1
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Hill CM, Indeglia A, Picone F, Murphy ME, Cipriano C, Maki RG, Gardini A. NAB2-STAT6 drives an EGR1-dependent neuroendocrine program in Solitary Fibrous Tumors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589533. [PMID: 38659891 PMCID: PMC11042251 DOI: 10.1101/2024.04.15.589533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The pathogenesis of many rare tumor types is poorly understood, preventing the design of effective treatments. Solitary fibrous tumors (SFTs) are neoplasms of mesenchymal origin that affect 1/1,000,000 individuals every year and are clinically assimilated to soft tissue sarcomas. SFTs can arise throughout the body and are usually managed surgically. However, 30-40% of SFTs will relapse local-regionally or metastasize. There are no systemic therapies with durable activity for malignant SFTs to date. The molecular hallmark of SFTs is a gene fusion between the NAB2 and STAT6 loci on chromosome 12, resulting in a chimeric protein of poorly characterized function called NAB2-STAT6. We use primary samples and an inducible cell model to discover that NAB2-STAT6 operates as a transcriptional coactivator for a specific set of enhancers and promoters that are normally targeted by the EGR1 transcription factor. In physiological conditions, NAB2 is primarily localized to the cytoplasm and only a small nuclear fraction is available to operate as a co-activator of EGR1 targets. NAB2-STAT6 redirects NAB1, NAB2, and additional EGR1 to the nucleus and bolster the expression of neuronal EGR1 targets. The STAT6 moiety of the fusion protein is a major driver of its nuclear localization and further contributes to NAB2's co-activating abilities. In primary tumors, NAB2-STAT6 activates a neuroendocrine gene signature that sets it apart from most sarcomas. These discoveries provide new insight into the pathogenesis of SFTs and reveal new targets with therapeutic potential.
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Affiliation(s)
- Connor M Hill
- The Wistar Institute, Philadelphia, PA, US
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S
| | - Alexandra Indeglia
- The Wistar Institute, Philadelphia, PA, US
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S
| | | | | | - Cara Cipriano
- Department of Orthopedic Surgery, University of Pennsylvania, Philadelphia, PA, U.S
| | - Robert G Maki
- Department of Orthopedic Surgery, University of Pennsylvania, Philadelphia, PA, U.S
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S
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2
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Bedois AMH, Parker HJ, Price AJ, Morrison JA, Bronner ME, Krumlauf R. Sea lamprey enlightens the origin of the coupling of retinoic acid signaling to vertebrate hindbrain segmentation. Nat Commun 2024; 15:1538. [PMID: 38378737 PMCID: PMC10879103 DOI: 10.1038/s41467-024-45911-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Retinoic acid (RA) is involved in antero-posterior patterning of the chordate body axis and, in jawed vertebrates, has been shown to play a major role at multiple levels of the gene regulatory network (GRN) regulating hindbrain segmentation. Knowing when and how RA became coupled to the core hindbrain GRN is important for understanding how ancient signaling pathways and patterning genes can evolve and generate diversity. Hence, we investigated the link between RA signaling and hindbrain segmentation in the sea lamprey Petromyzon marinus, an important jawless vertebrate model providing clues to decipher ancestral vertebrate features. Combining genomics, gene expression, and functional analyses of major components involved in RA synthesis (Aldh1as) and degradation (Cyp26s), we demonstrate that RA signaling is coupled to hindbrain segmentation in lamprey. Thus, the link between RA signaling and hindbrain segmentation is a pan vertebrate feature of the hindbrain and likely evolved at the base of vertebrates.
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Affiliation(s)
- Alice M H Bedois
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Andrew J Price
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Jason A Morrison
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, MO, 66160, USA.
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3
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Bedois AMH, Parker HJ, Bronner ME, Krumlauf R. Sea lamprey enlightens the origin of the coupling of retinoic acid signaling to vertebrate hindbrain segmentation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.07.548143. [PMID: 37461675 PMCID: PMC10350081 DOI: 10.1101/2023.07.07.548143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Retinoic acid (RA) is involved in antero-posterior patterning of the chordate body axis and, in jawed vertebrates, has been shown to play a major role at multiple levels of the gene regulatory network (GRN) regulating hindbrain segmentation. Knowing when and how RA became coupled to the core hindbrain GRN is important for understanding how ancient signaling pathways and patterning genes can evolve and generate diversity. Hence, we investigated the link between RA signaling and hindbrain segmentation in the sea lamprey Petromyzon marinus, an important jawless vertebrate model providing clues to decipher ancestral vertebrate features. Combining genomics, gene expression, and functional analyses of major components involved in RA synthesis (Aldh1as) and degradation (Cyp26s), we demonstrate that RA signaling is coupled to hindbrain segmentation in lamprey. Thus, the link between RA signaling and hindbrain segmentation is a pan vertebrate feature of the hindbrain and likely evolved at the base of vertebrates.
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Affiliation(s)
- Alice M. H. Bedois
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Hugo J. Parker
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Marianne E. Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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4
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Maurya VK, Ying Y, Lanza DG, Heaney JD, Lydon JP. A CRISPR/Cas9-engineered mouse carrying a conditional knockout allele for the early growth response-1 transcription factor. Genesis 2023; 61:e23515. [PMID: 36949241 PMCID: PMC10514223 DOI: 10.1002/dvg.23515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/02/2023] [Accepted: 03/10/2023] [Indexed: 03/24/2023]
Abstract
Early growth response 1 (EGR1) mediates transcriptional programs that are indispensable for cell division, differentiation, and apoptosis in numerous physiologies and pathophysiologies. Whole-body EGR1 knockouts in mice (Egr1KO ) have advanced our understanding of EGR1 function in an in vivo context. To extend the utility of the mouse to investigate EGR1 responses in a tissue- and/or cell-type-specific manner, we generated a mouse model in which exon 2 of the mouse Egr1 gene is floxed by CRISPR/Cas9 engineering. The floxed Egr1 alleles (Egr1f/f ) are designed to enable spatiotemporal control of Cre-mediated EGR1 ablation in the mouse. To confirm that the Egr1f/f alleles can be abrogated using a Cre driver, we crossed the Egr1f/f mouse with a global Cre driver to generate the Egr1 conditional knockout (Egr1d/d ) mouse in which EGR1 expression is ablated in all tissues. Genetic and protein analysis confirmed the absence of exon 2 and loss of EGR1 expression in the Egr1d/d mouse, respectively. Moreover, the Egr1d/d female exhibits overt reproductive phenotypes previously reported for the Egr1KO mouse. Therefore, studies described in this short technical report underscore the potential utility of the murine Egr1 floxed allele to further resolve EGR1 function at a tissue- and/or cell-type-specific level.
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Affiliation(s)
- Vineet K. Maurya
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030
| | - Yan Ying
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030
| | - Denise G. Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030
| | - Jason D. Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030
| | - John P. Lydon
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030
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5
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Spatio-temporal dynamics enhance cellular diversity, neuronal function and further maturation of human cerebral organoids. Commun Biol 2023; 6:173. [PMID: 36788328 PMCID: PMC9926461 DOI: 10.1038/s42003-023-04547-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
The bioengineerined and whole matured human brain organoids stand as highly valuable three-dimensional in vitro brain-mimetic models to recapitulate in vivo brain development, neurodevelopmental and neurodegenerative diseases. Various instructive signals affecting multiple biological processes including morphogenesis, developmental stages, cell fate transitions, cell migration, stem cell function and immune responses have been employed for generation of physiologically functional cerebral organoids. However, the current approaches for maturation require improvement for highly harvestable and functional cerebral organoids with reduced batch-to-batch variabilities. Here, we demonstrate two different engineering approaches, the rotating cell culture system (RCCS) microgravity bioreactor and a newly designed microfluidic platform (µ-platform) to improve harvestability, reproducibility and the survival of high-quality cerebral organoids and compare with those of traditional spinner and shaker systems. RCCS and µ-platform organoids have reached ideal sizes, approximately 95% harvestability, prolonged culture time with Ki-67 + /CD31 + /β-catenin+ proliferative, adhesive and endothelial-like cells and exhibited enriched cellular diversity (abundant neural/glial/ endothelial cell population), structural brain morphogenesis, further functional neuronal identities (glutamate secreting glutamatergic, GABAergic and hippocampal neurons) and synaptogenesis (presynaptic-postsynaptic interaction) during whole human brain development. Both organoids expressed CD11b + /IBA1 + microglia and MBP + /OLIG2 + oligodendrocytes at high levels as of day 60. RCCS and µ-platform organoids showing high levels of physiological fidelity a high level of physiological fidelity can serve as functional preclinical models to test new therapeutic regimens for neurological diseases and benefit from multiplexing.
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6
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Kim YI, O’Rourke R, Sagerström CG. scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525932. [PMID: 36747868 PMCID: PMC9900950 DOI: 10.1101/2023.01.27.525932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Rhombomeres serve to position neural progenitors in the embryonic hindbrain, thereby ensuring appropriate neural circuit formation, but the molecular identities of individual rhombomeres and the mechanism whereby they form have not been fully established. Here we apply scMultiome analysis in zebrafish to molecularly resolve all rhombomeres for the first time. We find that rhombomeres become molecularly distinct between 10hpf (end of gastrulation) and 13hpf (early segmentation). While the mature hindbrain consists of alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even characteristics in the early hindbrain. Instead, we find that each rhombomere displays a unique gene expression and chromatin profile. Prior to the appearance of distinct rhombomeres, we detect three hindbrain progenitor clusters (PHPDs) that correlate with the earliest visually observed segments in the hindbrain primordium and that represent prospective rhombomere r2/r3 (possibly including r1), r4 and r5/r6, respectively. We further find that the PHPDs form in response to Fgf and RA morphogens and that individual PHPD cells co-express markers of multiple mature rhombomeres. We propose that the PHPDs contain mixed-identity progenitors and that their subdivision into individual mature rhombomeres requires resolution of mixed transcription and chromatin states.
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Affiliation(s)
| | | | - Charles G. Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, 12801 E. 17th Avenue, Aurora, CO 80045
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7
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Azagra A, Meler A, de Barrios O, Tomás-Daza L, Collazo O, Monterde B, Obiols M, Rovirosa L, Vila-Casadesús M, Cabrera-Pasadas M, Gusi-Vives M, Graf T, Varela I, Sardina JL, Javierre BM, Parra M. The HDAC7-TET2 epigenetic axis is essential during early B lymphocyte development. Nucleic Acids Res 2022; 50:8471-8490. [PMID: 35904805 PMCID: PMC9410891 DOI: 10.1093/nar/gkac619] [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: 07/29/2021] [Revised: 06/23/2022] [Accepted: 07/05/2022] [Indexed: 12/02/2022] Open
Abstract
Correct B cell identity at each stage of cellular differentiation during B lymphocyte development is critically dependent on a tightly controlled epigenomic landscape. We previously identified HDAC7 as an essential regulator of early B cell development and its absence leads to a drastic block at the pro-B to pre-B cell transition. More recently, we demonstrated that HDAC7 loss in pro-B-ALL in infants associates with a worse prognosis. Here we delineate the molecular mechanisms by which HDAC7 modulates early B cell development. We find that HDAC7 deficiency drives global chromatin de-condensation, histone marks deposition and deregulates other epigenetic regulators and mobile elements. Specifically, the absence of HDAC7 induces TET2 expression, which promotes DNA 5-hydroxymethylation and chromatin de-condensation. HDAC7 deficiency also results in the aberrant expression of microRNAs and LINE-1 transposable elements. These findings shed light on the mechanisms by which HDAC7 loss or misregulation may lead to B cell–based hematological malignancies.
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Affiliation(s)
- Alba Azagra
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - Ainara Meler
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - Oriol de Barrios
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - Laureano Tomás-Daza
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Olga Collazo
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - Beatriz Monterde
- Instituto de Biomedicina y Biotecnología de Cantabria. Universidad de Cantabria-CSIC. 39011 Santander, Spain
| | - Mireia Obiols
- Epigenetic Control of Haematopoiesis Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain
| | - Llorenç Rovirosa
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain
| | - Maria Vila-Casadesús
- Centre for Genomic Regulation (CRG), PRBB Building, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Mónica Cabrera-Pasadas
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Mar Gusi-Vives
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation (CRG), PRBB Building, Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria. Universidad de Cantabria-CSIC. 39011 Santander, Spain
| | - José Luis Sardina
- Epigenetic Control of Haematopoiesis Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain
| | - Biola M Javierre
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain
| | - Maribel Parra
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
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8
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A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes. Nat Commun 2022; 13:1039. [PMID: 35210422 PMCID: PMC8873246 DOI: 10.1038/s41467-022-28666-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 02/04/2022] [Indexed: 12/15/2022] Open
Abstract
The contractile properties of adult myofibers are shaped by their Myosin heavy chain isoform content. Here, we identify by snATAC-seq a 42 kb super-enhancer at the locus regrouping the fast Myosin genes. By 4C-seq we show that active fast Myosin promoters interact with this super-enhancer by DNA looping, leading to the activation of a single promoter per nucleus. A rainbow mouse transgenic model of the locus including the super-enhancer recapitulates the endogenous spatio-temporal expression of adult fast Myosin genes. In situ deletion of the super-enhancer by CRISPR/Cas9 editing demonstrates its major role in the control of associated fast Myosin genes, and deletion of two fast Myosin genes at the locus reveals an active competition of the promoters for the shared super-enhancer. Last, by disrupting the organization of fast Myosin, we uncover positional heterogeneity within limb skeletal muscles that may underlie selective muscle susceptibility to damage in certain myopathies. The contractile properties of adult myofibers are shaped by their Myosin heavy chain isoform content. Here the authors show that a super enhancer controls the spatiotemporal expression of the genes at the fast myosin heavy chain locus by DNA looping and that this expression profile is recapitulated in a rainbow transgenic mouse model of the locus.
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9
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Qiu Y, Fung L, Schilling TF, Nie Q. Multiple morphogens and rapid elongation promote segmental patterning during development. PLoS Comput Biol 2021; 17:e1009077. [PMID: 34161317 PMCID: PMC8259987 DOI: 10.1371/journal.pcbi.1009077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 07/06/2021] [Accepted: 05/13/2021] [Indexed: 12/21/2022] Open
Abstract
The vertebrate hindbrain is segmented into rhombomeres (r) initially defined by distinct domains of gene expression. Previous studies have shown that noise-induced gene regulation and cell sorting are critical for the sharpening of rhombomere boundaries, which start out rough in the forming neural plate (NP) and sharpen over time. However, the mechanisms controlling simultaneous formation of multiple rhombomeres and accuracy in their sizes are unclear. We have developed a stochastic multiscale cell-based model that explicitly incorporates dynamic morphogenetic changes (i.e. convergent-extension of the NP), multiple morphogens, and gene regulatory networks to investigate the formation of rhombomeres and their corresponding boundaries in the zebrafish hindbrain. During pattern initiation, the short-range signal, fibroblast growth factor (FGF), works together with the longer-range morphogen, retinoic acid (RA), to specify all of these boundaries and maintain accurately sized segments with sharp boundaries. At later stages of patterning, we show a nonlinear change in the shape of rhombomeres with rapid left-right narrowing of the NP followed by slower dynamics. Rapid initial convergence improves boundary sharpness and segment size by regulating cell sorting and cell fate both independently and coordinately. Overall, multiple morphogens and tissue dynamics synergize to regulate the sizes and boundaries of multiple segments during development. In segmental pattern formation, chemical gradients control gene expression in a concentration-dependent manner to specify distinct gene expression domains. Despite the stochasticity inherent to such biological processes, precise and accurate borders form between segmental gene expression domains. Previous work has revealed synergy between gene regulation and cell sorting in sharpening borders that are initially rough. However, it is still poorly understood how size and boundary sharpness of multiple segments are regulated in a tissue that changes dramatically in its morphology as the embryo develops. Here we develop a stochastic multiscale cell-base model to investigate these questions. Two novel strategies synergize to promote accurate segment formation, a combination of long- and short-range morphogens plus rapid tissue convergence, with one responsible for pattern initiation and the other enabling pattern refinement.
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Affiliation(s)
- Yuchi Qiu
- Department of Mathematics, University of California, Irvine, California, United States of America
| | - Lianna Fung
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, United States of America
| | - Thomas F. Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, United States of America
- * E-mail: (TFS); (QN)
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, California, United States of America
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, United States of America
- * E-mail: (TFS); (QN)
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10
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Parker HJ, Krumlauf R. A Hox gene regulatory network for hindbrain segmentation. Curr Top Dev Biol 2020; 139:169-203. [DOI: 10.1016/bs.ctdb.2020.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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11
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Llères D, Moindrot B, Pathak R, Piras V, Matelot M, Pignard B, Marchand A, Poncelet M, Perrin A, Tellier V, Feil R, Noordermeer D. CTCF modulates allele-specific sub-TAD organization and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains. Genome Biol 2019; 20:272. [PMID: 31831055 PMCID: PMC6909504 DOI: 10.1186/s13059-019-1896-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Genomic imprinting is essential for mammalian development and provides a unique paradigm to explore intra-cellular differences in chromatin configuration. So far, the detailed allele-specific chromatin organization of imprinted gene domains has mostly been lacking. Here, we explored the chromatin structure of the two conserved imprinted domains controlled by paternal DNA methylation imprints-the Igf2-H19 and Dlk1-Dio3 domains-and assessed the involvement of the insulator protein CTCF in mouse cells. RESULTS Both imprinted domains are located within overarching topologically associating domains (TADs) that are similar on both parental chromosomes. At each domain, a single differentially methylated region is bound by CTCF on the maternal chromosome only, in addition to multiple instances of bi-allelic CTCF binding. Combinations of allelic 4C-seq and DNA-FISH revealed that bi-allelic CTCF binding alone, on the paternal chromosome, correlates with a first level of sub-TAD structure. On the maternal chromosome, additional CTCF binding at the differentially methylated region adds a further layer of sub-TAD organization, which essentially hijacks the existing paternal-specific sub-TAD organization. Perturbation of maternal-specific CTCF binding site at the Dlk1-Dio3 locus, using genome editing, results in perturbed sub-TAD organization and bi-allelic Dlk1 activation during differentiation. CONCLUSIONS Maternal allele-specific CTCF binding at the imprinted Igf2-H19 and the Dlk1-Dio3 domains adds an additional layer of sub-TAD organization, on top of an existing three-dimensional configuration and prior to imprinted activation of protein-coding genes. We speculate that this allele-specific sub-TAD organization provides an instructive or permissive context for imprinted gene activation during development.
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Affiliation(s)
- David Llères
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Benoît Moindrot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Rakesh Pathak
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Vincent Piras
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Mélody Matelot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Benoît Pignard
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Alice Marchand
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Mallory Poncelet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Aurélien Perrin
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Virgile Tellier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France.
| | - Daan Noordermeer
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France.
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12
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Frank D, Sela-Donenfeld D. Hindbrain induction and patterning during early vertebrate development. Cell Mol Life Sci 2019; 76:941-960. [PMID: 30519881 PMCID: PMC11105337 DOI: 10.1007/s00018-018-2974-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/28/2022]
Abstract
The hindbrain is a key relay hub of the central nervous system (CNS), linking the bilaterally symmetric half-sides of lower and upper CNS centers via an extensive network of neural pathways. Dedicated neural assemblies within the hindbrain control many physiological processes, including respiration, blood pressure, motor coordination and different sensations. During early development, the hindbrain forms metameric segmented units known as rhombomeres along the antero-posterior (AP) axis of the nervous system. These compartmentalized units are highly conserved during vertebrate evolution and act as the template for adult brainstem structure and function. TALE and HOX homeodomain family transcription factors play a key role in the initial induction of the hindbrain and its specification into rhombomeric cell fate identities along the AP axis. Signaling pathways, such as canonical-Wnt, FGF and retinoic acid, play multiple roles to initially induce the hindbrain and regulate Hox gene-family expression to control rhombomeric identity. Additional transcription factors including Krox20, Kreisler and others act both upstream and downstream to Hox genes, modulating their expression and protein activity. In this review, we will examine the earliest embryonic signaling pathways that induce the hindbrain and subsequent rhombomeric segmentation via Hox and other gene expression. We will examine how these signaling pathways and transcription factors interact to activate downstream targets that organize the segmented AP pattern of the embryonic vertebrate hindbrain.
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Affiliation(s)
- Dale Frank
- Department of Biochemistry, Faculty of Medicine, The Rappaport Family Institute for Research in the Medical Sciences, Technion-Israel Institute of Technology, 31096, Haifa, Israel.
| | - Dalit Sela-Donenfeld
- Koret School of Veterinary Medicine, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel.
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13
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Abstract
Studies of the vertebrate hindbrain have revealed parallel mechanisms that establish sharp segments with a distinct and homogeneous regional identity. Recent work has revealed roles of cell identity regulation and its relationships with cell segregation. At early stages, there is overlapping expression at segment borders of the Egr2 and Hoxb1 transcription factors that specify distinct identities, which is resolved by reciprocal repression. Computer simulations show that this dynamic regulation of cell identity synergises with cell segregation to generate sharp borders. Some intermingling between segments occurs at early stages, and ectopic egr2-expressing cells switch identity to match their new neighbours. This switching is mediated by coupling between egr2 expression and the level of retinoic acid signalling, which acts in a community effect to maintain homogeneous segmental identity. These findings reveal an interplay between cell segregation and the dynamic regulation of cell identity in the formation of sharp patterns in the hindbrain and raise the question of whether similar mechanisms occur in other tissues.
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14
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Torbey P, Thierion E, Collombet S, de Cian A, Desmarquet-Trin-Dinh C, Dura M, Concordet JP, Charnay P, Gilardi-Hebenstreit P. Cooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation. PLoS Genet 2018; 14:e1007581. [PMID: 30080860 PMCID: PMC6095606 DOI: 10.1371/journal.pgen.1007581] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/16/2018] [Accepted: 07/20/2018] [Indexed: 12/13/2022] Open
Abstract
Cis-regulation plays an essential role in the control of gene expression, and is particularly complex and poorly understood for developmental genes, which are subject to multiple levels of modulation. In this study, we performed a global analysis of the cis-acting elements involved in the control of the zebrafish developmental gene krox20. krox20 encodes a transcription factor required for hindbrain segmentation and patterning, a morphogenetic process highly conserved during vertebrate evolution. Chromatin accessibility analysis reveals a cis-regulatory landscape that includes 6 elements participating in the control of initiation and autoregulatory aspects of krox20 hindbrain expression. Combining transgenic reporter analyses and CRISPR/Cas9-mediated mutagenesis, we assign precise functions to each of these 6 elements and provide a comprehensive view of krox20 cis-regulation. Three important features emerged. First, cooperation between multiple cis-elements plays a major role in the regulation. Cooperation can surprisingly combine synergy and redundancy, and is not restricted to transcriptional enhancer activity (for example, 4 distinct elements cooperate through different modes to maintain autoregulation). Second, several elements are unexpectedly versatile, which allows them to be involved in different aspects of control of gene expression. Third, comparative analysis of the elements and their activities in several vertebrate species reveals that this versatility is underlain by major plasticity across evolution, despite the high conservation of the gene expression pattern. These characteristics are likely to be of broad significance for developmental genes.
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Affiliation(s)
- Patrick Torbey
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
| | - Elodie Thierion
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
| | - Samuel Collombet
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
| | - Anne de Cian
- Sorbonne Universités, Muséum National d’Histoire Naturelle, CNRS UMR 7196, INSERM U1154, Paris, France
| | - Carole Desmarquet-Trin-Dinh
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
| | - Mathilde Dura
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
| | - Jean-Paul Concordet
- Sorbonne Universités, Muséum National d’Histoire Naturelle, CNRS UMR 7196, INSERM U1154, Paris, France
| | - Patrick Charnay
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
- * E-mail: (PC); (PGH)
| | - Pascale Gilardi-Hebenstreit
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
- * E-mail: (PC); (PGH)
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15
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Barbieri E, Trizzino M, Welsh SA, Owens TA, Calabretta B, Carroll M, Sarma K, Gardini A. Targeted Enhancer Activation by a Subunit of the Integrator Complex. Mol Cell 2018; 71:103-116.e7. [PMID: 30008316 DOI: 10.1016/j.molcel.2018.05.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 04/11/2018] [Accepted: 05/24/2018] [Indexed: 01/12/2023]
Abstract
The control of cell fate is an epigenetic process initiated by transcription factors (TFs) that recognize DNA motifs and recruit activator complexes and transcriptional machineries to chromatin. Lineage specificity is thought to be provided solely by TF-motif pairing, while the recruited activators are passive. Here, we show that INTS13, a subunit of the Integrator complex, operates as monocytic/macrophagic differentiation factor. Integrator is a general activator of transcription at coding genes and is required for eRNA maturation. Here, we show that INTS13 functions as an independent sub-module and targets enhancers through Early Growth Response (EGR1/2) TFs and their co-factor NAB2. INTS13 binds poised monocytic enhancers eliciting chromatin looping and activation. Independent depletion of INTS13, EGR1, or NAB2 impairs monocytic differentiation of cell lines and primary human progenitors. Our data demonstrate that Integrator is not functionally homogeneous and has TF-specific regulatory potential, revealing a new enhancer regulatory axis that controls myeloid differentiation.
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Affiliation(s)
- Elisa Barbieri
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Marco Trizzino
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Sarah Ann Welsh
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Tori Alexandra Owens
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Bruno Calabretta
- Sidney Kimmel Cancer Center, Thomas Jefferson Medical School, Philadelphia, PA, USA
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - Kavitha Sarma
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA.
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16
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Lacomme M, Medevielle F, Bourbon HM, Thierion E, Kleinjan DJ, Roussat M, Pituello F, Bel-Vialar S. A long range distal enhancer controls temporal fine-tuning of PAX6 expression in neuronal precursors. Dev Biol 2018; 436:94-107. [PMID: 29486153 DOI: 10.1016/j.ydbio.2018.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/22/2018] [Accepted: 02/22/2018] [Indexed: 12/14/2022]
Abstract
Proper embryonic development relies on a tight control of spatial and temporal gene expression profiles in a highly regulated manner. One good example is the ON/OFF switching of the transcription factor PAX6 that governs important steps of neurogenesis. In the neural tube PAX6 expression is initiated in neural progenitors through the positive action of retinoic acid signaling and downregulated in neuronal precursors by the bHLH transcription factor NEUROG2. How these two regulatory inputs are integrated at the molecular level to properly fine tune temporal PAX6 expression is not known. In this study we identified and characterized a 940-bp long distal cis-regulatory module (CRM), located far away from the PAX6 transcription unit and which conveys positive input from RA signaling pathway and indirect repressive signal(s) from NEUROG2. These opposing regulatory signals are integrated through HOMZ, a 94 bp core region within E940 which is evolutionarily conserved in distant organisms such as the zebrafish. We show that within HOMZ, NEUROG2 and RA exert their opposite temporal activities through a short 60 bp region containing a functional RA-responsive element (RARE). We propose a model in which retinoic acid receptors (RARs) and NEUROG2 repressive target(s) compete on the same DNA motif to fine tune temporal PAX6 expression during the course of spinal neurogenesis.
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Affiliation(s)
- Marine Lacomme
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France; Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal, Québec, Canada
| | - François Medevielle
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Henri-Marc Bourbon
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Elodie Thierion
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Dirk-Jan Kleinjan
- 1UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Mélanie Roussat
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Fabienne Pituello
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Sophie Bel-Vialar
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
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17
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Andrey G, Mundlos S. The three-dimensional genome: regulating gene expression during pluripotency and development. Development 2017; 144:3646-3658. [PMID: 29042476 DOI: 10.1242/dev.148304] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The precise expression of genes in time and space during embryogenesis is largely influenced by communication between enhancers and promoters, which is propagated and governed by the physical proximity of these elements in the nucleus. Here, we review how chromatin domains organize the genome by guiding enhancers to their target genes thereby preventing non-specific interactions with other neighboring regions. We also discuss the dynamics of chromatin interactions between enhancers and promoters, as well as the consequent changes in gene expression, that occur in pluripotent cells and during development. Finally, we evaluate how genomic changes such as deletions, inversions and duplications affect 3D chromatin configuration overall and lead to ectopic enhancer-promoter contacts, and thus gene misexpression, which can contribute to abnormal development and disease.
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Affiliation(s)
- Guillaume Andrey
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany .,Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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