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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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2
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Polit L, Kerdivel G, Gregoricchio S, Esposito M, Guillouf C, Boeva V. CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes. BMC Bioinformatics 2021; 22:407. [PMID: 34404353 PMCID: PMC8371782 DOI: 10.1186/s12859-021-04320-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 07/30/2021] [Indexed: 01/02/2023] Open
Abstract
Background Multiple studies rely on ChIP-seq experiments to assess the effect of gene modulation and drug treatments on protein binding and chromatin structure. However, most methods commonly used for the normalization of ChIP-seq binding intensity signals across conditions, e.g., the normalization to the same number of reads, either assume a constant signal-to-noise ratio across conditions or base the estimates of correction factors on genomic regions with intrinsically different signals between conditions. Inaccurate normalization of ChIP-seq signal may, in turn, lead to erroneous biological conclusions. Results We developed a new R package, CHIPIN, that allows normalizing ChIP-seq signals across different conditions/samples when spike-in information is not available, but gene expression data are at hand. Our normalization technique is based on the assumption that, on average, no differences in ChIP-seq signals should be observed in the regulatory regions of genes whose expression levels are constant across samples/conditions. In addition to normalizing ChIP-seq signals, CHIPIN provides as output a number of graphs and calculates statistics allowing the user to assess the efficiency of the normalization and qualify the specificity of the antibody used. In addition to ChIP-seq, CHIPIN can be used without restriction on open chromatin ATAC-seq or DNase hypersensitivity data. We validated the CHIPIN method on several ChIP-seq data sets and documented its superior performance in comparison to several commonly used normalization techniques. Conclusions The CHIPIN method provides a new way for ChIP-seq signal normalization across conditions when spike-in experiments are not available. The method is implemented in a user-friendly R package available on GitHub: https://github.com/BoevaLab/CHIPIN Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04320-3.
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Affiliation(s)
- Lélia Polit
- Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France
| | - Gwenneg Kerdivel
- Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France
| | - Sebastian Gregoricchio
- INSERM UMR1170, Equipe Labellisée Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France
| | - Michela Esposito
- INSERM UMR1170, Equipe Labellisée Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France
| | - Christel Guillouf
- INSERM UMR1170, Equipe Labellisée Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France
| | - Valentina Boeva
- Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France. .,Department of Computer Science, Institute for Machine Learning, ETH Zurich, 8092, Zurich, Switzerland. .,Swiss Institute for Bioinformatics (SIB), Zürich, Switzerland.
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3
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Filandrová R, Vališ K, Černý J, Chmelík J, Slavata L, Fiala J, Rosůlek M, Kavan D, Man P, Chum T, Cebecauer M, Fabris D, Novák P. Motif orientation matters: Structural characterization of TEAD1 recognition of genomic DNA. Structure 2020; 29:345-356.e8. [PMID: 33333006 DOI: 10.1016/j.str.2020.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/09/2020] [Accepted: 11/24/2020] [Indexed: 11/29/2022]
Abstract
TEAD transcription factors regulate gene expression through interactions with DNA and other proteins. They are crucial for the development of eukaryotic organisms and to control the expression of genes involved mostly in cell proliferation and differentiation; however, their deregulation can lead to tumorigenesis. To study the interactions of TEAD1 with M-CAT motifs and their inverted versions, the KD of each complex was determined, and H/D exchange, quantitative chemical cross-linking, molecular docking, and smFRET were utilized for structural characterization. ChIP-qPCR was employed to correlate the results with a cell line model. The results obtained showed that although the inverted motif has 10× higher KD, the same residues were affected by the presence of M-CAT in both orientations. Molecular docking and smFRET revealed that TEAD1 binds the inverted motif rotated 180°. In addition, the inverted motif was proven to be occupied by TEAD1 in Jurkat cells, suggesting that the low-affinity binding sites present in the human genome may possess biological relevance.
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Affiliation(s)
- Růžena Filandrová
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Karel Vališ
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - Jiří Černý
- Institute of Biotechnology, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Josef Chmelík
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Lukáš Slavata
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Jan Fiala
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Michal Rosůlek
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Petr Man
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Tomáš Chum
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague 182 00, Czech Republic
| | - Marek Cebecauer
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague 182 00, Czech Republic
| | - Daniele Fabris
- University of Connecticut, Department of Chemistry, 55 N. Eagleville Road, Storrs, CT 06269, USA
| | - Petr Novák
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic.
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4
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Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome. Proc Natl Acad Sci U S A 2020; 117:19328-19338. [PMID: 32690705 DOI: 10.1073/pnas.2006038117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-Alu LIKE), which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of the highly rearranged structure of the gibbon genome by disrupting transcription of cell cycle genes. In this study, we investigated whether LAVA may have also contributed to the evolution of gene regulation by adopting enhancer function. We characterized fixed and polymorphic LAVA insertions across multiple gibbons and found 96 LAVA elements overlapping enhancer chromatin states. Moreover, LAVA was enriched in multiple transcription factor binding motifs, was bound by an important transcription factor (PU.1), and was associated with higher levels of gene expression in cis We found gibbon-specific signatures of purifying/positive selection at 27 LAVA insertions. Two of these insertions were fixed in the gibbon lineage and overlapped with enhancer chromatin states, representing putative co-opted LAVA enhancers. These putative enhancers were located within genes encoding SETD2 and RAD9A, two proteins that facilitate accurate repair of DNA double-strand breaks and prevent chromosomal rearrangement mutations. Co-option of LAVA in these genes may have influenced regulation of processes that preserve genome integrity. Our findings highlight the importance of considering lineage-specific TEs in studying evolution of gene regulatory elements.
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5
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Roos-Weil D, Decaudin C, Armand M, Della-Valle V, Diop MK, Ghamlouch H, Ropars V, Hérate C, Lara D, Durot E, Haddad R, Mylonas E, Damm F, Pflumio F, Stoilova B, Metzner M, Elemento O, Dessen P, Camara-Clayette V, Cosset FL, Verhoeyen E, Leblond V, Ribrag V, Cornillet-Lefebvre P, Rameau P, Azar N, Charlotte F, Morel P, Charbonnier JB, Vyas P, Mercher T, Aoufouchi S, Droin N, Guillouf C, Nguyen-Khac F, Bernard OA. A Recurrent Activating Missense Mutation in Waldenström Macroglobulinemia Affects the DNA Binding of the ETS Transcription Factor SPI1 and Enhances Proliferation. Cancer Discov 2019; 9:796-811. [PMID: 31018969 DOI: 10.1158/2159-8290.cd-18-0873] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/28/2019] [Accepted: 04/18/2019] [Indexed: 11/16/2022]
Abstract
The ETS-domain transcription factors divide into subfamilies based on protein similarities, DNA-binding sequences, and interaction with cofactors. They are regulated by extracellular clues and contribute to cellular processes, including proliferation and transformation. ETS genes are targeted through genomic rearrangements in oncogenesis. The PU.1/SPI1 gene is inactivated by point mutations in human myeloid malignancies. We identified a recurrent somatic mutation (Q226E) in PU.1/SPI1 in Waldenström macroglobulinemia, a B-cell lymphoproliferative disorder. It affects the DNA-binding affinity of the protein and allows the mutant protein to more frequently bind and activate promoter regions with respect to wild-type protein. Mutant SPI1 binding at promoters activates gene sets typically promoted by other ETS factors, resulting in enhanced proliferation and decreased terminal B-cell differentiation in model cell lines and primary samples. In summary, we describe oncogenic subversion of transcription factor function through subtle alteration of DNA binding leading to cellular proliferation and differentiation arrest. SIGNIFICANCE: The demonstration that a somatic point mutation tips the balance of genome-binding pattern provides a mechanistic paradigm for how missense mutations in transcription factor genes may be oncogenic in human tumors.This article is highlighted in the In This Issue feature, p. 681.
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Affiliation(s)
- Damien Roos-Weil
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Camille Decaudin
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Marine Armand
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Véronique Della-Valle
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - M'boyba K Diop
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,AMMICa, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - Hussein Ghamlouch
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Virginie Ropars
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Cécile Hérate
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Diane Lara
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,Sorbonne Université, INSERM UMRS 1138, Centre de Recherche des Cordeliers, Paris, France
| | - Eric Durot
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Rima Haddad
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) DSV-IRCM-SCSR-LSHL, Université Paris Diderot Sorbonne Paris Cité, Fontenay-aux-Roses, France
| | - Elena Mylonas
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Frederik Damm
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Francoise Pflumio
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) DSV-IRCM-SCSR-LSHL, Université Paris Diderot Sorbonne Paris Cité, Fontenay-aux-Roses, France
| | - Bilyana Stoilova
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine,NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine and Department of Haematology, Oxford University and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Marlen Metzner
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine,NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine and Department of Haematology, Oxford University and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Philippe Dessen
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,AMMICa, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - Valérie Camara-Clayette
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,AMMICa, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - François-Loïc Cosset
- CIRI-InternationalCenter for Infectiology Research, Team EVIR, Université de Lyon; INSERM, U1111; Ecole Normale Supérieure de Lyon; Université Lyon 1; CNRS, UMR5308, Lyon, France
| | - Els Verhoeyen
- CIRI-InternationalCenter for Infectiology Research, Team EVIR, Université de Lyon; INSERM, U1111; Ecole Normale Supérieure de Lyon; Université Lyon 1; CNRS, UMR5308, Lyon, France.,Université Côte d'Azur, INSERM, C3M, Nice, France
| | | | - Vincent Ribrag
- INSERM U1170, Gustave Roussy, Villejuif, France.,DITEP Gustave Roussy, Villejuif, Paris, France
| | - Pascale Cornillet-Lefebvre
- Laboratoire d'hématologie, Pôle de biologie, CHU de Reims-Hôpital Robert Debré, Avenuedu Général Koenig, Reims, France
| | - Philippe Rameau
- AMMICa, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - Nabih Azar
- Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | | | - Pierre Morel
- Centre Hospitalier Dr. Schaffner,Lens; Service d'Hématologie Clinique et Thérapie Cellulaire, CHU Amiens Picardie, Amiens cedex, France
| | - Jean-Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine,NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine and Department of Haematology, Oxford University and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Thomas Mercher
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Said Aoufouchi
- Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,CNRS UMR8200, Gustave Roussy, Villejuif, France
| | - Nathalie Droin
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,AMMICa, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - Christel Guillouf
- INSERM U1170, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Florence Nguyen-Khac
- Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France. .,Sorbonne Université, INSERM UMRS 1138, Centre de Recherche des Cordeliers, Paris, France
| | - Olivier A Bernard
- INSERM U1170, Gustave Roussy, Villejuif, France. .,Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France
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6
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Rothenberg EV, Hosokawa H, Ungerbäck J. Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development. Front Immunol 2019; 10:228. [PMID: 30842770 PMCID: PMC6391351 DOI: 10.3389/fimmu.2019.00228] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
PU.1 is an ETS-family transcription factor that plays a broad range of roles in hematopoiesis. A direct regulator of myeloid, dendritic-cell, and B cell functional programs, and a well-known antagonist of terminal erythroid cell differentiation, it is also expressed in the earliest stages of T-cell development of each cohort of intrathymic pro-T cells. Its expression in this context appears to give T-cell precursors initial, transient access to myeloid and dendritic cell developmental competence and therefore to represent a source of antagonism or delay of T-cell lineage commitment. However, it has remained uncertain until recently why T-cell development is also intensely dependent upon PU.1. Here, we review recent work that sheds light on the molecular biology of PU.1 action across the genome in pro-T cells and identifies the genes that depend on PU.1 for their correct regulation. This work indicates modes of chromatin engagement, pioneering, and cofactor recruitment (“coregulator theft”) by PU.1 as well as gene network interactions that not only affect specific target genes but also have system-wide regulatory consequences, amplifying the impact of PU.1 beyond its own direct binding targets. The genes directly regulated by PU.1 also suggest a far-reaching transformation of cell biology and signaling potential between the early stages of T-cell development when PU.1 is expressed and when it is silenced. These cell-biological functions can be important to distinguish fetal from adult T-cell development and have the potential to illuminate aspects of thymic function that have so far remained the most mysterious.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Hiroyuki Hosokawa
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Jonas Ungerbäck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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7
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Rimmelé P, Esposito M, Delestré L, Guervilly JH, Ridinger-Saison M, Despras E, Moreau-Gachelin F, Rosselli F, Guillouf C. The Spi1/PU.1 transcription factor accelerates replication fork progression by increasing PP1 phosphatase in leukemia. Oncotarget 2018; 8:37104-37114. [PMID: 28415748 PMCID: PMC5514894 DOI: 10.18632/oncotarget.16183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/03/2017] [Indexed: 11/25/2022] Open
Abstract
Oncogenes trigger replicative stress that can lead to genetic instability, which participates in cancer progression. Thus, determining how cells cope with replicative stress can help our understanding of oncogenesis and lead to the identification of new antitumor treatment targets. We previously showed that constitutive overexpression of the oncogenic transcription factor Spi1/PU.1 leads to pre-leukemic cells that have a shortened S phase duration with an increased replication fork speed and increased mutability in the absence of DNA breaks. Here, we demonstrate that the S phase checkpoint protein CHK1 is maintained in a low phosphorylation state in Spi1/PU.1-overexpressing cells and provide evidence that this is not due to negative control of its primary kinase ATR. Notably, we found that the expression of the CHK1 phosphatase PP1α is increased in Spi1/PU.1-overexpressing cells. By exogenously modulating its activity, we demonstrate that PP1α is required to maintain CHK1 in a dephosphorylated state and, more importantly, that it is responsible for the accelerated replication fork progression in Spi1/PU.1-overexpressing cells. These results identify a novel pathway by which an oncogene influences replication in the absence of DNA damage.
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Affiliation(s)
| | - Michela Esposito
- Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,Inserm U1170, Villejuif, France
| | - Laure Delestré
- Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,Inserm U1170, Villejuif, France
| | - Jean-Hugues Guervilly
- Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,CNRS UMR8200, Equipe Labellisée La Ligue Contre Le Cancer, Villejuif, France
| | | | - Emmanuelle Despras
- Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,CNRS UMR8200, Equipe Labellisée La Ligue Contre Le Cancer, Villejuif, France
| | | | - Filippo Rosselli
- Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,CNRS UMR8200, Equipe Labellisée La Ligue Contre Le Cancer, Villejuif, France
| | - Christel Guillouf
- Institut Curie, Paris, France.,Inserm U830, Paris, France.,Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,Inserm U1170, Villejuif, France.,CNRS, Paris, France
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8
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Boeva V. Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells. Front Genet 2016; 7:24. [PMID: 26941778 PMCID: PMC4763482 DOI: 10.3389/fgene.2016.00024] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/05/2016] [Indexed: 12/27/2022] Open
Abstract
Eukaryotic genomes contain a variety of structured patterns: repetitive elements, binding sites of DNA and RNA associated proteins, splice sites, and so on. Often, these structured patterns can be formalized as motifs and described using a proper mathematical model such as position weight matrix and IUPAC consensus. Two key tasks are typically carried out for motifs in the context of the analysis of genomic sequences. These are: identification in a set of DNA regions of over-represented motifs from a particular motif database, and de novo discovery of over-represented motifs. Here we describe existing methodology to perform these two tasks for motifs characterizing transcription factor binding. When applied to the output of ChIP-seq and ChIP-exo experiments, or to promoter regions of co-modulated genes, motif analysis techniques allow for the prediction of transcription factor binding events and enable identification of transcriptional regulators and co-regulators. The usefulness of motif analysis is further exemplified in this review by how motif discovery improves peak calling in ChIP-seq and ChIP-exo experiments and, when coupled with information on gene expression, allows insights into physical mechanisms of transcriptional modulation.
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Affiliation(s)
- Valentina Boeva
- Centre de Recherche, Institut CurieParis, France; INSERM, U900Paris, France; Mines ParisTechFontainebleau, France; PSL Research UniversityParis, France; Department of Development, Reproduction and Cancer, Institut CochinParis, France; INSERM, U1016Paris, France; Centre National de la Recherche Scientifique UMR 8104Paris, France; Université Paris Descartes UMR-S1016Paris, France
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9
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Champhekar A, Damle SS, Freedman G, Carotta S, Nutt SL, Rothenberg EV. Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1. Genes Dev 2015; 29:832-48. [PMID: 25846797 PMCID: PMC4403259 DOI: 10.1101/gad.259879.115] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/17/2015] [Indexed: 12/28/2022]
Abstract
In the thymus, high PU.1 expression persists through multiple cell divisions in early stages but then falls sharply during T-cell lineage commitment. Here, Champhekar et al. show that PU.1 is needed for full proliferation, restricting access to some non-T fates, and controlling the timing of T-cell developmental progression. Genome-wide transcriptome analysis identifies novel targets of PU.1-positive and PU.1-negative regulation affecting progenitor cell signaling and cell biology and indicating distinct regulatory effects on different subsets of progenitor cell transcription factors. The ETS family transcription factor PU.1 is essential for the development of several blood lineages, including T cells, but its function in intrathymic T-cell precursors has been poorly defined. In the thymus, high PU.1 expression persists through multiple cell divisions in early stages but then falls sharply during T-cell lineage commitment. PU.1 silencing is critical for T-cell commitment, but it has remained unknown how PU.1 activities could contribute positively to T-cell development. Here we employed conditional knockout and modified antagonist PU.1 constructs to perturb PU.1 function stage-specifically in early T cells. We show that PU.1 is needed for full proliferation, restricting access to some non-T fates, and controlling the timing of T-cell developmental progression such that removal or antagonism of endogenous PU.1 allows precocious access to T-cell differentiation. Dominant-negative effects reveal that this repression by PU.1 is mediated indirectly. Genome-wide transcriptome analysis identifies novel targets of PU.1 positive and negative regulation affecting progenitor cell signaling and cell biology and indicating distinct regulatory effects on different subsets of progenitor cell transcription factors. Thus, in addition to supporting early T-cell proliferation, PU.1 regulates the timing of activation of the core T-lineage developmental program.
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Affiliation(s)
- Ameya Champhekar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Sagar S Damle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - George Freedman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Sebastian Carotta
- Division of Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Stephen L Nutt
- Division of Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
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10
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Bruserud Ø, Nepstad I, Hauge M, Hatfield KJ, Reikvam H. STAT3 as a possible therapeutic target in human malignancies: lessons from acute myeloid leukemia. Expert Rev Hematol 2014; 8:29-41. [PMID: 25374305 DOI: 10.1586/17474086.2015.971005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
STAT3 is important for transcriptional regulation in human acute myeloid leukemia (AML). STAT3 has thousands of potential DNA binding sites but usually shows cell type specific binding preferences to a limited number of these. Furthermore, AML is a very heterogeneous disease, and studies of the prognostic impact of STAT3 in human AML have also given conflicting results. A more detailed characterization of STAT3 functions and the expression of various isoforms in human AML will therefore be required before it is possible to design clinical studies of STAT3 inhibitors in this disease, and it will be especially important to investigate whether the functions of STAT3 differ between patients. Several other malignancies also show extensive biological heterogeneity, and the present discussion and the suggested scientific approaches may thus be relevant for other cancer patients.
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Affiliation(s)
- Øystein Bruserud
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
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11
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Prange KHM, Singh AA, Martens JHA. The genome-wide molecular signature of transcription factors in leukemia. Exp Hematol 2014; 42:637-50. [PMID: 24814246 DOI: 10.1016/j.exphem.2014.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 04/22/2014] [Accepted: 04/23/2014] [Indexed: 01/08/2023]
Abstract
Transcription factors control expression of genes essential for the normal functioning of the hematopoietic system and regulate development of distinct blood cell types. During leukemogenesis, aberrant regulation of transcription factors such as RUNX1, CBFβ, MLL, C/EBPα, SPI1, GATA, and TAL1 is central to the disease. Here, we will discuss the mechanisms of transcription factor deregulation in leukemia and how in recent years next-generation sequencing approaches have helped to elucidate the molecular role of many of these aberrantly expressed transcription factors. We will focus on the complexes in which these factors reside, the role of posttranslational modification of these factors, their involvement in setting up higher order chromatin structures, and their influence on the local epigenetic environment. We suggest that only comprehensive knowledge on all these aspects will increase our understanding of aberrant gene expression in leukemia as well as open new entry points for therapeutic intervention.
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Affiliation(s)
- Koen H M Prange
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Abhishek A Singh
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.
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12
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Abstract
MYC dimerizes with MAX to bind DNA, with a preference for the E-box consensus CACGTG and several variant motifs. In cells, MYC binds DNA preferentially within transcriptionally active promoter regions. Although several thousand promoters are bound under physiological (low MYC) conditions, these represent only a fraction of all accessible, active promoters. MYC overexpression-as commonly observed in cancer cells-leads to invasion of virtually all active promoters, as well as of distal enhancer elements. We summarize here what is currently known about the mechanisms that may guide this process. We propose that binding site recognition is determined by low-affinity protein-protein interactions between MYC/MAX dimers and components of the basal transcriptional machinery, other chromatin-associated protein complexes, and/or DNA-bound transcription factors. DNA binding occurs subsequently, without an obligate requirement for sequence recognition. Local DNA scanning then leads to preferential stabilization of the MYC/MAX dimer on high-affinity DNA elements. This model is consistent with the invasion of all active promoters that occurs at elevated MYC levels, but posits that important differences in affinity persist between physiological target sites and the newly invaded elements, which may not all be bound in a productive regulatory mode. The implications of this model for transcriptional control by MYC in normal and cancer cells are discussed in the light of the latest literature.
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Affiliation(s)
- Arianna Sabò
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy
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13
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DNA methylation-mediated silencing of PU.1 in leukemia cells resistant to cell differentiation. SPRINGERPLUS 2013; 2:392. [PMID: 24010046 PMCID: PMC3758488 DOI: 10.1186/2193-1801-2-392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/13/2013] [Indexed: 11/20/2022]
Abstract
In mice, the proviral integration of the Friend Spleen Focus Forming Virus (SFFV) within the PU.1 locus of erythroid precursors results in the development of erythroleukemia. SFFV integrates several kilobases upstream of the PU.1 transcription initiation start site leading to the constitutive activation of the gene which in turn results in a block of erythroid differentiation. In this study we have mapped and sequenced the exact location of the retroviral integration site. We have shown that SFFV integrates downstream of a previously described upstream regulatory element (URE), precisely 2,976 bp downstream of the URE-distal element. We have also found that SFFV persists integrated within the same location in resistant cell lines that have lost their differentiation capacity and in which case PU.1 remains silent. We have examined the methylation status of PU.1 and found that in resistant cells the nearby CpG islands remained methylated in contrast to a non-methylated status of the parental cell lines. Treatment with 5-aza-2′-deoxycytidine caused resistant cells to differentiate yet only when combined with HMBA. Altogether these results strongly suggest that methylation plays a crucial role with regard to PU.1 silencing. However, although demethylation is required, it is not sufficient to overcome the differentiation impasse. We have also showed that activation blockage of the Epo/Epo-R pathway remains despite of the absence of PU.1.
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14
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Epigenetic silencing of Bim transcription by Spi-1/PU.1 promotes apoptosis resistance in leukaemia. Cell Death Differ 2013; 20:1268-78. [PMID: 23852375 DOI: 10.1038/cdd.2013.88] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/14/2013] [Accepted: 06/07/2013] [Indexed: 12/17/2022] Open
Abstract
Deregulation of transcriptional networks contributes to haematopoietic malignancies. The transcription factor Spi-1/PU.1 is a master regulator of haematopoiesis and its alteration leads to leukaemia. Spi-1 overexpression inhibits differentiation and promotes resistance to apoptosis in erythroleukaemia. Here, we show that Spi-1 inhibits mitochondrial apoptosis in vitro and in vivo through the transcriptional repression of Bim, a proapoptotic factor. BIM interacts with MCL-1 that behaves as a major player in the survival of the preleukaemic cells. The repression of BIM expression reduces the amount of BIM-MCL-1 complexes, thus increasing the fraction of potentially active antiapoptotic MCL-1. We then demonstrate that Spi-1 represses Bim transcription by binding to the Bim promoter and by promoting the trimethylation of histone 3 on lysine 27 (H3K27me3, a repressive histone mark) on the Bim promoter. The PRC2 repressive complex of Polycomb is directly responsible for the deposit of H3K27me3 mark at the Bim promoter. SUZ12 and the histone methyltransferase EZH2, two PRC2 subunits bind to the Bim promoter at the same location than H3K27me3, distinct of the Spi-1 DNA binding site. As Spi-1 interacts with SUZ12 and EZH2, these results indicate that Spi-1 modulates the activity of PRC2 without directly recruiting the complex to the site of its activity on the chromatin. Our results identify a new mechanism whereby Spi-1 represses transcription and provide mechanistic insights on the antiapoptotic function of a transcription factor mediated by the epigenetic control of gene expression.
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15
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Pham TH, Minderjahn J, Schmidl C, Hoffmeister H, Schmidhofer S, Chen W, Längst G, Benner C, Rehli M. Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1. Nucleic Acids Res 2013; 41:6391-402. [PMID: 23658224 PMCID: PMC3711439 DOI: 10.1093/nar/gkt355] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/03/2013] [Accepted: 04/15/2013] [Indexed: 11/16/2022] Open
Abstract
The transcription factor PU.1 is crucial for the development of many hematopoietic lineages and its binding patterns significantly change during differentiation processes. However, the 'rules' for binding or not-binding of potential binding sites are only partially understood. To unveil basic characteristics of PU.1 binding site selection in different cell types, we studied the binding properties of PU.1 during human macrophage differentiation. Using in vivo and in vitro binding assays, as well as computational prediction, we show that PU.1 selects its binding sites primarily based on sequence affinity, which results in the frequent autonomous binding of high affinity sites in DNase I inaccessible regions (25-45% of all occupied sites). Increasing PU.1 concentrations and the availability of cooperative transcription factor interactions during lineage differentiation both decrease affinity thresholds for in vivo binding and fine-tune cell type-specific PU.1 binding, which seems to be largely independent of DNA methylation. Occupied sites were predominantly detected in active chromatin domains, which are characterized by higher densities of PU.1 recognition sites and neighboring motifs for cooperative transcription factors. Our study supports a model of PU.1 binding control that involves motif-binding affinity, PU.1 concentration, cooperativeness with neighboring transcription factor sites and chromatin domain accessibility, which likely applies to all PU.1 expressing cells.
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Affiliation(s)
- Thu-Hang Pham
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Julia Minderjahn
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christian Schmidl
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Helen Hoffmeister
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Sandra Schmidhofer
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Wei Chen
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Gernot Längst
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christopher Benner
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany, Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, D-13092 Berlin, Germany, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0651, USA and Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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16
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Integrated analyses of genome-wide DNA occupancy and expression profiling identify key genes and pathways involved in cellular transformation by a Marek's disease virus oncoprotein, Meq. J Virol 2013; 87:9016-29. [PMID: 23740999 DOI: 10.1128/jvi.01163-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marek's disease (MD) is an economically significant disease in chickens that is caused by the highly oncogenic Marek's disease virus (MDV). A major unanswered question is the mechanism of MDV-induced tumor formation. Meq, a bZIP transcription factor discovered in the 1990s, is critically involved in viral oncogenicity, but only a few of its host target genes have been described, impeding our understanding of MDV-induced tumorigenesis. Using chromatin immunoprecipitation-sequencing (ChIP-seq) and microarray analysis, a high-confidence list of Meq binding sites in the chicken genome and a global transcriptome of Meq-responsive genes were generated. Meq binding sites were found to be enriched in the promoter regions of upregulated genes but not in those of downregulated genes. ChIP-seq was also performed for c-Jun, a known heterodimeric partner of Meq. The close location of binding sites of Meq and c-Jun was noted, suggesting cooperativity between these two factors in modulating transcription. Pathway analysis indicated that Meq transcriptionally regulates many genes that are part of several signaling pathways including the extracellular signal-regulated kinase /mitogen-activated protein kinase (ERK/MAPK), Jak-STAT, and ErbB pathways, which are critical for oncogenesis and/or include signaling mediators involved in apoptosis. Meq activates oncogenic signaling cascades by transcriptionally activating major kinases in the ERK/MAPK pathway and simultaneously repressing phosphatases, as verified using inhibitors of MEK and ERK1/2 in a cell proliferation assay. This study provides significant insights into the mechanistic basis of Meq-dependent cell transformation.
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17
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Boeva V, Lermine A, Barette C, Guillouf C, Barillot E. Nebula--a web-server for advanced ChIP-seq data analysis. ACTA ACUST UNITED AC 2012; 28:2517-9. [PMID: 22829625 DOI: 10.1093/bioinformatics/bts463] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
MOTIVATION ChIP-seq consists of chromatin immunoprecipitation and deep sequencing of the extracted DNA fragments. It is the technique of choice for accurate characterization of the binding sites of transcription factors and other DNA-associated proteins. We present a web service, Nebula, which allows inexperienced users to perform a complete bioinformatics analysis of ChIP-seq data. RESULTS Nebula was designed for both bioinformaticians and biologists. It is based on the Galaxy open source framework. Galaxy already includes a large number of functionalities for mapping reads and peak calling. We added the following to Galaxy: (i) peak calling with FindPeaks and a module for immunoprecipitation quality control, (ii) de novo motif discovery with ChIPMunk, (iii) calculation of the density and the cumulative distribution of peak locations relative to gene transcription start sites, (iv) annotation of peaks with genomic features and (v) annotation of genes with peak information. Nebula generates the graphs and the enrichment statistics at each step of the process. During Steps 3-5, Nebula optionally repeats the analysis on a control dataset and compares these results with those from the main dataset. Nebula can also incorporate gene expression (or gene modulation) data during these steps. In summary, Nebula is an innovative web service that provides an advanced ChIP-seq analysis pipeline providing ready-to-publish results. AVAILABILITY Nebula is available at http://nebula.curie.fr/ SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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18
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Powers JM, Trobridge GD. Identification of Hematopoietic Stem Cell Engraftment Genes in Gene Therapy Studies. ACTA ACUST UNITED AC 2011; 2013. [PMID: 24383045 PMCID: PMC3875223 DOI: 10.4172/2157-7633.s3-004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hematopoietic stem cell (HSC) therapy using replication-incompetent retroviral vectors is a promising approach to provide life-long correction for genetic defects. HSC gene therapy clinical studies have resulted in functional cures for several diseases, but in some studies clonal expansion or leukemia has occurred. This is due to the dyregulation of endogenous host gene expression from vector provirus insertional mutagenesis. Insertional mutagenesis screens using replicating retroviruses have been used extensively to identify genes that influence oncogenesis. However, retroviral mutagenesis screens can also be used to determine the role of genes in biological processes such as stem cell engraftment. The aim of this review is to describe the potential for vector insertion site data from gene therapy studies to provide novel insights into mechanisms of HSC engraftment. In HSC gene therapy studies dysregulation of host genes by replication-incompetent vector proviruses may lead to enrichment of repopulating clones with vector integrants near genes that influence engraftment. Thus, data from HSC gene therapy studies can be used to identify novel candidate engraftment genes. As HSC gene therapy use continues to expand, the vector insertion site data collected will be of great interest to help identify novel engraftment genes and may ultimately lead to new therapies to improve engraftment.
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Affiliation(s)
- John M Powers
- Department of Pharmaceutical Sciences, Washington State University, Pullman, Washington, USA
| | - Grant D Trobridge
- Department of Pharmaceutical Sciences, Washington State University, Pullman, Washington, USA ; School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
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