1
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Amin R, Ha NH, Qiu T, Holewinski R, Lam KC, Lopès A, Liu H, Tran AD, Lee MP, Gamage ST, Andresson T, Goldszmid RS, Meier JL, Hunter KW. Loss of NAT10 disrupts enhancer organization via p300 mislocalization and suppresses transcription of genes necessary for metastasis progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577116. [PMID: 38410432 PMCID: PMC10896336 DOI: 10.1101/2024.01.24.577116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Acetylation of protein and RNA represent a critical event for development and cancer progression. NAT10 is the only known RNA acetylase that catalyzes the N4-actylcytidine (ac4C) modification of RNAs. Here, we show that the loss of NAT10 significantly decreases lung metastasis in allograft and genetically engineered mouse models of breast cancer. NAT10 interacts with a mechanosensitive, metastasis susceptibility protein complex at the nuclear pore. In addition to its canonical role in RNA acetylation, we find that NAT10 interacts with p300 at gene enhancers. NAT10 loss is associated with p300 mislocalization into heterochromatin regions. NAT10 depletion disrupts enhancer organization, leading to alteration of gene transcription necessary for metastatic progression, including reduced myeloid cell-recruiting chemokines that results in a less metastasis-prone tumor microenvironment. Our study uncovers a distinct role of NAT10 in enhancer organization of metastatic tumor cells and suggests its involvement in the tumor-immune crosstalk dictating metastatic outcomes.
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2
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Salataj E, Spilianakis CG, Chaumeil J. Single-cell detection of primary transcripts, their genomic loci and nuclear factors by 3D immuno-RNA/DNA FISH in T cells. Front Immunol 2023; 14:1156077. [PMID: 37215121 PMCID: PMC10193148 DOI: 10.3389/fimmu.2023.1156077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Over the past decades, it has become increasingly clear that higher order chromatin folding and organization within the nucleus is involved in the regulation of genome activity and serves as an additional epigenetic mechanism that modulates cellular functions and gene expression programs in diverse biological processes. In particular, dynamic allelic interactions and nuclear locations can be of functional importance during the process of lymphoid differentiation and the regulation of immune responses. Analyses of the proximity between chromatin and/or nuclear regions can be performed on populations of cells with high-throughput sequencing approaches such as chromatin conformation capture ("3C"-based) or DNA adenine methyltransferase identification (DamID) methods, or, in individual cells, by the simultaneous visualization of genomic loci, their primary transcripts and nuclear compartments within the 3-dimensional nuclear space using Fluorescence In Situ Hybridization (FISH) and immunostaining. Here, we present a detailed protocol to simultaneously detect nascent RNA transcripts (3D RNA FISH), their genomic loci (3D DNA FISH) and/or their chromosome territories (CT paint DNA FISH) combined with the antibody-based detection of various nuclear factors (immunofluorescence). We delineate the application and effectiveness of this robust and reproducible protocol in several murine T lymphocyte subtypes (from differentiating thymic T cells, to activated splenic and peripheral T cells) as well as other murine cells, including embryonic stem cells, B cells, megakaryocytes and macrophages.
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Affiliation(s)
- Eralda Salataj
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Charalampos G. Spilianakis
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Julie Chaumeil
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
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3
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Wu J, Chen B, Liu Y, Ma L, Huang W, Lin Y. Modulating gene regulation function by chemically controlled transcription factor clustering. Nat Commun 2022; 13:2663. [PMID: 35562359 PMCID: PMC9106659 DOI: 10.1038/s41467-022-30397-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/29/2022] [Indexed: 12/21/2022] Open
Abstract
Recent studies have suggested that transcriptional protein condensates (or clusters) may play key roles in gene regulation and cell fate determination. However, it remains largely unclear how the gene regulation function is quantitatively tuned by transcription factor (TF) clustering and whether TF clustering may confer emergent behaviors as in cell fate control systems. Here, to address this, we construct synthetic TFs whose clustering behavior can be chemically controlled. Through single-parameter tuning of the system (i.e., TF clustering propensity), we provide lines of evidence supporting the direct transcriptional activation and amplification of target genes by TF clustering. Single-gene imaging suggests that such amplification results from the modulation of transcriptional dynamics. Importantly, TF clustering propensity modulates the gene regulation function by significantly tuning the effective TF binding affinity and to a lesser extent the ultrasensitivity, contributing to bimodality and sustained response behavior that are reminiscent of canonical cell fate control systems. Collectively, these results demonstrate that TF clustering can modulate the gene regulation function to enable emergent behaviors, and highlight the potential applications of chemically controlled protein clustering. Transcription factor (TF) condensates appear to be pervasive, yet their roles remain debated. Here, the authors use a synthetic biology approach to show that TF clusters causally amplify transcription and can confer bimodality and “memory”.
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Affiliation(s)
- Jiegen Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Baoqiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Yadi Liu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Liang Ma
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Wen Huang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Yihan Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China. .,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.
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4
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Benbarche S, Lopez CK, Salataj E, Aid Z, Thirant C, Laiguillon MC, Lecourt S, Belloucif Y, Vaganay C, Antonini M, Hu J, da Silva Babinet A, Ndiaye-Lobry D, Pardieu B, Petit A, Puissant A, Chaumeil J, Mercher T, Lobry C. Screening of ETO2-GLIS2-induced Super Enhancers identifies targetable cooperative dependencies in acute megakaryoblastic leukemia. SCIENCE ADVANCES 2022; 8:eabg9455. [PMID: 35138899 PMCID: PMC8827662 DOI: 10.1126/sciadv.abg9455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Super Enhancers (SEs) are clusters of regulatory elements associated with cell identity and disease. However, whether these elements are induced by oncogenes and can regulate gene modules cooperating for cancer cell transformation or maintenance remains elusive. To address this question, we conducted a genome-wide CRISPRi-based screening of SEs in ETO2-GLIS2+ acute megakaryoblastic leukemia. This approach revealed SEs essential for leukemic cell growth and survival that are induced by ETO2-GLIS2 expression. In particular, we identified a de novo SE specific of this leukemia subtype and regulating expression of tyrosine kinase-associated receptors KIT and PDGFRA. Combined expression of these two receptors was required for leukemic cell growth, and CRISPRi-mediated inhibition of this SE or treatment with tyrosine kinase inhibitors impaired progression of leukemia in vivo in patient-derived xenografts experiments. Our results show that fusion oncogenes, such as ETO2-GLIS2, can induce activation of SEs regulating essential gene modules synergizing for leukemia progression.
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Affiliation(s)
- Salima Benbarche
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
| | - Cécile K. Lopez
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Paris F-75013, France
| | - Eralda Salataj
- Université de Paris, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Zakia Aid
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Paris F-75013, France
| | - Cécile Thirant
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Paris F-75013, France
| | | | - Séverine Lecourt
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
| | - Yannis Belloucif
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | - Camille Vaganay
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | - Marion Antonini
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
| | - Jiang Hu
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | | | | | - Bryann Pardieu
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | - Arnaud Petit
- Hôpital Trousseau, Sorbonne Université, Assistance Publique - Hôpitaux de Paris CONECT-AML, Paris F-75012, France
| | - Alexandre Puissant
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | - Julie Chaumeil
- Université de Paris, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Thomas Mercher
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Paris F-75013, France
- Corresponding author. (C.L.); (T.M.)
| | - Camille Lobry
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
- Corresponding author. (C.L.); (T.M.)
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5
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Xiao L, Labaer J, Guo J. Highly Sensitive and Multiplexed In Situ RNA Profiling with Cleavable Fluorescent Tyramide. Cells 2021; 10:cells10061277. [PMID: 34063986 PMCID: PMC8224041 DOI: 10.3390/cells10061277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/11/2021] [Accepted: 05/18/2021] [Indexed: 12/29/2022] Open
Abstract
Understanding the composition, regulation, and function of complex biological systems requires tools that quantify multiple transcripts at their native cellular locations. However, the current multiplexed RNA imaging technologies are limited by their relatively low sensitivity or specificity, which hinders their applications in studying highly autofluorescent tissues, such as formalin-fixed paraffin-embedded (FFPE) tissues. To address this issue, here we develop a multiplexed in situ RNA profiling approach with a high sensitivity and specificity. In this approach, transcripts are first hybridized by target-specific oligonucleotide probes in pairs. Only when these two independent probes hybridize to the target in tandem will the subsequent signal amplification by oligonucleotide hybridization occur. Afterwards, horseradish peroxidase (HRP) is applied to further amplify the signal and stain the target with cleavable fluorescent tyramide (CFT). After imaging, the fluorophores are chemically cleaved and the hybridized probes are stripped by DNase and formamide. Through cycles of RNA staining, fluorescence imaging, signal cleavage, and probe stripping, many different RNA species can be profiled at the optical resolution. In applying this approach, we demonstrated that multiplexed in situ RNA analysis can be successfully achieved in both fixed, frozen, and FFPE tissues.
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Affiliation(s)
| | | | - Jia Guo
- Correspondence: ; Tel.: +1-480-727-2096
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6
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Visualization of Nuclear and Cytoplasmic Long Noncoding RNAs at Single-Cell Level by RNA-FISH. Methods Mol Biol 2021; 2157:251-280. [PMID: 32820409 DOI: 10.1007/978-1-0716-0664-3_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The RNA fluorescence in situ hybridization (RNA-FISH) methodology offers an attractive strategy to deepen our knowledge on the long noncoding RNA biology. In this chapter, we provide a comprehensive overview of the current RNA-FISH protocols available for imaging nuclear and cytoplasmic lncRNAs within cells or tissues. We describe a multicolor approach optimized for the simultaneous visualization of these transcripts with their specific molecular interactors, such as proteins or DNA sequences. Common challenges faced by this methodology such as cell-type specific permeabilization, target accessibility, image acquisition, and post-acquisition analyses are also discussed.
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7
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Aguilar M, Prieto P. Telomeres and Subtelomeres Dynamics in the Context of Early Chromosome Interactions During Meiosis and Their Implications in Plant Breeding. FRONTIERS IN PLANT SCIENCE 2021; 12:672489. [PMID: 34149773 PMCID: PMC8212018 DOI: 10.3389/fpls.2021.672489] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/06/2021] [Indexed: 05/08/2023]
Abstract
Genomic architecture facilitates chromosome recognition, pairing, and recombination. Telomeres and subtelomeres play an important role at the beginning of meiosis in specific chromosome recognition and pairing, which are critical processes that allow chromosome recombination between homologs (equivalent chromosomes in the same genome) in later stages. In plant polyploids, these terminal regions are even more important in terms of homologous chromosome recognition, due to the presence of homoeologs (equivalent chromosomes from related genomes). Although telomeres interaction seems to assist homologous pairing and consequently, the progression of meiosis, other chromosome regions, such as subtelomeres, need to be considered, because the DNA sequence of telomeres is not chromosome-specific. In addition, recombination operates at subtelomeres and, as it happens in rye and wheat, homologous recognition and pairing is more often correlated with recombining regions than with crossover-poor regions. In a plant breeding context, the knowledge of how homologous chromosomes initiate pairing at the beginning of meiosis can contribute to chromosome manipulation in hybrids or interspecific genetic crosses. Thus, recombination in interspecific chromosome associations could be promoted with the aim of transferring desirable agronomic traits from related genetic donor species into crops. In this review, we summarize the importance of telomeres and subtelomeres on chromatin dynamics during early meiosis stages and their implications in recombination in a plant breeding framework.
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Affiliation(s)
- Miguel Aguilar
- Área de Fisiología Vegetal, Universidad de Córdoba, Córdoba, Spain
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
- *Correspondence: Pilar Prieto, ; orcid.org/0000-0002-8160-808X
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8
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Bianchi JJ, Murigneux V, Bedora-Faure M, Lescale C, Deriano L. Breakage-Fusion-Bridge Events Trigger Complex Genome Rearrangements and Amplifications in Developmentally Arrested T Cell Lymphomas. Cell Rep 2020; 27:2847-2858.e4. [PMID: 31167132 PMCID: PMC6581794 DOI: 10.1016/j.celrep.2019.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 02/15/2019] [Accepted: 05/01/2019] [Indexed: 12/30/2022] Open
Abstract
To reveal the relative contribution of the recombination activating gene (RAG)1/2 nuclease to lymphomagenesis, we conducted a genome-wide analysis of T cell lymphomas from p53-deficient mice expressing or lacking RAG2. We found that while p53−/− lymphoblastic T cells harbor primarily ectopic DNA deletions, Rag2−/−p53−/− T cell lymphomas display complex genomic rearrangements associated with amplification of the chromosomal location 9qA4-5.3. We show that this amplicon is generated by breakage-fusion-bridge during mitosis and arises distinctly in T cell lymphomas originating from an early progenitor stage. Notably, we report amplification of the corresponding syntenic region (11q23) in a subset of human leukemia leading to the overexpression of several cancer genes, including MLL/KMT2A. Our findings provide direct evidence that lymphocytes undergo malignant transformation through distinct genome architectural routes that are determined by both RAG-dependent and RAG-independent DNA damage and a block in cell development. Lymphomas from RAG2/p53- and p53-deficient mice bear distinct genome architectures Block in T cell development leads to 9qA4-5.3 rearrangements and amplifications Breakage-fusion-bridge events trigger 9qA4-5.3 aberrations in early T cell lymphomas The syntenic region 11q23 is amplified in some human hematological cancers
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Affiliation(s)
- Joy J Bianchi
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France; Cellule Pasteur, University of Paris René Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Valentine Murigneux
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Marie Bedora-Faure
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Chloé Lescale
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.
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9
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Garsuault D, Bouyer C, Nguyen E, Kandhari R, Prochazkova-Carlotti M, Chevret E, Forgez P, Ségal-Bendirdjian E. Complex context relationships between DNA methylation and accessibility, histone marks, and hTERT gene expression in acute promyelocytic leukemia cells: perspectives for all-trans retinoic acid in cancer therapy. Mol Oncol 2020; 14:1310-1326. [PMID: 32239597 PMCID: PMC7266276 DOI: 10.1002/1878-0261.12681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/19/2020] [Accepted: 03/28/2020] [Indexed: 02/06/2023] Open
Abstract
Telomerase (hTERT) reactivation and sustained expression is a key event in the process of cellular transformation. Therefore, the identification of the mechanisms regulating hTERT expression is of great interest for the development of new anticancer therapies. Although the epigenetic state of hTERT gene promoter is important, we still lack a clear understanding of the mechanisms by which epigenetic changes affect hTERT expression. Retinoids are well-known inducers of granulocytic maturation in acute promyelocytic leukemia (APL). We have previously shown that retinoids repressed hTERT expression in the absence of maturation leading to growth arrest and cell death. Exploring the mechanisms of this repression, we showed that transcription factor binding was dependent on the epigenetic status of hTERT promoter. In the present study, we used APL cells lines and publicly available datasets from APL patients to further investigate the integrated epigenetic events that promote hTERT promoter transition from its silent to its active state, and inversely. We showed, in APL patients, that the methylation of the distal domain of hTERT core promoter was altered and correlated with the outcome of the disease. Further studies combining complementary approaches carried out on APL cell lines highlighted the significance of a domain outside the minimal promoter, localized around 5 kb upstream from the transcription start site, in activating hTERT. This domain is characterized by DNA hypomethylation and H3K4Me3 deposition. Our findings suggest a cooperative interplay between hTERT promoter methylation, chromatin accessibility, and histone modifications that force the revisiting of previously proposed concepts regarding hTERT epigenetic regulation. They represent, therefore, a major advance in predicting sensitivity to retinoid-induced hTERT repression and, more generally, in the potential development of therapies targeting hTERT expression in cancers.
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Affiliation(s)
- Delphine Garsuault
- Team: Cellular Homeostasis, Cancer, and Therapies, INSERM UMR-S 1124, Université de Paris, France.,Université de Paris, Paris Sorbonne Cité, France.,Paris-Sud University, Paris-Saclay University, Orsay, France
| | - Claire Bouyer
- Team: Cellular Homeostasis, Cancer, and Therapies, INSERM UMR-S 1124, Université de Paris, France.,Université de Paris, Paris Sorbonne Cité, France
| | - Eric Nguyen
- Team: Cellular Homeostasis, Cancer, and Therapies, INSERM UMR-S 1124, Université de Paris, France.,Université de Paris, Paris Sorbonne Cité, France
| | - Rohan Kandhari
- Team: Cellular Homeostasis, Cancer, and Therapies, INSERM UMR-S 1124, Université de Paris, France.,Indian Institute of Technology, BHU, Varanasi, India
| | | | - Edith Chevret
- Team Cutaneous Lymphoma Oncogenesis, INSERM U1053, Bordeaux, France
| | - Patricia Forgez
- Team: Cellular Homeostasis, Cancer, and Therapies, INSERM UMR-S 1124, Université de Paris, France.,Université de Paris, Paris Sorbonne Cité, France
| | - Evelyne Ségal-Bendirdjian
- Team: Cellular Homeostasis, Cancer, and Therapies, INSERM UMR-S 1124, Université de Paris, France.,Université de Paris, Paris Sorbonne Cité, France.,BioMedTech Facilities, CNRS UMS2009/INSERM US36, Université de Paris, France
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10
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Galindo-Campos MA, Bedora-Faure M, Farrés J, Lescale C, Moreno-Lama L, Martínez C, Martín-Caballero J, Ampurdanés C, Aparicio P, Dantzer F, Cerutti A, Deriano L, Yélamos J. Coordinated signals from the DNA repair enzymes PARP-1 and PARP-2 promotes B-cell development and function. Cell Death Differ 2019; 26:2667-2681. [PMID: 30996287 DOI: 10.1038/s41418-019-0326-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 02/07/2023] Open
Abstract
Poly (ADP-ribose) polymerase (PARP)-1 and PARP-2 regulate the function of various DNA-interacting proteins by transferring ADP-ribose emerging from catalytic cleavage of cellular β-NAD+. Hence, mice lacking PARP-1 or PARP-2 show DNA perturbations ranging from altered DNA integrity to impaired DNA repair. These effects stem from the central role that PARP-1 and PARP-2 have on the cellular response to DNA damage. Failure to mount a proper response culminates in cell death. Accordingly, PARP inhibitors are emerging as promising drugs in cancer therapy. However, the full impact of these inhibitors on immunity, including B-cell antibody production, remains elusive. Given that mice carrying dual PARP-1 and PARP-2 deficiency develop early embryonic lethality, we crossed PARP-1-deficient mice with mice carrying a B-cell-conditional PARP-2 gene deletion. We found that the resulting dually PARP-1 and PARP-2-deficient mice had perturbed bone-marrow B-cell development as well as profound peripheral depletion of transitional and follicular but not marginal zone B-cells. Of note, bone-marrow B-cell progenitors and peripheral mature B-cells were conserved in mice carrying either PARP-1 or PARP-2 deficiency. In dually PARP-1 and PARP-2-deficient mice, B-cell lymphopenia was associated with increased DNA damage and accentuated death in actively proliferating B-cells. Moreover, dual PARP-1 and PARP-2 deficiency impaired antibody responses to T-independent carbohydrate but not to T-dependent protein antigens. Notwithstanding the pivotal role of PARP-1 and PARP-2 in DNA repair, combined PARP-1 and PARP-2 deficiency did not perturb the DNA-editing processes required for the generation of a protective antibody repertoire, including Ig V(D)J gene recombination and IgM-to-IgG class switching. These findings provide key information as to the potential impact of PARP inhibitors on humoral immunity, which will facilitate the development of safer PARP-targeting regimens against cancer.
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Affiliation(s)
- Miguel A Galindo-Campos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Marie Bedora-Faure
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015, Paris, France
| | - Jordi Farrés
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Chloé Lescale
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015, Paris, France
| | - Lucia Moreno-Lama
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Carlos Martínez
- Experimental Pathology Unit, IMIB-LAIB-Arrixaca, Murcia, Spain
| | | | - Coral Ampurdanés
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Pedro Aparicio
- Department of Biochemistry, Molecular Biology and Immunology, University of Murcia, Murcia, Spain
| | - Françoise Dantzer
- Biotechnology and Cell Signaling, UMR7242-CNRS, Laboratory of Excellence Medalis, ESBS, Illkirch, France
| | - Andrea Cerutti
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain.,Inflammatory and Cardiovascular Disorders Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015, Paris, France.
| | - José Yélamos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain. .,Department of Immunology, Hospital del Mar, Barcelona, Spain.
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11
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Schiroli G, Conti A, Ferrari S, Della Volpe L, Jacob A, Albano L, Beretta S, Calabria A, Vavassori V, Gasparini P, Salataj E, Ndiaye-Lobry D, Brombin C, Chaumeil J, Montini E, Merelli I, Genovese P, Naldini L, Di Micco R. Precise Gene Editing Preserves Hematopoietic Stem Cell Function following Transient p53-Mediated DNA Damage Response. Cell Stem Cell 2019; 24:551-565.e8. [PMID: 30905619 PMCID: PMC6458988 DOI: 10.1016/j.stem.2019.02.019] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/21/2018] [Accepted: 02/26/2019] [Indexed: 01/06/2023]
Abstract
Precise gene editing in hematopoietic stem and progenitor cells (HSPCs) holds promise for treating genetic diseases. However, responses triggered by programmable nucleases in HSPCs are poorly characterized and may negatively impact HSPC engraftment and long-term repopulation capacity. Here, we induced either one or several DNA double-stranded breaks (DSBs) with optimized zinc-finger and CRISPR/Cas9 nucleases and monitored DNA damage response (DDR) foci induction, cell-cycle progression, and transcriptional responses in HSPC subpopulations, with up to single-cell resolution. p53-mediated DDR pathway activation was the predominant response to even single-nuclease-induced DSBs across all HSPC subtypes analyzed. Excess DSB load and/or adeno-associated virus (AAV)-mediated delivery of DNA repair templates induced cumulative p53 pathway activation, constraining proliferation, yield, and engraftment of edited HSPCs. However, functional impairment was reversible when DDR burden was low and could be overcome by transient p53 inhibition. These findings provide molecular and functional evidence for feasible and seamless gene editing in HSPCs. DNA DSBs induced by programmable nucleases transiently activate the DDR in HSPCs Single-cell transcriptomics show that induced DSBs activate the p53 pathway AAV6-mediated genome editing aggravates p53 activation and delays HSPC proliferation Transient p53 inhibition alleviates clonogenic and repopulation defects in edited HSPCs
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Affiliation(s)
- Giulia Schiroli
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Anastasia Conti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Lucrezia Della Volpe
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Aurelien Jacob
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Milano-Bicocca University, 20126 Milan, Italy
| | - Luisa Albano
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Stefano Beretta
- Milano-Bicocca University, 20126 Milan, Italy; Institute for Biomedical Technologies, National Research Council, 20090 Segrate, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Valentina Vavassori
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Patrizia Gasparini
- Tumor Genomics Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133 Milan, Italy
| | - Eralda Salataj
- Inserm U1016, Institut Cochin, 75014 Paris, France; CNRS UMR8104, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, France
| | - Delphine Ndiaye-Lobry
- Inserm U1016, Institut Cochin, 75014 Paris, France; CNRS UMR8104, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, France
| | - Chiara Brombin
- CUSSB-University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Julie Chaumeil
- Inserm U1016, Institut Cochin, 75014 Paris, France; CNRS UMR8104, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, France
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Ivan Merelli
- Institute for Biomedical Technologies, National Research Council, 20090 Segrate, Italy
| | - Pietro Genovese
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Vita-Salute San Raffaele University, 20132 Milan, Italy.
| | - Raffaella Di Micco
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.
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12
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Roch B, Abramowski V, Chaumeil J, de Villartay JP. Cernunnos/Xlf Deficiency Results in Suboptimal V(D)J Recombination and Impaired Lymphoid Development in Mice. Front Immunol 2019; 10:443. [PMID: 30923523 PMCID: PMC6426757 DOI: 10.3389/fimmu.2019.00443] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/19/2019] [Indexed: 12/23/2022] Open
Abstract
Xlf/Cernunnos is unique among the core factors of the non-homologous end joining (NHEJ) DNA double strand breaks (DSBs) repair pathway, in the sense that it is not essential for V(D)J recombination in vivo and in vitro. Unlike other NHEJ deficient mice showing a SCID phenotype, Xlf−/− mice present a unique immune phenotype with a moderate B- and T-cell lymphopenia, a decreased cellularity in the thymus, and a characteristic TCRα repertoire bias associated with the P53-dependent apoptosis of CD4+CD8+ DP thymocytes. Here, we thoroughly analyzed Xlf−/− mice immune phenotype and showed that it is specifically related to the DP stage but independent of the MHC-driven antigen presentation and T-cell activation during positive selection. Instead, we show that V(D)J recombination is subefficient in Xlf−/− mice in vivo, exemplified by the presence of unrepaired DSBs in the thymus. This results in a moderate developmental delay of both B- and T-lymphocytes at key V(D)J recombination dependent stages. Furthermore, subefficient V(D)J recombination waves are accumulating during TCRα rearrangement, causing the typical TCRα repertoire bias with loss of distal Vα and Jα rearrangements.
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Affiliation(s)
- Benoit Roch
- Laboratory "Genome Dynamics in the Immune System", INSERM UMR1163, Paris, France.,Institut Imagine, Université Paris Descartes Sorbonne Paris Cité, Paris, France
| | - Vincent Abramowski
- Laboratory "Genome Dynamics in the Immune System", INSERM UMR1163, Paris, France.,Institut Imagine, Université Paris Descartes Sorbonne Paris Cité, Paris, France
| | - Julie Chaumeil
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris-Descartes, Paris, France
| | - Jean-Pierre de Villartay
- Laboratory "Genome Dynamics in the Immune System", INSERM UMR1163, Paris, France.,Institut Imagine, Université Paris Descartes Sorbonne Paris Cité, Paris, France
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13
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Grigoryan A, Guidi N, Senger K, Liehr T, Soller K, Marka G, Vollmer A, Markaki Y, Leonhardt H, Buske C, Lipka DB, Plass C, Zheng Y, Mulaw MA, Geiger H, Florian MC. LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells. Genome Biol 2018; 19:189. [PMID: 30404662 PMCID: PMC6223039 DOI: 10.1186/s13059-018-1557-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 10/04/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The decline of hematopoietic stem cell (HSC) function upon aging contributes to aging-associated immune remodeling and leukemia pathogenesis. Aged HSCs show changes to their epigenome, such as alterations in DNA methylation and histone methylation and acetylation landscapes. We previously showed a correlation between high Cdc42 activity in aged HSCs and the loss of intranuclear epigenetic polarity, or epipolarity, as indicated by the specific distribution of H4K16ac. RESULTS Here, we show that not all histone modifications display a polar localization and that a reduction in H4K16ac amount and loss of epipolarity are specific to aged HSCs. Increasing the levels of H4K16ac is not sufficient to restore polarity in aged HSCs and the restoration of HSC function. The changes in H4K16ac upon aging and rejuvenation of HSCs are correlated with a change in chromosome 11 architecture and alterations in nuclear volume and shape. Surprisingly, by taking advantage of knockout mouse models, we demonstrate that increased Cdc42 activity levels correlate with the repression of the nuclear envelope protein LaminA/C, which controls chromosome 11 distribution, H4K16ac polarity, and nuclear volume and shape in aged HSCs. CONCLUSIONS Collectively, our data show that chromatin architecture changes in aged stem cells are reversible by decreasing the levels of Cdc42 activity, revealing an unanticipated way to pharmacologically target LaminA/C expression and revert alterations of the epigenetic architecture in aged HSCs.
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Affiliation(s)
- Ani Grigoryan
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081, Ulm, Germany
| | - Novella Guidi
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081, Ulm, Germany
| | - Katharina Senger
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081, Ulm, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, 07743, Jena, Germany
| | - Karin Soller
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081, Ulm, Germany
| | - Gina Marka
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081, Ulm, Germany
| | - Angelika Vollmer
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081, Ulm, Germany
| | - Yolanda Markaki
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians University Munich, Großhaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians University Munich, Großhaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Christian Buske
- Institute of Experimental Cancer Research, Comprehensive Cancer Center Ulm, University Hospital Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Daniel B Lipka
- Regulation of Cellular Differentiation Group, INF280, 69120, Heidelberg, Germany
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF280, 69120, Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF280, 69120, Heidelberg, Germany
| | - Yi Zheng
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH, USA
| | - Medhanie A Mulaw
- Institute of Experimental Cancer Research, Comprehensive Cancer Center Ulm, University Hospital Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Hartmut Geiger
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081, Ulm, Germany
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH, USA
| | - Maria Carolina Florian
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081, Ulm, Germany.
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Gran Via de l'Hospitalet, 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
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14
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Karki S, Kennedy DE, Mclean K, Grzybowski AT, Maienschein-Cline M, Banerjee S, Xu H, Davis E, Mandal M, Labno C, Powers SE, Le Beau MM, Dinner AR, Singh H, Ruthenburg AJ, Clark MR. Regulated Capture of Vκ Gene Topologically Associating Domains by Transcription Factories. Cell Rep 2018; 24:2443-2456. [PMID: 30157436 PMCID: PMC6310487 DOI: 10.1016/j.celrep.2018.07.091] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 04/25/2018] [Accepted: 07/27/2018] [Indexed: 12/28/2022] Open
Abstract
Expression of vast repertoires of antigen receptors by lymphocytes, with each cell expressing a single receptor, requires stochastic activation of individual variable (V) genes for transcription and recombination. How this occurs remains unknown. Using single-cell RNA sequencing (scRNA-seq) and allelic variation, we show that individual pre-B cells monoallelically transcribe divergent arrays of Vκ genes, thereby opening stochastic repertoires for subsequent Vκ-Jκ recombination. Transcription occurs upon translocation of Vκ genes to RNA polymerase II arrayed on the nuclear matrix in transcription factories. Transcription is anchored by CTCF-bound sites or E2A-loaded Vκ promotors and continues over large genomic distances delimited only by topological associating domains (TADs). Prior to their monoallelic activation, Vκ loci are transcriptionally repressed by cyclin D3, which prevents capture of Vκ gene containing TADs by transcription factories. Cyclin D3 also represses protocadherin, olfactory, and other monoallelically expressed genes, suggesting a widely deployed mechanism for coupling monoallelic gene activation with cell cycle exit.
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Affiliation(s)
- Sophiya Karki
- Department of Medicine, Section of Rheumatology and The Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Domenick E Kennedy
- Department of Medicine, Section of Rheumatology and The Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Kaitlin Mclean
- Department of Medicine, Section of Rheumatology and The Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Adrian T Grzybowski
- Department of Molecular Genetics and Cell Biology and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | | | - Shiladitya Banerjee
- Department of Physics & Astronomy, University College London, London WC1E6BT, UK
| | - Heping Xu
- Division of Immunobiology, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Elizabeth Davis
- Section of Hematology/Oncology, University of Chicago, Chicago, IL, USA
| | - Malay Mandal
- Department of Medicine, Section of Rheumatology and The Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Christine Labno
- Integrated Light Microscopy Core Facility, University of Chicago, Chicago, IL, USA
| | - Sarah E Powers
- Department of Biology, Lewis University, Romeoville, IL, USA
| | | | - Aaron R Dinner
- James Frank Institute, University of Chicago, Chicago, IL, USA
| | - Harinder Singh
- Division of Immunobiology, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Alexander J Ruthenburg
- Department of Molecular Genetics and Cell Biology and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Marcus R Clark
- Department of Medicine, Section of Rheumatology and The Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA.
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15
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A new approach of gene co-expression network inference reveals significant biological processes involved in porcine muscle development in late gestation. Sci Rep 2018; 8:10150. [PMID: 29977047 PMCID: PMC6033925 DOI: 10.1038/s41598-018-28173-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/14/2018] [Indexed: 12/28/2022] Open
Abstract
The integration of genetic information in the cellular and nuclear environments is crucial for deciphering the way in which the genome functions under different physiological conditions. Experimental techniques of 3D nuclear mapping, a high-flow approach such as transcriptomic data analyses, and statistical methods for the development of co-expressed gene networks, can be combined to develop an integrated approach for depicting the regulation of gene expression. Our work focused more specifically on the mechanisms involved in the transcriptional regulation of genes expressed in muscle during late foetal development in pig. The data generated by a transcriptomic analysis carried out on muscle of foetuses from two extreme genetic lines for birth mortality are used to construct networks of differentially expressed and co-regulated genes. We developed an innovative co-expression networking approach coupling, by means of an iterative process, a new statistical method for graph inference with data of gene spatial co-localization (3D DNA FISH) to construct a robust network grouping co-expressed genes. This enabled us to highlight relevant biological processes related to foetal muscle maturity and to discover unexpected gene associations between IGF2, MYH3 and DLK1/MEG3 in the nuclear space, genes that are up-regulated at this stage of muscle development.
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16
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Mondal M, Liao R, Nazaroff CD, Samuel AD, Guo J. Highly multiplexed single-cell in situ RNA and DNA analysis with bioorthogonal cleavable fluorescent oligonucleotides. Chem Sci 2018; 9:2909-2917. [PMID: 29732074 PMCID: PMC5914540 DOI: 10.1039/c7sc05089e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/08/2018] [Indexed: 11/21/2022] Open
Abstract
The ability to profile transcripts and genomic loci comprehensively in single cells in situ is essential to advance our understanding of normal physiology and disease pathogenesis. Here we report a highly multiplexed single-cell in situ RNA and DNA analysis approach using bioorthogonal cleavable fluorescent oligonucleotides. In this approach, oligonucleotides tethered to fluorophores through an azide-based cleavable linker are used to detect their nucleic acids targets by in situ hybridization. After fluorescence imaging, the fluorophores in the whole specimen are efficiently cleaved in 30 minutes without loss of RNA or DNA integrity. Through reiterative cycles of hybridization, imaging, and cleavage, this method has the potential to quantify hundreds to thousands of different RNA species or genomic loci in single cells in situ at the single-molecule sensitivity. Applying this approach, we demonstrate that different nucleic acids can be detected in each hybridization cycle by multi-color staining, and at least ten continuous hybridization cycles can be carried out in the same specimen. We also show that the integrated single-cell in situ analysis of DNA, RNA and protein can be achieved using cleavable fluorescent oligonucleotides combined with cleavable fluorescent antibodies. This highly multiplexed imaging platform will have wide applications in systems biology and biomedical research.
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Affiliation(s)
- Manas Mondal
- Biodesign Institute , School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , USA .
| | - Renjie Liao
- Biodesign Institute , School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , USA .
| | - Christopher D Nazaroff
- Biodesign Institute , School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , USA .
- Division of Pulmonary Medicine , Department of Biochemistry and Molecular Biology , Mayo Clinic Arizona , Scottsdale , Arizona 85259 , USA
| | - Adam D Samuel
- Biodesign Institute , School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , USA .
| | - Jia Guo
- Biodesign Institute , School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , USA .
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17
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Expanded Satellite Repeats Amplify a Discrete CENP-A Nucleosome Assembly Site on Chromosomes that Drive in Female Meiosis. Curr Biol 2017; 27:2365-2373.e8. [PMID: 28756949 DOI: 10.1016/j.cub.2017.06.069] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/23/2017] [Accepted: 06/27/2017] [Indexed: 11/20/2022]
Abstract
Female meiosis provides an opportunity for selfish genetic elements to violate Mendel's law of segregation by increasing the chance of segregating to the egg [1]. Centromeres and other repetitive sequences can drive in meiosis by cheating the segregation process [2], but the underlying mechanisms are unknown. Here, we show that centromeres with more satellite repeats house more nucleosomes that confer centromere identity, containing the histone H3 variant CENP-A, and bias their segregation to the egg relative to centromeres with fewer repeats. CENP-A nucleosomes predominantly occupy a single site within the repeating unit that becomes limiting for centromere assembly on smaller centromeres. We propose that amplified repetitive sequences act as selfish elements by promoting expansion of CENP-A chromatin and increased transmission through the female germline.
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18
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Lescale C, Lenden Hasse H, Blackford AN, Balmus G, Bianchi JJ, Yu W, Bacoccina L, Jarade A, Clouin C, Sivapalan R, Reina-San-Martin B, Jackson SP, Deriano L. Specific Roles of XRCC4 Paralogs PAXX and XLF during V(D)J Recombination. Cell Rep 2016; 16:2967-2979. [PMID: 27601299 PMCID: PMC5033762 DOI: 10.1016/j.celrep.2016.08.069] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/02/2016] [Accepted: 08/23/2016] [Indexed: 11/04/2022] Open
Abstract
Paralog of XRCC4 and XLF (PAXX) is a member of the XRCC4 superfamily and plays a role in nonhomologous end-joining (NHEJ), a DNA repair pathway critical for lymphocyte antigen receptor gene assembly. Here, we find that the functions of PAXX and XLF in V(D)J recombination are masked by redundant joining activities. Thus, combined PAXX and XLF deficiency leads to an inability to join RAG-cleaved DNA ends. Additionally, we demonstrate that PAXX function in V(D)J recombination depends on its interaction with Ku. Importantly, we show that, unlike XLF, the role of PAXX during the repair of DNA breaks does not overlap with ATM and the RAG complex. Our findings illuminate the role of PAXX in V(D)J recombination and support a model in which PAXX and XLF function during NHEJ repair of DNA breaks, whereas XLF, the RAG complex, and the ATM-dependent DNA damage response promote end joining by stabilizing DNA ends.
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Affiliation(s)
- Chloé Lescale
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Hélène Lenden Hasse
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Andrew N Blackford
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Gabriel Balmus
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Maintenance of Genome Stability, Genome Campus, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Joy J Bianchi
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France; Cellule Pasteur, University of Paris René Descartes, Sorbonne Paris Cité, Paris 75015, France
| | - Wei Yu
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Léa Bacoccina
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Angélique Jarade
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Christophe Clouin
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Rohan Sivapalan
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM-U964, CNRS-UMR7104, University of Strasbourg, 67400 Illkirch, France
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Maintenance of Genome Stability, Genome Campus, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Ludovic Deriano
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France.
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19
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Fu Y, Rocha PP, Luo VM, Raviram R, Deng Y, Mazzoni EO, Skok JA. CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci. Nat Commun 2016; 7:11707. [PMID: 27222091 PMCID: PMC4894952 DOI: 10.1038/ncomms11707] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 04/21/2016] [Indexed: 12/18/2022] Open
Abstract
Imaging systems that allow visualization of specific loci and nuclear structures are highly relevant for investigating how organizational changes within the nucleus play a role in regulating gene expression and other cellular processes. Here we present a live imaging system for targeted detection of genomic regions. Our approach involves generating chimaeric transcripts of viral RNAs (MS2 and PP7) and single-guide RNAs (sgRNAs), which when co-expressed with a cleavage-deficient Cas9 can recruit fluorescently tagged viral RNA-binding proteins (MCP and PCP) to specific genomic sites. This allows for rapid, stable, low-background visualization of target loci. We demonstrate the efficiency and flexibility of our method by simultaneously labelling major and minor satellite regions as well as two individual loci on mouse chromosome 12. This system provides a tool for dual-colour labelling, which is important for tracking the dynamics of chromatin interactions and for validating epigenetic processes identified in fixed cells.
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Affiliation(s)
- Yi Fu
- Department of Pathology, New York University School of Medicine, 550 First Avenue, Sml 311, New York, New York 10016, USA
- Department of Biology, New York University, New York, New York 10003, USA
| | - Pedro P. Rocha
- Department of Pathology, New York University School of Medicine, 550 First Avenue, Sml 311, New York, New York 10016, USA
| | - Vincent M. Luo
- Department of Pathology, New York University School of Medicine, 550 First Avenue, Sml 311, New York, New York 10016, USA
- Department of Biology, New York University, New York, New York 10003, USA
| | - Ramya Raviram
- Department of Pathology, New York University School of Medicine, 550 First Avenue, Sml 311, New York, New York 10016, USA
- Department of Biology, New York University, New York, New York 10003, USA
| | - Yan Deng
- Microscopy Core, New York University School of Medicine, New York, New York 10016, USA
| | - Esteban O. Mazzoni
- Department of Biology, New York University, New York, New York 10003, USA
| | - Jane A. Skok
- Department of Pathology, New York University School of Medicine, 550 First Avenue, Sml 311, New York, New York 10016, USA
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20
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Lescale C, Abramowski V, Bedora-Faure M, Murigneux V, Vera G, Roth DB, Revy P, de Villartay JP, Deriano L. RAG2 and XLF/Cernunnos interplay reveals a novel role for the RAG complex in DNA repair. Nat Commun 2016; 7:10529. [PMID: 26833222 PMCID: PMC4740868 DOI: 10.1038/ncomms10529] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/22/2015] [Indexed: 12/22/2022] Open
Abstract
XRCC4-like factor (XLF) functions in classical non-homologous end-joining (cNHEJ) but is dispensable for the repair of DNA double-strand breaks (DSBs) generated during V(D)J recombination. A long-standing hypothesis proposes that, in addition to its canonical nuclease activity, the RAG1/2 proteins participate in the DNA repair phase of V(D)J recombination. Here we show that in the context of RAG2 lacking the C-terminus domain (Rag2c/c mice), XLF deficiency leads to a profound lymphopenia associated with a severe defect in V(D)J recombination and, in the absence of p53, increased genomic instability at V(D)J sites. In addition, Rag2c/cXLF−/−p53−/− mice develop aggressive pro-B cell lymphomas bearing complex chromosomal translocations and gene amplifications involving Igh and c-myc/pvt1 loci. Our results reveal an unanticipated functional interplay between the RAG complex and XLF in repairing RAG-induced DSBs and maintaining genome integrity during antigen receptor gene assembly. Antigen receptor diversity relies on careful DNA cleavage and repair. Here the authors identify a functional interplay between RAG2 and XLF during V(D)J recombination, revealing an important role for the RAG complex in repairing induced DNA double-strand breaks and maintaining genome integrity.
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Affiliation(s)
- Chloé Lescale
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, CNRS-URA 1961, Paris 75015, France
| | - Vincent Abramowski
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France
| | - Marie Bedora-Faure
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, CNRS-URA 1961, Paris 75015, France
| | - Valentine Murigneux
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, CNRS-URA 1961, Paris 75015, France
| | - Gabriella Vera
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France
| | - David B Roth
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Patrick Revy
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France
| | - Jean-Pierre de Villartay
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France
| | - Ludovic Deriano
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, CNRS-URA 1961, Paris 75015, France
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21
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Anton T, Bultmann S, Leonhardt H, Markaki Y. Visualization of specific DNA sequences in living mouse embryonic stem cells with a programmable fluorescent CRISPR/Cas system. Nucleus 2014; 5:163-72. [PMID: 24637835 PMCID: PMC4049922 DOI: 10.4161/nucl.28488] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Labeling and tracing of specific sequences in living cells has been a major challenge in studying the spatiotemporal dynamics of native chromatin. Here we repurposed the prokaryotic CRISPR/Cas adaptive immunity system to specifically detect endogenous genomic loci in mouse embryonic stem cells. We constructed a catalytically inactive version of the Cas9 endonuclease, fused it with eGFP (dCas9-eGFP) and co-expressed small guide RNAs (gRNAs) to target pericentric, centric, and telomeric repeats, which are enriched in distinct nuclear structures. With major satellite specific gRNAs we obtained a characteristic chromocenter (CC) pattern, while gRNAs targeting minor satellites and telomeres highlighted smaller foci coinciding with centromere protein B (CENP-B) and telomeric repeat-binding factor 2 (TRF2), respectively. DNA sequence specific labeling by gRNA/dCas9-eGFP complexes was directly shown with 3D-fluorescent in situ hybridization (3D-FISH). Structured illumination microscopy (3D-SIM) of gRNA/dCas9-eGFP expressing cells revealed chromatin ultrastructures and demonstrated the potential of this approach for chromatin conformation studies by super resolution microscopy. This programmable dCas9 labeling system opens new perspectives to study functional nuclear architecture.
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Affiliation(s)
- Tobias Anton
- Department of Biology II; Center for Integrated Protein Science Munich (CIPSM); Ludwig Maximilians University Munich; Planegg-Martinsried, Germany
| | - Sebastian Bultmann
- Department of Biology II; Center for Integrated Protein Science Munich (CIPSM); Ludwig Maximilians University Munich; Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Department of Biology II; Center for Integrated Protein Science Munich (CIPSM); Ludwig Maximilians University Munich; Planegg-Martinsried, Germany
| | - Yolanda Markaki
- Department of Biology II; Center for Integrated Protein Science Munich (CIPSM); Ludwig Maximilians University Munich; Planegg-Martinsried, Germany
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22
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Chaumeil J, Micsinai M, Ntziachristos P, Roth DB, Aifantis I, Kluger Y, Deriano L, Skok JA. The RAG2 C-terminus and ATM protect genome integrity by controlling antigen receptor gene cleavage. Nat Commun 2014; 4:2231. [PMID: 23900513 PMCID: PMC3903180 DOI: 10.1038/ncomms3231] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 07/02/2013] [Indexed: 01/16/2023] Open
Abstract
Tight control of antigen-receptor gene rearrangement is required to preserve genome integrity and prevent the occurrence of leukemia and lymphoma. Nonetheless, mistakes can happen, leading to the generation of aberrant rearrangements, such as Tcra/d-Igh inter-locus translocations that are a hallmark of ATM deficiency. Current evidence indicates that these translocations arise from the persistence of unrepaired breaks converging at different stages of thymocyte differentiation. Here we show that a defect in feedback control of RAG2 activity gives rise to bi-locus breaks and damage on Tcra/d and Igh in the same T cell at the same developmental stage, which provides a direct mechanism for generating these inter-locus rearrangements. Both the RAG2 C-terminus and ATM prevent bi-locus RAG-mediated cleavage through modulation of 3D conformation (higher order loops) and nuclear organization of the two loci. This limits the number of potential substrates for translocation and provides an important mechanism for protecting genome stability.
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Affiliation(s)
- Julie Chaumeil
- Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
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23
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Bantignies F, Cavalli G. Topological organization of Drosophila Hox genes using DNA fluorescent in situ hybridization. Methods Mol Biol 2014; 1196:103-20. [PMID: 25151160 DOI: 10.1007/978-1-4939-1242-1_7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
DNA fluorescent in situ hybridization (FISH) is the method of choice to study genomic organization at the single-cell level. It has been recently used to study the topological organization of the homeotic bithorax complex (BX-C) in Drosophila as well as to describe long-range genomic interactions between the BX-C and the Antennapedia complex (ANT-C), in addition to other genomic loci. Coupled with immunofluorescence, FISH can be used to study the relative positioning of homeotic genes with nuclear subcompartments, such as Polycomb-group (PcG) bodies, transcription factories, or the nuclear lamina. Here, we describe two multicolor 3D-FISH protocols; one for whole mount Drosophila embryos or larval discs and one for Drosophila-cultured cells. Both methods can be applied to any single copy locus of interest and are compatible with immunostaining (FISH-I).
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Affiliation(s)
- Frédéric Bantignies
- Institut de Génétique Humaine, CNRS UPR-1142, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France,
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24
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Chaumeil J, Micsinai M, Ntziachristos P, Deriano L, Wang JMH, Ji Y, Nora EP, Rodesch MJ, Jeddeloh JA, Aifantis I, Kluger Y, Schatz DG, Skok JA. Higher-order looping and nuclear organization of Tcra facilitate targeted rag cleavage and regulated rearrangement in recombination centers. Cell Rep 2013; 3:359-70. [PMID: 23416051 DOI: 10.1016/j.celrep.2013.01.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/01/2013] [Accepted: 01/16/2013] [Indexed: 11/16/2022] Open
Abstract
V(D)J recombination is essential for generating a diverse array of B and T cell receptors that can recognize and combat foreign antigens. As with any recombination event, tight control is essential to prevent the occurrence of genetic anomalies that drive cellular transformation. One important aspect of regulation is directed targeting of the RAG recombinase. Indeed, RAG accumulates at the 3' end of individual antigen receptor loci poised for rearrangement; however, it is not known whether focal binding is involved in regulating cleavage, and what mechanisms lead to enrichment of RAG in this region. Here, we show that monoallelic looping out of the 3' end of the T cell receptor α (Tcra) locus, coupled with transcription and increased chromatin/nuclear accessibility, is linked to focal RAG binding and ATM-mediated regulation of monoallelic cleavage on looped-out 3' regions. Our data identify higher-order loop formation as a key determinant of directed RAG targeting and the maintenance of genome stability.
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Affiliation(s)
- Julie Chaumeil
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
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