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Lemma RB, Fuglerud BM, Frampton J, Gabrielsen OS. MYB: A Key Transcription Factor in the Hematopoietic System Subject to Many Levels of Control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:3-29. [PMID: 39017837 DOI: 10.1007/978-3-031-62731-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
MYB is a master regulator and pioneer factor highly expressed in hematopoietic progenitor cells (HPCs) where it contributes to the reprogramming processes operating during hematopoietic development. MYB plays a complex role being involved in several lineages of the hematopoietic system. At the molecular level, the MYB gene is subject to intricate regulation at many levels through several enhancer and promoter elements, through transcriptional elongation control, as well as post-transcriptional regulation. The protein is modulated by post-translational modifications (PTMs) such as SUMOylation restricting the expression of its downstream targets. Together with a range of interaction partners, cooperating transcription factors (TFs) and epigenetic regulators, MYB orchestrates a fine-tuned symphony of genes expressed during various stages of haematopoiesis. At the same time, the complex MYB system is vulnerable, being a target for unbalanced control and cancer development.
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Affiliation(s)
- Roza Berhanu Lemma
- Department of Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | | | - Jon Frampton
- Department of Cancer & Genomic Sciences, College of Medicine & Health, University of Birmingham, Edgbaston, Birmingham, UK
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Lemma RB, Ledsaak M, Fuglerud BM, Rodríguez-Castañeda F, Eskeland R, Gabrielsen OS. MYB regulates the SUMO protease SENP1 and its novel interaction partner UXT, modulating MYB target genes and the SUMO landscape. J Biol Chem 2023; 299:105062. [PMID: 37468105 PMCID: PMC10463205 DOI: 10.1016/j.jbc.2023.105062] [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: 11/18/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
SUMOylation is a post-translational modification frequently found on nuclear proteins, including transcription factors (TFs) and coactivators. By controlling the activity of several TFs, SUMOylation may have far-reaching effects. MYB is an example of a developmental TF subjected to SUMO-mediated regulation, through both SUMO conjugation and SUMO binding. How SUMO affects MYB target genes is unknown. Here, we explored the global effect of reduced SUMOylation of MYB on its downstream gene programs. RNA-Seq in K562 cells after MYB knockdown and rescue with mutants having an altered SUMO status revealed a number of differentially regulated genes and distinct gene ontology term enrichments. Clearly, the SUMO status of MYB both quantitatively and qualitatively affects its regulome. The transcriptome data further revealed that MYB upregulates the SUMO protease SENP1, a key enzyme that removes SUMO conjugation from SUMOylated proteins. Given this role of SENP1 in the MYB regulome, we expanded the analysis, mapped interaction partners of SENP1, and identified UXT as a novel player affecting the SUMO system by acting as a repressor of SENP1. MYB inhibits the expression of UXT suggesting that MYB is able not only to control a specific gene program directly but also indirectly by affecting the SUMO landscape through SENP1 and UXT. These findings suggest an autoactivation loop whereby MYB, through enhancing SENP1 and reducing UXT, is itself being activated by a reduced level of repressive SUMOylation. We propose that overexpressed MYB, seen in multiple cancers, may drive this autoactivation loop and contribute to oncogenic activation of MYB.
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Affiliation(s)
- Roza Berhanu Lemma
- Department of Biosciences, University of Oslo, Oslo, Norway; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.
| | - Marit Ledsaak
- Department of Biosciences, University of Oslo, Oslo, Norway; Faculty of Medicine, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | | | - Ragnhild Eskeland
- Department of Biosciences, University of Oslo, Oslo, Norway; Faculty of Medicine, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Faculty of Medicine, Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Nyquist MD, Coleman IM, Lucas JM, Li D, Hanratty B, Meade H, Mostaghel EA, Plymate SR, Corey E, Haffner MC, Nelson PS. Supraphysiological Androgens Promote the Tumor Suppressive Activity of the Androgen Receptor through cMYC Repression and Recruitment of the DREAM Complex. Cancer Res 2023; 83:2938-2951. [PMID: 37352376 PMCID: PMC10472100 DOI: 10.1158/0008-5472.can-22-2613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 02/24/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
The androgen receptor (AR) pathway regulates key cell survival programs in prostate epithelium. The AR represents a near-universal driver and therapeutic vulnerability in metastatic prostate cancer, and targeting AR has a remarkable therapeutic index. Though most approaches directed toward AR focus on inhibiting AR signaling, laboratory and now clinical data have shown that high dose, supraphysiological androgen treatment (SPA) results in growth repression and improved outcomes in subsets of patients with prostate cancer. A better understanding of the mechanisms contributing to SPA response and resistance could help guide patient selection and combination therapies to improve efficacy. To characterize SPA signaling, we integrated metrics of gene expression changes induced by SPA together with cistrome data and protein-interactomes. These analyses indicated that the dimerization partner, RB-like, E2F, and multivulval class B (DREAM) complex mediates growth repression and downregulation of E2F targets in response to SPA. Notably, prostate cancers with complete genomic loss of RB1 responded to SPA treatment, whereas loss of DREAM complex components such as RBL1/2 promoted resistance. Overexpression of MYC resulted in complete resistance to SPA and attenuated the SPA/AR-mediated repression of E2F target genes. These findings support a model of SPA-mediated growth repression that relies on the negative regulation of MYC by AR leading to repression of E2F1 signaling via the DREAM complex. The integrity of MYC signaling and DREAM complex assembly may consequently serve as determinants of SPA responses and as pathways mediating SPA resistance. SIGNIFICANCE Determining the molecular pathways by which supraphysiological androgens promote growth arrest and treatment responses in prostate cancer provides opportunities for biomarker-selected clinical trials and the development of strategies to augment responses.
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Affiliation(s)
- Michael D. Nyquist
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ilsa M. Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jared M. Lucas
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Dapei Li
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Brian Hanratty
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Hannah Meade
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Elahe A. Mostaghel
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, Washington
| | - Stephen R. Plymate
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, Washington
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington
| | - Michael C. Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Peter S. Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Urology, University of Washington, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle, Washington
- Department of Medicine, University of Washington, Seattle, Washington
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Bengtsen M, Winje IM, Eftestøl E, Landskron J, Sun C, Nygård K, Domanska D, Millay DP, Meza-Zepeda LA, Gundersen K. Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle. PLoS Genet 2021; 17:e1009907. [PMID: 34752468 PMCID: PMC8604348 DOI: 10.1371/journal.pgen.1009907] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 11/19/2021] [Accepted: 10/23/2021] [Indexed: 01/04/2023] Open
Abstract
Muscle cells have different phenotypes adapted to different usage, and can be grossly divided into fast/glycolytic and slow/oxidative types. While most muscles contain a mixture of such fiber types, we aimed at providing a genome-wide analysis of the epigenetic landscape by ChIP-Seq in two muscle extremes, the fast/glycolytic extensor digitorum longus (EDL) and slow/oxidative soleus muscles. Muscle is a heterogeneous tissue where up to 60% of the nuclei can be of a different origin. Since cellular homogeneity is critical in epigenome-wide association studies we developed a new method for purifying skeletal muscle nuclei from whole tissue, based on the nuclear envelope protein Pericentriolar material 1 (PCM1) being a specific marker for myonuclei. Using antibody labelling and a magnetic-assisted sorting approach, we were able to sort out myonuclei with 95% purity in muscles from mice, rats and humans. The sorting eliminated influence from the other cell types in the tissue and improved the myo-specific signal. A genome-wide comparison of the epigenetic landscape in EDL and soleus reflected the differences in the functional properties of the two muscles, and revealed distinct regulatory programs involving distal enhancers, including a glycolytic super-enhancer in the EDL. The two muscles were also regulated by different sets of transcription factors; e.g. in soleus, binding sites for MEF2C, NFATC2 and PPARA were enriched, while in EDL MYOD1 and SIX1 binding sites were found to be overrepresented. In addition, more novel transcription factors for muscle regulation such as members of the MAF family, ZFX and ZBTB14 were identified. Complex tissues like skeletal muscle contain a variety of cells which confound the analysis of each cell type when based on homogenates, thus only about half of the cell nuclei in muscles reside inside the muscle cells. We here describe a labelling and sorting technique that allowed us to study the epigenetic landscape in purified muscle cell nuclei leaving the other cell types out. Differences between a fast/glycolytic and a slow/oxidative muscle were studied. While all skeletal muscle fibers have a similar make up and basic function, they differ in their physiology and the way they are used. Thus, some fibers are fast contracting but fatigable, and are used for short lasting explosive tasks such as sprinting. Other fibers are slow and are used for more prolonged tasks such as standing or long distance running. Since fiber type correlate with metabolic profile these features can also be related to metabolic diseases. We here show that the epigenetic landscape differed in gene loci corresponding to the differences in functional properties, and revealed that the two types are enriched in different gene regulatory networks. Exercise can alter muscle phenotype, and the epigenetic landscape might be related to how plastic different properties are.
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Affiliation(s)
- Mads Bengtsen
- Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Einar Eftestøl
- Department of Biosciences, University of Oslo, Oslo, Norway
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | | | - Chengyi Sun
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Kamilla Nygård
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Diana Domanska
- Department of Pathology, University of Oslo, Oslo, Norway
| | - Douglas P. Millay
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Leonardo A. Meza-Zepeda
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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Dúcka M, Kučeríková M, Trčka F, Červinka J, Biglieri E, Šmarda J, Borsig L, Beneš P, Knopfová L. c-Myb interferes with inflammatory IL1α-NF-κB pathway in breast cancer cells. Neoplasia 2021; 23:326-336. [PMID: 33621853 PMCID: PMC7905261 DOI: 10.1016/j.neo.2021.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/12/2021] [Accepted: 01/20/2021] [Indexed: 12/14/2022] Open
Abstract
The transcription factor c-Myb can be involved in the activation of many genes with protumorigenic function; however, its role in breast cancer (BC) development is still under discussion. c-Myb is considered as a tumor-promoting factor in the early phases of BC, on the other hand, its expression in BC patients relates to a good prognosis. Previously, we have shown that c-Myb controls the capacity of BC cells to form spontaneous lung metastasis. Reduced seeding of BC cells to the lungs is linked to high expression of c-Myb and a decline in expression of a specific set of inflammatory genes. Here, we unraveled a c-Myb-IL1α-NF-κB signaling axis that takes place in tumor cells. We report that an overexpression of c-Myb interfered with the activity of NF-κB in several BC cell lines. We identified IL1α to be essential for this interference since it was abrogated in the IL1α-deficient cells. Overexpression of IL1α, as well as addition of recombinant IL1α protein, activated NF-κB signaling and restored expression of the inflammatory signature genes suppressed by c-Myb. The endogenous levels of c-Myb negatively correlated with IL1α on both transcriptional and protein levels across BC cell lines. We concluded that inhibition of IL1α expression by c-Myb reduces NF-κB activity and disconnects the inflammatory circuit, a potentially targetable mechanism to mimic the antimetastatic effect of c-Myb with therapeutic perspective.
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Affiliation(s)
- Monika Dúcka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, Center for Biological and Cellular Engineering, St. Anne's University Hospital, Brno, Czech Republic
| | - Martina Kučeríková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Filip Trčka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, Center for Biological and Cellular Engineering, St. Anne's University Hospital, Brno, Czech Republic
| | - Jakub Červinka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, Center for Biological and Cellular Engineering, St. Anne's University Hospital, Brno, Czech Republic
| | - Elisabetta Biglieri
- Institute of Physiology, University of Zurich and Comprehensive Cancer Center, Zurich, Switzerland
| | - Jan Šmarda
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lubor Borsig
- Institute of Physiology, University of Zurich and Comprehensive Cancer Center, Zurich, Switzerland
| | - Petr Beneš
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, Center for Biological and Cellular Engineering, St. Anne's University Hospital, Brno, Czech Republic
| | - Lucia Knopfová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, Center for Biological and Cellular Engineering, St. Anne's University Hospital, Brno, Czech Republic.
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Boulanger M, Chakraborty M, Tempé D, Piechaczyk M, Bossis G. SUMO and Transcriptional Regulation: The Lessons of Large-Scale Proteomic, Modifomic and Genomic Studies. Molecules 2021; 26:molecules26040828. [PMID: 33562565 PMCID: PMC7915335 DOI: 10.3390/molecules26040828] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
One major role of the eukaryotic peptidic post-translational modifier SUMO in the cell is transcriptional control. This occurs via modification of virtually all classes of transcriptional actors, which include transcription factors, transcriptional coregulators, diverse chromatin components, as well as Pol I-, Pol II- and Pol III transcriptional machineries and their regulators. For many years, the role of SUMOylation has essentially been studied on individual proteins, or small groups of proteins, principally dealing with Pol II-mediated transcription. This provided only a fragmentary view of how SUMOylation controls transcription. The recent advent of large-scale proteomic, modifomic and genomic studies has however considerably refined our perception of the part played by SUMO in gene expression control. We review here these developments and the new concepts they are at the origin of, together with the limitations of our knowledge. How they illuminate the SUMO-dependent transcriptional mechanisms that have been characterized thus far and how they impact our view of SUMO-dependent chromatin organization are also considered.
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Affiliation(s)
- Mathias Boulanger
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Mehuli Chakraborty
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Denis Tempé
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Marc Piechaczyk
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
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Næs G, Storesund JO, Udayakumar P, Ledsaak M, Gabrielsen OS. Dissecting the transactivation domain (tAD) of the transcription factor c-Myb to assess recent models of tAD function. FEBS Open Bio 2020; 10:2329-2342. [PMID: 32937031 PMCID: PMC7609802 DOI: 10.1002/2211-5463.12978] [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: 05/11/2020] [Revised: 08/25/2020] [Accepted: 09/10/2020] [Indexed: 11/29/2022] Open
Abstract
Transcription factors use a DNA-binding domain to localize their action and a transactivation domain (tAD) to stimulate activation of the associated gene. Recent work has renewed interest in how tADs activate genes, which remains poorly understood. Key features in the new models are exposure of short linear motifs (SLMs) and liquid-liquid phase separation (LLPS). Inspired by the new models for tAD function, we decided to revisit the tAD of the haematopoietic transcription factor c-Myb by performing a mutational analysis to see how these new models fit and potentially explain the tAD behaviour of this master regulator. We know that c-Myb has an acidic tAD, which contains a well-characterized SLM in the form of a LxxLL motif. By testing 12 alanine-scanning mutants and three mutants with major reorganization of its tAD in two mammalian reporter systems, we found a pattern of effects very close to what would be expected from the SLM-exposure model, with strong effects exerted by both acidic replacements and SLM mutation. When the same mutants were tested in a yeast system, the pattern of effects was dramatically different, with the SLM mutation exerting no effect, and tAD behaviour was much less affected by small alterations, as would be expected from a LLPS model. These observations are discussed in the light of the two new tAD models, and a two-step hypothesis for transactivation, combining both models, is proposed.
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Affiliation(s)
- Guro Næs
- Department of BiosciencesUniversity of OsloNorway
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Rodríguez-Castañeda F, Lemma RB, Cuervo I, Bengtsen M, Moen LM, Ledsaak M, Eskeland R, Gabrielsen OS. The SUMO protease SENP1 and the chromatin remodeler CHD3 interact and jointly affect chromatin accessibility and gene expression. J Biol Chem 2018; 293:15439-15454. [PMID: 30082317 DOI: 10.1074/jbc.ra118.002844] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/12/2018] [Indexed: 01/22/2023] Open
Abstract
The small ubiquitin-like modifier (SUMO) post-translationally modifies lysine residues of transcription factors and co-regulators and thereby contributes to an important layer of control of the activities of these transcriptional regulators. Likewise, deSUMOylation of these factors by the sentrin-specific proteases (SENPs) also plays a role in gene regulation, but whether SENPs functionally interact with other regulatory factors that control gene expression is unclear. In the present work, we focused on SENP1, specifically, on its role in activation of gene expression investigated through analysis of the SENP1 interactome, which revealed that SENP1 physically interacts with the chromatin remodeler chromodomain helicase DNA-binding protein 3 (CHD3). Using several additional methods, including GST pulldown and co-immunoprecipitation assays, we validated and mapped this interaction, and using CRISPR-Cas9-generated CHD3- and SENP1-KO cells (in the haploid HAP1 cell line), we investigated whether these two proteins are functionally linked in regulating chromatin remodeling and gene expression. Genome-wide ATAC-Seq analysis of the CHD3- and SENP1-KO cells revealed a large degree of overlap in differential chromatin openness between these two mutant cell lines. Moreover, motif analysis and comparison with ChIP-Seq profiles in K562 cells pointed to an association of CHD3 and SENP1 with CCCTC-binding factor (CTCF) and SUMOylated chromatin-associated factors. Lastly, genome-wide RNA-Seq also indicated that these two proteins co-regulate the expression of several genes. We propose that the functional link between chromatin remodeling by CHD3 and deSUMOylation by SENP1 uncovered here provides another level of control of gene expression.
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Affiliation(s)
| | - Roza Berhanu Lemma
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and
| | - Ignacio Cuervo
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and
| | - Mads Bengtsen
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and
| | - Lisa Marie Moen
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and
| | - Marit Ledsaak
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and
| | - Ragnhild Eskeland
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and.,the Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, P.O. Box 1112 Blindern, N-0317 Oslo, Norway
| | - Odd Stokke Gabrielsen
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and
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Fuglerud BM, Ledsaak M, Rogne M, Eskeland R, Gabrielsen OS. The pioneer factor activity of c-Myb involves recruitment of p300 and induction of histone acetylation followed by acetylation-induced chromatin dissociation. Epigenetics Chromatin 2018; 11:35. [PMID: 29954426 PMCID: PMC6022509 DOI: 10.1186/s13072-018-0208-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/26/2018] [Indexed: 12/17/2022] Open
Abstract
Background The concept of pioneer transcription factors is emerging as an essential part of the epigenetic regulation, taking place during cell development and differentiation. However, the precise molecular mechanism underlying pioneer factor activity remains poorly understood. We recently reported that the transcription factor c-Myb acts as a pioneer factor in haematopoiesis, and a point mutation in its DNA binding domain, D152V, is able to abrogate this function. Results Here, we show that specific histone modifications, including H3K27ac, prevent binding of c-Myb to histone tails, representing a novel effect of histone modifications, namely restricting binding of a pioneer factor to chromatin. Furthermore, we have taken advantage of the pioneer-defect D152V mutant to investigate mechanisms of c-Myb’s pioneer factor activity. We show that c-Myb-dependent transcriptional activation of a gene in inaccessible chromatin relies on c-Myb binding to histones, as well as on c-Myb interacting with the histone acetyltransferase p300. ChIP assays show that both wild type and the D152V mutant of c-Myb bind to a selected target gene at its promoter and enhancer, but only wild-type c-Myb causes opening and activation of the locus. Enhancement of histone acetylation restores activation of the same gene in the absence of c-Myb, suggesting that facilitating histone acetylation is a crucial part of the pioneer factor function of c-Myb. Conclusions We suggest a pioneer factor model in which c-Myb binds to regions of closed chromatin and then recruits histone acetyltransferases. By binding to histones, c-Myb facilitates histone acetylation, acting as a cofactor for p300 at c-Myb bound sites. The resulting H3K27ac leads to chromatin opening and detachment of c-Myb from the acetylated chromatin. We propose that the latter phenomenon, acetylation-induced chromatin dissociation, represents a mechanism for controlling the dynamics of pioneer factor binding to chromatin. Electronic supplementary material The online version of this article (10.1186/s13072-018-0208-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bettina M Fuglerud
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway
| | - Marit Ledsaak
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway
| | - Marie Rogne
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway
| | - Ragnhild Eskeland
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, 0379, Norway
| | - Odd S Gabrielsen
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway.
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Fuglerud BM, Lemma RB, Wanichawan P, Sundaram AYM, Eskeland R, Gabrielsen OS. A c-Myb mutant causes deregulated differentiation due to impaired histone binding and abrogated pioneer factor function. Nucleic Acids Res 2017; 45:7681-7696. [PMID: 28472346 PMCID: PMC5570105 DOI: 10.1093/nar/gkx364] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/26/2017] [Indexed: 12/21/2022] Open
Abstract
The transcription factor c-Myb is involved in early differentiation and proliferation of haematopoietic cells, where it operates as a regulator of self-renewal and multi-lineage differentiation. Deregulated c-Myb plays critical roles in leukaemias and other human cancers. Due to its role as a master regulator, we hypothesized it might function as a pioneer transcription factor. Our approach to test this was to analyse a mutant of c-Myb, D152V, previously reported to cause haematopoietic defects in mice by an unknown mechanism. Our transcriptome data from K562 cells indicates that this mutation specifically affects c-Myb's ability to regulate genes involved in differentiation, causing failure in c-Myb's ability to block differentiation. Furthermore, we see a major effect of this mutation in assays where chromatin opening is involved. We show that each repeat in the minimal DNA-binding domain of c-Myb binds to histones and that D152V disrupts histone binding of the third repeat. ATAC-seq data indicates this mutation impairs the ability of c-Myb to cause chromatin opening at specific sites. Taken together, our findings support that c-Myb acts as a pioneer factor and show that D152V impairs this function. The D152V mutant is the first mutant of a transcription factor specifically destroying pioneer factor function.
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Affiliation(s)
- Bettina M Fuglerud
- Department of Biosciences, University of Oslo, P.O.Box 1066 Blindern, N-0316 Oslo, Norway
| | - Roza B Lemma
- Department of Biosciences, University of Oslo, P.O.Box 1066 Blindern, N-0316 Oslo, Norway
| | - Pimthanya Wanichawan
- Department of Biosciences, University of Oslo, P.O.Box 1066 Blindern, N-0316 Oslo, Norway.,Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, P.O.Box 4956 Nydalen, N-0424 Oslo, Norway.,Center for Heart Failure Research, Oslo University Hospital and University of Oslo, P.O.Box 4956 Nydalen, N-0424 Oslo, Norway
| | - Arvind Y M Sundaram
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, P.O.Box 4950 Nydalen, N-0424 Oslo, Norway
| | - Ragnhild Eskeland
- Department of Biosciences, University of Oslo, P.O.Box 1066 Blindern, N-0316 Oslo, Norway.,Norwegian Center for Stem Cell Research, Department of Immunology, Oslo University Hospital, P.O.Box 1112 Blindern, N-0317 Oslo, Norway
| | - Odd S Gabrielsen
- Department of Biosciences, University of Oslo, P.O.Box 1066 Blindern, N-0316 Oslo, Norway
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Bengtsen M, Sørensen L, Aabel L, Ledsaak M, Matre V, Gabrielsen OS. The adaptor protein ARA55 and the nuclear kinase HIPK1 assist c-Myb in recruiting p300 to chromatin. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:751-760. [DOI: 10.1016/j.bbagrm.2017.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/26/2017] [Accepted: 05/03/2017] [Indexed: 02/01/2023]
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12
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Rosonina E, Akhter A, Dou Y, Babu J, Sri Theivakadadcham VS. Regulation of transcription factors by sumoylation. Transcription 2017; 8:220-231. [PMID: 28379052 PMCID: PMC5574528 DOI: 10.1080/21541264.2017.1311829] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Transcription factors (TFs) are among the most frequently detected targets of sumoylation, and effects of the modification have been studied for about 200 individual TFs to date. TF sumoylation is most often associated with reduced target gene expression, which can be mediated by enhanced interactions with corepressors or by interference with protein modifications that promote transcription. However, recent studies show that sumoylation also regulates gene expression by controlling the levels of TFs that are associated with chromatin. SUMO can mediate this by modulating TF DNA-binding activity, promoting clearance of TFs from chromatin, or indirectly, by influencing TF abundance or localization.
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Affiliation(s)
- Emanuel Rosonina
- a Department of Biology , York University , Toronto , ON , Canada
| | - Akhi Akhter
- a Department of Biology , York University , Toronto , ON , Canada
| | - Yimo Dou
- a Department of Biology , York University , Toronto , ON , Canada
| | - John Babu
- a Department of Biology , York University , Toronto , ON , Canada
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13
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Pichler A, Fatouros C, Lee H, Eisenhardt N. SUMO conjugation - a mechanistic view. Biomol Concepts 2017; 8:13-36. [PMID: 28284030 DOI: 10.1515/bmc-2016-0030] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/06/2017] [Indexed: 02/08/2023] Open
Abstract
The regulation of protein fate by modification with the small ubiquitin-related modifier (SUMO) plays an essential and crucial role in most cellular pathways. Sumoylation is highly dynamic due to the opposing activities of SUMO conjugation and SUMO deconjugation. SUMO conjugation is performed by the hierarchical action of E1, E2 and E3 enzymes, while its deconjugation involves SUMO-specific proteases. In this review, we summarize and compare the mechanistic principles of how SUMO gets conjugated to its substrate. We focus on the interplay of the E1, E2 and E3 enzymes and discuss how specificity could be achieved given the limited number of conjugating enzymes and the thousands of substrates.
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Affiliation(s)
- Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Chronis Fatouros
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Heekyoung Lee
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Nathalie Eisenhardt
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
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