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Xu N, Liu Y, Nai S, Tao Y, Ding Y, Jia L, Geng Q, Li J, Bai Y, Wei GH, Dong MQ, Luo L, Zhao M, Xu X, Li XX, Li J, Huang L. UBE3D Is Involved in Blue Light-Induced Retinal Damage by Regulating Double-Strand Break Repair. Invest Ophthalmol Vis Sci 2022; 63:7. [PMID: 36094642 PMCID: PMC9482326 DOI: 10.1167/iovs.63.10.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose Age-related macular degeneration (AMD) is currently the leading cause of blindness worldwide. Previously, we identified ubiquitin-protein ligase E3D (UBE3D) as an AMD-associated protein for East Asian populations, and here we further demonstrate that UBE3D could be associated with DNA damage response. Methods The established I-SceI-inducible GFP reporter system was used to explore the effect of UBE3D on homologous recombination. Immunoprecipitation-mass spectrometry (MS) was used to explore potential UBE3D-interacting proteins and validated with coimmunoprecipitation assays and the pulldown assays. Micrococcal nuclease (MNase) assays were used to investigate the function of UBE3D on heterochromatin de-condensation upon DNA damage. An aged mouse model of blue light-induced eye damage was constructed, and electroretinography (ERG) and optical coherence tomography (OCT) were performed to compare the differences between wild-type and UBE3D+/- mice. Results First, we show that GFP-UBE3D is recruited to damage sites by PCNA, through a PCNA-interacting protein (PIP) box. Furthermore, UBE3D interacts with KAP1 via R377R378 and oxidation of the AMD-associated V379M mutation abolishes KAP1-UBE3D binding. By MNase assays, UBE3D depletion reduces the chromatin relaxation levels upon DNA damage. In addition, UBE3D depletion renders less KAP1 recruitment. Compared with wild type, blue light induces less damage in UBE3D+/- mice as measured by ERG and OCT, consistent with our biochemical results. Conclusions Hence, we propose that one potential mechanism that UBE3D-V379M contributes to AMD pathogenesis might be via defective DNA damage repair linked with oxidative stress and our results offered a potential direction for the treatment of AMD.
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Affiliation(s)
- Ningda Xu
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
| | - Yue Liu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Shanshan Nai
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Yong Tao
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University, Chaoyang District, Beijing, China
| | - Yuehe Ding
- National Institute of Biological Sciences, Beijing, China
| | - Lemei Jia
- National Institute of Biological Sciences, Beijing, China
| | - Qizhi Geng
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Jie Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Yujing Bai
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University, Shanghai, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Linyi Luo
- Department of Ophthalmology and Visual Sciences, Affiliated Dongguan Hospital, Southern Medical University, Guangdong, China
| | - Mingwei Zhao
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xiao-Xin Li
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
- Department of Ophthalmology, Xiamen Eye Center of Xiamen University, Xiamen, China
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Lvzhen Huang
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
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Nguyen TL, Pradeep S, Judson-Torres RL, Reed J, Teitell MA, Zangle TA. Quantitative Phase Imaging: Recent Advances and Expanding Potential in Biomedicine. ACS NANO 2022; 16:11516-11544. [PMID: 35916417 PMCID: PMC10112851 DOI: 10.1021/acsnano.1c11507] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Quantitative phase imaging (QPI) is a label-free, wide-field microscopy approach with significant opportunities for biomedical applications. QPI uses the natural phase shift of light as it passes through a transparent object, such as a mammalian cell, to quantify biomass distribution and spatial and temporal changes in biomass. Reported in cell studies more than 60 years ago, ongoing advances in QPI hardware and software are leading to numerous applications in biology, with a dramatic expansion in utility over the past two decades. Today, investigations of cell size, morphology, behavior, cellular viscoelasticity, drug efficacy, biomass accumulation and turnover, and transport mechanics are supporting studies of development, physiology, neural activity, cancer, and additional physiological processes and diseases. Here, we review the field of QPI in biology starting with underlying principles, followed by a discussion of technical approaches currently available or being developed, and end with an examination of the breadth of applications in use or under development. We comment on strengths and shortcomings for the deployment of QPI in key biomedical contexts and conclude with emerging challenges and opportunities based on combining QPI with other methodologies that expand the scope and utility of QPI even further.
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53
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Podgornaya OI. Nuclear organization by satellite DNA, SAF-A/hnRNPU and matrix attachment regions. Semin Cell Dev Biol 2022; 128:61-68. [PMID: 35484025 DOI: 10.1016/j.semcdb.2022.04.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/18/2022] [Accepted: 04/18/2022] [Indexed: 12/15/2022]
Abstract
The need of large-scale chromatin organization in the nucleus has become more and more appreciated. The higher order nuclear organization ultimately regulate a plethora of biological processes including transcription, DNA replication, and DNA repair. In this context, it is of critical importance to understand the mechanisms that allow higher order nuclear organization. Scaffold Attachment Factor A (SAF-A/hnRNPU), which was originally identified as the component of nuclear matrix, has emerged as an important regulator of higher order nuclear organization. It is shown that SAF-A/hnRNPU binds to tandem repeats (TRs) and scaffold/matrix attachment regions (S/MAR) in a sequence-non-specific, but structure-specific manner (e.g. DNA curvature). Recent studies showed that SAF-A interacts with chromatin-associated RNAs (caRNAs) to regulate interphase chromatin structures in a transcription-dependent manner. It is proposed that SAF-A/hnRNPU and caRNAs form a dynamic, transcriptionally responsive chromatin mesh that organizes chromatin in a large scale. The common structural features of S/MAR and pericentromeric (periCEN) TR promotes SAF-A-mediated association with each other. Collectively a model is presented wherein SAF-A/hnRNPU and periCEN TR are the key players in large-scale nuclear organization that supports general transcription.
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Affiliation(s)
- O I Podgornaya
- Institute of Cytology RAS, St. Petersburg State University, Russia.
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54
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Belmont AS. Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture. Cold Spring Harb Perspect Biol 2022; 14:a041268. [PMID: 34400557 PMCID: PMC9248822 DOI: 10.1101/cshperspect.a041268] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This work reviews nuclear compartments, defined broadly to include distinct nuclear structures, bodies, and chromosome domains. It first summarizes original cytological observations before comparing concepts of nuclear compartments emerging from microscopy versus genomic approaches and then introducing new multiplexed imaging approaches that promise in the future to meld both approaches. I discuss how previous models of radial distribution of chromosomes or the binary division of the genome into A and B compartments are now being refined by the recognition of more complex nuclear compartmentalization. The poorly understood question of how these nuclear compartments are established and maintained is then discussed, including through the modern perspective of phase separation, before moving on to address possible functions of nuclear compartments, using the possible role of nuclear speckles in modulating gene expression as an example. Finally, the review concludes with a discussion of future questions for this field.
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Affiliation(s)
- Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
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Mirny L, Dekker J. Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. Cold Spring Harb Perspect Biol 2022; 14:a040147. [PMID: 34518339 PMCID: PMC9248823 DOI: 10.1101/cshperspect.a040147] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Microscopy and genomic approaches provide detailed descriptions of the three-dimensional folding of chromosomes and nuclear organization. The fundamental question is how activity of molecules at the nanometer scale can lead to complex and orchestrated spatial organization at the scale of chromosomes and the whole nucleus. At least three key mechanisms can bridge across scales: (1) tethering of specific loci to nuclear landmarks leads to massive reorganization of the nucleus; (2) spatial compartmentalization of chromatin, which is driven by molecular affinities, results in spatial isolation of active and inactive chromatin; and (3) loop extrusion activity of SMC (structural maintenance of chromosome) complexes can explain many features of interphase chromatin folding and underlies key phenomena during mitosis. Interestingly, many features of chromosome organization ultimately result from collective action and the interplay between these mechanisms, and are further modulated by transcription and topological constraints. Finally, we highlight some outstanding questions that are critical for our understanding of nuclear organization and function. We believe many of these questions can be answered in the coming years.
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Affiliation(s)
- Leonid Mirny
- Institute for Medical Engineering and Science, and Department of Physics, MIT, Cambridge, Massachusetts 02139, USA
| | - Job Dekker
- Howard Hughes Medical Institute, and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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Acke A, Van Belle S, Louis B, Vitale R, Rocha S, Voet T, Debyser Z, Hofkens J. Expansion microscopy allows high resolution single cell analysis of epigenetic readers. Nucleic Acids Res 2022; 50:e100. [PMID: 35716125 PMCID: PMC9508849 DOI: 10.1093/nar/gkac521] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 05/04/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Interactions between epigenetic readers and histone modifications play a pivotal role in gene expression regulation and aberrations can enact etiopathogenic roles in both developmental and acquired disorders like cancer. Typically, epigenetic interactions are studied by mass spectrometry or chromatin immunoprecipitation sequencing. However, in these methods, spatial information is completely lost. Here, we devise an expansion microscopy based method, termed Expansion Microscopy for Epigenetics or ExEpi, to preserve spatial information and improve resolution. We calculated relative co-localization ratios for two epigenetic readers, lens epithelium derived growth factor (LEDGF) and bromodomain containing protein 4 (BRD4), with marks for heterochromatin (H3K9me3 and H3K27me3) and euchromatin (H3K36me2, H3K36me3 and H3K9/14ac). ExEpi confirmed their preferred epigenetic interactions, showing co-localization for LEDGF with H3K36me3/me2 and for BRD4 with H3K9/14ac. Moreover addition of JQ1, a known BET-inhibitor, abolished BRD4 interaction with H3K9/14ac with an IC50 of 137 nM, indicating ExEpi could serve as a platform for epigenetic drug discovery. Since ExEpi retains spatial information, the nuclear localization of marks and readers was determined, which is one of the main advantages of ExEpi. The heterochromatin mark, H3K9me3, is located in the nuclear rim whereas LEDGF co-localization with H3K36me3 and BRD4 co-localization with H3K9/14ac occur further inside the nucleus.
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Affiliation(s)
- Aline Acke
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, KU Leuven, Leuven, Flanders, Belgium
| | - Siska Van Belle
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Flanders, Belgium
| | - Boris Louis
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, KU Leuven, Leuven, Flanders, Belgium.,Division of Chemical Physics and NanoLund, Lund University, Lund, Sweden
| | - Raffaele Vitale
- Dynamics, Nanoscopy and Chemometrics (DYNACHEM) Group, U. Lille, CNRS, LASIRE, Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Cité Scientifique, F-59000Lille, France
| | - Susana Rocha
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, KU Leuven, Leuven, Flanders, Belgium
| | - Thierry Voet
- Department of Human Genetics, KU Leuven, Leuven, Flanders, Belgium.,LISCO, KU Leuven Institute for Single-Cell Omics, Leuven 3000, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Flanders, Belgium
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, KU Leuven, Leuven, Flanders, Belgium.,Max Plank Institute for Polymer Research, Ackermannweg 10, Mainz, D-55128, Germany.,LISCO, KU Leuven Institute for Single-Cell Omics, Leuven 3000, Belgium
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Chomiak AA, Guo Y, Kopsidas CA, McDaniel DP, Lowe CC, Pan H, Zhou X, Zhou Q, Doughty ML, Feng Y. Nde1 is required for heterochromatin compaction and stability in neocortical neurons. iScience 2022; 25:104354. [PMID: 35601919 PMCID: PMC9121328 DOI: 10.1016/j.isci.2022.104354] [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: 10/05/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 11/20/2022] Open
Abstract
The NDE1 gene encodes a scaffold protein essential for brain development. Although biallelic NDE1 loss of function (LOF) causes microcephaly with profound mental retardation, NDE1 missense mutations and copy number variations are associated with multiple neuropsychiatric disorders. However, the etiology of the diverse phenotypes resulting from NDE1 aberrations remains elusive. Here we demonstrate Nde1 controls neurogenesis through facilitating H4K20 trimethylation-mediated heterochromatin compaction. This mechanism patterns diverse chromatin landscapes and stabilizes constitutive heterochromatin of neocortical neurons. We demonstrate that NDE1 can undergo dynamic liquid-liquid phase separation, partitioning to the nucleus and interacting with pericentromeric and centromeric satellite repeats. Nde1 LOF results in nuclear architecture aberrations and DNA double-strand breaks, as well as instability and derepression of pericentromeric satellite repeats in neocortical neurons. These findings uncover a pivotal role of NDE1/Nde1 in establishing and protecting neuronal heterochromatin. They suggest that heterochromatin instability predisposes a wide range of brain dysfunction.
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Affiliation(s)
- Alison A. Chomiak
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Superior Street, Chicago, IL 60611, USA
| | - Yan Guo
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Superior Street, Chicago, IL 60611, USA
| | - Caroline A. Kopsidas
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Dennis P. McDaniel
- Biomedical Instrumentation Center, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Clara C. Lowe
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Hongna Pan
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Xiaoming Zhou
- Department of Medicine, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Qiong Zhou
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Martin L. Doughty
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Yuanyi Feng
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
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Müller B, Serafin F, Laucke LL, Rheinhard W, Wimmer T, Stieger K. Characterization of Double-Strand Break Repair Protein Ku80 Location Within the Murine Retina. Invest Ophthalmol Vis Sci 2022; 63:22. [PMID: 35737378 PMCID: PMC9233284 DOI: 10.1167/iovs.63.6.22] [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] [Indexed: 11/24/2022] Open
Abstract
Purpose To characterize the spatial distribution of the DNA-double strand break-repair protein Ku80 in the murine retina. Even though robust data exist on the complexity of DNA repair mechanisms in dividing cells in vitro, almost nothing is known about it in post-mitotic neurons or photoreceptors (PRs). This knowledge is an important prerequisite for in vivo therapeutic approaches by genome editing in retina and PRs. Recently, it was shown that mouse rod PRs are incapable of repairing double-strand breaks induced by radiation. Material and Methods Retinae from wild-type, rd10, and RPGR-KI mouse lines were obtained and stained with antibodies against Ku80, and cellular markers CtBP2, beta-Dystropglycan, Lamin B, and peanut agglutinin. Organotypic explant cultures were generated and maintained for up to 10 days. Laser microdissection was performed to obtain photoreceptor nuclei, and Ku80 expression was compared to whole retina by real-time PCR (RT-PCR). Results Strong Ku80 immunoreactivity was observed in rod but not cone photoreceptor terminals localized in the outer plexiform layer of the retina in all three mouse lines. During retinal explant culture, we observed that Ku80-positive globules translocate into the heterochromatin region of nuclei in the outer nuclear layer (ONL). By quantitative PCR, we showed upregulation of relative Ku80 expression in the ONL during wild-type retinal explant culture. Discussion The unexpected localization of Ku80 to murine rod terminals indicates another tissue-specific modification to the canonical DNA repair mechanisms and warrants further investigation.
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Affiliation(s)
- Brigitte Müller
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Franziska Serafin
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Leonie Luise Laucke
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Wilhelm Rheinhard
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Tobias Wimmer
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
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Müller M, Fäh T, Schaefer M, Hermes V, Luitz J, Stalder P, Arora R, Ngondo RP, Ciaudo C. AGO1 regulates pericentromeric regions in mouse embryonic stem cells. Life Sci Alliance 2022; 5:e202101277. [PMID: 35236760 PMCID: PMC8897595 DOI: 10.26508/lsa.202101277] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/17/2022] [Accepted: 02/17/2022] [Indexed: 01/09/2023] Open
Abstract
Argonaute proteins (AGOs), which play an essential role in cytosolic post-transcriptional gene silencing, have been also reported to function in nuclear processes like transcriptional activation or repression, alternative splicing and, chromatin organization. As most of these studies have been conducted in human cancer cell lines, the relevance of AGOs nuclear functions in the context of mouse early embryonic development remains uninvestigated. Here, we examined a possible role of the AGO1 protein on the distribution of constitutive heterochromatin in mouse embryonic stem cells (mESCs). We observed a specific redistribution of the repressive histone mark H3K9me3 and the heterochromatin protein HP1α, away from pericentromeric regions upon Ago1 depletion. Furthermore, we demonstrated that major satellite transcripts are strongly up-regulated in Ago1_KO mESCs and that their levels are partially restored upon AGO1 rescue. We also observed a similar redistribution of H3K9me3 and HP1α in Drosha_KO mESCs, suggesting a role for microRNAs (miRNAs) in the regulation of heterochromatin distribution in mESCs. Finally, we showed that specific miRNAs with complementarity to major satellites can partially regulate the expression of these transcripts.
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Affiliation(s)
- Madlen Müller
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zürich, Zürich, Switzerland
| | - Tara Fäh
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Moritz Schaefer
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zürich, Zürich, Switzerland
| | - Victoria Hermes
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Janina Luitz
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Patrick Stalder
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zürich, Zürich, Switzerland
| | - Rajika Arora
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Richard Patryk Ngondo
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Constance Ciaudo
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
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A Nuclear Belt Fastens on Neural Cell Fate. Cells 2022; 11:cells11111761. [PMID: 35681456 PMCID: PMC9179901 DOI: 10.3390/cells11111761] [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: 04/14/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/22/2022] Open
Abstract
Successful embryonic and adult neurogenesis require proliferating neural stem and progenitor cells that are intrinsically and extrinsically guided into a neuronal fate. In turn, migration of new-born neurons underlies the complex cytoarchitecture of the brain. Proliferation and migration are therefore essential for brain development, homeostasis and function in adulthood. Among several tightly regulated processes involved in brain formation and function, recent evidence points to the nuclear envelope (NE) and NE-associated components as critical new contributors. Classically, the NE was thought to merely represent a barrier mediating selective exchange between the cytoplasm and nucleoplasm. However, research over the past two decades has highlighted more sophisticated and diverse roles for NE components in progenitor fate choice and migration of their progeny by tuning gene expression via interactions with chromatin, transcription factors and epigenetic factors. Defects in NE components lead to neurodevelopmental impairments, whereas age-related changes in NE components are proposed to influence neurodegenerative diseases. Thus, understanding the roles of NE components in brain development, maintenance and aging is likely to reveal new pathophysiological mechanisms for intervention. Here, we review recent findings for the previously underrepresented contribution of the NE in neuronal commitment and migration, and envision future avenues for investigation.
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Komoto T, Fujii M, Awazu A. Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation of mouse embryonic stem cells. Biophys Physicobiol 2022; 19:1-14. [PMID: 35797402 PMCID: PMC9174021 DOI: 10.2142/biophysico.bppb-v19.0018] [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: 03/03/2022] [Accepted: 05/02/2022] [Indexed: 12/01/2022] Open
Abstract
X chromosome inactivation center (Xic) pairing occurs during the differentiation of embryonic stem (ES) cells from female mouse embryos, and is related to X chromosome inactivation, the circadian clock, intra-nucleus architecture, and metabolism. However, the mechanisms underlying the identification and approach of X chromosome pairs in the crowded nucleus are unclear. To elucidate the driving force of Xic pairing, we developed a coarse-grained molecular dynamics model of intranuclear chromosomes in ES cells and in cells 2 days after the onset of differentiation (2-day cells) by considering intrachromosomal epigenetic-structural feature-dependent mechanics. The analysis of the experimental data showed that X-chromosomes exhibit the rearrangement of their distributions of open/closed chromatin regions on their surfaces during cell differentiation. By simulating models where the excluded volume effects of closed chromatin regions are stronger than those of open chromatin regions, such rearrangement of open/closed chromatin regions on X-chromosome surfaces promoted the mutual approach of the Xic pair. These findings suggested that local intrachromosomal epigenetic features may contribute to the regulation of cell species-dependent differences in intranuclear architecture.
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Affiliation(s)
- Tetsushi Komoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Masashi Fujii
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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Ke Q, Gong L, Zhu X, Qi R, Zou M, Chen B, Liu W, Huang S, Liu Y, Li DWC. Multinucleated Retinal Pigment Epithelial Cells Adapt to Vision and Exhibit Increased DNA Damage Response. Cells 2022; 11:cells11091552. [PMID: 35563857 PMCID: PMC9103592 DOI: 10.3390/cells11091552] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/18/2022] [Accepted: 04/28/2022] [Indexed: 01/27/2023] Open
Abstract
Multinucleated retinal pigment epithelium (RPE) cells have been reported in humans and other mammals. Rodents have an extremely high percentage of multinucleated cells (more than 80%). Both mouse and human multinucleated RPE cells exhibit specific regional distributions that are potentially correlated with photoreceptor density. However, detailed investigations of multinucleated RPE in different species and their behavior after DNA damage are missing. Here, we compared the composition of multinucleated RPE cells in nocturnal and diurnal animals that possess distinct rod and cone proportions. We further investigated the reactive oxygen species (ROS) production and DNA damage response in mouse mononucleated and multinucleated RPE cells and determined the effect of p53 dosage on the DNA damage response in these cells. Our results revealed an unrealized association between multinucleated RPE cells and nocturnal vision. In addition, we found multinucleated RPE cells exhibited increased ROS production and DNA damage after X-ray irradiation. Furthermore, haploinsufficiency of p53 led to increased DNA damage frequency after irradiation, and mononucleated RPE cells were more sensitive to a change in p53 dosage. In conclusion, this study provides novel information on in vivo PRE topography and the DNA damage response, which may reflect specific requirements for vision adaption and macular function.
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63
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de Lima MF, Lisboa MDO, Terceiro LEL, Rangel-Pozzo A, Mai S. Chromosome Territories in Hematological Malignancies. Cells 2022; 11:1368. [PMID: 35456046 PMCID: PMC9028803 DOI: 10.3390/cells11081368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
Chromosomes are organized in distinct nuclear areas designated as chromosome territories (CT). The structural formation of CT is a consequence of chromatin packaging and organization that ultimately affects cell function. Chromosome positioning can identify structural signatures of genomic organization, especially for diseases where changes in gene expression contribute to a given phenotype. The study of CT in hematological diseases revealed chromosome position as an important factor for specific chromosome translocations. In this review, we highlight the history of CT theory, current knowledge on possible clinical applications of CT analysis, and the impact of CT in the development of hematological neoplasia such as multiple myeloma, leukemia, and lymphomas. Accumulating data on nuclear architecture in cancer allow one to propose the three-dimensional nuclear genomic landscape as a novel cancer biomarker for the future.
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Affiliation(s)
- Matheus Fabiao de Lima
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Mateus de Oliveira Lisboa
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná—PUCPR, Curitiba 80215-901, Brazil;
| | - Lucas E. L. Terceiro
- Department of Pathology, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 3P5, Canada;
| | - Aline Rangel-Pozzo
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Sabine Mai
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
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64
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Cremer C, Birk U. Spatially modulated illumination microscopy: application perspectives in nuclear nanostructure analysis. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A: MATHEMATICAL, PHYSICAL AND ENGINEERING SCIENCES 2022; 380:20210152. [PMID: 0 DOI: 10.1098/rsta.2021.0152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/02/2021] [Indexed: 05/19/2023]
Abstract
Thousands of genes and the complex biochemical networks for their transcription are packed in the micrometer sized cell nucleus. To control biochemical processes, spatial organization plays a key role. Hence the structure of the cell nucleus of higher organisms has emerged as a main topic of advanced light microscopy. So far, a variety of methods have been applied for this, including confocal laser scanning fluorescence microscopy, 4Pi-, STED- and localization microscopy approaches, as well as (laterally) structured illumination microscopy (SIM). Here, we summarize the state of the art and discuss application perspectives for nuclear nanostructure analysis of spatially modulated illumination (SMI). SMI is a widefield-based approach to using axially structured illumination patterns to determine the axial extension (size) of small, optically isolated fluorescent objects between less than or equal to 200 nm and greater than or equal to 40 nm diameter with a precision down to the few nm range; in addition, it allows the axial positioning of such structures down to the 1 nm scale. Combined with SIM, a three-dimensional localization precision of less than or equal to 1 nm is expected to become feasible using fluorescence yields typical for single molecule localization microscopy applications. Together with its nanosizing capability, this may eventually be used to analyse macromolecular complexes and other nanostructures with a topological resolution, further narrowing the gap to Cryoelectron microscopy.
This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 2)’.
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Affiliation(s)
- Christoph Cremer
- Max-Planck Institute for Polymer Research, and Institute of Molecular Biology (IMB), D-55128 Mainz, Germany
- Kirchhoff Institute for Physics (KIP), Interdisciplinary Center for Scientific Computing (IWR), and Institute of Pharmacy and Molecular Biotechnology (IPMB), University Heidelberg, D-69120 Heidelberg, Germany
| | - Udo Birk
- Institute for Photonics and ICT (IPI), University of Applied Sciences (FH Graubünden), CH-7000 Chur, Switzerland
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65
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Nothof SA, Magdinier F, Van-Gils J. Chromatin Structure and Dynamics: Focus on Neuronal Differentiation and Pathological Implication. Genes (Basel) 2022; 13:genes13040639. [PMID: 35456445 PMCID: PMC9029427 DOI: 10.3390/genes13040639] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Chromatin structure is an essential regulator of gene expression. Its state of compaction contributes to the regulation of genetic programs, in particular during differentiation. Epigenetic processes, which include post-translational modifications of histones, DNA methylation and implication of non-coding RNA, are powerful regulators of gene expression. Neurogenesis and neuronal differentiation are spatio-temporally regulated events that allow the formation of the central nervous system components. Here, we review the chromatin structure and post-translational histone modifications associated with neuronal differentiation. Studying the impact of histone modifications on neuronal differentiation improves our understanding of the pathophysiological mechanisms of chromatinopathies and opens up new therapeutic avenues. In addition, we will discuss techniques for the analysis of histone modifications on a genome-wide scale and the pathologies associated with the dysregulation of the epigenetic machinery.
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Affiliation(s)
- Sophie A. Nothof
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Frédérique Magdinier
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Julien Van-Gils
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
- Reference Center AD SOOR, AnDDI-RARE, Inserm U 1211, Medical Genetics Department, Bordeaux University, Center Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France
- Correspondence:
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66
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Ball JM, Chen S, Li W. Mitochondria in cone photoreceptors act as microlenses to enhance photon delivery and confer directional sensitivity to light. SCIENCE ADVANCES 2022; 8:eabn2070. [PMID: 35235359 PMCID: PMC8890704 DOI: 10.1126/sciadv.abn2070] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/03/2022] [Indexed: 05/10/2023]
Abstract
Mammalian photoreceptors aggregate numerous mitochondria, organelles chiefly for energy production, in the ellipsoid region immediately adjacent to the light-sensitive outer segment to support the high metabolic demands of phototransduction. However, these complex, lipid-rich organelles are also poised to affect light passage into the outer segment. Here, we show, via live imaging and simulations, that despite this risk of light scattering or absorption, these tightly packed mitochondria "focus" light for entry into the outer segment and that mitochondrial remodeling affects such light concentration. This "microlens"-like feature of cone mitochondria delivers light with an angular dependence akin to the Stiles-Crawford effect (SCE), providing a simple explanation for this essential visual phenomenon that improves resolution. This new insight into the optical role of mitochondria is relevant for the interpretation of clinical ophthalmological imaging, lending support for the use of SCE as an early diagnostic tool in retinal disease.
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Affiliation(s)
- John M. Ball
- Retinal Neurophysiology Section, National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Shan Chen
- Retinal Neurophysiology Section, National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Wei Li
- Corresponding author. (J.M.B.); (W.L.)
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Heisterkamp P, Borsch O, Lezama ND, Gasparini S, Fathima A, Carvalho LS, Wagner F, Karl MO, Schlierf M, Ader M. Evidence for endogenous exchange of cytoplasmic material between a subset of cone and rod photoreceptors within the adult mammalian retina via direct cell-cell connections. Exp Eye Res 2022; 219:109033. [DOI: 10.1016/j.exer.2022.109033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/08/2022] [Accepted: 03/08/2022] [Indexed: 12/13/2022]
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Zhang X, Zhang BW, Xiang L, Wu H, Sahiri Alexander SUPITA, Zhou P, Zi-Yu Dai M, Wang X, Xiong W, Zhang Y, Jin ZB, Deng LW. MLL5 is involved in retinal photoreceptor maturation through facilitating CRX-mediated photoreceptor gene transactivation. iScience 2022; 25:104058. [PMID: 35359806 PMCID: PMC8961232 DOI: 10.1016/j.isci.2022.104058] [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: 08/23/2021] [Revised: 12/11/2021] [Accepted: 03/07/2022] [Indexed: 11/06/2022] Open
Abstract
Histone methylation, particularly at the H3K4 position, is thought to contribute to the specification of photoreceptor cell fate; however, the mechanisms linking histone methylation with transcription factor transactivation and photoreceptor gene expression have not yet been determined. Here, we demonstrate that MLL5 is abundantly expressed in the mouse retina. Mll5 deficiency impaired electroretinogram responses, alongside attenuated expression of a number of retina genes. Mechanistic studies revealed that MLL5 interacts with the retina-specific transcription factor, CRX, contributing to its binding to photoreceptor-specific gene promoters. Moreover, depletion of MLL5 impairs H3K4 methylation and H3K79 methylation, which subsequently compromises CRX-CBP assembly and H3 acetylation on photoreceptor promoters. Our data support a scenario in which recognition of H3K4 methylation by MLL5 is required for photoreceptor-specific gene transcription through maintaining a permissive chromatin state and proper CRX-CBP recruitment at promoter sites. MLL5 is essential for the expression of critical photoreceptor genes MLL5 depletion reduces H3K4/K79 methylation at photoreceptor gene promoters MLL5 interacts with CRX via its CD4 domain Recognition of H3K4me2/3 by MLL5 is a prerequisite for CRX recruitment to chromatin
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69
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Salbaum KA, Shelton ER, Serwane F. Retina organoids: Window into the biophysics of neuronal systems. BIOPHYSICS REVIEWS 2022; 3:011302. [PMID: 38505227 PMCID: PMC10903499 DOI: 10.1063/5.0077014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/16/2021] [Indexed: 03/21/2024]
Abstract
With a kind of magnetism, the human retina draws the eye of neuroscientist and physicist alike. It is attractive as a self-organizing system, which forms as a part of the central nervous system via biochemical and mechanical cues. The retina is also intriguing as an electro-optical device, converting photons into voltages to perform on-the-fly filtering before the signals are sent to our brain. Here, we consider how the advent of stem cell derived in vitro analogs of the retina, termed retina organoids, opens up an exploration of the interplay between optics, electrics, and mechanics in a complex neuronal network, all in a Petri dish. This review presents state-of-the-art retina organoid protocols by emphasizing links to the biochemical and mechanical signals of in vivo retinogenesis. Electrophysiological recording of active signal processing becomes possible as retina organoids generate light sensitive and synaptically connected photoreceptors. Experimental biophysical tools provide data to steer the development of mathematical models operating at different levels of coarse-graining. In concert, they provide a means to study how mechanical factors guide retina self-assembly. In turn, this understanding informs the engineering of mechanical signals required to tailor the growth of neuronal network morphology. Tackling the complex developmental and computational processes in the retina requires an interdisciplinary endeavor combining experiment and theory, physics, and biology. The reward is enticing: in the next few years, retina organoids could offer a glimpse inside the machinery of simultaneous cellular self-assembly and signal processing, all in an in vitro setting.
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Affiliation(s)
| | - Elijah R. Shelton
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
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70
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Zibetti C. Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives. Cells 2022; 11:cells11050806. [PMID: 35269428 PMCID: PMC8908986 DOI: 10.3390/cells11050806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outcome on gene expression, by coordinating variations in chromatin landscapes to drive divergent retinal specification programs. Recent studies have furthered the understanding of the epigenetic contribution to the progression of age-related macular degeneration, a leading cause of blindness in the elderly. The knowledge of the epigenomic mechanisms that control the acquisition and stabilization of retinal cell fates and are evoked upon damage, holds the potential for the treatment of retinal degeneration. Herein, this review presents the state-of-the-art approaches to investigate the retinal epigenome during development, disease, and reprogramming. A pipeline is then reviewed to functionally interrogate the epigenetic and transcriptional networks underlying cell fate specification, relying on a truly unbiased screening of open chromatin states. The related work proposes an inferential model to identify gene regulatory networks, features the first footprinting analysis and the first tentative, systematic query of candidate pioneer factors in the retina ever conducted in any model organism, leading to the identification of previously uncharacterized master regulators of retinal cell identity, such as the nuclear factor I, NFI. This pipeline is virtually applicable to the study of genetic programs and candidate pioneer factors in any developmental context. Finally, challenges and limitations intrinsic to the current next-generation sequencing techniques are discussed, as well as recent advances in super-resolution imaging, enabling spatio-temporal resolution of the genome.
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Affiliation(s)
- Cristina Zibetti
- Department of Ophthalmology, Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, Building 36, 0455 Oslo, Norway
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71
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Brändle F, Frühbauer B, Jagannathan M. Principles and functions of pericentromeric satellite DNA clustering into chromocenters. Semin Cell Dev Biol 2022; 128:26-39. [PMID: 35144860 DOI: 10.1016/j.semcdb.2022.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/29/2022]
Abstract
Simple non-coding tandem repeats known as satellite DNA are observed widely across eukaryotes. These repeats occupy vast regions at the centromere and pericentromere of chromosomes but their contribution to cellular function has remained incompletely understood. Here, we review the literature on pericentromeric satellite DNA and discuss its organization and functions across eukaryotic species. We specifically focus on chromocenters, DNA-dense nuclear foci that contain clustered pericentromeric satellite DNA repeats from multiple chromosomes. We first discuss chromocenter formation and the roles that epigenetic modifications, satellite DNA transcripts and sequence-specific satellite DNA-binding play in this process. We then review the newly emerging functions of chromocenters in genome encapsulation, the maintenance of cell fate and speciation. We specifically highlight how the rapid divergence of satellite DNA repeats impacts reproductive isolation between closely related species. Together, we underline the importance of this so-called 'junk DNA' in fundamental biological processes.
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Affiliation(s)
- Franziska Brändle
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Benjamin Frühbauer
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Madhav Jagannathan
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland.
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72
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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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73
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Cheng Q, Delafrouz P, Liang J, Liu C, Shen J. Modeling and simulation of cell nuclear architecture reorganization process. JOURNAL OF COMPUTATIONAL PHYSICS 2022; 449:110808. [PMID: 36185393 PMCID: PMC9524197 DOI: 10.1016/j.jcp.2021.110808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We develop a special phase field/diffusive interface method to model the nuclear architecture reorganization process. In particular, we use a Lagrange multiplier approach in the phase field model to preserve the specific physical and geometrical constraints for the biological events. We develop several efficient and robust linear and weakly nonlinear schemes for this new model. To validate the model and numerical methods, we present ample numerical simulations which in particular reproduce several processes of nuclear architecture reorganization from the experiment literature.
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Affiliation(s)
- Qing Cheng
- Department of Mathematics,Purdue University, West Lafayette, IN 47907, USA
| | - Pourya Delafrouz
- Department of Bioengineering, University of Illinois at Chicago, SEO, MC-063, Chicago, IL, 60607-7052, USA
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, SEO, MC-063, Chicago, IL, 60607-7052, USA
| | - Chun Liu
- Department of Applied Mathematics, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jie Shen
- Department of Mathematics,Purdue University, West Lafayette, IN 47907, USA
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74
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Williams DL, Sikora VM, Hammer MA, Amin S, Brinjikji T, Brumley EK, Burrows CJ, Carrillo PM, Cromer K, Edwards SJ, Emri O, Fergle D, Jenkins MJ, Kaushik K, Maydan DD, Woodard W, Clowney EJ. May the Odds Be Ever in Your Favor: Non-deterministic Mechanisms Diversifying Cell Surface Molecule Expression. Front Cell Dev Biol 2022; 9:720798. [PMID: 35087825 PMCID: PMC8787164 DOI: 10.3389/fcell.2021.720798] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 11/24/2021] [Indexed: 12/30/2022] Open
Abstract
How does the information in the genome program the functions of the wide variety of cells in the body? While the development of biological organisms appears to follow an explicit set of genomic instructions to generate the same outcome each time, many biological mechanisms harness molecular noise to produce variable outcomes. Non-deterministic variation is frequently observed in the diversification of cell surface molecules that give cells their functional properties, and is observed across eukaryotic clades, from single-celled protozoans to mammals. This is particularly evident in immune systems, where random recombination produces millions of antibodies from only a few genes; in nervous systems, where stochastic mechanisms vary the sensory receptors and synaptic matching molecules produced by different neurons; and in microbial antigenic variation. These systems employ overlapping molecular strategies including allelic exclusion, gene silencing by constitutive heterochromatin, targeted double-strand breaks, and competition for limiting enhancers. Here, we describe and compare five stochastic molecular mechanisms that produce variety in pathogen coat proteins and in the cell surface receptors of animal immune and neuronal cells, with an emphasis on the utility of non-deterministic variation.
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Affiliation(s)
- Donnell L. Williams
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
| | - Veronica Maria Sikora
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Max A. Hammer
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Sayali Amin
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Taema Brinjikji
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Emily K. Brumley
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Connor J. Burrows
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Paola Michelle Carrillo
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Kirin Cromer
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Summer J. Edwards
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Olivia Emri
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Fergle
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - M. Jamal Jenkins
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
| | - Krishangi Kaushik
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Daniella D. Maydan
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Wrenn Woodard
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - E. Josephine Clowney
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
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75
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Löscher M, Seiz C, Hurst J, Schnichels S. Topical Drug Delivery to the Posterior Segment of the Eye. Pharmaceutics 2022; 14:pharmaceutics14010134. [PMID: 35057030 PMCID: PMC8779621 DOI: 10.3390/pharmaceutics14010134] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 02/07/2023] Open
Abstract
Topical drug delivery to the posterior segment of the eye is a very complex challenge. However, topical delivery is highly desired, to achieve an easy-to-use treatment option for retinal diseases. In this review, we focus on the drug characteristics that are relevant to succeed in this challenge. An overview on the ocular barriers that need to be overcome and some relevant animal models to study ocular pharmacokinetics are given. Furthermore, a summary of substances that were able to reach the posterior segment after eye drop application is provided, as well as an outline of investigated delivery systems to improve ocular drug delivery. Some promising results of substances delivered to the retina suggest that topical treatment of retinal diseases might be possible in the future, which warrants further research.
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76
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RNA gradients: Shapers of 3D genome architecture. Curr Opin Cell Biol 2022; 74:7-12. [PMID: 34998095 DOI: 10.1016/j.ceb.2021.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 01/13/2023]
Abstract
A growing body of evidence points to a role of nuclear RNAs (nucRNAs) in shaping the three-dimensional (3D) architecture of the genome within the nucleus of a eukaryotic cell. nucRNAs are non-homogeneously distributed within the nucleus where they can form global and local gradients that might contribute to instructing the formation and coordinating the function of different types of 3D genome structures. In this article, we highlight the available literature supporting a role of nucRNAs as 3D genome shapers and propose that nucRNA gradients are key mediators of genome structure and function.
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77
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Ito K, Takizawa T. Nuclear Architecture in the Nervous System. Results Probl Cell Differ 2022; 70:419-442. [PMID: 36348117 DOI: 10.1007/978-3-031-06573-6_15] [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: 06/16/2023]
Abstract
Neurons and glial cells in the nervous system exhibit different gene expression programs for neural development and function. These programs are controlled by the epigenetic regulatory layers in the nucleus. The nucleus is a well-organized subcellular organelle that includes chromatin, the nuclear lamina, and nuclear bodies. These subnuclear components operate together as epigenetic regulators of neural development and function and are collectively called the nuclear architecture. In the nervous system, dynamic rearrangement of the nuclear architecture has been observed in each cell type, especially in neurons, allowing for their specialized functions, including learning and memory formation. Although the importance of nuclear architecture has been debated for decades, the paradigm has been changing rapidly, owing to the development of new technologies. Here, we reviewed the latest studies on nuclear geometry, nuclear bodies, and heterochromatin compartments, as well as summarized recent novel insights regarding radial positioning, chromatin condensation, and chromatin interaction between genes and cis-regulatory elements.
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Affiliation(s)
- Kenji Ito
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, Pennsylvania, USA
| | - Takumi Takizawa
- Department of Pediatrics, Gunma University Graduate School of Medicine, Maebashi, Japan.
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78
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Mahmood SR, El Said NH, Percipalle P. The Role of Nuclear Actin in Genome Organization and Gene Expression Regulation During Differentiation. Results Probl Cell Differ 2022; 70:607-624. [PMID: 36348124 DOI: 10.1007/978-3-031-06573-6_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the cell nucleus, actin participates in numerous essential processes. Actin is involved in chromatin as part of specific ATP-dependent chromatin remodeling complexes and associates with the RNA polymerase machinery to regulate transcription at multiple levels. Emerging evidence has also shown that the nuclear actin pool controls the architecture of the mammalian genome playing an important role in its hierarchical organization into transcriptionally active and repressed compartments, contributing to the clustering of RNA polymerase II into transcriptional hubs. Here, we review the most recent literature and discuss how actin involvement in genome organization impacts the regulation of gene programs that are activated or repressed during differentiation and development. As in the cytoplasm, we propose that nuclear actin is involved in key nuclear tasks in complex with different types of actin-binding proteins that regulate actin function and bridge interactions between actin and various nuclear components.
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Affiliation(s)
- Syed Raza Mahmood
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
- Department of Biology, New York University, New York, NY, USA
| | - Nadine Hosny El Said
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - Piergiorgio Percipalle
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.
- Department of Biology, New York University, New York, NY, USA.
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.
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79
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The Physical Behavior of Interphase Chromosomes: Polymer Theory and Coarse-Grain Computer Simulations. Methods Mol Biol 2022; 2301:235-258. [PMID: 34415539 DOI: 10.1007/978-1-0716-1390-0_12] [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
Fluorescence in situ hybridization and chromosome conformation capture methods point to the same conclusion: that chromosomes appear to the external observer as compact structures with a highly nonrandom three-dimensional organization. In this work, we recapitulate the efforts made by us and other groups to rationalize this behavior in terms of the mathematical language and tools of polymer physics. After a brief introduction dedicated to some crucial experiments dissecting the structure of interphase chromosomes, we discuss at a nonspecialistic level some fundamental aspects of theoretical and numerical polymer physics. Then, we inglobe biological and polymer aspects into a polymer model for interphase chromosomes which moves from the observation that mutual topological constraints, such as those typically present between polymer chains in ordinary melts, induce slow chain dynamics and "constraint" chromosomes to resemble double-folded randomly branched polymer conformations. By explicitly turning these ideas into a multi-scale numerical algorithm which is described here in full details, we can design accurate model polymer conformations for interphase chromosomes and offer them for systematic comparison to experiments. The review is concluded by discussing the limitations of our approach and pointing to promising perspectives for future work.
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80
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Maillard F, Elie N, Villain-Naud N, Lepoittevin M, Martinez AS, Lelong C. Male triploid oysters of Crassostrea gigas exhibit defects in mitosis and meiosis during early spermatogenesis. FEBS Open Bio 2021; 12:1438-1452. [PMID: 34935310 PMCID: PMC9340784 DOI: 10.1002/2211-5463.13356] [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: 07/07/2021] [Revised: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 11/07/2022] Open
Abstract
The Pacific oyster, Crassostrea gigas is a successive irregular hermaphrodite mollusc which has an annual breeding cycle. Oysters are naturally diploid organisms, but triploid oysters have been developed for use in shellfish aquaculture, with the aim of obtaining sterile animals with commercial value. However, studies have shown that some triploid oysters are partially able to undergo gametogenesis, with numerous proliferating cells closed to diploids (3n alpha) or a partial one with an accumulation of locked germ cells (3n beta). The aim of our study therefore was to understand the regulation of spermatogenesis in both groups of triploid oysters (alpha and beta) from the beginning of spermatogenesis, during mitosis and meiosis events. Our results demonstrate that the reduced spermatogenesis in triploids results from a deregulation of the development of the germinal lineage and the establishment of the gonadal tract led by a lower number of tubules. Morphological cellular investigation also revealed an abnormal condensation of germ cell nuclei and the presence of clear patches in the nucleoplasm of triploid cells, which were more pronounced in beta oysters. Furthermore, studies of molecular and cellular regulation showed a downregulation of mitotic spindle checkpoint in beta oysters, resulting in disturbance of chromosomal segregation, notably on Spindle Assembly Checkpoint involved in the binding of microtubules to chromosomes. Taken together, our results suggest that the lower reproductive ability of triploid oysters may be due to cellular and molecular events such as impairment of spermatogenesis and disruptions of mitosis and meiosis, occurring early and at various stages of the gametogenetic cycle.
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Affiliation(s)
- Floriane Maillard
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France
| | - Nicolas Elie
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Microscopie Appliquée à la Biologie, SF4206 Interaction Cellule-Organisme-Environnement (ICORE), Université de Caen Normandie, Esplanade de la paix, 14032, Caen CEDEX, France
| | - Nadège Villain-Naud
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France
| | - Mélanie Lepoittevin
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France
| | - Anne-Sophie Martinez
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France
| | - Christophe Lelong
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France.,Oestrogènes et Reproduction (OeReCa), EA2608, Université de Caen Normandie, Esplanade de la paix, 14032, Caen CEDEX, France
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81
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Seelbinder B, Ghosh S, Schneider SE, Scott AK, Berman AG, Goergen CJ, Margulies KB, Bedi K, Casas E, Swearingen AR, Brumbaugh J, Calve S, Neu CP. Nuclear deformation guides chromatin reorganization in cardiac development and disease. Nat Biomed Eng 2021; 5:1500-1516. [PMID: 34857921 PMCID: PMC9300284 DOI: 10.1038/s41551-021-00823-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 10/20/2021] [Indexed: 01/31/2023]
Abstract
In cardiovascular tissues, changes in the mechanical properties of the extracellular matrix are associated with cellular de-differentiation and with subsequent functional declines. However, the underlying mechanoreceptive mechanisms are largely unclear. Here, by generating high-resolution, full-field strain maps of cardiomyocyte nuclei during contraction in vitro, complemented with evidence from tissues from patients with cardiomyopathy and from mice with reduced cardiac performance, we show that cardiomyocytes establish a distinct nuclear organization during maturation, characterized by the reorganization of H3K9me3-marked chromatin towards the nuclear border. Specifically, we show that intranuclear tension is spatially correlated with H3K9me3-marked chromatin, that reductions in nuclear deformation (through environmental stiffening or through the disruption of complexes of the linker of nucleoskeleton and cytoskeleton) abrogate chromatin reorganization and lead to the dissociation of H3K9me3-marked chromatin from the nuclear periphery, and that the suppression of H3K9 methylation induces chromatin reorganization and reduces the expression of cardiac developmental genes. Overall, our findings indicate that, by integrating environmental mechanical cues, the nuclei of cardiomyocytes guide and stabilize the fate of cells through the reorganization of epigenetically marked chromatin.
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Affiliation(s)
- Benjamin Seelbinder
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO)
| | - Soham Ghosh
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO)
| | | | - Adrienne K. Scott
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO)
| | - Alycia G. Berman
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette (IN)
| | - Craig J. Goergen
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette (IN)
| | | | - Kenneth Bedi
- Cardiovascular Institute, University of Pennsylvania, Philadelphia (PA)
| | - Eduard Casas
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder (CO)
| | - Alison R. Swearingen
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder (CO)
| | - Justin Brumbaugh
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder (CO)
| | - Sarah Calve
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO),Weldon School of Biomedical Engineering, Purdue University, West Lafayette (IN)
| | - Corey P. Neu
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO),Corresponding Author
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82
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Wong X, Hoskins VE, Melendez-Perez AJ, Harr JC, Gordon M, Reddy KL. Lamin C is required to establish genome organization after mitosis. Genome Biol 2021; 22:305. [PMID: 34775987 PMCID: PMC8591896 DOI: 10.1186/s13059-021-02516-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/08/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The dynamic 3D organization of the genome is central to gene regulation and development. The nuclear lamina influences genome organization through the tethering of lamina-associated domains (LADs) to the nuclear periphery. Evidence suggests that lamins A and C are the predominant lamins involved in the peripheral association of LADs, potentially serving different roles. RESULTS Here, we examine chromosome architecture in mouse cells in which lamin A or lamin C are downregulated. We find that lamin C, and not lamin A, is required for the 3D organization of LADs and overall chromosome organization. Striking differences in localization are present as cells exit mitosis and persist through early G1 and are linked to differential phosphorylation. Whereas lamin A associates with the nascent nuclear envelope (NE) during telophase, lamin C remains in the interior, surrounding globular LAD aggregates enriched on euchromatic regions. Lamin C association with the NE is delayed until several hours into G1 and correlates temporally and spatially with the post-mitotic NE association of LADs. Post-mitotic LAD association with the NE, and global 3D genome organization, is perturbed only in cells depleted of lamin C, and not lamin A. CONCLUSIONS Lamin C regulates LAD dynamics during exit from mitosis and is a key regulator of genome organization in mammalian cells. This reveals an unexpectedly central role for lamin C in genome organization, including inter-chromosomal LAD-LAD segregation and LAD scaffolding at the NE, raising intriguing questions about the individual and overlapping roles of lamin A/C in cellular function and disease.
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Affiliation(s)
- Xianrong Wong
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.,Current Address: Laboratory of Developmental and Regenerative Biology, A*STAR Skin Research Labs, Agency for Science, Technology and Research (A*STAR), Immunos, Singapore, 138648, Singapore
| | - Victoria E Hoskins
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.,McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ashley J Melendez-Perez
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Jennifer C Harr
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.,Department of Biological Sciences, St. Mary's University, San Antonio, TX, 78228, USA
| | - Molly Gordon
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.,Department of Cell Biology, Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Karen L Reddy
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA. .,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
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83
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Daghsni M, Aldiri I. Building a Mammalian Retina: An Eye on Chromatin Structure. Front Genet 2021; 12:775205. [PMID: 34764989 PMCID: PMC8576187 DOI: 10.3389/fgene.2021.775205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Regulation of gene expression by chromatin structure has been under intensive investigation, establishing nuclear organization and genome architecture as a potent and effective means of regulating developmental processes. The substantial growth in our knowledge of the molecular mechanisms underlying retinogenesis has been powered by several genome-wide based tools that mapped chromatin organization at multiple cellular and biochemical levels. Studies profiling the retinal epigenome and transcriptome have allowed the systematic annotation of putative cis-regulatory elements associated with transcriptional programs that drive retinal neural differentiation, laying the groundwork to understand spatiotemporal retinal gene regulation at a mechanistic level. In this review, we outline recent advances in our understanding of the chromatin architecture in the mammalian retina during development and disease. We focus on the emerging roles of non-coding regulatory elements in controlling retinal cell-type specific transcriptional programs, and discuss potential implications in untangling the etiology of eye-related disorders.
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Affiliation(s)
- Marwa Daghsni
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Issam Aldiri
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Louis J. Fox Center for Vision Restoration, University of Pittsburgh, Pittsburgh, PA, United States
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84
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Abstract
Emergence of a captivating phenomenon aggregation induced emission (AIE) in the early years of 21st century attracted worldwide researchers. In the last two decades various novel AIE active biocompatible small molecules, macromolecules and polymers have been developed for diverse biomedical applications. Imaging of specific organelle such as mitochondria, ribosomes, nuclei and many others play important in the controlling and successful treatment of various diseases. Conventional luminescent probe molecules used in the imaging at cellular or subcellular level exhibit very weak emission on dispersion or on aggregation in aqueous media. AIE luminogens development is indispensable to overcome the notorious aggregation-caused quenching (ACQ) issue inherited by conventional fluorophores. In the present chapter we mostly highlighted over one decade development of various AIE active luminogens utilized for imaging of cell nucleus, nucleon and nucleic acids. The development of those AIE luminogens exhibits promising results in the early diagnosis of cancer diseases.
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85
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Kalargyrou AA, Basche M, Hare A, West EL, Smith AJ, Ali RR, Pearson RA. Nanotube-like processes facilitate material transfer between photoreceptors. EMBO Rep 2021; 22:e53732. [PMID: 34494703 PMCID: PMC8567251 DOI: 10.15252/embr.202153732] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Neuronal communication is typically mediated via synapses and gap junctions. New forms of intercellular communication, including nanotubes (NTs) and extracellular vesicles (EVs), have been described for non-neuronal cells, but their role in neuronal communication is not known. Recently, transfer of cytoplasmic material between donor and host neurons ("material transfer") was shown to occur after photoreceptor transplantation. The cellular mechanism(s) underlying this surprising finding are unknown. Here, using transplantation, primary neuronal cultures and the generation of chimeric retinae, we show for the first time that mammalian photoreceptor neurons can form open-end NT-like processes. These processes permit the transfer of cytoplasmic and membrane-bound molecules in culture and after transplantation and can mediate gain-of-function in the acceptor cells. Rarely, organelles were also observed to transfer. Strikingly, use of chimeric retinae revealed that material transfer can occur between photoreceptors in the intact adult retina. Conversely, while photoreceptors are capable of releasing EVs, at least in culture, these are taken up by glia and not by retinal neurons. Our findings provide the first evidence of functional NT-like processes forming between sensory neurons in culture and in vivo.
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Affiliation(s)
- Aikaterini A Kalargyrou
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
| | - Mark Basche
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
| | - Aura Hare
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
| | - Emma L West
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
| | - Alexander J Smith
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
| | - Robin R Ali
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
- Kellogg Eye CenterUniversity of MichiganAnn ArborMIUSA
| | - Rachael A Pearson
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
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86
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Maslova A, Krasikova A. FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains. Front Cell Dev Biol 2021; 9:753097. [PMID: 34805161 PMCID: PMC8597843 DOI: 10.3389/fcell.2021.753097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
The intimate relationships between genome structure and function direct efforts toward deciphering three-dimensional chromatin organization within the interphase nuclei at different genomic length scales. For decades, major insights into chromatin structure at the level of large-scale euchromatin and heterochromatin compartments, chromosome territories, and subchromosomal regions resulted from the evolution of light microscopy and fluorescence in situ hybridization. Studies of nanoscale nucleosomal chromatin organization benefited from a variety of electron microscopy techniques. Recent breakthroughs in the investigation of mesoscale chromatin structures have emerged from chromatin conformation capture methods (C-methods). Chromatin has been found to form hierarchical domains with high frequency of local interactions from loop domains to topologically associating domains and compartments. During the last decade, advances in super-resolution light microscopy made these levels of chromatin folding amenable for microscopic examination. Here we are reviewing recent developments in FISH-based approaches for detection, quantitative measurements, and validation of contact chromatin domains deduced from C-based data. We specifically focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains. Vivid examples of chromatin domain FISH-visualization by means of conventional, super-resolution light and electron microscopy in different model organisms are provided.
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Affiliation(s)
| | - Alla Krasikova
- Laboratory of Nuclear Structure and Dynamics, Cytology and Histology Department, Saint Petersburg State University, Saint Petersburg, Russia
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87
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Takei Y, Zheng S, Yun J, Shah S, Pierson N, White J, Schindler S, Tischbirek CH, Yuan GC, Cai L. Single-cell nuclear architecture across cell types in the mouse brain. Science 2021; 374:586-594. [PMID: 34591592 DOI: 10.1126/science.abj1966] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Diverse cell types in tissues have distinct gene expression programs, chromatin states, and nuclear architectures. To correlate such multimodal information across thousands of single cells in mouse brain tissue sections, we use integrated spatial genomics, imaging thousands of genomic loci along with RNAs and epigenetic markers simultaneously in individual cells. We reveal that cell type–specific association and scaffolding of DNA loci around nuclear bodies organize the nuclear architecture and correlate with differential expression levels in different cell types. At the submegabase level, active and inactive X chromosomes access similar domain structures in single cells despite distinct epigenetic and expression states. This work represents a major step forward in linking single-cell three-dimensional nuclear architecture, gene expression, and epigenetic modifications in a native tissue context.
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Affiliation(s)
- Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shiwei Zheng
- Department of Genetics and Genomic Sciences and Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jina Yun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sheel Shah
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nico Pierson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jonathan White
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Simone Schindler
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Carsten H Tischbirek
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences and Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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88
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Sirés A, Turch-Anguera M, Bogdanov P, Sampedro J, Ramos H, Ruíz Lasa A, Huo J, Xu S, Lam KP, López-Soriano J, Pérez-García MJ, Hernández C, Simó R, Solé M, Comella JX. Faim knockout leads to gliosis and late-onset neurodegeneration of photoreceptors in the mouse retina. J Neurosci Res 2021; 99:3103-3120. [PMID: 34713467 DOI: 10.1002/jnr.24978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/13/2021] [Accepted: 09/21/2021] [Indexed: 01/08/2023]
Abstract
Fas Apoptotic Inhibitory Molecule protein (FAIM) is a death receptor antagonist and an apoptosis regulator. It encodes two isoforms, namely FAIM-S (short) and FAIM-L (long), both with significant neuronal functions. FAIM-S, which is ubiquitously expressed, is involved in neurite outgrowth. In contrast, FAIM-L is expressed only in neurons and it protects them from cell death. Interestingly, FAIM-L is downregulated in patients and mouse models of Alzheimer's disease before the onset of neurodegeneration, and Faim transcript levels are decreased in mouse models of retinal degeneration. However, few studies have addressed the role of FAIM in the central nervous system, yet alone the retina. The retina is a highly specialized tissue, and its degeneration has proved to precede pathological mechanisms of neurodegenerative diseases. Here we describe that Faim depletion in mice damages the retina persistently and leads to late-onset photoreceptor death in older mice. Immunohistochemical analyses showed that Faim knockout (Faim-/- ) mice present ubiquitinated aggregates throughout the retina from early ages. Moreover, retinal cells released stress signals that can signal to Müller cells, as shown by immunofluorescence and qRT-PCR. Müller cells monitor retinal homeostasis and trigger a gliotic response in Faim-/- mice that becomes pathogenic when sustained. In this regard, we observed pronounced vascular leakage at later ages, which may be caused by persistent inflammation. These results suggest that FAIM is an important player in the maintenance of retinal homeostasis, and they support the premise that FAIM is a plausible early marker for late photoreceptor and neuronal degeneration.
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Affiliation(s)
- Anna Sirés
- Cell Signaling and Apoptosis Group, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain.,Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Mireia Turch-Anguera
- Cell Signaling and Apoptosis Group, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.,Diabetes and Metabolism Research Unit, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Patricia Bogdanov
- Diabetes and Metabolism Research Unit, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Joel Sampedro
- Diabetes and Metabolism Research Unit, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Hugo Ramos
- Diabetes and Metabolism Research Unit, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Agustín Ruíz Lasa
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain.,Research Center and Memory Clinic. Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Jianxin Huo
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Shengli Xu
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Kong-Peng Lam
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Joaquín López-Soriano
- Cell Signaling and Apoptosis Group, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain.,Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - M Jose Pérez-García
- Cell Signaling and Apoptosis Group, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | - Cristina Hernández
- Diabetes and Metabolism Research Unit, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Rafael Simó
- Diabetes and Metabolism Research Unit, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Montse Solé
- Cell Signaling and Apoptosis Group, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain.,Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Joan X Comella
- Cell Signaling and Apoptosis Group, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain.,Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
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89
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Nishihara H, Stanyon R, Tanabe H, Koga A. Replacement of owl monkey centromere satellite by a newly evolved variant was a recent and rapid process. Genes Cells 2021; 26:979-986. [PMID: 34570411 DOI: 10.1111/gtc.12898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 11/29/2022]
Abstract
Alpha satellite DNA is a major DNA component of primate centromeres. We previously reported that Azara's owl monkey has two types of alpha satellite DNA, OwlAlp1 and OwlAlp2. OwlAlp2 (344 bp) exhibits a sequence similarity throughout its entire length with alpha satellite DNA of closely related species. OwlAlp1 (185 bp) corresponds to the part of OwlAlp2. Based on the observation that the CENP-A protein binds to OwlAlp1, we proposed that OwlAlp1 is a relatively new repetitive DNA that replaced OwlAlp2 as the centromeric satellite DNA. However, a detailed picture of the evolutionary process of this centromere DNA replacement remains largely unknown. Here, we performed a phylogenetic analysis of OwlAlp1 and OwlAlp2 sequences, and also compared our results to alpha satellite DNA sequences of other primate species. We found that: (i) OwlAlp1 exhibits a higher similarity to OwlAlp2 than to alpha satellite DNA of other species, (ii) OwlAlp1 has a single origin, and (iii) sequence variation is lower in OwlAlp1 than in OwlAlp2. We conclude that OwlAlp1 underwent a recent and rapid expansion in the owl monkey lineage. This centromere DNA replacement could have been facilitated by the heterochromatin reorganization that is associated with the adaptation of owl monkeys to a nocturnal lifestyle.
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Affiliation(s)
- Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Roscoe Stanyon
- Department of Biology, University of Florence, Florence, Italy
| | - Hideyuki Tanabe
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Japan
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama, Japan
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90
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Smith CL, Lan Y, Jain R, Epstein JA, Poleshko A. Global chromatin relabeling accompanies spatial inversion of chromatin in rod photoreceptors. SCIENCE ADVANCES 2021; 7:eabj3035. [PMID: 34559565 PMCID: PMC8462898 DOI: 10.1126/sciadv.abj3035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
The nuclear architecture of rod photoreceptor cells in nocturnal mammals is unlike that of other animal cells. Murine rod cells have an “inverted” chromatin organization with euchromatin at the nuclear periphery and heterochromatin packed in the center of the nucleus. In conventional nuclear architecture, euchromatin is mostly in the interior, and heterochromatin is largely at the nuclear periphery. We demonstrate that inverted nuclear architecture is achieved through global relabeling of the rod cell epigenome. During rod cell maturation, H3K9me2-labeled nuclear peripheral heterochromatin is relabeled with H3K9me3 and repositioned to the nuclear center, while transcriptionally active euchromatin is labeled with H3K9me2 and positioned at the nuclear periphery. Global chromatin relabeling is correlated with spatial rearrangement, suggesting a critical role for histone modifications, specifically H3K9 methylation, in nuclear architecture. These results reveal a dramatic example of genome-wide epigenetic relabeling of chromatin that accompanies altered nuclear architecture in a postnatal, postmitotic cell.
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Affiliation(s)
- Cheryl L. Smith
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yemin Lan
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rajan Jain
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Penn Cardiovascular Institute, and Institute of Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan A. Epstein
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Penn Cardiovascular Institute, and Institute of Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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91
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MacPhillamy C, Pitchford WS, Alinejad-Rokny H, Low WY. Opportunity to improve livestock traits using 3D genomics. Anim Genet 2021; 52:785-798. [PMID: 34494283 DOI: 10.1111/age.13135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 11/30/2022]
Abstract
The advent of high-throughput chromosome conformation capture and sequencing (Hi-C) has enabled researchers to probe the 3D architecture of the mammalian genome in a genome-wide manner. Simultaneously, advances in epigenomic assays, such as chromatin immunoprecipitation and sequencing (ChIP-seq) and DNase-seq, have enabled researchers to study cis-regulatory interactions and chromatin accessibility across the same genome-wide scale. The use of these data has revealed many unique insights into gene regulation and disease pathomechanisms in several model organisms. With the advent of these high-throughput sequencing technologies, there has been an ever-increasing number of datasets available for study; however, this is often limited to model organisms. Livestock species play critical roles in the economies of developing and developed nations alike. Despite this, they are greatly underrepresented in the 3D genomics space; Hi-C and related technologies have the potential to revolutionise livestock breeding by enabling a more comprehensive understanding of how production traits are controlled. The growth in human and model organism Hi-C data has seen a surge in the availability of computational tools for use in 3D genomics, with some tools using machine learning techniques to predict features and improve dataset quality. In this review, we provide an overview of the 3D genome and discuss the status of 3D genomics in livestock before delving into advancing the field by drawing inspiration from research in human and mouse. We end by offering future directions for livestock research in the field of 3D genomics.
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Affiliation(s)
- C MacPhillamy
- Davies Livestock Research Centre, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, SA, 5371, Australia
| | - W S Pitchford
- Davies Livestock Research Centre, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, SA, 5371, Australia
| | - H Alinejad-Rokny
- Biological & Medical Machine Learning Lab, The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia.,School of Computer Science and Engineering, The University of New South Wales (UNSW Sydney), Sydney, NSW, 2052, Australia
| | - W Y Low
- Davies Livestock Research Centre, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, SA, 5371, Australia
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92
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Mejia-Ramirez E, Geiger H, Florian MC. Loss of epigenetic polarity is a hallmark of hematopoietic stem cell aging. Hum Mol Genet 2021; 29:R248-R254. [PMID: 32821941 DOI: 10.1093/hmg/ddaa189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/01/2023] Open
Abstract
Changes of polarity in somatic stem cells upon aging or disease lead to a functional deterioration of stem cells and consequently loss of tissue homeostasis, likely due to changes in the mode (symmetry versus asymmetry) of stem cell divisions. Changes in polarity of epigenetic markers (or 'epi-polarity') in stem cells, which are linked to alterations in chromatin architecture, might explain how a decline in the frequency of epipolar stem cells can have a long-lasting impact on the function of especially aging stem cells. The drift in epipolarity might represent a novel therapeutic target to improve stem cell function upon aging or disease. Here we review basic biological principles of epigenetic polarity, with a special focus on epipolarity and aging of hematopoietic stem cells.
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Affiliation(s)
- Eva Mejia-Ramirez
- Program of Regenerative Medicine, IDIBELL and Program for Clinical Translation of Regenerative Medicine in Catalonia (P-CMRC), Av. Granvia 199, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Hartmut Geiger
- Institute of Molecular Medicine, University of Ulm, James-Franck-Ring 11c, 89081, Ulm, Germany
| | - M Carolina Florian
- Program of Regenerative Medicine, IDIBELL and Program for Clinical Translation of Regenerative Medicine in Catalonia (P-CMRC), Av. Granvia 199, 08908 L'Hospitalet de Llobregat, Barcelona, Spain.,Institute of Molecular Medicine, University of Ulm, James-Franck-Ring 11c, 89081, Ulm, Germany
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93
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Wu J, Liu LL, Cao M, Hu A, Hu D, Luo Y, Wang H, Zhong JN. DNA methylation plays important roles in retinal development and diseases. Exp Eye Res 2021; 211:108733. [PMID: 34418429 DOI: 10.1016/j.exer.2021.108733] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/16/2022]
Abstract
DNA methylation is important in developing and post-mitotic cells in various tissues. Recent studies have shown that DNA methylation is highly dynamic, and plays important roles during retinal development and aging. In addition, the dynamic regulation of DNA methylation is involved in the occurrence and development of age-related macular degeneration and diabetic retinopathy and shows potential in disease diagnoses and prognoses. This review introduces the epigenetic concepts of DNA methylation and demethylation with an emphasis on their regulatory roles in retinal development and related diseases. Moreover, we propose exciting ideas such as its crosstalk with other epigenetic modifications and retinal regeneration, to provide a potential direction for understanding retinal diseases from the epigenetic perspective.
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Affiliation(s)
- Jing Wu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, Lishui Municipal Central Hospital, Lishui, 323000, Zhejiang Province, China
| | - Lin-Lin Liu
- Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Miao Cao
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Ang Hu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Die Hu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Yan Luo
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Hui Wang
- Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China.
| | - Jia-Ning Zhong
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China.
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94
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Dileep V, Tsai LH. Three-dimensional chromatin organization in brain function and dysfunction. Curr Opin Neurobiol 2021; 69:214-221. [PMID: 34111830 DOI: 10.1016/j.conb.2021.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/20/2021] [Accepted: 04/29/2021] [Indexed: 01/24/2023]
Abstract
The three-dimensional (3D) organization of chromatin within the nucleus is now recognized as a bona fide epigenetic property influencing genome function, replication, and maintenance. In the recent years, several studies have revealed how 3D chromatin organization is associated with brain function and its emerging role in disorders of the brain. 3D chromatin organization plays a crucial role in the development of different cell types of the nervous system and some neuronal cell types have adapted unique modifications to this organization that deviates from all other cell types. In post-mitotic neurons, dynamic changes in chromatin interactions in response to neuronal activity underlie learning and memory formation. Finally, new evidence directly links 3D chromatin organization to several disorders of the brain. These recent findings position 3D chromatin organization as a fundamental regulatory mechanism poised to reveal the etiology of brain function and dysfunctions.
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Affiliation(s)
- Vishnu Dileep
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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95
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Solovyeva A, Levakin I, Zorin E, Adonin L, Khotimchenko Y, Podgornaya O. Transposons-Based Clonal Diversity in Trematode Involves Parts of CR1 (LINE) in Eu- and Heterochromatin. Genes (Basel) 2021; 12:1129. [PMID: 34440303 PMCID: PMC8392823 DOI: 10.3390/genes12081129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 01/21/2023] Open
Abstract
Trematode parthenitae have long been believed to form clonal populations, but clonal diversity has been discovered in this asexual stage of the lifecycle. Clonal polymorphism in the model species Himasthla elongata has been previously described, but the source of this phenomenon remains unknown. In this work, we traced cercarial clonal diversity using a simplified amplified fragment length polymorphism (SAFLP) method and characterised the nature of fragments in diverse electrophoretic bands. The repetitive elements were identified in both the primary sequence of the H. elongata genome and in the transcriptome data. Long-interspersed nuclear elements (LINEs) and long terminal repeat retrotransposons (LTRs) were found to represent an overwhelming majority of the genome and the transposon transcripts. Most sequenced fragments from SAFLP pattern contained the reverse transcriptase (RT, ORF2) domains of LINEs, and only a few sequences belonged to ORFs of LTRs and ORF1 of LINEs. A fragment corresponding to a CR1-like (LINE) spacer region was discovered and named CR1-renegade (CR1-rng). In addition to RT-containing CR1 transcripts, we found short CR1-rng transcripts in the redia transcriptome and short contigs in the mobilome. Probes against CR1-RT and CR1-rng presented strikingly different pictures in FISH mapping, despite both being fragments of CR1. In silico data and Southern blotting indicated that CR1-rng is not tandemly organised. CR1 involvement in clonal diversity is discussed.
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Affiliation(s)
- Anna Solovyeva
- Institute of Cytology of the Russian Academy of Science, Tikhoretsky Ave 4, 194064 Saint Petersburg, Russia;
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Nab 1, 199034 Saint Petersburg, Russia;
| | - Ivan Levakin
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Nab 1, 199034 Saint Petersburg, Russia;
| | - Evgeny Zorin
- All-Russia Research Institute for Agricultural Microbiology, Pushkin 8, 196608 Saint Petersburg, Russia;
| | - Leonid Adonin
- Moscow Institute of Physics and Technology, Institutskiy per 9, 141701 Dolgoprudny, Russia;
| | - Yuri Khotimchenko
- School of Biomedicine, Far Eastern Federal University, Sukhanova St 8, 690091 Vladivostok, Russia;
| | - Olga Podgornaya
- Institute of Cytology of the Russian Academy of Science, Tikhoretsky Ave 4, 194064 Saint Petersburg, Russia;
- Department of Cytology and Histology, Saint Petersburg State University, Universitetskaya Nab 7/9, 199034 Saint Petersburg, Russia
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96
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Inhibition of Epigenetic Modifiers LSD1 and HDAC1 Blocks Rod Photoreceptor Death in Mouse Models of Retinitis Pigmentosa. J Neurosci 2021; 41:6775-6792. [PMID: 34193554 DOI: 10.1523/jneurosci.3102-20.2021] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 06/11/2021] [Accepted: 06/18/2021] [Indexed: 11/21/2022] Open
Abstract
Epigenetic modifiers are increasingly being investigated as potential therapeutics to modify and overcome disease phenotypes. Diseases of the nervous system present a particular problem as neurons are postmitotic and demonstrate relatively stable gene expression patterns and chromatin organization. We have explored the ability of epigenetic modifiers to prevent degeneration of rod photoreceptors in a mouse model of retinitis pigmentosa (RP), using rd10 mice of both sexes. The histone modification eraser enzymes lysine demethylase 1 (LSD1) and histone deacetylase 1 (HDAC1) are known to have dramatic effects on the development of rod photoreceptors. In the RP mouse model, inhibitors of these enzymes blocked rod degeneration, preserved vision, and affected the expression of multiple genes including maintenance of rod-specific transcripts and downregulation of those involved in inflammation, gliosis, and cell death. The neuroprotective activity of LSD1 inhibitors includes two pathways. First, through targeting histone modifications, they increase accessibility of chromatin and upregulate neuroprotective genes, such as from the Wnt pathway. We propose that this process is going in rod photoreceptors. Second, through nonhistone targets, they inhibit transcription of inflammatory genes and inflammation. This process is going in microglia, and lack of inflammation keeps rod photoreceptors alive.SIGNIFICANCE STATEMENT Retinal degenerations are a leading cause of vision loss. RP is genetically very heterogeneous, and the multiple pathways leading to cell death are one reason for the slow progress in identifying suitable treatments for patients. Here we demonstrate that inhibition of LSD1and HDAC1 in a mouse model of RP leads to preservation of rod photoreceptors and visual function, retaining of expression of rod-specific genes, and with decreased inflammation, cell death, and Müller cell gliosis. We propose that these epigenetic inhibitors cause more open and accessible chromatin, allowing expression of neuroprotective genes. A second mechanism that allows rod photoreceptor survival is suppression of inflammation by epigenetic inhibitors in microglia. Manipulation of epigenetic modifiers is a new strategy to fight neurodegeneration in RP.
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97
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Zhou M, Liu Y, Ma C. Distinct Nuclear Architecture of Photoreceptors and Light-Induced Behaviors in Different Strains of Mice. Transl Vis Sci Technol 2021; 10:37. [PMID: 34003922 PMCID: PMC7910638 DOI: 10.1167/tvst.10.2.37] [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] [Indexed: 11/24/2022] Open
Abstract
Purpose The mouse retina is considered a remarkable model for studying gene functions. However, variations in genetic background influence phenotypes in the mammalian retina. Therefore this study aimed to investigate the effects of the genetic background on the nuclear architecture of photoreceptor cells and the light-induced behavior in C57BL/6, 129 × 1/svj, and ICR mice. Methods The nuclear architecture of photoreceptor cells was investigated using various staining methods on postnatal day 21 (P21). Murine behavior was observed using a light-dark compartment test. Results The outer nuclear layer and retina were significantly thicker in C57BL/6 mice than in 129 × 1/svj mice. The percentage of photoreceptors with one chromocenter was significantly higher in C57BL/6 mice than in 129 × 1/svj and ICR mice on P21. The numbers of photoreceptor cells in C57BL/6 and ICR mice were significantly higher than those in 129 × 1/svj mice. The behavior test revealed that the walking distance and velocity in the light compartment were increased in C57BL/6 and ICR mice compared to 129 × 1/svj mice. Conclusions Different mouse strains had a distinct nuclear architecture of photoreceptors on P21, and C57BL/6 and ICR mice were more active than 129 × 1/svj mice in response to light-induced stress. Translational Relevance This study demonstrates a technique for assessing retinal structures and nuclear architecture in various strains of mice, which are often used to model human retinal disease. Hence, this study may help to elucidate the effect of genetic or disease-induced variance in retinal architecture and the organization of photoreceptor nuclear content on visual function in humans.
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Affiliation(s)
- Mingxue Zhou
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing Institute of Traditional Chinese Medicine, Beijing, China
| | - Yutong Liu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Chao Ma
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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98
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Lu JY, Chang L, Li T, Wang T, Yin Y, Zhan G, Han X, Zhang K, Tao Y, Percharde M, Wang L, Peng Q, Yan P, Zhang H, Bi X, Shao W, Hong Y, Wu Z, Ma R, Wang P, Li W, Zhang J, Chang Z, Hou Y, Zhu B, Ramalho-Santos M, Li P, Xie W, Na J, Sun Y, Shen X. Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome. Cell Res 2021; 31:613-630. [PMID: 33514913 PMCID: PMC8169921 DOI: 10.1038/s41422-020-00466-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/17/2020] [Indexed: 01/30/2023] Open
Abstract
Organization of the genome into euchromatin and heterochromatin appears to be evolutionarily conserved and relatively stable during lineage differentiation. In an effort to unravel the basic principle underlying genome folding, here we focus on the genome itself and report a fundamental role for L1 (LINE1 or LINE-1) and B1/Alu retrotransposons, the most abundant subclasses of repetitive sequences, in chromatin compartmentalization. We find that homotypic clustering of L1 and B1/Alu demarcates the genome into grossly exclusive domains, and characterizes and predicts Hi-C compartments. Spatial segregation of L1-rich sequences in the nuclear and nucleolar peripheries and B1/Alu-rich sequences in the nuclear interior is conserved in mouse and human cells and occurs dynamically during the cell cycle. In addition, de novo establishment of L1 and B1 nuclear segregation is coincident with the formation of higher-order chromatin structures during early embryogenesis and appears to be critically regulated by L1 and B1 transcripts. Importantly, depletion of L1 transcripts in embryonic stem cells drastically weakens homotypic repeat contacts and compartmental strength, and disrupts the nuclear segregation of L1- or B1-rich chromosomal sequences at genome-wide and individual sites. Mechanistically, nuclear co-localization and liquid droplet formation of L1 repeat DNA and RNA with heterochromatin protein HP1α suggest a phase-separation mechanism by which L1 promotes heterochromatin compartmentalization. Taken together, we propose a genetically encoded model in which L1 and B1/Alu repeats blueprint chromatin macrostructure. Our model explains the robustness of genome folding into a common conserved core, on which dynamic gene regulation is overlaid across cells.
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Affiliation(s)
- J Yuyang Lu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lei Chang
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, and College of Future Technology, Peking University, Beijing, 100871, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, 510005, China
| | - Tong Li
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ting Wang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yafei Yin
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ge Zhan
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xue Han
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ke Zhang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yibing Tao
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Michelle Percharde
- MRC London Institute of Medical Sciences (LMS), London, W120NN, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, W120NN, UK
| | - Liang Wang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qi Peng
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Pixi Yan
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hui Zhang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xianju Bi
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wen Shao
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yantao Hong
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhongyang Wu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Runze Ma
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Peizhe Wang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wenzhi Li
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jing Zhang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zai Chang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yingping Hou
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, and College of Future Technology, Peking University, Beijing, 100871, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Miguel Ramalho-Santos
- Lunenfeld-Tanenbaum Research Institute, University of Toronto, Toronto, Ontario, M5T 3H7, Canada
| | - Pilong Li
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wei Xie
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jie Na
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, and College of Future Technology, Peking University, Beijing, 100871, China.
| | - Xiaohua Shen
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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99
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Challenging Safety and Efficacy of Retinal Gene Therapies by Retinogenesis. Int J Mol Sci 2021; 22:ijms22115767. [PMID: 34071252 PMCID: PMC8198227 DOI: 10.3390/ijms22115767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 11/28/2022] Open
Abstract
Gene-expression programs modulated by transcription factors (TFs) mediate key developmental events. Here, we show that the synthetic transcriptional repressor (TR; ZF6-DB), designed to treat Rhodopsin-mediated autosomal dominant retinitis pigmentosa (RHO-adRP), does not perturb murine retinal development, while maintaining its ability to block Rho expression transcriptionally. To express ZF6-DB into the developing retina, we pursued two approaches, (i) the retinal delivery (somatic expression) of ZF6-DB by Adeno-associated virus (AAV) vector (AAV-ZF6-DB) gene transfer during retinogenesis and (ii) the generation of a transgenic mouse (germ-line transmission, TR-ZF6-DB). Somatic and transgenic expression of ZF6-DB during retinogenesis does not affect retinal function of wild-type mice. The P347S mouse model of RHO-adRP, subretinally injected with AAV-ZF6-DB, or crossed with TR-ZF6-DB or shows retinal morphological and functional recovery. We propose the use of developmental transitions as an effective mode to challenge the safety of retinal gene therapies operating at genome, transcriptional, and transcript levels.
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100
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Aboelnour E, Bonev B. Decoding the organization, dynamics, and function of the 4D genome. Dev Cell 2021; 56:1562-1573. [PMID: 33984271 DOI: 10.1016/j.devcel.2021.04.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/15/2021] [Accepted: 04/21/2021] [Indexed: 11/15/2022]
Abstract
Understanding how complex cell-fate decisions emerge at the molecular level is a key challenge in developmental biology. Despite remarkable progress in decoding the contribution of the linear epigenome, how spatial genome architecture functionally informs changes in gene expression remains unclear. In this review, we discuss recent insights in elucidating the molecular landscape of genome folding, emphasizing the multilayered nature of the 3D genome, its importance for gene regulation, and its spatiotemporal dynamics. Finally, we discuss how these new concepts and emergent technologies will enable us to address some of the outstanding questions in development and disease.
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Affiliation(s)
- Erin Aboelnour
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Boyan Bonev
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Germany.
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