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Wang C, Hu M, Yu K, Liu W, Hu A, Kuang Y, Huang L, Gajendran B, Zacksenhaus E, Xiao X, Ben-David Y. An intricate regulatory circuit between FLI1 and GATA1/GATA2/LDB1/ERG dictates erythroid vs. megakaryocytic differentiation. Mol Med Rep 2024; 29:107. [PMID: 38695236 PMCID: PMC11082641 DOI: 10.3892/mmr.2024.13231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/21/2024] [Indexed: 05/12/2024] Open
Abstract
During hematopoiesis, megakaryocytic erythroid progenitors (MEPs) differentiate into megakaryocytic or erythroid lineages in response to specific transcriptional factors, yet the regulatory mechanism remains to be elucidated. Using the MEP‑like cell line HEL western blotting, RT‑qPCR, lentivirus‑mediated downregulation, flow cytometry as well as chromatin immunoprecipitation (ChIp) assay demonstrated that the E26 transformation‑specific (ETS) transcription factor friend leukemia integration factor 1 (Fli‑1) inhibits erythroid differentiation. The present study using these methods showed that while FLI1‑mediated downregulation of GATA binding protein 1 (GATA1) suppresses erythropoiesis, its direct transcriptional induction of GATA2 promotes megakaryocytic differentiation. GATA1 is also involved in megakaryocytic differentiation through regulation of GATA2. By contrast to FLI1, the ETS member erythroblast transformation‑specific‑related gene (ERG) negatively controls GATA2 and its overexpression through exogenous transfection blocks megakaryocytic differentiation. In addition, FLI1 regulates expression of LIM Domain Binding 1 (LDB1) during erythroid and megakaryocytic commitment, whereas shRNA‑mediated depletion of LDB1 downregulates FLI1 and GATA2 but increases GATA1 expression. In agreement, LDB1 ablation using shRNA lentivirus expression blocks megakaryocytic differentiation and modestly suppresses erythroid maturation. These results suggested that a certain threshold level of LDB1 expression enables FLI1 to block erythroid differentiation. Overall, FLI1 controlled the commitment of MEP to either erythroid or megakaryocytic lineage through an intricate regulation of GATA1/GATA2, LDB1 and ERG, exposing multiple targets for cell fate commitment and therapeutic intervention.
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Affiliation(s)
- Chunlin Wang
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550014, P.R. China
- Institute of Pharmacology and Biological Activity, Natural Products Research Center of Guizhou Province, Guiyang, Guizhou 550014, P.R. China
| | - Maoting Hu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550014, P.R. China
- Institute of Pharmacology and Biological Activity, Natural Products Research Center of Guizhou Province, Guiyang, Guizhou 550014, P.R. China
| | - Kunlin Yu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550014, P.R. China
- Institute of Pharmacology and Biological Activity, Natural Products Research Center of Guizhou Province, Guiyang, Guizhou 550014, P.R. China
| | - Wuling Liu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550014, P.R. China
- Institute of Pharmacology and Biological Activity, Natural Products Research Center of Guizhou Province, Guiyang, Guizhou 550014, P.R. China
| | - Anling Hu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550014, P.R. China
- Institute of Pharmacology and Biological Activity, Natural Products Research Center of Guizhou Province, Guiyang, Guizhou 550014, P.R. China
| | - Yi Kuang
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550014, P.R. China
- Institute of Pharmacology and Biological Activity, Natural Products Research Center of Guizhou Province, Guiyang, Guizhou 550014, P.R. China
| | - Lei Huang
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550014, P.R. China
- Institute of Pharmacology and Biological Activity, Natural Products Research Center of Guizhou Province, Guiyang, Guizhou 550014, P.R. China
| | - Babu Gajendran
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550014, P.R. China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, Guizhou 550025, P.R. China
| | - Eldad Zacksenhaus
- Department of Medicine, University of Toronto, Toronto, Ontario M5S3H2, Canada
- Division of Advanced Diagnostics, Toronto General Research Institute, University Health Network, Toronto, Ontario M5G1L7, Canada
| | - Xiao Xiao
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550014, P.R. China
- Institute of Pharmacology and Biological Activity, Natural Products Research Center of Guizhou Province, Guiyang, Guizhou 550014, P.R. China
| | - Yaacov Ben-David
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550014, P.R. China
- Institute of Pharmacology and Biological Activity, Natural Products Research Center of Guizhou Province, Guiyang, Guizhou 550014, P.R. China
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2
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Fagnan A, Aid Z, Baille M, Drakul A, Robert E, Lopez CK, Thirant C, Lecluse Y, Rivière J, Ignacimouttou C, Salmoiraghi S, Anguita E, Naimo A, Marzac C, Pflumio F, Malinge S, Wichmann C, Huang Y, Lobry C, Chaumeil J, Soler E, Bourquin J, Nerlov C, Bernard OA, Schwaller J, Mercher T. The ETO2 transcriptional cofactor maintains acute leukemia by driving a MYB/EP300-dependent stemness program. Hemasphere 2024; 8:e90. [PMID: 38903535 PMCID: PMC11187848 DOI: 10.1002/hem3.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/13/2024] [Accepted: 05/01/2024] [Indexed: 06/22/2024] Open
Abstract
Transcriptional cofactors of the ETO family are recurrent fusion partners in acute leukemia. We characterized the ETO2 regulome by integrating transcriptomic and chromatin binding analyses in human erythroleukemia xenografts and controlled ETO2 depletion models. We demonstrate that beyond its well-established repressive activity, ETO2 directly activates transcription of MYB, among other genes. The ETO2-activated signature is associated with a poorer prognosis in erythroleukemia but also in other acute myeloid and lymphoid leukemia subtypes. Mechanistically, ETO2 colocalizes with EP300 and MYB at enhancers supporting the existence of an ETO2/MYB feedforward transcription activation loop (e.g., on MYB itself). Both small-molecule and PROTAC-mediated inhibition of EP300 acetyltransferases strongly reduced ETO2 protein, chromatin binding, and ETO2-activated transcripts. Taken together, our data show that ETO2 positively enforces a leukemia maintenance program that is mediated in part by the MYB transcription factor and that relies on acetyltransferase cofactors to stabilize ETO2 scaffolding activity.
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Affiliation(s)
- Alexandre Fagnan
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Zakia Aid
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Marie Baille
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Aneta Drakul
- Division of Oncology and Children's Research CentreUniversity Children's Hospital ZurichZurichSwitzerland
| | - Elie Robert
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Cécile K. Lopez
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Cécile Thirant
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Yann Lecluse
- Gustave Roussy, Plateforme Imagerie et Cytométrie, Université Paris‐Saclay, UMS AMMICA, INSERM US23, CNRS UMS 3655VillejuifFrance
| | - Julie Rivière
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Cathy Ignacimouttou
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Silvia Salmoiraghi
- Department of Oncology and HematologyAzienda Socio Sanitaria Territoriale Papa Giovanni XXIII, FROM Research Foundation, Papa Giovanni XXIII HospitalBergamoItaly
| | - Eduardo Anguita
- Hematology Department, Hospital Clínico San Carlos (HCSC), IML, IdISSC, Department of MedicineUniversidad Complutense de Madrid (UCM)MadridSpain
| | - Audrey Naimo
- Gustave Roussy, Genomic PlatformUniversité Paris‐Saclay, UMS AMMICA, INSERM US23, CNRS UMS 3655VillejuifFrance
| | - Christophe Marzac
- Department of HematologyLeukemia Interception Program, Personalized Cancer Prevention Center, Gustave RoussyVillejuifFrance
| | - Françoise Pflumio
- Equipe Labellisée Ligue Contre le CancerParisFrance
- Unité de Recherche (UMR)‐E008 Stabilité Génétique, Cellules Souches et Radiations, Team Niche and Cancer in Hematopoiesis, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Université de Paris‐Université Paris‐SaclayFontenay‐aux‐RosesFrance
- OPALE Carnot Institute, The Organization for Partnerships in LeukemiaParisFrance
| | - Sébastien Malinge
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Telethon Kids Institute, Perth Children's HospitalNedlandsAustralia
| | - Christian Wichmann
- Department of Transfusion Medicine, Cell Therapeutics and HaemostasisLudwig‐Maximilians‐University of MunichMunichGermany
| | - Yun Huang
- Division of Oncology and Children's Research CentreUniversity Children's Hospital ZurichZurichSwitzerland
| | - Camille Lobry
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- INSERM U944, CNRS UMR7212Institut de Recherche Saint Louis and Université de ParisParisFrance
| | - Julie Chaumeil
- Université de Paris, Institut Cochin, INSERM, CNRSParisFrance
| | - Eric Soler
- IGMM, University of Montpellier, CNRS, Montpellier, France & Université de Paris, Laboratory of Excellence GR‐ExParisFrance
| | - Jean‐Pierre Bourquin
- Division of Oncology and Children's Research CentreUniversity Children's Hospital ZurichZurichSwitzerland
| | - Claus Nerlov
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe HospitalUniversity of OxfordOxfordUK
| | | | - Juerg Schwaller
- Department of BiomedicineUniversity Children's Hospital Beider Basel (UKBB), University of BaselBaselSwitzerland
| | - Thomas Mercher
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
- OPALE Carnot Institute, The Organization for Partnerships in LeukemiaParisFrance
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3
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Bower G, Hollingsworth EW, Jacinto S, Clock B, Cao K, Liu M, Dziulko A, Alcaina-Caro A, Xu Q, Skowronska-Krawczyk D, Lopez-Rios J, Dickel DE, Bardet AF, Pennacchio LA, Visel A, Kvon EZ. Conserved Cis-Acting Range Extender Element Mediates Extreme Long-Range Enhancer Activity in Mammals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.595809. [PMID: 38826394 PMCID: PMC11142232 DOI: 10.1101/2024.05.26.595809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
While most mammalian enhancers regulate their cognate promoters over moderate distances of tens of kilobases (kb), some enhancers act over distances in the megabase range. The sequence features enabling such extreme-distance enhancer-promoter interactions remain elusive. Here, we used in vivo enhancer replacement experiments in mice to show that short- and medium-range enhancers cannot initiate gene expression at extreme-distance range. We uncover a novel conserved cis-acting element, Range EXtender (REX), that confers extreme-distance regulatory activity and is located next to a long-range enhancer of Sall1. The REX element itself has no endogenous enhancer activity. However, addition of the REX to other short- and mid-range enhancers substantially increases their genomic interaction range. In the most extreme example observed, addition of the REX increased the range of an enhancer by an order of magnitude, from its native 71kb to 840kb. The REX element contains highly conserved [C/T]AATTA homeodomain motifs. These motifs are enriched around long-range limb enhancers genome-wide, including the ZRS, a benchmark long-range limb enhancer of Shh. Mutating the [C/T]AATTA motifs within the ZRS does not affect its limb-specific enhancer activity at short range, but selectively abolishes its long-range activity, resulting in severe limb reduction in knock-in mice. In summary, we identify a sequence signature globally associated with long-range enhancer-promoter interactions and describe a prototypical REX element that is necessary and sufficient to confer extreme-distance gene activation by remote enhancers.
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Affiliation(s)
- Grace Bower
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Ethan W. Hollingsworth
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
- Medical Scientist Training Program, University of California, Irvine, CA 92967, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Benjamin Clock
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Kaitlyn Cao
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Mandy Liu
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Adam Dziulko
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ana Alcaina-Caro
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, 41013, Spain
| | - Qianlan Xu
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, University of California, Irvine, CA, USA
| | - Dorota Skowronska-Krawczyk
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, University of California, Irvine, CA, USA
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, 41013, Spain
| | - Diane E. Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anaïs F. Bardet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U1258, 67400 Illkirch, France
| | - Len A. Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Evgeny Z. Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
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4
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Deleuze V, Garcia L, Rouaisnel B, Salma M, Kinoo A, Andrieu-Soler C, Soler E. Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions. iScience 2023; 26:107641. [PMID: 37670779 PMCID: PMC10475484 DOI: 10.1016/j.isci.2023.107641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/09/2023] [Accepted: 08/11/2023] [Indexed: 09/07/2023] Open
Abstract
Targeted genome editing holds great promise in biology. However, efficient genome modification, including gene knock-in (KI), remains an unattained goal in multiple cell types and loci due to poor transfection efficiencies and low target genes expression, impeding the positive selection of recombined cells. Here, we describe a genome editing approach to achieve efficient gene targeting using hard to transfect erythroid cell lines. We demonstrate robust fluorescent protein KI efficiency in low expressed transcription factor (TF) genes (e.g., Myb or Zeb1). We further show the ability to target two independent loci in individual cells, exemplified by MYB-GFP and NuMA-Cherry double KI, allowing multicolor labeling of regulatory factors at physiological endogenous levels. Our KI tagging approach allowed us to perform genome-wide TF analysis at increased signal-to-noise ratios, and highlighted previously unidentified MYB target genes and pathways. Overall, we establish a versatile CRISPR-Cas9-based platform, offering attractive opportunities for the dissection of the erythroid differentiation process.
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Affiliation(s)
| | - Leonor Garcia
- IGMM, University Montpellier, CNRS, Montpellier, France
| | | | - Mohammad Salma
- IGMM, University Montpellier, CNRS, Montpellier, France
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France
| | - Alexia Kinoo
- IGMM, University Montpellier, CNRS, Montpellier, France
| | - Charlotte Andrieu-Soler
- IGMM, University Montpellier, CNRS, Montpellier, France
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France
| | - Eric Soler
- IGMM, University Montpellier, CNRS, Montpellier, France
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France
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5
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Li D, Zhao XY, Zhou S, Hu Q, Wu F, Lee HY. Multidimensional profiling reveals GATA1-modulated stage-specific chromatin states and functional associations during human erythropoiesis. Nucleic Acids Res 2023; 51:6634-6653. [PMID: 37254808 PMCID: PMC10359633 DOI: 10.1093/nar/gkad468] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 04/18/2023] [Accepted: 05/13/2023] [Indexed: 06/01/2023] Open
Abstract
Mammalian erythroid development can be divided into three stages: hematopoietic stem and progenitor cell (HSPC), erythroid progenitor (Ery-Pro), and erythroid precursor (Ery-Pre). However, the mechanisms by which the 3D genome changes to establish the stage-specific transcription programs that are critical for erythropoiesis remain unclear. Here, we analyze the chromatin landscape at multiple levels in defined populations from primary human erythroid culture. While compartments and topologically associating domains remain largely unchanged, ∼50% of H3K27Ac-marked enhancers are dynamic in HSPC versus Ery-Pre. The enhancer anchors of enhancer-promoter loops are enriched for occupancy of respective stage-specific transcription factors (TFs), indicating these TFs orchestrate the enhancer connectome rewiring. The master TF of erythropoiesis, GATA1, is found to occupy most erythroid gene promoters at the Ery-Pro stage, and mediate conspicuous local rewiring through acquiring binding at the distal regions in Ery-Pre, promoting productive erythroid transcription output. Knocking out GATA1 binding sites precisely abrogates local rewiring and corresponding gene expression. Interestingly, knocking down GATA1 can transiently revert the cell state to an earlier stage and prolong the window of progenitor state. This study reveals mechanistic insights underlying chromatin rearrangements during development by integrating multidimensional chromatin landscape analyses to associate with transcription output and cellular states.
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Affiliation(s)
- Dong Li
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xin-Ying Zhao
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shuo Zhou
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qi Hu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Fan Wu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Hsiang-Ying Lee
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100871, China
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6
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Piqué-Borràs MR, Jevtic Z, Bagger FO, Seguin J, Sivalingam R, Bezerra MF, Louwagie A, Juge S, Nellas I, Ivanek R, Tzankov A, Moll UM, Cantillo O, Schulz-Heddergott R, Fagnan A, Mercher T, Schwaller J. The NFIA-ETO2 fusion blocks erythroid maturation and induces pure erythroid leukemia in cooperation with mutant TP53. Blood 2023; 141:2245-2260. [PMID: 36735909 PMCID: PMC10646783 DOI: 10.1182/blood.2022017273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 02/05/2023] Open
Abstract
The NFIA-ETO2 fusion is the product of a t(1;16)(p31;q24) chromosomal translocation, so far, exclusively found in pediatric patients with pure erythroid leukemia (PEL). To address the role for the pathogenesis of the disease, we facilitated the expression of the NFIA-ETO2 fusion in murine erythroblasts (EBs). We observed that NFIA-ETO2 significantly increased proliferation and impaired erythroid differentiation of murine erythroleukemia cells and of primary fetal liver-derived EBs. However, NFIA-ETO2-expressing EBs acquired neither aberrant in vitro clonogenic activity nor disease-inducing potential upon transplantation into irradiated syngenic mice. In contrast, in the presence of 1 of the most prevalent erythroleukemia-associated mutations, TP53R248Q, expression of NFIA-ETO2 resulted in aberrant clonogenic activity and induced a fully penetrant transplantable PEL-like disease in mice. Molecular studies support that NFIA-ETO2 interferes with erythroid differentiation by preferentially binding and repressing erythroid genes that contain NFI binding sites and/or are decorated by ETO2, resulting in a activity shift from GATA- to ETS-motif-containing target genes. In contrast, TP53R248Q does not affect erythroid differentiation but provides self-renewal and survival potential, mostly via downregulation of known TP53 targets. Collectively, our work indicates that NFIA-ETO2 initiates PEL by suppressing gene expression programs of terminal erythroid differentiation and cooperates with TP53 mutation to induce erythroleukemia.
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Affiliation(s)
- Maria-Riera Piqué-Borràs
- University Children’s Hospital Basel, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Zivojin Jevtic
- University Children’s Hospital Basel, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Frederik Otzen Bagger
- University Children’s Hospital Basel, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Seguin
- University Children’s Hospital Basel, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Rathick Sivalingam
- University Children’s Hospital Basel, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Matheus Filgueira Bezerra
- University Children’s Hospital Basel, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Amber Louwagie
- University Children’s Hospital Basel, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Sabine Juge
- University Children’s Hospital Basel, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Ioannis Nellas
- University Children’s Hospital Basel, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Robert Ivanek
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Alexandar Tzankov
- Institute for Pathology, University Hospital Basel, Basel, Switzerland
| | - Ute M. Moll
- Institute of Molecular Oncology, University of Göttingen, Göttingen, Germany
- Department of Pathology, Stony Brook University, Stony Brook, NY
| | - Oriano Cantillo
- University Children’s Hospital Basel, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Alexandre Fagnan
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Cancer Center, Université Paris Diderot, Université Paris-Sud, OPALE Carnot Institute, PEDIAC Program, Villejuif, France
| | - Thomas Mercher
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Cancer Center, Université Paris Diderot, Université Paris-Sud, OPALE Carnot Institute, PEDIAC Program, Villejuif, France
| | - Juerg Schwaller
- University Children’s Hospital Basel, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
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7
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Salma M, Andrieu-Soler C, Deleuze V, Soler E. High-throughput methods for the analysis of transcription factors and chromatin modifications: Low input, single cell and spatial genomic technologies. Blood Cells Mol Dis 2023; 101:102745. [PMID: 37121019 DOI: 10.1016/j.bcmd.2023.102745] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023]
Abstract
Genome-wide analysis of transcription factors and epigenomic features is instrumental to shed light on DNA-templated regulatory processes such as transcription, cellular differentiation or to monitor cellular responses to environmental cues. Two decades of technological developments have led to a rich set of approaches progressively pushing the limits of epigenetic profiling towards single cells. More recently, disruptive technologies using innovative biochemistry came into play. Assays such as CUT&RUN, CUT&Tag and variations thereof show considerable potential to survey multiple TFs or histone modifications in parallel from a single experiment and in native conditions. These are in the path to become the dominant assays for genome-wide analysis of TFs and chromatin modifications in bulk, single-cell, and spatial genomic applications. The principles together with pros and cons are discussed.
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Affiliation(s)
- Mohammad Salma
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France
| | - Charlotte Andrieu-Soler
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France
| | - Virginie Deleuze
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France
| | - Eric Soler
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France.
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8
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Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis. Nat Struct Mol Biol 2023; 30:463-474. [PMID: 36914797 DOI: 10.1038/s41594-023-00939-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/08/2023] [Indexed: 03/16/2023]
Abstract
Mammalian erythropoiesis involves progressive chromatin compaction and subsequent enucleation in terminal differentiation, but the mechanisms underlying the three-dimensional chromatin reorganization remain obscure. Here, we systematically analyze the higher-order chromatin in purified populations of primary human erythroblasts. Our results reveal that heterochromatin regions undergo substantial compression, with H3K9me3 markers relocalizing to the nuclear periphery and forming a significant number of long-range interactions, and that ~58% of the topologically associating domain (TAD) boundaries are disrupted, while certain TADs enriched for markers of the active transcription state and erythroid master regulators, GATA1 and KLF1, are selectively maintained during terminal erythropoiesis. Finally, we demonstrate that GATA1 is involved in safeguarding selected essential chromatin domains during terminal erythropoiesis. Our study therefore delineates the molecular characteristics of a development-driven chromatin compaction process, which reveals transcription competence as a key indicator of the selected domain maintenance to ensure appropriate gene expression during the extreme compaction of chromatin.
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9
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Shin B, Rothenberg EV. Multi-modular structure of the gene regulatory network for specification and commitment of murine T cells. Front Immunol 2023; 14:1108368. [PMID: 36817475 PMCID: PMC9928580 DOI: 10.3389/fimmu.2023.1108368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023] Open
Abstract
T cells develop from multipotent progenitors by a gradual process dependent on intrathymic Notch signaling and coupled with extensive proliferation. The stages leading them to T-cell lineage commitment are well characterized by single-cell and bulk RNA analyses of sorted populations and by direct measurements of precursor-product relationships. This process depends not only on Notch signaling but also on multiple transcription factors, some associated with stemness and multipotency, some with alternative lineages, and others associated with T-cell fate. These factors interact in opposing or semi-independent T cell gene regulatory network (GRN) subcircuits that are increasingly well defined. A newly comprehensive picture of this network has emerged. Importantly, because key factors in the GRN can bind to markedly different genomic sites at one stage than they do at other stages, the genes they significantly regulate are also stage-specific. Global transcriptome analyses of perturbations have revealed an underlying modular structure to the T-cell commitment GRN, separating decisions to lose "stem-ness" from decisions to block alternative fates. Finally, the updated network sheds light on the intimate relationship between the T-cell program, which depends on the thymus, and the innate lymphoid cell (ILC) program, which does not.
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Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ellen V. Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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10
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Elucidation of the Role of FAM210B in Mitochondrial Metabolism and Erythropoiesis. Mol Cell Biol 2022; 42:e0014322. [PMID: 36374104 PMCID: PMC9753634 DOI: 10.1128/mcb.00143-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Mitochondria play essential and specific roles during erythroid differentiation. Recently, FAM210B, encoding a mitochondrial inner membrane protein, has been identified as a novel target of GATA-1, as well as an erythropoietin-inducible gene. While FAM210B protein is involved in regulate mitochondrial metabolism and heme biosynthesis, its detailed function remains unknown. Here, we generated both knockout and knockdown of endogenous FAM210B in human induced pluripotent stem-derived erythroid progenitor (HiDEP) cells using CRISPR/Cas9 methodology. Intriguingly, erythroid differentiation was more pronounced in the FAM210B-depleted cells, and this resulted in increased frequency of orthochromatic erythroblasts and decreased frequencies of basophilic/polychromatic erythroblasts. Comprehensive metabolite analysis and functional analysis indicated that oxygen consumption rates and the NAD (NAD+)/NADH ratio were significantly decreased, while lactate production was significantly increased in FAM210B deletion HiDEP cells, indicating involvement of FAM210B in mitochondrial energy metabolism in erythroblasts. Finally, we purified FAM210B-interacting protein from K562 cells that stably expressed His/biotin-tagged FAM210B. Mass spectrometry analysis of the His/biotin-purified material indicated interactions with multiple subunits of mitochondrial ATP synthases, such as subunit alpha (ATP5A) and beta (ATP5B). Our results suggested that FAM210B contributes prominently to erythroid differentiation by regulating mitochondrial energy metabolism. Our results provide insights into the pathophysiology of dysregulated hematopoiesis.
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11
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Wang MX, Yan L, Chen J, Zhao JM, Zhu J, Yu SH. Reinforced erythroid differentiation inhibits leukemogenic potential of t(8;21) leukemia. FASEB J 2022; 36:e22562. [PMID: 36125067 DOI: 10.1096/fj.202200026rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 08/12/2022] [Accepted: 09/09/2022] [Indexed: 11/11/2022]
Abstract
Oncoprotein AML1-ETO (AE) derived from t(8;21)(q22;q22) translocation is typically present in a portion of French-American-British-M2 subtype of acute myeloid leukemia (AML). Although these patients have relatively favorable prognoses, substantial numbers of them would relapse after conventional therapy. Here, we explored whether reinforcing the endogenous differentiation potential of t(8;21) AML cells would diminish the associated malignancy. In doing so, we noticed an expansion of immature erythroid blasts featured in both AML1-ETO9a (AE9a) and AE plus c-KIT (N822K) (AK) murine leukemic models. Interestingly, in the AE9a murine model, a spontaneous step-wise erythroid differentiation path, as characterized by the differential expression of CD43/c-Kit and the upregulation of several key erythroid transcription factors (TFs), accompanied the decline or loss of leukemia-initiating potential. Notably, overexpression of one of the key erythroid TFs, Ldb1, potently disrupted the repopulation of AE9a leukemic cells in vivo, suggesting a new promising intervention strategy of t(8;21) AML through enforcing their erythroid differentiation.
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Affiliation(s)
- Meng-Xi Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Yan
- Department of Hematology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun-Mei Zhao
- Department of Hematology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jiang Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Life Sciences and Biotechnology, Shanghai Jiao-Tong University, Shanghai, China.,Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shan-He Yu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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12
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Asgarian Z, Oliveira MG, Stryjewska A, Maragkos I, Rubin AN, Magno L, Pachnis V, Ghorbani M, Hiebert SW, Denaxa M, Kessaris N. MTG8 interacts with LHX6 to specify cortical interneuron subtype identity. Nat Commun 2022; 13:5217. [PMID: 36064547 PMCID: PMC9445035 DOI: 10.1038/s41467-022-32898-6] [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: 01/19/2022] [Accepted: 08/23/2022] [Indexed: 11/09/2022] Open
Abstract
Cortical interneurons originating in the embryonic medial ganglionic eminence (MGE) diverge into a range of different subtypes found in the adult mouse cerebral cortex. The mechanisms underlying this divergence and the timing when subtype identity is set up remain unclear. We identify the highly conserved transcriptional co-factor MTG8 as being pivotal in the development of a large subset of MGE cortical interneurons that co-expresses Somatostatin (SST) and Neuropeptide Y (NPY). MTG8 interacts with the pan-MGE transcription factor LHX6 and together the two factors are sufficient to promote expression of critical cortical interneuron subtype identity genes. The SST-NPY cortical interneuron fate is initiated early, well before interneurons migrate into the cortex, demonstrating an early onset specification program. Our findings suggest that transcriptional co-factors and modifiers of generic lineage specification programs may hold the key to the emergence of cortical interneuron heterogeneity from the embryonic telencephalic germinal zones. There is a large diversity of inhibitory interneurons in the mammalian cerebral cortex. How this emerges during embryogenesis remains unclear. Here, the authors identify MTG8 as a co-factor of LHX6 and a new regulator of cortical interneuron development.
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Affiliation(s)
- Zeinab Asgarian
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK
| | - Marcio Guiomar Oliveira
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK
| | - Agata Stryjewska
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK
| | - Ioannis Maragkos
- Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Anna Noren Rubin
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK
| | - Lorenza Magno
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK
| | | | - Mohammadmersad Ghorbani
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.,Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Scott Wayne Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Myrto Denaxa
- Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Nicoletta Kessaris
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK.
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13
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Liu G, Wang L, Wess J, Dean A. Enhancer looping protein LDB1 regulates hepatocyte gene expression by cooperating with liver transcription factors. Nucleic Acids Res 2022; 50:9195-9211. [PMID: 36018801 PMCID: PMC9458430 DOI: 10.1093/nar/gkac707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/22/2022] [Indexed: 12/24/2022] Open
Abstract
Enhancers establish proximity with distant target genes to regulate temporospatial gene expression and specify cell identity. Lim domain binding protein 1 (LDB1) is a conserved and widely expressed protein that functions as an enhancer looping factor. Previous studies in erythroid cells and neuronal cells showed that LDB1 forms protein complexes with different transcription factors to regulate cell-specific gene expression. Here, we show that LDB1 regulates expression of liver genes by occupying enhancer elements and cooperating with hepatic transcription factors HNF4A, FOXA1, TCF7 and GATA4. Using the glucose transporter SLC2A2 gene, encoding GLUT2, as an example, we find that LDB1 regulates gene expression by mediating enhancer-promoter interactions. In vivo, we find that LDB1 deficiency in primary mouse hepatocytes dysregulates metabolic gene expression and changes the enhancer landscape. Conditional deletion of LDB1 in adult mouse liver induces glucose intolerance. However, Ldb1 knockout hepatocytes show improved liver pathology under high-fat diet conditions associated with increased expression of genes related to liver fatty acid metabolic processes. Thus, LDB1 is linked to liver metabolic functions under normal and obesogenic conditions.
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Affiliation(s)
- Guoyou Liu
- Correspondence may also be addressed to Guoyou Liu. Tel: +1 301 435 9396;
| | - Lei Wang
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jürgen Wess
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann Dean
- To whom correspondence should be addressed. Tel: +1 301 496 6068;
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14
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Gregoricchio S, Polit L, Esposito M, Berthelet J, Delestré L, Evanno E, Diop M, Gallais I, Aleth H, Poplineau M, Zwart W, Rosenbauer F, Rodrigues-Lima F, Duprez E, Boeva V, Guillouf C. HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia. Nucleic Acids Res 2022; 50:7938-7958. [PMID: 35871293 PMCID: PMC9371914 DOI: 10.1093/nar/gkac613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/18/2022] [Accepted: 06/30/2022] [Indexed: 11/23/2022] Open
Abstract
Although originally described as transcriptional activator, SPI1/PU.1, a major player in haematopoiesis whose alterations are associated with haematological malignancies, has the ability to repress transcription. Here, we investigated the mechanisms underlying gene repression in the erythroid lineage, in which SPI1 exerts an oncogenic function by blocking differentiation. We show that SPI1 represses genes by binding active enhancers that are located in intergenic or gene body regions. HDAC1 acts as a cooperative mediator of SPI1-induced transcriptional repression by deacetylating SPI1-bound enhancers in a subset of genes, including those involved in erythroid differentiation. Enhancer deacetylation impacts on promoter acetylation, chromatin accessibility and RNA pol II occupancy. In addition to the activities of HDAC1, polycomb repressive complex 2 (PRC2) reinforces gene repression by depositing H3K27me3 at promoter sequences when SPI1 is located at enhancer sequences. Moreover, our study identified a synergistic relationship between PRC2 and HDAC1 complexes in mediating the transcriptional repression activity of SPI1, ultimately inducing synergistic adverse effects on leukaemic cell survival. Our results highlight the importance of the mechanism underlying transcriptional repression in leukemic cells, involving complex functional connections between SPI1 and the epigenetic regulators PRC2 and HDAC1.
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Affiliation(s)
- Sebastian Gregoricchio
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute , Amsterdam , The Netherlands
| | - Lélia Polit
- CNRS UMR8104, Inserm U1016, Université Paris Cité, Cochin Institute , F-75014 Paris , France
| | - Michela Esposito
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | | | - Laure Delestré
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | - Emilie Evanno
- Curie Institute , Inserm U830, F- 75005 Paris, France
| | - M’Boyba Diop
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | | | - Hanna Aleth
- Institute of Molecular Tumor Biology, University of Münster , Münster, Germany
| | - Mathilde Poplineau
- CNRS UMR7258, Inserm U1068, Université Aix Marseille, Paoli-Calmettes Institute , CRCM, F-13009 Marseille , France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute , Amsterdam , The Netherlands
| | - Frank Rosenbauer
- Institute of Molecular Tumor Biology, University of Münster , Münster, Germany
| | | | - Estelle Duprez
- CNRS UMR7258, Inserm U1068, Université Aix Marseille, Paoli-Calmettes Institute , CRCM, F-13009 Marseille , France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | - Valentina Boeva
- CNRS UMR8104, Inserm U1016, Université Paris Cité, Cochin Institute , F-75014 Paris , France
- Department of Computer Science and Department of Biology , ETH Zurich, 8092 Zurich , Switzerland
| | - Christel Guillouf
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
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15
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Andrieu-Soler C, Soler E. Erythroid Cell Research: 3D Chromatin, Transcription Factors and Beyond. Int J Mol Sci 2022; 23:ijms23116149. [PMID: 35682828 PMCID: PMC9181152 DOI: 10.3390/ijms23116149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 02/04/2023] Open
Abstract
Studies of the regulatory networks and signals controlling erythropoiesis have brought important insights in several research fields of biology and have been a rich source of discoveries with far-reaching implications beyond erythroid cells biology. The aim of this review is to highlight key recent discoveries and show how studies of erythroid cells bring forward novel concepts and refine current models related to genome and 3D chromatin organization, signaling and disease, with broad interest in life sciences.
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Affiliation(s)
| | - Eric Soler
- IGMM, Université Montpellier, CNRS, 34093 Montpellier, France;
- Laboratory of Excellence GR-Ex, Université de Paris, 75015 Paris, France
- Correspondence:
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16
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Ben-David Y, Gajendran B, Sample KM, Zacksenhaus E. Current insights into the role of Fli-1 in hematopoiesis and malignant transformation. Cell Mol Life Sci 2022; 79:163. [PMID: 35412146 PMCID: PMC11072361 DOI: 10.1007/s00018-022-04160-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/05/2022] [Accepted: 01/19/2022] [Indexed: 11/27/2022]
Abstract
Fli-1, a member of the ETS family of transcription factors, was discovered in 1991 through retroviral insertional mutagenesis as a driver of mouse erythroleukemias. In the past 30 years, nearly 2000 papers have defined its biology and impact on normal development and cancer. In the hematopoietic system, Fli-1 controls self-renewal of stem cells and their differentiation into diverse mature blood cells. Fli-1 also controls endothelial survival and vasculogenesis, and high and low levels of Fli-1 are implicated in the auto-immune diseases systemic lupus erythematosus and systemic sclerosis, respectively. In addition, aberrant Fli-1 expression is observed in, and is essential for, the growth of multiple hematological malignancies and solid cancers. Here, we review the historical context and latest research on Fli-1, focusing on its role in hematopoiesis, immune response, and malignant transformation. The importance of identifying Fli-1 modulators (both agonists and antagonists) and their potential clinical applications is discussed.
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Affiliation(s)
- Yaacov Ben-David
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Province Science City, High Tech Zone, Baiyun District, Guiyang, 550014, Guizhou Province, People's Republic of China.
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Babu Gajendran
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Province Science City, High Tech Zone, Baiyun District, Guiyang, 550014, Guizhou Province, People's Republic of China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Klarke M Sample
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Province Science City, High Tech Zone, Baiyun District, Guiyang, 550014, Guizhou Province, People's Republic of China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Eldad Zacksenhaus
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Research Institute, Max Bell Research Centre, University Health Network, 101 College Street, Toronto, ON, Canada
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17
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Application of Weighted Gene Coexpression Network Analysis to Identify Key Modules and Hub Genes in Systemic Juvenile Idiopathic Arthritis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9957569. [PMID: 34435051 PMCID: PMC8382540 DOI: 10.1155/2021/9957569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/22/2021] [Indexed: 12/14/2022]
Abstract
Systemic juvenile idiopathic arthritis (sJIA) is a severe autoinflammatory disorder with a still not clearly defined molecular mechanism. To better understand the disease, we used scattered datasets from public domains and performed a weighted gene coexpression network analysis (WGCNA) to identify key modules and hub genes underlying sJIA pathogenesis. Two gene expression datasets, GSE7753 and GSE13501, were used to construct the WGCNA. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were applied to the genes and hub genes in the sJIA modules. Cytoscape was used to screen and visualize the hub genes. We further compared the hub genes with the genome-wide association study (GWAS) genes and used a consensus WGCNA to verify that our conclusions were conservative and reproducible across multiple independent datasets. A total of 5,414 genes were obtained for WGCNA, from which highly correlated genes were divided into 17 modules. The red module demonstrated the highest correlation with the sJIA module (r = 0.8, p = 3e−29), whereas the green-yellow module was found to be closely related to the non-sJIA module (r = 0.62, p = 1e−14). Functional enrichment analysis demonstrated that the red module was mostly enriched in the activation of immune responses, infection, nucleosomes, and erythrocytes, and the green-yellow module was mostly enriched in immune responses and inflammation. Additionally, the hub genes in the red module were highly enriched in erythrocyte differentiation, including ALAS2, AHSP, TRIM10, TRIM58, and KLF1. The hub genes from the green-yellow module were mainly associated with immune responses, as exemplified by the genes KLRB1, KLRF1, CD160, and KIRs. We identified sJIA-related modules and several hub genes that might be associated with the development of sJIA. Particularly, the modules may help understand the mechanisms of sJIA, and the hub genes may become biomarkers and therapeutic targets of sJIA in the future.
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18
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Mechanisms of Binding Specificity among bHLH Transcription Factors. Int J Mol Sci 2021; 22:ijms22179150. [PMID: 34502060 PMCID: PMC8431614 DOI: 10.3390/ijms22179150] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 12/25/2022] Open
Abstract
The transcriptome of every cell is orchestrated by the complex network of interaction between transcription factors (TFs) and their binding sites on DNA. Disruption of this network can result in many forms of organism malfunction but also can be the substrate of positive natural selection. However, understanding the specific determinants of each of these individual TF-DNA interactions is a challenging task as it requires integrating the multiple possible mechanisms by which a given TF ends up interacting with a specific genomic region. These mechanisms include DNA motif preferences, which can be determined by nucleotide sequence but also by DNA’s shape; post-translational modifications of the TF, such as phosphorylation; and dimerization partners and co-factors, which can mediate multiple forms of direct or indirect cooperative binding. Binding can also be affected by epigenetic modifications of putative target regions, including DNA methylation and nucleosome occupancy. In this review, we describe how all these mechanisms have a role and crosstalk in one specific family of TFs, the basic helix-loop-helix (bHLH), with a very conserved DNA binding domain and a similar DNA preferred motif, the E-box. Here, we compile and discuss a rich catalog of strategies used by bHLH to acquire TF-specific genome-wide landscapes of binding sites.
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19
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A Positive Regulatory Feedback Loop between EKLF/KLF1 and TAL1/SCL Sustaining the Erythropoiesis. Int J Mol Sci 2021; 22:ijms22158024. [PMID: 34360789 PMCID: PMC8347936 DOI: 10.3390/ijms22158024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 11/25/2022] Open
Abstract
The erythroid Krüppel-like factor EKLF/KLF1 is a hematopoietic transcription factor binding to the CACCC DNA motif and participating in the regulation of erythroid differentiation. With combined use of microarray-based gene expression profiling and the promoter-based ChIP-chip assay of E14.5 fetal liver cells from wild type (WT) and EKLF-knockout (Eklf−/−) mouse embryos, we identified the pathways and direct target genes activated or repressed by EKLF. This genome-wide study together with the molecular/cellular analysis of the mouse erythroleukemic cells (MEL) indicate that among the downstream direct target genes of EKLF is Tal1/Scl. Tal1/Scl encodes another DNA-binding hematopoietic transcription factor TAL1/SCL, known to be an Eklf activator and essential for definitive erythroid differentiation. Further identification of the authentic Tal gene promoter in combination with the in vivo genomic footprinting approach and DNA reporter assay demonstrate that EKLF activates the Tal gene through binding to a specific CACCC motif located in its promoter. These data establish the existence of a previously unknow positive regulatory feedback loop between two DNA-binding hematopoietic transcription factors, which sustains mammalian erythropoiesis.
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20
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A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker. Nat Commun 2021; 12:3806. [PMID: 34155213 PMCID: PMC8217497 DOI: 10.1038/s41467-021-23980-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/19/2021] [Indexed: 02/08/2023] Open
Abstract
Many single nucleotide variants (SNVs) associated with human traits and genetic diseases are thought to alter the activity of existing regulatory elements. Some SNVs may also create entirely new regulatory elements which change gene expression, but the mechanism by which they do so is largely unknown. Here we show that a single base change in an otherwise unremarkable region of the human α-globin cluster creates an entirely new promoter and an associated unidirectional transcript. This SNV downregulates α-globin expression causing α-thalassaemia. Of note, the new promoter lying between the α-globin genes and their associated super-enhancer disrupts their interaction in an orientation-dependent manner. Together these observations show how both the order and orientation of the fundamental elements of the genome determine patterns of gene expression and support the concept that active genes may act to disrupt enhancer-promoter interactions in mammals as in Drosophila. Finally, these findings should prompt others to fully evaluate SNVs lying outside of known regulatory elements as causing changes in gene expression by creating new regulatory elements. The role of promoters as potential insulator elements has been largely unexplored in mammals. Here the authors show that a single nucleotide variant in the α-globin locus forms a new promoter and acts as an orientation-dependent enhancer-blocking insulator element.
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21
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Boontanrart MY, Schröder MS, Stehli GM, Banović M, Wyman SK, Lew RJ, Bordi M, Gowen BG, DeWitt MA, Corn JE. ATF4 Regulates MYB to Increase γ-Globin in Response to Loss of β-Globin. Cell Rep 2021; 32:107993. [PMID: 32755585 DOI: 10.1016/j.celrep.2020.107993] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/20/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
β-Hemoglobinopathies can trigger rapid production of red blood cells in a process known as stress erythropoiesis. Cellular stress prompts differentiating erythroid precursors to express high levels of fetal γ-globin. However, the mechanisms underlying γ-globin production during cellular stress are still poorly defined. Here, we use CRISPR-Cas genome editing to model the stress caused by reduced levels of adult β-globin. We find that decreased β-globin is sufficient to induce robust re-expression of γ-globin, and RNA sequencing (RNA-seq) of differentiating isogenic erythroid precursors implicates ATF4 as a causal regulator of this response. ATF4 binds within the HBS1L-MYB intergenic enhancer and regulates expression of MYB, a known γ-globin regulator. Overall, the reduction of ATF4 upon β-globin knockout decreases the levels of MYB and BCL11A. Identification of ATF4 as a key regulator of globin compensation adds mechanistic insight to the poorly understood phenomenon of stress-induced globin compensation and could inform strategies to treat hemoglobinopathies.
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Affiliation(s)
- Mandy Y Boontanrart
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | | | - Marija Banović
- Department of Biology, ETH Zurich, Zurich 8092, Switzerland
| | - Stacia K Wyman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel J Lew
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Matteo Bordi
- Department of Biology, ETH Zurich, Zurich 8092, Switzerland
| | - Benjamin G Gowen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mark A DeWitt
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zurich, Zurich 8092, Switzerland; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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22
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Jakobczyk H, Debaize L, Soubise B, Avner S, Rouger-Gaudichon J, Commet S, Jiang Y, Sérandour AA, Rio AG, Carroll JS, Wichmann C, Lie-A-Ling M, Lacaud G, Corcos L, Salbert G, Galibert MD, Gandemer V, Troadec MB. Reduction of RUNX1 transcription factor activity by a CBFA2T3-mimicking peptide: application to B cell precursor acute lymphoblastic leukemia. J Hematol Oncol 2021; 14:47. [PMID: 33743795 PMCID: PMC7981807 DOI: 10.1186/s13045-021-01051-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/24/2021] [Indexed: 12/27/2022] Open
Abstract
Background B Cell Precursor Acute Lymphoblastic Leukemia (BCP-ALL) is the most common pediatric cancer. Identifying key players involved in proliferation of BCP-ALL cells is crucial to propose new therapeutic targets. Runt Related Transcription Factor 1 (RUNX1) and Core-Binding Factor Runt Domain Alpha Subunit 2 Translocated To 3 (CBFA2T3, ETO2, MTG16) are master regulators of hematopoiesis and are implicated in leukemia. Methods We worked with BCP-ALL mononuclear bone marrow patients’ cells and BCP-ALL cell lines, and performed Chromatin Immunoprecipitations followed by Sequencing (ChIP-Seq), co-immunoprecipitations (co-IP), proximity ligation assays (PLA), luciferase reporter assays and mouse xenograft models. Results We demonstrated that CBFA2T3 transcript levels correlate with RUNX1 expression in the pediatric t(12;21) ETV6-RUNX1 BCP-ALL. By ChIP-Seq in BCP-ALL patients’ cells and cell lines, we found that RUNX1 is recruited on its promoter and on an enhancer of CBFA2T3 located − 2 kb upstream CBFA2T3 promoter and that, subsequently, the transcription factor RUNX1 drives both RUNX1 and CBFA2T3 expression. We demonstrated that, mechanistically, RUNX1 and CBFA2T3 can be part of the same complex allowing CBFA2T3 to strongly potentiate the activity of the transcription factor RUNX1. Finally, we characterized a CBFA2T3-mimicking peptide that inhibits the interaction between RUNX1 and CBFA2T3, abrogating the activity of this transcription complex and reducing BCP-ALL lymphoblast proliferation. Conclusions Altogether, our findings reveal a novel and important activation loop between the transcription regulator CBFA2T3 and the transcription factor RUNX1 that promotes BCP-ALL proliferation, supporting the development of an innovative therapeutic approach based on the NHR2 subdomain of CBFA2T3 protein. Supplementary Information The online version contains supplementary material available at 10.1186/s13045-021-01051-z.
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Affiliation(s)
- Hélène Jakobczyk
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, 35000, Rennes, France
| | - Lydie Debaize
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, 35000, Rennes, France
| | - Benoit Soubise
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200, Brest, France
| | - Stéphane Avner
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, 35000, Rennes, France
| | - Jérémie Rouger-Gaudichon
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, 35000, Rennes, France.,Département d'onco-hematologie pediatrique, Centre Hospitalier Universitaire de Caen Normandie, Caen, France
| | - Séverine Commet
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200, Brest, France.,CHRU Brest, Service de génétique, laboratoire de génétique chromosomique, 22 avenue Camille Desmoulins, 29238, Brest Cedex 3, France
| | - Yan Jiang
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200, Brest, France.,Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | | | - Anne-Gaëlle Rio
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, 35000, Rennes, France
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Christian Wichmann
- Department of Transfusion Medicine, Cell Therapeutics and Haemostasis, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Michael Lie-A-Ling
- Cancer Research UK Manchester Institute, University of Manchester, Aderley Park, Macclesfield, SK10 4TG, UK
| | - Georges Lacaud
- Cancer Research UK Manchester Institute, University of Manchester, Aderley Park, Macclesfield, SK10 4TG, UK
| | - Laurent Corcos
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200, Brest, France
| | - Gilles Salbert
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, 35000, Rennes, France
| | - Marie-Dominique Galibert
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, 35000, Rennes, France.,Service de Génétique et Génomique Moléculaire, Centre Hospitalier Universitaire de Rennes (CHU-Rennes), 35033, Rennes, France
| | - Virginie Gandemer
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, 35000, Rennes, France.,Department of Pediatric Hemato-Oncology, Centre Hospitalier Universitaire de Rennes (CHU-Rennes), 35203, Rennes, France
| | - Marie-Bérengère Troadec
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, 35000, Rennes, France. .,Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200, Brest, France. .,CHRU Brest, Service de génétique, laboratoire de génétique chromosomique, 22 avenue Camille Desmoulins, 29238, Brest Cedex 3, France.
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23
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Giraud G, Kolovos P, Boltsis I, van Staalduinen J, Guyot B, Weiss-Gayet M, IJcken WV, Morlé F, Grosveld F. Interplay between FLI-1 and the LDB1 complex in murine erythroleukemia cells and during megakaryopoiesis. iScience 2021; 24:102210. [PMID: 33733070 PMCID: PMC7940982 DOI: 10.1016/j.isci.2021.102210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/22/2020] [Accepted: 02/17/2021] [Indexed: 11/29/2022] Open
Abstract
Transcription factors are key players in a broad range of cellular processes such as cell-fate decision. Understanding how they act to control these processes is of critical importance for therapy purposes. FLI-1 controls several hematopoietic lineage differentiation including megakaryopoiesis and erythropoiesis. Its aberrant expression is often observed in cancer and is associated with poor prognosis. We showed that FLI-1 interacts with the LDB1 complex, which also plays critical roles in erythropoiesis and megakaryopoiesis. In this study, we aimed to unravel how FLI-1 and the LDB1 complex act together in murine erythroleukemia cells and in megakaryocyte. Combining omics techniques, we show that FLI-1 enables the recruitment of the LDB1 complex to regulatory sequences of megakaryocytic genes and to enhancers. We show as well for the first time that FLI-1 is able to modulate the 3D chromatin organization by promoting chromatin looping between enhancers and promoters most likely through the LDB1 complex. FLI-1 is important for the recruitment of the LDB1 complex FLI-1 is important for chromatin looping FLI-1 and the LDB1 complex co-regulate megakaryopoiesis
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Affiliation(s)
- Guillaume Giraud
- Department of Cell Biology, Erasmus Medical Centre, 3015CN Rotterdam, the Netherlands
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | - Ilias Boltsis
- Department of Cell Biology, Erasmus Medical Centre, 3015CN Rotterdam, the Netherlands
| | - Jente van Staalduinen
- Department of Cell Biology, Erasmus Medical Centre, 3015CN Rotterdam, the Netherlands
| | - Boris Guyot
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Department of Immunity, Virus and Microenvironment, Lyon, France
| | - Michele Weiss-Gayet
- Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217 - Université de Lyon - Université Claude Bernard Lyon 1, Lyon, France
| | - Wilfred van IJcken
- Biomics Center, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | - François Morlé
- Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217 - Université de Lyon - Université Claude Bernard Lyon 1, Lyon, France
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, 3015CN Rotterdam, the Netherlands
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24
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Ramalingam V, Natarajan M, Johnston J, Zeitlinger J. TATA and paused promoters active in differentiated tissues have distinct expression characteristics. Mol Syst Biol 2021; 17:e9866. [PMID: 33543829 PMCID: PMC7863008 DOI: 10.15252/msb.20209866] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/22/2020] [Accepted: 01/07/2021] [Indexed: 12/18/2022] Open
Abstract
Core promoter types differ in the extent to which RNA polymerase II (Pol II) pauses after initiation, but how this affects their tissue-specific gene expression characteristics is not well understood. While promoters with Pol II pausing elements are active throughout development, TATA promoters are highly active in differentiated tissues. We therefore used a genomics approach on late-stage Drosophila embryos to analyze the properties of promoter types. Using tissue-specific Pol II ChIP-seq, we found that paused promoters have high levels of paused Pol II throughout the embryo, even in tissues where the gene is not expressed, while TATA promoters only show Pol II occupancy when the gene is active. The promoter types are associated with different chromatin accessibility in ATAC-seq data and have different expression characteristics in single-cell RNA-seq data. The two promoter types may therefore be optimized for different properties: paused promoters show more consistent expression when active, while TATA promoters have lower background expression when inactive. We propose that tissue-specific genes have evolved to use two different strategies for their differential expression across tissues.
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Affiliation(s)
- Vivekanandan Ramalingam
- Stowers Institute for Medical ResearchKansas CityMOUSA
- Department of Pathology and Laboratory MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
- Present address:
Department of GeneticsStanford UniversityStanfordCAUSA
| | - Malini Natarajan
- Stowers Institute for Medical ResearchKansas CityMOUSA
- Present address:
Department of Molecular Biology, Cell Biology and BiochemistryBrown UniversityProvidenceRIUSA
| | - Jeff Johnston
- Stowers Institute for Medical ResearchKansas CityMOUSA
- Present address:
Center for Pediatric Genomic MedicineChildren's MercyKansas CityMOUSA
| | - Julia Zeitlinger
- Stowers Institute for Medical ResearchKansas CityMOUSA
- Department of Pathology and Laboratory MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
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25
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When basic science reaches into rational therapeutic design: from historical to novel leads for the treatment of β-globinopathies. Curr Opin Hematol 2021; 27:141-148. [PMID: 32167946 DOI: 10.1097/moh.0000000000000577] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW β-hemoglobinopathies, such as β-Thalassemias (β-Thal) and sickle cell disease (SCD) are among the most common inherited genetic disorders in humans worldwide. These disorders are characterized by a quantitative (β-Thal) or qualitative (SCD) defects in adult hemoglobin production, leading to anemia, ineffective erythropoiesis and severe secondary complications. Reactivation of the fetal globin genes (γ-globin), making-up fetal hemoglobin (HbF), which are normally silenced in adults, represents a major strategy to ameliorate anemia and disease severity. RECENT FINDINGS Following the identification of the first 'switching factors' for the reactivation of fetal globin gene expression more than 10 years ago, a multitude of novel leads have recently been uncovered. SUMMARY Recent findings provided invaluable functional insights into the genetic and molecular networks controlling globin genes expression, revealing that complex repression systems evolved in erythroid cells to maintain HbF silencing in adults. This review summarizes these unique and exciting discoveries of the regulatory factors controlling the globin switch. New insights and novel leads for therapeutic strategies based on the pharmacological induction of HbF are discussed. This represents a major breakthrough for rational drug design in the treatment of β-Thal and SCD.
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26
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Meyer A, Herkt S, Kunze-Schumacher H, Kohrs N, Ringleb J, Schneider L, Kuvardina ON, Oellerich T, Häupl B, Krueger A, Seifried E, Bonig H, Lausen J. The transcription factor TAL1 and miR-17-92 create a regulatory loop in hematopoiesis. Sci Rep 2020; 10:21438. [PMID: 33293632 PMCID: PMC7722897 DOI: 10.1038/s41598-020-78629-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
A network of gene regulatory factors such as transcription factors and microRNAs establish and maintain gene expression patterns during hematopoiesis. In this network, transcription factors regulate each other and are involved in regulatory loops with microRNAs. The microRNA cluster miR-17-92 is located within the MIR17HG gene and encodes six mature microRNAs. It is important for hematopoietic differentiation and plays a central role in malignant disease. However, the transcription factors downstream of miR-17-92 are largely elusive and the transcriptional regulation of miR-17-92 is not fully understood. Here we show that miR-17-92 forms a regulatory loop with the transcription factor TAL1. The miR-17-92 cluster inhibits expression of TAL1 and indirectly leads to decreased stability of the TAL1 transcriptional complex. We found that TAL1 and its heterodimerization partner E47 regulate miR-17-92 transcriptionally. Furthermore, miR-17-92 negatively influences erythroid differentiation, a process that depends on gene activation by the TAL1 complex. Our data give example of how transcription factor activity is fine-tuned during normal hematopoiesis. We postulate that disturbance of the regulatory loop between TAL1 and the miR-17-92 cluster could be an important step in cancer development and progression.
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Affiliation(s)
- Annekarin Meyer
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany
| | - Stefanie Herkt
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany
| | - Heike Kunze-Schumacher
- Institute for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Nicole Kohrs
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Paul-Ehrlich-Strasse 42-44, 60596, Frankfurt am Main, Germany
| | - Julia Ringleb
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Paul-Ehrlich-Strasse 42-44, 60596, Frankfurt am Main, Germany
| | - Lucas Schneider
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany
| | - Olga N Kuvardina
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Frankfurt Cancer Institute, Goethe University, 60596, Frankfurt, Germany
| | - Björn Häupl
- Department of Medicine II, Hematology/Oncology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Frankfurt Cancer Institute, Goethe University, 60596, Frankfurt, Germany
| | - Andreas Krueger
- Institute for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Erhard Seifried
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany.,Department of Medicine, Division of Hematology, University of Washington, Seattle, WA, 98195, USA
| | - Joern Lausen
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany. .,Department of Eukaryotic Genetics, Institute of Industrial Genetics, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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27
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Scheenstra MR, Martínez-Botía P, Acebes-Huerta A, Brouwer RWW, Caballero-Sánchez N, Gillemans N, De Bleser P, Nota B, De Cuyper IM, Salunkhe V, Woltman AM, van de Laar L, Rijkers E, Demmers JAA, van IJcken WFJ, Philipsen S, van den Berg TK, Kuijpers TW, Gutiérrez L. Comparison of the PU.1 transcriptional regulome and interactome in human and mouse inflammatory dendritic cells. J Leukoc Biol 2020; 110:735-751. [PMID: 33289106 DOI: 10.1002/jlb.6a1219-711rrr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022] Open
Abstract
Dendritic cells (DCs) are key immune modulators and are able to mount immune responses or tolerance. DC differentiation and activation imply a plethora of molecular and cellular responses, including transcriptional changes. PU.1 is a highly expressed transcription factor in DCs and coordinates relevant aspects of DC biology. Due to their role as immune regulators, DCs pose as a promising immunotherapy tool. However, some of their functional features, such as survival, activation, or migration, are compromised due to the limitations to simulate in vitro the physiologic DC differentiation process. A better knowledge of transcriptional programs would allow the identification of potential targets for manipulation with the aim of obtaining "qualified" DCs for immunotherapy purposes. Most of the current knowledge regarding DC biology derives from studies using mouse models, which not always find a parallel in human. In the present study, we dissect the PU.1 transcriptional regulome and interactome in mouse and human DCs, in the steady state or LPS activated. The PU.1 transcriptional regulome was identified by performing PU.1 chromatin immunoprecipitation followed by high-throughput sequencing and pairing these data with RNAsequencing data. The PU.1 interactome was identified by performing PU.1 immunoprecipitation followed by mass spectrometry analysis. Our results portray PU.1 as a pivotal factor that plays an important role in the regulation of genes required for proper DC activation and function, and assures the repression of nonlineage genes. The interspecies differences between human and mouse DCs are surprisingly substantial, highlighting the need to study the biology of human DCs.
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Affiliation(s)
- Maaike R Scheenstra
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | | | - Andrea Acebes-Huerta
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Nynke Gillemans
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Pieter De Bleser
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Data Mining and Modeling for Biomedicine, Ghent, Belgium
| | - Benjamin Nota
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Iris M De Cuyper
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Vishal Salunkhe
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Andrea M Woltman
- Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, The Netherlands
- Current Address: Institute of Medical Education Research Rotterdam, Erasmus MC, Rotterdam, The Netherlands
| | - Lianne van de Laar
- Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Wilfred F J van IJcken
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Timo K van den Berg
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Taco W Kuijpers
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
- Laboratory of Immunotherapy, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Center, Vrije University, Amsterdam, The Netherlands
| | - Laura Gutiérrez
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- University of Oviedo, Oviedo, Spain
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28
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Guo X, Plank-Bazinet J, Krivega I, Dale RK, Dean A. Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin organization. Nucleic Acids Res 2020; 48:10226-10240. [PMID: 32960220 DOI: 10.1093/nar/gkaa736] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/19/2020] [Accepted: 09/18/2020] [Indexed: 11/14/2022] Open
Abstract
The underlying mechanism of transcriptional co-repressor ETO2 during early erythropoiesis and hemoglobin switching is unclear. We find that absence of ETO2 in mice interferes with down-regulation of PU.1 and GATA2 in the fetal liver, impeding a key step required for commitment to erythroid maturation. In human β-globin transgenic Eto2 null mice and in human CD34+ erythroid progenitor cells with reduced ETO2, loss of ETO2 results in ineffective silencing of embryonic/fetal globin gene expression, impeding hemoglobin switching during erythroid differentiation. ETO2 occupancy genome-wide occurs virtually exclusively at LDB1-complex binding sites in enhancers and ETO2 loss leads to increased enhancer activity and expression of target genes. ETO2 recruits the NuRD nucleosome remodeling and deacetylation complex to regulate histone acetylation and nucleosome occupancy in the β-globin locus control region and γ-globin gene. Loss of ETO2 elevates LDB1, MED1 and Pol II in the locus and facilitates fetal γ-globin/LCR looping and γ-globin transcription. Absence of the ETO2 hydrophobic heptad repeat region impairs ETO2-NuRD interaction and function in antagonizing γ-globin/LCR looping. Our results reveal a pivotal role for ETO2 in erythropoiesis and globin gene switching through its repressive role in the LDB1 complex, affecting the transcription factor and epigenetic environment and ultimately restructuring chromatin organization.
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Affiliation(s)
- Xiang Guo
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
| | - Jennifer Plank-Bazinet
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
| | - Ivan Krivega
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
| | - Ryan K Dale
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
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Fagnan A, Bagger FO, Piqué-Borràs MR, Ignacimouttou C, Caulier A, Lopez CK, Robert E, Uzan B, Gelsi-Boyer V, Aid Z, Thirant C, Moll U, Tauchmann S, Kurtovic-Kozaric A, Maciejewski J, Dierks C, Spinelli O, Salmoiraghi S, Pabst T, Shimoda K, Deleuze V, Lapillonne H, Sweeney C, De Mas V, Leite B, Kadri Z, Malinge S, de Botton S, Micol JB, Kile B, Carmichael CL, Iacobucci I, Mullighan CG, Carroll M, Valent P, Bernard OA, Delabesse E, Vyas P, Birnbaum D, Anguita E, Garçon L, Soler E, Schwaller J, Mercher T. Human erythroleukemia genetics and transcriptomes identify master transcription factors as functional disease drivers. Blood 2020; 136:698-714. [PMID: 32350520 PMCID: PMC8215330 DOI: 10.1182/blood.2019003062] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 03/25/2020] [Indexed: 12/11/2022] Open
Abstract
Acute erythroleukemia (AEL or acute myeloid leukemia [AML]-M6) is a rare but aggressive hematologic malignancy. Previous studies showed that AEL leukemic cells often carry complex karyotypes and mutations in known AML-associated oncogenes. To better define the underlying molecular mechanisms driving the erythroid phenotype, we studied a series of 33 AEL samples representing 3 genetic AEL subgroups including TP53-mutated, epigenetic regulator-mutated (eg, DNMT3A, TET2, or IDH2), and undefined cases with low mutational burden. We established an erythroid vs myeloid transcriptome-based space in which, independently of the molecular subgroup, the majority of the AEL samples exhibited a unique mapping different from both non-M6 AML and myelodysplastic syndrome samples. Notably, >25% of AEL patients, including in the genetically undefined subgroup, showed aberrant expression of key transcriptional regulators, including SKI, ERG, and ETO2. Ectopic expression of these factors in murine erythroid progenitors blocked in vitro erythroid differentiation and led to immortalization associated with decreased chromatin accessibility at GATA1-binding sites and functional interference with GATA1 activity. In vivo models showed development of lethal erythroid, mixed erythroid/myeloid, or other malignancies depending on the cell population in which AEL-associated alterations were expressed. Collectively, our data indicate that AEL is a molecularly heterogeneous disease with an erythroid identity that results in part from the aberrant activity of key erythroid transcription factors in hematopoietic stem or progenitor cells.
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Affiliation(s)
- Alexandre Fagnan
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Frederik Otzen Bagger
- University Children's Hospital Beider Basel (UKBB), Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
- Swiss Institute of Bioinformatics, Basel, Basel, Switzerland
| | - Maria-Riera Piqué-Borràs
- University Children's Hospital Beider Basel (UKBB), Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Cathy Ignacimouttou
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Alexis Caulier
- Equipe d'Accueil (EA) 4666, Hématopoïèse et Immunologie (HEMATIM), Université de Picardie Jules Verne (UPJV), Amiens, France
- Service Hématologie Biologique, Centre Hospitalier Universitaire (CHU) Amiens, Amiens, France
| | - Cécile K Lopez
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Elie Robert
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Benjamin Uzan
- Unité Mixte de Recherche 967 (UMR 967), INSERM-Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA)/Direction de la Recherche Fondamentale (DRF)/Institut de Biologie François Jacob (IBFJ)/Institut de Radiobiologie Cellulaire et Moléculaire (IRCM)/Laboratoire des cellules Souches Hématopoïétiques et des Leucémies (LSHL)-Université Paris-Diderot-Université Paris-Sud, Fontenay-aux-Roses, France
| | - Véronique Gelsi-Boyer
- U1068 and
- UMR7258, Centre de Recherche en Cancérologie de Marseille, Centre National de la Recherche Scientifique (CNRS)/INSERM/Institut Paoli Calmettes/Aix-Marseille Université, Marseille, France
| | - Zakia Aid
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Cécile Thirant
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Ute Moll
- Institute of Molecular Oncology, University Medical Center Göttingen, Göttingen, Germany
- Department of Pathology, Stony Brook University, Stony Brook, NY
| | - Samantha Tauchmann
- University Children's Hospital Beider Basel (UKBB), Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Amina Kurtovic-Kozaric
- Clinical Center of the University of Sarajevo, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Jaroslaw Maciejewski
- Department of Translational Hematology and Oncologic Research, Cleveland Clinic Taussig Cancer Institute, Cleveland, OH
| | - Christine Dierks
- Hämatologie, Onkologie und Stammzelltransplantation, Klinik für Innere Medizin I, Freiburg, Germany
| | - Orietta Spinelli
- UOC Ematologia, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Silvia Salmoiraghi
- UOC Ematologia, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII Hospital, Bergamo, Italy
- FROM Research Foundation, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Thomas Pabst
- Department of Oncology, Inselspital, University Hospital Bern/University of Bern, Bern, Switzerland
| | - Kazuya Shimoda
- Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Virginie Deleuze
- IGMM, University of Montpellier, CNRS, Montpellier, France
- Université de Paris, Laboratory of Excellence GR-Ex, Paris, France
| | - Hélène Lapillonne
- Centre de Recherche Saint Antoine (CRSA)-Unité INSERM, Sorbonne Université/Assistance Publique-Hôpitaux de Paris (AP-HP)/Hôpital Trousseau, Paris, France
| | - Connor Sweeney
- Medical Research Council Molecular Haematology Unit (MRC MHU), Biomedical Research Centre (BRC) Hematology Theme, Oxford Biomedical Research Centre, Oxford Centre for Haematology, Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Véronique De Mas
- Team 16, Hematology Laboratory, Center of Research of Cancerology of Toulouse, U1037, INSERM/Institut Universitaire du Cancer de Toulouse (IUCT) Oncopole, Toulouse, France
| | - Betty Leite
- Genomic Platform, Unité Mixte de Service - Analyse Moléculaire, Modélisation et Imagerie de la maladie Cancéreuse (UMS AMMICA), Gustave Roussy/Université Paris-Saclay, Villejuif, France
| | - Zahra Kadri
- Division of Innovative Therapies, UMR-1184, Immunologie des Maladies Virales, Auto-immunes, Hématologiques et Bactériennes (IMVA-HB) and Infectious Disease Models and Innovative Therapies (IDMIT) Center, CEA/INSERM/Paris-Saclay University, Fontenay-aux-Roses, France
| | - Sébastien Malinge
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, Australia
| | - Stéphane de Botton
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Jean-Baptiste Micol
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
| | - Benjamin Kile
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | | | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania, PA
| | - Peter Valent
- Division of Hematology and Hemostaseology, Department of Internal Medicine I and
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Olivier A Bernard
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Eric Delabesse
- Team 16, Hematology Laboratory, Center of Research of Cancerology of Toulouse, U1037, INSERM/Institut Universitaire du Cancer de Toulouse (IUCT) Oncopole, Toulouse, France
| | - Paresh Vyas
- Medical Research Council Molecular Haematology Unit (MRC MHU), Biomedical Research Centre (BRC) Hematology Theme, Oxford Biomedical Research Centre, Oxford Centre for Haematology, Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Daniel Birnbaum
- U1068 and
- UMR7258, Centre de Recherche en Cancérologie de Marseille, Centre National de la Recherche Scientifique (CNRS)/INSERM/Institut Paoli Calmettes/Aix-Marseille Université, Marseille, France
| | - Eduardo Anguita
- Hematology Department
- Instituto de Medicina de Laboratorio (IML), and
- Instituto de Investigación Sanitaria San Carlos, (IdISSC), Hospital Clínico San Carlos (HCSC), Madrid, Spain; and
- Department of Medicine, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Loïc Garçon
- Equipe d'Accueil (EA) 4666, Hématopoïèse et Immunologie (HEMATIM), Université de Picardie Jules Verne (UPJV), Amiens, France
- Service Hématologie Biologique, Centre Hospitalier Universitaire (CHU) Amiens, Amiens, France
| | - Eric Soler
- IGMM, University of Montpellier, CNRS, Montpellier, France
- Université de Paris, Laboratory of Excellence GR-Ex, Paris, France
| | - Juerg Schwaller
- University Children's Hospital Beider Basel (UKBB), Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Thomas Mercher
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
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LDB1 Enforces Stability on Direct and Indirect Oncoprotein Partners in Leukemia. Mol Cell Biol 2020; 40:MCB.00652-19. [PMID: 32229578 DOI: 10.1128/mcb.00652-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/14/2020] [Indexed: 12/22/2022] Open
Abstract
The LMO2/LDB1 macromolecular complex is critical in hematopoietic stem and progenitor cell specification and in the development of acute leukemia. This complex is comprised of core subunits of LMO2 and LDB1 as well as single-stranded DNA-binding protein (SSBP) cofactors and DNA-binding basic helix-loop-helix (bHLH) and GATA transcription factors. We analyzed the steady-state abundance and kinetic stability of LMO2 and its partners via Halo protein tagging in conjunction with variant proteins deficient in binding their respective direct protein partners. We discovered a hierarchy of protein stabilities (with half-lives in descending order) as follows: LDB1 > SSBP > LMO2 > TAL1. Importantly, LDB1 is a remarkably stable protein that confers enhanced stability upon direct and indirect partners, thereby nucleating the formation of the multisubunit protein complex. The data imply that free subunits are more rapidly degraded than those incorporated within the LMO2/LDB1 complex. Our studies provided significant insights into LMO2/LDB1 macromolecular protein complex assembly and stability, which has implications for understanding its role in blood cell formation and for therapeutically targeting this complex in human leukemias.
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31
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Fong HT, Hagen T, Inoue T. LDB1 and the SWI/SNF complex participate in both transcriptional activation and repression by Caenorhabditis elegans BLIMP1/PRDM1. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194577. [PMID: 32417234 DOI: 10.1016/j.bbagrm.2020.194577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 01/05/2023]
Abstract
Transcription factors of the BLIMP1/PRDM1 family are important regulators of development. BLIMP1/PRDM1 can both activate and repress gene expression, however, the mechanism of activation is not well understood. Therefore, we looked for factors involved in gene activation by C. elegans BLMP-1, the ortholog of BLIMP1/PRDM1. BLMP-1 activates the expression of bed-3, a gene involved in vulval development. By screening nuclear proteins that function in vulval development, we identified two proteins (LDB-1 and HAM-3) required for BLMP-1 dependent bed-3 expression. LDB-1 is the sole C. elegans member of the LIM Binding Protein (LDB) family, whereas HAM-3 is an accessory subunit of the SWI/SNF complex (ortholog of human SMARCD3/BAF60C). A core SWI/SNF subunit SWSN-1 (ortholog of human SMARCC1/BAF155) is also involved. We found that LDB-1 and HAM-3 bind to BLMP-1, suggesting that BLMP-1 recruits LDB-1 and the SWI/SNF complex to activate bed-3 expression. Interestingly, LDB-1 and HAM-3 are involved in both transcriptional activation and repression. In particular, BLMP-1, LDB-1 and HAM-3 co-regulate a set of hypodermal genes including bed-3 (activated), col-124 (activated) and lin-29 (repressed). On the other hand, LDB-1 and HAM-3 are not required for activation or repression of some genes regulated by BLMP-1 (e.g. T09D3.8, nas-10). We also found that human LDB1, SMARCD3/BAF60C and SMARCC1/BAF155 all physically interact with human BLIMP1/PRDM1 in vitro and are closely associated with BLIMP1/PRDM1 in vivo. Taken together, these results identify LDB1 and SWI/SNF as likely conserved cofactors of BLIMP1/PRDM1, which participate in activation and repression of a subset of BLIMP1/PRDM1-regulated genes.
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Affiliation(s)
- Hei Tung Fong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Thilo Hagen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore.
| | - Takao Inoue
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore.
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32
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Wu S, Cui T, Zhang X, Tian T. A non-linear reverse-engineering method for inferring genetic regulatory networks. PeerJ 2020; 8:e9065. [PMID: 32391205 PMCID: PMC7195839 DOI: 10.7717/peerj.9065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/05/2020] [Indexed: 12/19/2022] Open
Abstract
Hematopoiesis is a highly complex developmental process that produces various types of blood cells. This process is regulated by different genetic networks that control the proliferation, differentiation, and maturation of hematopoietic stem cells (HSCs). Although substantial progress has been made for understanding hematopoiesis, the detailed regulatory mechanisms for the fate determination of HSCs are still unraveled. In this study, we propose a novel approach to infer the detailed regulatory mechanisms. This work is designed to develop a mathematical framework that is able to realize nonlinear gene expression dynamics accurately. In particular, we intended to investigate the effect of possible protein heterodimers and/or synergistic effect in genetic regulation. This approach includes the Extended Forward Search Algorithm to infer network structure (top-down approach) and a non-linear mathematical model to infer dynamical property (bottom-up approach). Based on the published experimental data, we study two regulatory networks of 11 genes for regulating the erythrocyte differentiation pathway and the neutrophil differentiation pathway. The proposed algorithm is first applied to predict the network topologies among 11 genes and 55 non-linear terms which may be for heterodimers and/or synergistic effect. Then, the unknown model parameters are estimated by fitting simulations to the expression data of two different differentiation pathways. In addition, the edge deletion test is conducted to remove possible insignificant regulations from the inferred networks. Furthermore, the robustness property of the mathematical model is employed as an additional criterion to choose better network reconstruction results. Our simulation results successfully realized experimental data for two different differentiation pathways, which suggests that the proposed approach is an effective method to infer the topological structure and dynamic property of genetic regulations.
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Affiliation(s)
- Siyuan Wu
- School of Mathematics, Monash University, Clayton, VIC, Australia
| | - Tiangang Cui
- School of Mathematics, Monash University, Clayton, VIC, Australia
| | - Xinan Zhang
- School of Mathematics and Statistics, Central China Normal University, Wuhan, PR China
| | - Tianhai Tian
- School of Mathematics, Monash University, Clayton, VIC, Australia
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33
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Gutiérrez L, Caballero N, Fernández-Calleja L, Karkoulia E, Strouboulis J. Regulation of GATA1 levels in erythropoiesis. IUBMB Life 2019; 72:89-105. [PMID: 31769197 DOI: 10.1002/iub.2192] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/14/2019] [Indexed: 12/15/2022]
Abstract
GATA1 is considered as the "master" transcription factor in erythropoiesis. It regulates at the transcriptional level all aspects of erythroid maturation and function, as revealed by gene knockout studies in mice and by genome-wide occupancies in erythroid cells. The GATA1 protein contains two zinc finger domains and an N-terminal transactivation domain. GATA1 translation results in the production of the full-length protein and of a shorter variant (GATA1s) lacking the N-terminal transactivation domain, which is functionally deficient in supporting erythropoiesis. GATA1 protein abundance is highly regulated in erythroid cells at different levels, including transcription, mRNA translation, posttranslational modifications, and protein degradation, in a differentiation-stage-specific manner. Maintaining high GATA1 protein levels is essential in the early stages of erythroid maturation, whereas downregulating GATA1 protein levels is a necessary step in terminal erythroid differentiation. The importance of maintaining proper GATA1 protein homeostasis in erythropoiesis is demonstrated by the fact that both GATA1 loss and its overexpression result in lethal anemia. Importantly, alterations in any of those GATA1 regulatory checkpoints have been recognized as an important cause of hematological disorders such as dyserythropoiesis (with or without thrombocytopenia), β-thalassemia, Diamond-Blackfan anemia, myelodysplasia, or leukemia. In this review, we provide an overview of the multilevel regulation of GATA1 protein homeostasis in erythropoiesis and of its deregulation in hematological disease.
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Affiliation(s)
- Laura Gutiérrez
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Department of Medicine, Universidad de Oviedo, Oviedo, Spain
| | - Noemí Caballero
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Luis Fernández-Calleja
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Elena Karkoulia
- Institute of Molecular Biology and Biotechnology, Foundation of Research & Technology Hellas, Heraklion, Crete, Greece
| | - John Strouboulis
- Cancer Comprehensive Center, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
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34
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Yu X, Martella A, Kolovos P, Stevens M, Stadhouders R, Grosveld FG, Andrieu-Soler C. The dynamic emergence of GATA1 complexes identified in in vitro embryonic stem cell differentiation and in vivo mouse fetal liver. Haematologica 2019; 105:1802-1812. [PMID: 31582556 PMCID: PMC7327653 DOI: 10.3324/haematol.2019.216010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 10/03/2019] [Indexed: 01/20/2023] Open
Abstract
GATA1 is an essential transcriptional regulator of myeloid hematopoietic differentiation towards red blood cells. During erythroid differentiation, GATA1 forms different complexes with other transcription factors such as LDB1, TAL1, E2A and LMO2 ("the LDB1 complex") or with FOG1. The functions of GATA1 complexes have been studied extensively in definitive erythroid differentiation; however, the temporal and spatial formation of these complexes during erythroid development is unknown. We applied proximity ligation assay (PLA) to detect, localize and quantify individual interactions during embryonic stem cell differentiation and in mouse fetal liver (FL) tissue. We show that GATA1/LDB1 interactions appear before the proerythroblast stage and increase in a subset of the CD71+/TER119- cells to activate the terminal erythroid differentiation program in 12.5 day FL. Using Ldb1 and Gata1 knockdown FL cells, we studied the functional contribution of the GATA1/LDB1 complex during differentiation. This shows that the active LDB1 complex appears quite late at the proerythroblast stage of differentiation and confirms the power of PLA in studying the dynamic interaction of proteins in cell differentiation at the single cell level. We provide dynamic insight into the temporal and spatial formation of the GATA1 and LDB1 transcription factor complexes during hematopoietic development and differentiation.
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Affiliation(s)
- Xiao Yu
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands.,Current address: Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Andrea Martella
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands.,AstraZeneca, R&D Innovative Medicines, Cambridge Science Park, Milton Road, Cambridge, UK
| | - Petros Kolovos
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands.,Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Mary Stevens
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands
| | - Ralph Stadhouders
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands.,Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands
| | - Charlotte Andrieu-Soler
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands .,Institut de Génétique Moléculaire Montpellier, Université de Montpellier, CNRS, Montpellier, France.,Université de Paris, Laboratoire d'excellence (LabEx) du globule rouge GR-Ex, Paris, France
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35
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Romano O, Miccio A. GATA factor transcriptional activity: Insights from genome-wide binding profiles. IUBMB Life 2019; 72:10-26. [PMID: 31574210 DOI: 10.1002/iub.2169] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/05/2019] [Indexed: 01/07/2023]
Abstract
The members of the GATA family of transcription factors have homologous zinc fingers and bind to similar sequence motifs. Recent advances in genome-wide technologies and the integration of bioinformatics data have led to a better understanding of how GATA factors regulate gene expression; GATA-factor-induced transcriptional and epigenetic changes have now been analyzed at unprecedented levels of detail. Here, we review the results of genome-wide studies of GATA factor occupancy in human and murine cell lines and primary cells (as determined by chromatin immunoprecipitation sequencing), and then discuss the molecular mechanisms underlying the mediation of transcriptional and epigenetic regulation by GATA factors.
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Affiliation(s)
- Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Annarita Miccio
- Laboratory of chromatin and gene regulation during development, Imagine Institute, INSERM UMR, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
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36
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Ohneda K, Ohmori S, Yamamoto M. Mouse Tryptase Gene Expression is Coordinately Regulated by GATA1 and GATA2 in Bone Marrow-Derived Mast Cells. Int J Mol Sci 2019; 20:ijms20184603. [PMID: 31533351 PMCID: PMC6770354 DOI: 10.3390/ijms20184603] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/12/2022] Open
Abstract
Mast cell tryptases have crucial roles in allergic and inflammatory diseases. The mouse tryptase genes represent a cluster of loci on chromosome 16p3.3. While their functional studies have been extensively performed, transcriptional regulation of tryptase genes is poorly understood. In this study, we examined the molecular basis of the tryptase gene expression in bone marrow-derived mast cells (BMMCs) of C57BL/6 mice and in MEDMC-BRC6 mast cells. The expression of the Tpsb2 and Tpsg1 genes, which reside at the 3′-end of the tryptase locus, is significantly decreased by the reduction of the GATA transcription factors GATA1 or GATA2. Chromatin immunoprecipitation assays have shown that the GATA factors bind at multiple regions within the locus, including 1.0 and 72.8 kb upstream of the Tpsb2 gene, and that GATA1 and GATA2 facilitate each other’s DNA binding activity to these regions. Deletion of the −72.8 kb region by genome editing significantly reduced the Tpsb2 and Tpsg1 mRNA levels in MEDMC-BRC6 cells. Furthermore, binding of CTCF and the cohesin subunit Rad21 was found upstream of the −72.8 kb region and was significantly reduced in the absence of GATA1. These results suggest that mouse tryptase gene expression is coordinately regulated by GATA1 and GATA2 in BMMCs.
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Affiliation(s)
- Kinuko Ohneda
- Department of Pharmacy, Faculty of Pharmacy, Takasaki University of Health and Welfare, Takasaki 370-0033, Japan;
- Correspondence: ; Tel.: +81-22-274-5990
| | - Shin’ya Ohmori
- Department of Pharmacy, Faculty of Pharmacy, Takasaki University of Health and Welfare, Takasaki 370-0033, Japan;
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8573, Japan;
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37
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Kim MY, Kim JS, Son SH, Lim CS, Eum HY, Ha DH, Park MA, Baek EJ, Ryu BY, Kang HC, Uversky VN, Kim CG. Mbd2-CP2c loop drives adult-type globin gene expression and definitive erythropoiesis. Nucleic Acids Res 2019; 46:4933-4949. [PMID: 29547954 PMCID: PMC6007553 DOI: 10.1093/nar/gky193] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/12/2018] [Indexed: 01/18/2023] Open
Abstract
During hematopoiesis, red blood cells originate from the hematopoietic stem cell reservoir. Although the regulation of erythropoiesis and globin expression has been intensively investigated, the underlining mechanisms are not fully understood, including the interplay between transcription factors and epigenetic factors. Here, we uncover that the Mbd2-free NuRD chromatin remodeling complex potentiates erythroid differentiation of proerythroblasts via managing functions of the CP2c complexes. We found that both Mbd2 and Mbd3 expression is downregulated during differentiation of MEL cells in vitro and in normal erythropoiesis in mouse bone marrow, and Mbd2 downregulation is crucial for erythropoiesis. In uninduced MEL cells, the Mbd2-NuRD complex is recruited to the promoter via Gata1/Fog1, and, via direct binding through p66α, it acts as a transcriptional inhibitor of the CP2c complexes, preventing their DNA binding and promoting degradation of the CP2c family proteins to suppress globin gene expression. Conversely, during erythropoiesis in vitro and in vivo, the Mbd2-free NuRD does not dissociate from the chromatin and acts as a transcriptional coactivator aiding the recruitment of the CP2c complexes to chromatin, and thereby leading to the induction of the active hemoglobin synthesis and erythroid differentiation. Our study highlights the regulation of erythroid differentiation by the Mbd2-CP2c loop.
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Affiliation(s)
- Min Young Kim
- Department of Life Science and Research Institute of Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Ji Sook Kim
- Department of Life Science and Research Institute of Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Seung Han Son
- Department of Life Science and Research Institute of Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Chang Su Lim
- Department of Life Science and Research Institute of Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Hea Young Eum
- Department of Life Science and Research Institute of Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Dae Hyun Ha
- Department of Life Science and Research Institute of Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Mi Ae Park
- Department of Life Science and Research Institute of Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Eun Jung Baek
- Department of Laboratory Medicine, College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Buom-Yong Ryu
- Department of Animal Science & Technology, Chung-Ang University, Ansung, Gyeonggi-do 17546, Korea
| | - Ho Chul Kang
- Department of Physiology and Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region 142290, Russia
| | - Chul Geun Kim
- Department of Life Science and Research Institute of Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
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Enhancer long-range contacts: The multi-adaptor protein LDB1 is the tie that binds. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:625-633. [DOI: 10.1016/j.bbagrm.2019.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/20/2022]
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DNA·RNA triple helix formation can function as a cis-acting regulatory mechanism at the human β-globin locus. Proc Natl Acad Sci U S A 2019; 116:6130-6139. [PMID: 30867287 DOI: 10.1073/pnas.1900107116] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We have identified regulatory mechanisms in which an RNA transcript forms a DNA duplex·RNA triple helix with a gene or one of its regulatory elements, suggesting potential auto-regulatory mechanisms in vivo. We describe an interaction at the human β-globin locus, in which an RNA segment embedded in the second intron of the β-globin gene forms a DNA·RNA triplex with the HS2 sequence within the β-globin locus control region, a major regulator of globin expression. We show in human K562 cells that the triplex is stable in vivo. Its formation causes displacement from HS2 of major transcription factors and RNA Polymerase II, and consequently in loss of factors and polymerase that bind to the human ε- and γ-globin promoters, which are activated by HS2 in K562 cells. This results in reduced expression of these genes. These effects are observed when a small length of triplex-forming RNA is introduced into cells, or when a full-length intron-containing human β-globin transcript is expressed. Related results are obtained in human umbilical cord blood-derived erythroid progenitor-2 cells, in which β-globin expression is similarly affected by triplex formation. These results suggest a model in which RNAs conforming to the strict sequence rules for DNA·RNA triplex formation may participate in feedback regulation of genes in cis.
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40
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Zhang Z, Parker MP, Graw S, Novikova LV, Fedosyuk H, Fontes JD, Koestler DC, Peterson KR, Slawson C. O-GlcNAc homeostasis contributes to cell fate decisions during hematopoiesis. J Biol Chem 2019; 294:1363-1379. [PMID: 30523150 PMCID: PMC6349094 DOI: 10.1074/jbc.ra118.005993] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/29/2018] [Indexed: 11/06/2022] Open
Abstract
The addition of a single β-d-GlcNAc sugar (O-GlcNAc) by O-GlcNAc-transferase (OGT) and O-GlcNAc removal by O-GlcNAcase (OGA) maintain homeostatic O-GlcNAc levels on cellular proteins. Changes in protein O-GlcNAcylation regulate cellular differentiation and cell fate decisions, but how these changes affect erythropoiesis, an essential process in blood cell formation, remains unclear. Here, we investigated the role of O-GlcNAcylation in erythropoiesis by using G1E-ER4 cells, which carry the erythroid-specific transcription factor GATA-binding protein 1 (GATA-1) fused to the estrogen receptor (GATA-1-ER) and therefore undergo erythropoiesis after β-estradiol (E2) addition. We observed that during G1E-ER4 differentiation, overall O-GlcNAc levels decrease, and physical interactions of GATA-1 with both OGT and OGA increase. RNA-Seq-based transcriptome analysis of G1E-ER4 cells differentiated in the presence of the OGA inhibitor Thiamet-G (TMG) revealed changes in expression of 433 GATA-1 target genes. ChIP results indicated that the TMG treatment decreases the occupancy of GATA-1, OGT, and OGA at the GATA-binding site of the lysosomal protein transmembrane 5 (Laptm5) gene promoter. TMG also reduced the expression of genes involved in differentiation of NB4 and HL60 human myeloid leukemia cells, suggesting that O-GlcNAcylation is involved in the regulation of hematopoietic differentiation. Sustained treatment of G1E-ER4 cells with TMG before differentiation reduced hemoglobin-positive cells and increased stem/progenitor cell surface markers. Our results show that alterations in O-GlcNAcylation disrupt transcriptional programs controlling erythropoietic lineage commitment, suggesting a role for O-GlcNAcylation in regulating hematopoietic cell fate.
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Affiliation(s)
- Zhen Zhang
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160
| | - Matthew P Parker
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160
| | | | - Lesya V Novikova
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160
| | - Halyna Fedosyuk
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160
| | - Joseph D Fontes
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160; Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Devin C Koestler
- Biostatistics, Kansas City, Kansas 66160; Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Kenneth R Peterson
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160; Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160; Anatomy and Cell Biology, Kansas City, Kansas 66160.
| | - Chad Slawson
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160; Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160.
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Abstract
In this review from Murre, the evolution of HLH genes, the structures of HLH domains, and the elaborate activities of HLH proteins in multicellular life are discussed. Helix–loop–helix (HLH) proteins are dimeric transcription factors that control lineage- and developmental-specific gene programs. Genes encoding for HLH proteins arose in unicellular organisms >600 million years ago and then duplicated and diversified from ancestral genes across the metazoan and plant kingdoms to establish multicellularity. Hundreds of HLH proteins have been identified with diverse functions in a wide variety of cell types. HLH proteins orchestrate lineage specification, commitment, self-renewal, proliferation, differentiation, and homing. HLH proteins also regulate circadian clocks, protect against hypoxic stress, promote antigen receptor locus assembly, and program transdifferentiation. HLH proteins deposit or erase epigenetic marks, activate noncoding transcription, and sequester chromatin remodelers across the chromatin landscape to dictate enhancer–promoter communication and somatic recombination. Here the evolution of HLH genes, the structures of HLH domains, and the elaborate activities of HLH proteins in multicellular life are discussed.
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Affiliation(s)
- Cornelis Murre
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92903, USA
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42
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Temporal autoregulation during human PU.1 locus SubTAD formation. Blood 2018; 132:2643-2655. [PMID: 30315124 DOI: 10.1182/blood-2018-02-834721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 10/06/2018] [Indexed: 12/20/2022] Open
Abstract
Epigenetic control of gene expression occurs within discrete spatial chromosomal units called topologically associating domains (TADs), but the exact spatial requirements of most genes are unknown; this is of particular interest for genes involved in cancer. We therefore applied high-resolution chromosomal conformation capture sequencing to map the three-dimensional (3D) organization of the human locus encoding the key myeloid transcription factor PU.1 in healthy monocytes and acute myeloid leukemia (AML) cells. We identified a dynamic ∼75-kb unit (SubTAD) as the genomic region in which spatial interactions between PU.1 gene regulatory elements occur during myeloid differentiation and are interrupted in AML. Within this SubTAD, proper initiation of the spatial chromosomal interactions requires PU.1 autoregulation and recruitment of the chromatin-adaptor protein LDB1 (LIM domain-binding protein 1). However, once these spatial interactions have occurred, LDB1 stabilizes them independently of PU.1 autoregulation. Thus, our data support that PU.1 autoregulates its expression in a "hit-and-run" manner by initiating stable chromosomal loops that result in a transcriptionally active chromatin architecture.
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43
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Peters MJ, Parker SK, Grim J, Allard CAH, Levin J, Detrich HW. Divergent Hemogen genes of teleosts and mammals share conserved roles in erythropoiesis: analysis using transgenic and mutant zebrafish. Biol Open 2018; 7:bio.035576. [PMID: 30097520 PMCID: PMC6124579 DOI: 10.1242/bio.035576] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hemogen is a vertebrate transcription factor that performs important functions in erythropoiesis and testicular development and may contribute to neoplasia. Here we identify zebrafish Hemogen and show that it is considerably smaller (∼22 kDa) than its human ortholog (∼55 kDa), a striking difference that is explained by an underlying modular structure. We demonstrate that Hemogens are largely composed of 21-25 amino acid repeats, some of which may function as transactivation domains (TADs). Hemogen expression in embryonic and adult zebrafish is detected in hematopoietic, renal, neural and gonadal tissues. Using Tol2- and CRISPR/Cas9-generated transgenic zebrafish, we show that Hemogen expression is controlled by two Gata1-dependent regulatory sequences that act alone and together to control spatial and temporal expression during development. Partial depletion of Hemogen in embryos by morpholino knockdown reduces the number of erythrocytes in circulation. CRISPR/Cas9-generated zebrafish lines containing either a frameshift mutation or an in-frame deletion in a putative, C-terminal TAD display anemia and embryonic tail defects. This work expands our understanding of Hemogen and provides mutant zebrafish lines for future study of the mechanism of this important transcription factor. Summary: Transgenic and mutant zebrafish lines were created to characterize the expression and functions of Hemogen, a transcription factor involved in the formation of red blood cells and other processes.
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Affiliation(s)
- Michael J Peters
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA 01908, USA
| | - Sandra K Parker
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA 01908, USA
| | - Jeffrey Grim
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA 01908, USA
| | - Corey A H Allard
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA 01908, USA
| | - Jonah Levin
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA 01908, USA
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA 01908, USA
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44
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Moore KS, Yagci N, van Alphen F, Meijer AB, ‘t Hoen PAC, von Lindern M. Strap associates with Csde1 and affects expression of select Csde1-bound transcripts. PLoS One 2018; 13:e0201690. [PMID: 30138317 PMCID: PMC6107111 DOI: 10.1371/journal.pone.0201690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 07/22/2018] [Indexed: 02/06/2023] Open
Abstract
Erythropoiesis is regulated at many levels, including control of mRNA translation. Changing environmental conditions, such as hypoxia or the availability of nutrients and growth factors, require a rapid response enacted by the enhanced or repressed translation of existing transcripts. Cold shock domain protein e1 (Csde1/Unr) is an RNA-binding protein required for erythropoiesis and strongly upregulated in erythroblasts relative to other hematopoietic progenitors. The aim of this study is to identify the Csde1-containing protein complexes and investigate their role in post-transcriptional expression control of Csde1-bound transcripts. We show that Serine/Threonine kinase receptor-associated protein (Strap/Unrip), was the protein most strongly associated with Csde1 in erythroblasts. Strap is a WD40 protein involved in signaling and RNA splicing, but its role when associated with Csde1 is unknown. Reduced expression of Strap did not alter the pool of transcripts bound by Csde1. Instead, it altered the mRNA and/or protein expression of several Csde1-bound transcripts that encode for proteins essential for translational regulation during hypoxia, such as Hmbs, eIF4g3 and Pabpc4. Also affected by Strap knockdown were Vim, a Gata-1 target crucial for erythrocyte enucleation, and Elavl1, which stabilizes Gata-1 mRNA. The major cellular processes affected by both Csde1 and Strap were ribosome function and cell cycle control.
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Affiliation(s)
- Kat S. Moore
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Nurcan Yagci
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Floris van Alphen
- Sanquin Research, Department of Research Facilities, Amsterdam, The Netherlands
| | - Alexander B. Meijer
- Sanquin Research, Department of Research Facilities, Amsterdam, The Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Peter A. C. ‘t Hoen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marieke von Lindern
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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45
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Xiao D, Jin K, Xiang M. Necessity and Sufficiency of Ldb1 in the Generation, Differentiation and Maintenance of Non-photoreceptor Cell Types During Retinal Development. Front Mol Neurosci 2018; 11:271. [PMID: 30127719 PMCID: PMC6087769 DOI: 10.3389/fnmol.2018.00271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/17/2018] [Indexed: 12/28/2022] Open
Abstract
During mammalian retinal development, the multipotent progenitors differentiate into all classes of retinal cells under the delicate control of transcriptional factors. The deficiency of a transcription cofactor, the LIM-domain binding protein Ldb1, has been shown to cause proliferation and developmental defects in multiple tissues including cardiovascular, hematopoietic, and nervous systems; however, it remains unclear whether and how it regulates retinal development. By expression profiling, RNA in situ hybridization and immunostaining, here we show that Ldb1 is expressed in the progenitors during early retinal development, but later its expression gradually shifts to non-photoreceptor cell types including bipolar, amacrine, horizontal, ganglion, and Müller glial cells. Retina-specific ablation of Ldb1 in mice resulted in microphthalmia, optic nerve hypoplasia, retinal thinning and detachment, and profound vision impairment as determined by electroretinography. In the mutant retina, there was precocious differentiation of amacrine and horizontal cells, indicating a requirement of Ldb1 in maintaining the retinal progenitor pool. Additionally, all non-photoreceptor cell types were greatly reduced which appeared to be caused by a generation defect and/or retinal degeneration via excessive cell apoptosis. Furthermore, we showed that misexpressed Ldb1 was sufficient to promote the generation of bipolar, amacrine, horizontal, ganglion, and Müller glial cells at the expense of photoreceptors. Together, these results demonstrate that Ldb1 is not only necessary but also sufficient for the development and/or maintenance of non-photoreceptor cell types, and implicate that the pleiotropic functions of Ldb1 during retinal development are context-dependent and determined by its interaction with diverse LIM-HD (LIM-homeodomain) and LMO (LIM domain-only) binding protein partners.
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Affiliation(s)
- Dongchang Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Kangxin Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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46
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Gilmour J, Assi SA, Noailles L, Lichtinger M, Obier N, Bonifer C. The Co-operation of RUNX1 with LDB1, CDK9 and BRD4 Drives Transcription Factor Complex Relocation During Haematopoietic Specification. Sci Rep 2018; 8:10410. [PMID: 29991720 PMCID: PMC6039467 DOI: 10.1038/s41598-018-28506-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/25/2018] [Indexed: 01/09/2023] Open
Abstract
Haematopoietic cells arise from endothelial cells within the dorsal aorta of the embryo via a process called the endothelial-haematopoietic transition (EHT). This process crucially depends on the transcription factor RUNX1 which rapidly activates the expression of genes essential for haematopoietic development. Using an inducible version of RUNX1 in a mouse embryonic stem cell differentiation model we showed that prior to the EHT, haematopoietic genes are primed by the binding of the transcription factor FLI1. Once expressed, RUNX1 relocates FLI1 towards its binding sites. However, the nature of the transcription factor assemblies recruited by RUNX1 to reshape the chromatin landscape and initiate mRNA synthesis are unclear. Here, we performed genome-wide analyses of RUNX1-dependent binding of factors associated with transcription elongation to address this question. We demonstrate that RUNX1 induction moves FLI1 from distal ETS/GATA sites to RUNX1/ETS sites and recruits the basal transcription factors CDK9, BRD4, the Mediator complex and the looping factor LDB1. Our study explains how the expression of a single transcription factor can drive rapid and replication independent transitions in cellular shape which are widely observed in development and disease.
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Affiliation(s)
- Jane Gilmour
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Laura Noailles
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Monika Lichtinger
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Nadine Obier
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Centre for Clinical Research, University of Freiburg Medical School, Freiburg, Germany
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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47
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Philipsen S, Hardison RC. Evolution of hemoglobin loci and their regulatory elements. Blood Cells Mol Dis 2018; 70:2-12. [PMID: 28811072 PMCID: PMC5807248 DOI: 10.1016/j.bcmd.2017.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/13/2017] [Accepted: 08/03/2017] [Indexed: 11/21/2022]
Abstract
Across the expanse of vertebrate evolution, each species produces multiple forms of hemoglobin in erythroid cells at appropriate times and in the proper amounts. The multiple hemoglobins are encoded in two globin gene clusters in almost all species. One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. This preservation of synteny may reflect the presence of a powerful enhancer of globin gene expression in the NPRL3 gene. Despite substantial divergence in noncoding DNA sequences among mammals, several epigenetic features of the globin gene regulatory regions are preserved across vertebrates. The preserved features include multiple DNase hypersensitive sites, at least one of which is an enhancer, and binding by key lineage-restricted transcription factors such as GATA1 and TAL1, which in turn recruit coactivators such as P300 that catalyze acetylation of histones. The maps of epigenetic features are strongly correlated with activity in gene regulation, and resources for accessing and visualizing such maps are readily available to the community of researchers and students.
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Affiliation(s)
- Sjaak Philipsen
- Department of Cell Biology Ee1071b, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institute for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.
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48
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Yamamoto R, Kawahara M, Ito S, Satoh J, Tatsumi G, Hishizawa M, Suzuki T, Andoh A. Selective dissociation between LSD1 and GFI1B by a LSD1 inhibitor NCD38 induces the activation of ERG super-enhancer in erythroleukemia cells. Oncotarget 2018; 9:21007-21021. [PMID: 29765516 PMCID: PMC5940392 DOI: 10.18632/oncotarget.24774] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 02/24/2018] [Indexed: 12/22/2022] Open
Abstract
Lysine-specific demethylase 1 (LSD1) is a histone modifier for transcriptional repression involved in the regulation of hematopoiesis. We previously reported that a LSD1 inhibitor NCD38 induces transdifferentiation from erythroid lineage to granulomonocytic lineage and exerts anti-leukemia effect through de-repression of the specific super-enhancers of hematopoietic regulators including ERG in a human erythroleukemia cell line, HEL. However, the mechanistic basis for this specificity of NCD38 has remained unclear. Herein, we report major partners associated with LSD1 and clarify the mechanism in HEL cells. Proteome analysis identified 54 candidate proteins associated with LSD1, including several transcription factors such as GFI1B and RUNX1 as well as BRAF-histone deacetylase complex (BHC) components such as CoREST, HDAC1, and HDAC2. NCD38 selectively disrupted the interaction of LSD1 with GFI1B but not with RUNX1, CoREST, HDAC1 and HDAC2. Erg was downregulated in murine erythroid progenitors with prominent upregulation of Gfi1b. NCD38 induced ERG and attenuated an erythroid marker CD235a in HEL while this attenuation was mimicked by the lentiviral overexpression of ERG. The ERG super-enhancer contained the conserved binding motif of GFI1B and was actually occupied by GFI1B. NCD38 dissociated LSD1 and CoREST but not GFI1B from the ERG super-enhancer. Collectively, the selective separation of LSD1 from GFI1B by NCD38 restores the ERG super-enhancer activation and consequently upregulates ERG expression, inducing the transdifferentiation linked to the anti-leukemia effect.
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Affiliation(s)
- Ryusuke Yamamoto
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Masahiro Kawahara
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan.,Department of Medicine, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Shinji Ito
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Junko Satoh
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Goichi Tatsumi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Masakatsu Hishizawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Takayoshi Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, Japan.,CREST, Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
| | - Akira Andoh
- Department of Medicine, Shiga University of Medical Science, Otsu, Shiga, Japan
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49
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Abstract
Lineage-specific transcription factors are critical for long-range enhancer interactions, but direct or indirect contributions of architectural proteins such as CCCTC-binding factor (CTCF) to enhancer function remain less clear. The LDB1 complex mediates enhancer-gene interactions at the β-globin locus through LDB1 self-interaction. We find that an LDB1-bound enhancer upstream of carbonic anhydrase 2 (Car2) activates its expression by interacting directly with CTCF at the gene promoter. Both LDB1 and CTCF are required for enhancer-Car2 looping, and the domain of LDB1 contacted by CTCF is necessary to rescue Car2 transcription in LDB1-deficient cells. Genome-wide studies and CRISPR/Cas9 genome editing indicate that LDB1-CTCF enhancer looping underlies activation of a substantial fraction of erythroid genes. Our results provide a mechanism by which long-range interactions of architectural protein CTCF can be tailored to achieve a tissue-restricted pattern of chromatin loops and gene expression.
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50
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Mantsoki A, Devailly G, Joshi A. Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells. BMC DEVELOPMENTAL BIOLOGY 2018; 18:2. [PMID: 29458328 PMCID: PMC5819258 DOI: 10.1186/s12861-018-0163-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/05/2018] [Indexed: 01/04/2023]
Abstract
Background Mammalian embryonic stem cells display a unique epigenetic and transcriptional state to facilitate pluripotency by maintaining lineage-specification genes in a poised state. Two epigenetic and transcription processes involved in maintaining poised state are bivalent chromatin, characterized by the simultaneous presence of activating and repressive histone methylation marks, and RNA polymerase II (RNAPII) promoter proximal pausing. However, the dynamics of histone modifications and RNAPII at promoters in diverse cellular contexts remains underexplored. Results We collected genome wide data for bivalent chromatin marks H3K4me3 and H3K27me3, and RNAPII (8WG16) occupancy together with expression profiling in eight different cell types, including ESCs, in mouse. The epigenetic and transcription profiles at promoters grouped in over thirty clusters with distinct functional identities and transcription control. Conclusion The clustering analysis identified distinct bivalent clusters where genes in one cluster retained bivalency across cell types while in the other were mostly cell type specific, but neither showed a high RNAPII pausing. We noted that RNAPII pausing is more associated with active genes than bivalent genes in a cell type, and was globally reduced in differentiated cell types compared to multipotent. Electronic supplementary material The online version of this article (10.1186/s12861-018-0163-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Mantsoki
- Division of Developmental Biology, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Guillaume Devailly
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Toulouse, Haute-Garonne, France
| | - Anagha Joshi
- Division of Developmental Biology, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
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