - Katsuhiko Shirahige
- Institute for Quantitative Bioscience, Tokyo University, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Camilla Björkegren
- Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden
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31
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López-Jiménez E, González-Aguilera C. Role of Chromatin Replication in Transcriptional Plasticity, Cell Differentiation and Disease. Genes (Basel) 2022; 13:genes13061002. [PMID: 35741764 PMCID: PMC9222293 DOI: 10.3390/genes13061002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Chromatin organization is essential to maintain a correct regulation of gene expression and establish cell identity. However, during cell division, the replication of the genetic material produces a global disorganization of chromatin structure. In this paper, we describe the new scientific breakthroughs that have revealed the nature of the post-replicative chromatin and the mechanisms that facilitate its restoration. Moreover, we highlight the implications of these chromatin alterations in gene expression control and their impact on key biological processes, such as cell differentiation, cell reprogramming or human diseases linked to cell proliferation, such as cancer.
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Affiliation(s)
- Elena López-Jiménez
- Faculty of Medicine, National Heart and Lung Institute, Margaret Turner Warwick Centre for Fibrosing Lung Disease, Royal Brompton Campus, Imperial College London, London SW3 6LY, UK;
| | - Cristina González-Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
- Correspondence:
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32
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Cheung CY, Huang TT, Chow N, Zhang S, Zhao Y, Chau MP, Chan WC, Wong CCL, Boassa D, Phan S, Ellisman MH, Yates JR, Xu S, Yu Z, Zhang Y, Zhang R, Ng LL, Ko BCB. Unconventional tonicity-regulated nuclear trafficking of NFAT5 mediated by KPNB1, XPOT and RUVBL2. J Cell Sci 2022; 135:275560. [PMID: 35635291 PMCID: PMC9377714 DOI: 10.1242/jcs.259280] [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: 08/18/2021] [Accepted: 05/20/2022] [Indexed: 11/20/2022] Open
Abstract
NFAT5 is the only known mammalian tonicity-responsive transcription factor with essential role in cellular adaptation to hypertonic stress. It is also implicated in diverse physiological and pathological processes. NFAT5 activity is tightly regulated by extracellular tonicity, but the underlying mechanisms remain elusive. We demonstrated that NFAT5 enters the nucleus via the nuclear pore complex. We found that NFAT5 utilizes a unique nuclear localization signal (NFAT5-NLS) for nuclear import. siRNA screening revealed that only karyopherin β1 (KPNB1), but not karyopherin alpha, is responsible for the nuclear import of NFAT5 via direct interaction with the NFAT5-NLS. Proteomics analysis and siRNA screening further revealed that nuclear export of NFAT5 under hypotonicity is driven by Exportin-T, where the process requires RuvB-Like AAA type ATPase 2 (RUVBL2) as an indispensable chaperone. Our findings have identified an unconventional tonicity-dependent nucleocytoplasmic trafficking pathway for NFAT5, a critical step in orchestrating rapid cellular adaptation to change in extracellular tonicity. These findings offer an opportunity for the development of novel NFAT5 targeting strategies that are potentially useful for the treatment of diseases associated with NFAT5 dysregulation.
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Affiliation(s)
- Chris Y Cheung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ting-Ting Huang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ning Chow
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Shuqi Zhang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yanxiang Zhao
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Mary P Chau
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Wing Cheung Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Catherine C L Wong
- Center for Precision Medicine Muti-Omics Research, Health Science Center, Peking University, China Clinical Laboratory Department, The Cancer Hospital of the University of Chinese Academy of Sciences, Beijing, China
| | - Daniela Boassa
- Department of Neurosciences, University of California, San Diego, USA.,Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Sebastien Phan
- Department of Neurosciences, University of California, San Diego, USA.,Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Mark H Ellisman
- Department of Neurosciences, University of California, San Diego, USA.,Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | - SongXiao Xu
- The Clinical Laboratory Department, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Zicheng Yu
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yajing Zhang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Rui Zhang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ling Ling Ng
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ben C B Ko
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
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33
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Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy. Sci Rep 2022; 12:8582. [PMID: 35595799 PMCID: PMC9122977 DOI: 10.1038/s41598-022-12568-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/10/2022] [Indexed: 11/18/2022] Open
Abstract
The three-dimensional (3D) genome structure plays a fundamental role in gene regulation and cellular functions. Recent studies in 3D genomics inferred the very basic functional chromatin folding structures known as chromatin loops, the long-range chromatin interactions that are mediated by protein factors and dynamically extruded by cohesin. We combined the use of FISH staining of a very short (33 kb) chromatin fragment, interferometric photoactivated localization microscopy (iPALM), and traveling salesman problem-based heuristic loop reconstruction algorithm from an image of the one of the strongest CTCF-mediated chromatin loops in human lymphoblastoid cells. In total, we have generated thirteen good quality images of the target chromatin region with 2–22 nm oligo probe localization precision. We visualized the shape of the single chromatin loops with unprecedented genomic resolution which allowed us to study the structural heterogeneity of chromatin looping. We were able to compare the physical distance maps from all reconstructed image-driven computational models with contact frequencies observed by ChIA-PET and Hi-C genomic-driven methods to examine the concordance between single cell imaging and population based genomic data.
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34
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Nollmann M, Bennabi I, Götz M, Gregor T. The Impact of Space and Time on the Functional Output of the Genome. Cold Spring Harb Perspect Biol 2022; 14:a040378. [PMID: 34230036 PMCID: PMC8733053 DOI: 10.1101/cshperspect.a040378] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Over the past two decades, it has become clear that the multiscale spatial and temporal organization of the genome has important implications for nuclear function. This review centers on insights gained from recent advances in light microscopy on our understanding of transcription. We discuss spatial and temporal aspects that shape nuclear order and their consequences on regulatory components, focusing on genomic scales most relevant to function. The emerging picture is that spatiotemporal constraints increase the complexity in transcriptional regulation, highlighting new challenges, such as uncertainty about how information travels from molecular factors through the genome and space to generate a functional output.
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Affiliation(s)
- Marcelo Nollmann
- Centre de Biologie Structurale, CNRS UMR5048, INSERM U1054, Univ Montpellier, 34090 Montpellier, France
| | - Isma Bennabi
- Department of Stem Cell and Developmental Biology, CNRS UMR3738, Institut Pasteur, 75015 Paris, France
| | - Markus Götz
- Centre de Biologie Structurale, CNRS UMR5048, INSERM U1054, Univ Montpellier, 34090 Montpellier, France
| | - Thomas Gregor
- Department of Stem Cell and Developmental Biology, CNRS UMR3738, Institut Pasteur, 75015 Paris, France
- Joseph Henry Laboratory of Physics & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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35
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Zhou J. Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale. Nat Genet 2022; 54:725-734. [PMID: 35551308 DOI: 10.1038/s41588-022-01065-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 03/29/2022] [Indexed: 11/09/2022]
Abstract
To learn how genomic sequence influences multiscale three-dimensional (3D) genome architecture, this manuscript presents a sequence-based deep-learning approach, Orca, that predicts directly from sequence the 3D genome architecture from kilobase to whole-chromosome scale. Orca captures the sequence dependencies of structures including chromatin compartments and topologically associating domains, as well as diverse types of interactions from CTCF-mediated to enhancer-promoter interactions and Polycomb-mediated interactions with cell-type specificity. Orca enables various applications including predicting structural variant effects on multiscale genome organization and it recapitulated effects of experimentally studied variants at varying sizes (300 bp to 90 Mb). Moreover, Orca enables in silico virtual screens to probe the sequence basis of 3D genome organization at different scales. At the submegabase scale, it predicted specific transcription factor motifs underlying cell-type-specific genome interactions. At the compartment scale, virtual screens of sequence activities suggest a model for the sequence basis of chromatin compartments with a prominent role of transcription start sites.
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Affiliation(s)
- Jian Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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36
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Deng S, Feng Y, Pauklin S. 3D chromatin architecture and transcription regulation in cancer. J Hematol Oncol 2022; 15:49. [PMID: 35509102 PMCID: PMC9069733 DOI: 10.1186/s13045-022-01271-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 12/18/2022] Open
Abstract
Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role in developing abnormalities and diseases such as cancer. This review discusses key 3D chromatin structures (topologically associating domain, lamina-associated domain, and enhancer-promoter interactions) and corresponding structural protein elements mediating 3D chromatin interactions [CCCTC-binding factor, polycomb group protein, cohesin, and Brother of the Regulator of Imprinted Sites (BORIS) protein] with a highlight of their associations with cancer. We also summarise the recent development of technologies and bioinformatics approaches to study the 3D chromatin interactions in gene expression regulation, including crosslinking and proximity ligation methods in the bulk cell population (ChIA-PET and HiChIP) or single-molecule resolution (ChIA-drop), and methods other than proximity ligation, such as GAM, SPRITE, and super-resolution microscopy techniques.
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Affiliation(s)
- Siwei Deng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Siim Pauklin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK.
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37
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Brown JM, De Ornellas S, Parisi E, Schermelleh L, Buckle VJ. RASER-FISH: non-denaturing fluorescence in situ hybridization for preservation of three-dimensional interphase chromatin structure. Nat Protoc 2022; 17:1306-1331. [PMID: 35379945 DOI: 10.1038/s41596-022-00685-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/10/2022] [Indexed: 11/09/2022]
Abstract
DNA fluorescence in situ hybridization (FISH) has been a central technique in advancing our understanding of how chromatin is organized within the nucleus. With the increasing resolution offered by super-resolution microscopy, the optimal maintenance of chromatin structure within the nucleus is essential for accuracy in measurements and interpretation of data. However, standard 3D-FISH requires potentially destructive heat denaturation in the presence of chaotropic agents such as formamide to allow access to the DNA strands for labeled FISH probes. To avoid the need to heat-denature, we developed Resolution After Single-strand Exonuclease Resection (RASER)-FISH, which uses exonuclease digestion to generate single-stranded target DNA for efficient probe binding over a 2 d process. Furthermore, RASER-FISH is easily combined with immunostaining of nuclear proteins or the detection of RNAs. Here, we provide detailed procedures for RASER-FISH in mammalian cultured cells to detect single loci, chromatin tracks and topologically associating domains with conventional and super-resolution 3D structured illumination microscopy. Moreover, we provide a validation and characterization of our method, demonstrating excellent preservation of chromatin structure and nuclear integrity, together with improved hybridization efficiency, compared with classic 3D-FISH protocols.
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Affiliation(s)
- Jill M Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Sara De Ornellas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Eva Parisi
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
- School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Lothar Schermelleh
- Micron Oxford Advanced Bioimaging Unit, Department of Biochemistry, Oxford University, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK.
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38
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Llimos G, Gardeux V, Koch U, Kribelbauer JF, Hafner A, Alpern D, Pezoldt J, Litovchenko M, Russeil J, Dainese R, Moia R, Mahmoud AM, Rossi D, Gaidano G, Plass C, Lutsik P, Gerhauser C, Waszak SM, Boettiger A, Radtke F, Deplancke B. A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation. Nat Commun 2022; 13:2042. [PMID: 35440565 PMCID: PMC9018852 DOI: 10.1038/s41467-022-29625-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. These molecularly coordinated regions are named “variable chromatin modules” (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect a VCM-modulating noncoding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a large change in TF binding activity and chromatin state at an enhancer cluster spanning >150 kb, coinciding with subtle, long-range chromatin compaction and robust AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology. Non-coding variants can regulate transcription factor binding and gene expression at variable chromatin modules. Here, the authors show that a germline variant induces transcription factor nucleation through chromatin compaction leading to AXIN2 up-regulation and is associated to better prognosis in chronic lymphocytic leukaemia.
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Affiliation(s)
- Gerard Llimos
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vincent Gardeux
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ute Koch
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Judith F Kribelbauer
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Antonina Hafner
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Daniel Alpern
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joern Pezoldt
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria Litovchenko
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Cancer Research UK Lung Cancer Centre of Excellence, University College London (UCL) Cancer Institute, Cancer Genome Evolution Research Group, London, UK
| | - Julie Russeil
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Riccardo Dainese
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Riccardo Moia
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Abdurraouf Mokhtar Mahmoud
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Davide Rossi
- Oncology Institute of Southern Switzerland, Università della Svizzera italiana, Bellinzona, Switzerland.,Institute of Oncology Research, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Clarissa Gerhauser
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - Alistair Boettiger
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Freddy Radtke
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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39
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Sefer E. A comparison of topologically associating domain callers over mammals at high resolution. BMC Bioinformatics 2022; 23:127. [PMID: 35413815 PMCID: PMC9006547 DOI: 10.1186/s12859-022-04674-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Topologically associating domains (TADs) are locally highly-interacting genome regions, which also play a critical role in regulating gene expression in the cell. TADs have been first identified while investigating the 3D genome structure over High-throughput Chromosome Conformation Capture (Hi-C) interaction dataset. Substantial degree of efforts have been devoted to develop techniques for inferring TADs from Hi-C interaction dataset. Many TAD-calling methods have been developed which differ in their criteria and assumptions in TAD inference. Correspondingly, TADs inferred via these callers vary in terms of both similarities and biological features they are enriched in. RESULT We have carried out a systematic comparison of 27 TAD-calling methods over mammals. We use Micro-C, a recent high-resolution variant of Hi-C, to compare TADs at a very high resolution, and classify the methods into 3 categories: feature-based methods, Clustering methods, Graph-partitioning methods. We have evaluated TAD boundaries, gaps between adjacent TADs, and quality of TADs across various criteria. We also found particularly CTCF and Cohesin proteins to be effective in formation of TADs with corner dots. We have also assessed the callers performance on simulated datasets since a gold standard for TADs is missing. TAD sizes and numbers change remarkably between TAD callers and dataset resolutions, indicating that TADs are hierarchically-organized domains, instead of disjoint regions. A core subset of feature-based TAD callers regularly perform the best while inferring reproducible domains, which are also enriched for TAD related biological properties. CONCLUSION We have analyzed the fundamental principles of TAD-calling methods, and identified the existing situation in TAD inference across high resolution Micro-C interaction datasets over mammals. We come up with a systematic, comprehensive, and concise framework to evaluate the TAD-calling methods performance across Micro-C datasets. Our research will be useful in selecting appropriate methods for TAD inference and evaluation based on available data, experimental design, and biological question of interest. We also introduce our analysis as a benchmarking tool with publicly available source code.
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Affiliation(s)
- Emre Sefer
- Department of Computer Science, Ozyegin University, Istanbul, Turkey.
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40
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Vaasjo LO. LncRNAs and Chromatin Modifications Pattern m6A Methylation at the Untranslated Regions of mRNAs. Front Genet 2022; 13:866772. [PMID: 35368653 PMCID: PMC8968631 DOI: 10.3389/fgene.2022.866772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 12/16/2022] Open
Abstract
New roles for RNA in mediating gene expression are being discovered at an alarming rate. A broad array of pathways control patterning of N6-methyladenosine (m6A) methylation on RNA transcripts. This review comprehensively discusses long non-coding RNAs (lncRNAs) as an additional dynamic regulator of m6A methylation, with a focus on the untranslated regions (UTRs) of mRNAs. Although there is extensive literature describing m6A modification of lncRNA, the function of lncRNA in guiding m6A writers has not been thoroughly explored. The independent control of lncRNA expression, its heterogeneous roles in RNA metabolism, and its interactions with epigenetic machinery, alludes to their potential in dynamic patterning of m6A methylation. While epigenetic regulation by histone modification of H3K36me3 has been demonstrated to pattern RNA m6A methylation, these modifications were specific to the coding and 3′UTR regions. However, there are observations that 5′UTR m6A is distinct from that of the coding and 3′UTR regions, and substantial evidence supports the active regulation of 5′UTR m6A methylation. Consequently, two potential mechanisms in patterning the UTRs m6A methylation are discussed; (1) Anti-sense lncRNA (AS-lncRNA) can either bind directly to the UTR, or (2) act indirectly via recruitment of chromatin-modifying complexes to pattern m6A. Both pathways can guide the m6A writer complex, facilitate m6A methylation and modulate protein translation. Findings in the lncRNA-histone-m6A axis could potentially contribute to the discovery of new functions of lncRNAs and clarify lncRNA-m6A findings in translational medicine.
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Affiliation(s)
- Lee O. Vaasjo
- Cellular and Molecular Biology, Tulane University, New Orleans, LA, United States
- Neuroscience Program, Brain Institute, Tulane University, New Orleans, LA, United States
- *Correspondence: Lee O. Vaasjo,
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41
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Chebrout M, Koné MC, Jan HU, Cournut M, Letheule M, Fleurot R, Aguirre-Lavin T, Peynot N, Jouneau A, Beaujean N, Bonnet-Garnier A. Transcription of rRNA in early mouse embryos promotes chromatin reorganization and expression of major satellite repeats. J Cell Sci 2022; 135:274059. [DOI: 10.1242/jcs.258798] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 01/09/2022] [Indexed: 11/20/2022] Open
Abstract
During the first cell cycles of the early development, the chromatin of the embryo is highly reprogrammed alongside that embryonic genome starts its own transcription. The spatial organization of the genome is a major process that contributes to regulating gene transcription in time and space, however, it is poorly studied in the context of early embryos. To study the cause and effect link between transcription and spatial organization in embryos, we focused on the ribosomal genes, that are first silent and begin to transcribe during the 2-cell stage in the mouse. We demonstrated that ribosomal sequences and early unprocessed rRNAs are spatially organized in a very peculiar manner from the 2-cell to the 16-cell. Using drugs interfering with ribosomal DNA transcription, we show that this organization, totally different from somatic cells, depends on an active transcription of ribosomal genes and induces a unique chromatin environment that favors transcription of major satellite sequences after the 4-cell stage.
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Affiliation(s)
- Martine Chebrout
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Maïmouna Coura Koné
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Habib U. Jan
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Marie Cournut
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Martine Letheule
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Renaud Fleurot
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Tiphaine Aguirre-Lavin
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Nathalie Peynot
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Alice Jouneau
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Nathalie Beaujean
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Amélie Bonnet-Garnier
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
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42
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Li CC, Zhang G, Du J, Liu D, Li Z, Ni Y, Zhou J, Li Y, Hou S, Zheng X, Lan Y, Liu B, He A. Pre-configuring chromatin architecture with histone modifications guides hematopoietic stem cell formation in mouse embryos. Nat Commun 2022; 13:346. [PMID: 35039499 PMCID: PMC8764075 DOI: 10.1038/s41467-022-28018-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/03/2022] [Indexed: 11/09/2022] Open
Abstract
The gene activity underlying cell differentiation is regulated by a diverse set of transcription factors (TFs), histone modifications, chromatin structures and more. Although definitive hematopoietic stem cells (HSCs) are known to emerge via endothelial-to-hematopoietic transition (EHT), how the multi-layered epigenome is sequentially unfolded in a small portion of endothelial cells (ECs) transitioning into the hematopoietic fate remains elusive. With optimized low-input itChIP-seq and Hi-C assays, we performed multi-omics dissection of the HSC ontogeny trajectory across early arterial ECs (eAECs), hemogenic endothelial cells (HECs), pre-HSCs and long-term HSCs (LT-HSCs) in mouse embryos. Interestingly, HSC regulatory regions are already pre-configurated with active histone modifications as early as eAECs, preceding chromatin looping dynamics within topologically associating domains. Chromatin looping structures between enhancers and promoters only become gradually strengthened over time. Notably, RUNX1, a master TF for hematopoiesis, enriched at half of these loops is observed early from eAECs through pre-HSCs but its enrichment further increases in HSCs. RUNX1 and co-TFs together constitute a central, progressively intensified enhancer-promoter interactions. Thus, our study provides a framework to decipher how temporal epigenomic configurations fulfill cell lineage specification during development.
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Affiliation(s)
- Chen C Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Guangyu Zhang
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Junjie Du
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Di Liu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Zongcheng Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China
| | - Yanli Ni
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China
| | - Jie Zhou
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China
| | - Yunqiao Li
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Siyuan Hou
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Xiaona Zheng
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.
| | - Bing Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China.
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China.
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.
| | - Aibin He
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
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43
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Baur B, Lee DI, Haag J, Chasman D, Gould M, Roy S. Deciphering the Role of 3D Genome Organization in Breast Cancer Susceptibility. Front Genet 2022; 12:788318. [PMID: 35087569 PMCID: PMC8787344 DOI: 10.3389/fgene.2021.788318] [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: 10/02/2021] [Accepted: 12/21/2021] [Indexed: 11/25/2022] Open
Abstract
Cancer risk by environmental exposure is modulated by an individual's genetics and age at exposure. This age-specific period of susceptibility is referred to as the "Window of Susceptibility" (WOS). Rats have a similar WOS for developing breast cancer. A previous study in rat identified an age-specific long-range regulatory interaction for the cancer gene, Pappa, that is associated with breast cancer susceptibility. However, the global role of three-dimensional genome organization and downstream gene expression programs in the WOS is not known. Therefore, we generated Hi-C and RNA-seq data in rat mammary epithelial cells within and outside the WOS. To systematically identify higher-order changes in 3D genome organization, we developed NE-MVNMF that combines network enhancement followed by multitask non-negative matrix factorization. We examined three-dimensional genome organization dynamics at the level of individual loops as well as higher-order domains. Differential chromatin interactions tend to be associated with differentially up-regulated genes with the WOS and recapitulate several human SNP-gene interactions associated with breast cancer susceptibility. Our approach identified genomic blocks of regions with greater overall differences in contact count between the two time points when the cluster assignments change and identified genes and pathways implicated in early carcinogenesis and cancer treatment. Our results suggest that WOS-specific changes in 3D genome organization are linked to transcriptional changes that may influence susceptibility to breast cancer.
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Affiliation(s)
- Brittany Baur
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
| | - Da-Inn Lee
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
| | - Jill Haag
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States
| | - Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
| | - Michael Gould
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States
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44
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Jost D. Polymer Modeling of 3D Epigenome Folding: Application to Drosophila. Methods Mol Biol 2022; 2301:293-305. [PMID: 34415542 DOI: 10.1007/978-1-0716-1390-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mechanistic modeling in biology allows to investigate, based on first principles, if putative hypotheses are compatible with observations and to drive further experimental works. Along this line, polymer modeling has been instrumental in 3D genomics to better understand the impact of key mechanisms on the spatial genome organization. Here, I describe how polymer-based models can be practically used to study the role of epigenome in chromosome folding. I illustrate this methodology in the context of Drosophila epigenome folding.
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Affiliation(s)
- Daniel Jost
- University of Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France.
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45
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Lochs SJA, Kind J. Simultaneous Quantification of Spatial Genome Positioning and Transcriptomics in Single Cells with scDam&T-Seq. Methods Mol Biol 2022; 2532:215-241. [PMID: 35867252 DOI: 10.1007/978-1-0716-2497-5_11] [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: 06/15/2023]
Abstract
Spatial genome organization is considered to play an important role in mammalian cells, by guiding gene expression programs and supporting lineage specification. Yet it is still an outstanding question in the field what the direct impact of spatial genome organization on gene expression is. To elucidate this relationship further, we have recently developed scDam&T-seq, a method that simultaneously quantifies protein-DNA interactions and transcriptomes in single cells. This method efficiently combines two preexisting methods: DamID for measuring protein-DNA contacts and CEL-Seq2 for quantification of the transcriptome in single cells. scDam&T-seq has been successfully applied to measure DNA contacts with the nuclear lamina, while at the same time revealing the effect of these contacts on gene expression. This method is applicable to many different proteins of interest and can thereby aid in studying the relationship between protein-DNA interactions and gene expression in single cells.
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Affiliation(s)
- Silke J A Lochs
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Radboud University & Oncode Institute, Utrecht, The Netherlands
| | - Jop Kind
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Radboud University & Oncode Institute, Utrecht, The Netherlands.
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46
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Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin. Genome Res 2021; 32:28-43. [PMID: 34963660 PMCID: PMC8744683 DOI: 10.1101/gr.275827.121] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/02/2021] [Indexed: 11/25/2022]
Abstract
Chromosome organization and dynamics are involved in regulating many fundamental processes such as gene transcription and DNA repair. Experiments unveiled that chromatin motion is highly heterogeneous inside cell nuclei, ranging from a liquid-like, mobile state to a gel-like, rigid regime. Using polymer modeling, we investigate how these different physical states and dynamical heterogeneities may emerge from the same structural mechanisms. We found that the formation of topologically associating domains (TADs) is a key driver of chromatin motion heterogeneity. In particular, we showed that the local degree of compaction of the TAD regulates the transition from a weakly compact, fluid state of chromatin to a more compact, gel state exhibiting anomalous diffusion and coherent motion. Our work provides a comprehensive study of chromosome dynamics and a unified view of chromatin motion enabling interpretation of the wide variety of dynamical behaviors observed experimentally across different biological conditions, suggesting that the "liquid" or "solid" state of chromatin are in fact two sides of the same coin.
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47
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Rezaei-Lotfi S, Vujovic F, Simonian M, Hunter N, Farahani RM. Programmed genomic instability regulates neural transdifferentiation of human brain microvascular pericytes. Genome Biol 2021; 22:334. [PMID: 34886891 PMCID: PMC8656028 DOI: 10.1186/s13059-021-02555-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 11/22/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Transdifferentiation describes transformation in vivo of specialized cells from one lineage into another. While there is extensive literature on forced induction of lineage reprogramming in vitro, endogenous mechanisms that govern transdifferentiation remain largely unknown. The observation that human microvascular pericytes transdifferentiate into neurons provided an opportunity to explore the endogenous molecular basis for lineage reprogramming. RESULTS We show that abrupt destabilization of the higher-order chromatin topology that chaperones lineage memory of pericytes is driven by transient global transcriptional arrest. This leads within minutes to localized decompression of the repressed competing higher-order chromatin topology and expression of pro-neural genes. Transition to neural lineage is completed by probabilistic induction of R-loops in key myogenic loci upon re-initiation of RNA polymerase activity, leading to depletion of the myogenic transcriptome and emergence of the neurogenic transcriptome. CONCLUSIONS These findings suggest that the global transcriptional landscape not only shapes the functional cellular identity of pericytes, but also stabilizes lineage memory by silencing the competing neural program within a repressed chromatin state.
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Affiliation(s)
- Saba Rezaei-Lotfi
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006 Australia
| | - Filip Vujovic
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006 Australia
| | - Mary Simonian
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
| | - Ramin M. Farahani
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006 Australia
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48
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Histone variant H2A.Z regulates zygotic genome activation. Nat Commun 2021; 12:7002. [PMID: 34853314 PMCID: PMC8636486 DOI: 10.1038/s41467-021-27125-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
During embryogenesis, the genome shifts from transcriptionally quiescent to extensively active in a process known as Zygotic Genome Activation (ZGA). In Drosophila, the pioneer factor Zelda is known to be essential for the progression of development; still, it regulates the activation of only a small subset of genes at ZGA. However, thousands of genes do not require Zelda, suggesting that other mechanisms exist. By conducting GRO-seq, HiC and ChIP-seq in Drosophila embryos, we demonstrate that up to 65% of zygotically activated genes are enriched for the histone variant H2A.Z. H2A.Z enrichment precedes ZGA and RNA Polymerase II loading onto chromatin. In vivo knockdown of maternally contributed Domino, a histone chaperone and ATPase, reduces H2A.Z deposition at transcription start sites, causes global downregulation of housekeeping genes at ZGA, and compromises the establishment of the 3D chromatin structure. We infer that H2A.Z is essential for the de novo establishment of transcriptional programs during ZGA via chromatin reorganization. During embryogenesis, the genome becomes transcriptionally active in a process known as zygotic genome activation (ZGA); how ZGA is initiated is still an open question. Here the authors show histone variant H2A.Z deposition precedes RNA polymerase II binding on chromatin, before ZGA. H2A.Z loss causes transcriptional downregulation of ZGA genes and leads to changes in the 3D genome organization.
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49
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Venkatachalapathy S, Jokhun DS, Andhari M, Shivashankar GV. Single cell imaging-based chromatin biomarkers for tumor progression. Sci Rep 2021; 11:23041. [PMID: 34845273 PMCID: PMC8630115 DOI: 10.1038/s41598-021-02441-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022] Open
Abstract
Tumour progression within the tissue microenvironment is accompanied by complex biomechanical alterations of the extracellular environment. While histopathology images provide robust biochemical markers for tumor progression in clinical settings, a quantitative single cell score using nuclear morphology and chromatin organization integrated with the long range mechanical coupling within the tumor microenvironment is missing. We propose that the spatial chromatin organization in individual nuclei characterises the cell state and their alterations during tumor progression. In this paper, we first built an image analysis pipeline and implemented it to classify nuclei from patient derived breast tissue biopsies of various cancer stages based on their nuclear and chromatin features. Replacing H&E with DNA binding dyes such as Hoescht stained tissue biopsies, we improved the classification accuracy. Using the nuclear morphology and chromatin organization features, we constructed a pseudo-time model to identify the chromatin state changes that occur during tumour progression. This enabled us to build a single-cell mechano-genomic score that characterises the cell state during tumor progression from a normal to a metastatic state. To gain further insights into the alterations in the local tissue microenvironments, we also used the nuclear orientations to identify spatial neighbourhoods that have been posited to drive tumor progression. Collectively, we demonstrate that image-based single cell chromatin and nuclear features are important single cell biomarkers for phenotypic mapping of tumor progression.
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Affiliation(s)
- Saradha Venkatachalapathy
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, 117411, Singapore.,Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Doorgesh S Jokhun
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, 117411, Singapore
| | - Madhavi Andhari
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, 117411, Singapore.,Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, 741246, India
| | - G V Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, 117411, Singapore. .,FIRC Institute for Molecular Oncology, 20139, Milan, Italy. .,Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland. .,Paul Scherrer Institut, 5232, Villigen, Switzerland.
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50
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Yamaguchi N, Ito T. Expression profiling of H3K27me3 demethylase genes during plant development and in response to environmental stress in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2021; 16:1950445. [PMID: 34227901 PMCID: PMC8526033 DOI: 10.1080/15592324.2021.1950445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/26/2021] [Accepted: 06/28/2021] [Indexed: 05/21/2023]
Abstract
Histone modification influences gene expression. Among histone modifications, H3K27me3 is associated with downregulation of nearby genes via chromatin compaction. In Arabidopsis thaliana, a subset of JUMONJI C DOMAIN-CONTAINING PROTEIN (JMJ) proteins play a critical role in removal of H3K27me3 during plant development or in response to environmental cues. However, the regulation of H3K27me3 demethylase gene expression is not yet fully characterized. In this study, we computationally characterized the expression patterns of JMJ H3K27me3 demethylase genes using public transcriptome datasets created across plant development and after various environmental cues. Consistent with the available transcriptome datasets, GUS staining validated that JMJ30 was highly expressed in the L1 layer of the shoot apical meristem. Furthermore, expression data for panel of five H3K27me3 demethylase genes revealed JMJ30 to be the most highly affected by abiotic and biotic stress. In addition, JMJ30 expression was variable between Arabidopsis thaliana accessions. Finally, the expression of a JMJ30 orthologue from the related species Arabidopsis halleri, AhgJMJ30, fluctuated under field conditions. Taken together, our results suggest that transcriptional changes of H3K27me3 demethylase genes may play key roles in development and environmental responses.
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Affiliation(s)
- Nobutoshi Yamaguchi
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi-shi, Saitama, Japan
- CONTACT Nobutoshi Yamaguchi
| | - Toshiro Ito
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
- Toshiro Ito Biological Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
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