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Zhang W, Chronis C, Chen X, Zhang H, Spalinskas R, Pardo M, Chen L, Wu G, Zhu Z, Yu Y, Yu L, Choudhary J, Nichols J, Parast MM, Greber B, Sahlén P, Plath K. The BAF and PRC2 Complex Subunits Dpf2 and Eed Antagonistically Converge on Tbx3 to Control ESC Differentiation. Cell Stem Cell 2020; 24:138-152.e8. [PMID: 30609396 PMCID: PMC6486830 DOI: 10.1016/j.stem.2018.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 06/21/2018] [Accepted: 12/05/2018] [Indexed: 01/01/2023]
Abstract
BAF complexes are composed of different subunits with varying functional and developmental roles, although many subunits have not been examined in depth. Here we show that the Baf45 subunit Dpf2 maintains pluripotency and ESC differentiation potential. Dpf2 co-occupies enhancers with Oct4, Sox2, p300, and the BAF subunit Brg1, and deleting Dpf2 perturbs ESC self-renewal, induces repression of Tbx3, and impairs mesendodermal differentiation without dramatically altering Brg1 localization. Mesendodermal differentiation can be rescued by restoring Tbx3 expression, whose distal enhancer is positively regulated by Dpf2-dependent H3K27ac maintenance and recruitment of pluripotency TFs and Brg1. In contrast, the PRC2 subunit Eed binds an intragenic Tbx3 enhancer to oppose Dpf2-dependent Tbx3 expression and mesendodermal differentiation. The PRC2 subunit Ezh2 likewise opposes Dpf2-dependent differentiation through a distinct mechanism involving Nanog repression. Together, these findings delineate distinct mechanistic roles for specific BAF and PRC2 subunits during ESC differentiation. Dpf2 and Eed antagonistically regulate mesendodermal differentiation of ESCs via Tbx3 Dpf2 and Eed bind different Tbx3 enhancers to control its expression Dpf2 controls H3K27ac and the access of pluripotency TFs at critical target sites Ezh2 and Eed counteract Dpf2 function in differentiation through distinct mechanisms
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Affiliation(s)
- Wensheng Zhang
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China; Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA; Bioinformatics Program, Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Xi Chen
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Heyao Zhang
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China
| | - Rapolas Spalinskas
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Mercedes Pardo
- The Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Liangliang Chen
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China
| | - Guangming Wu
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Zhexin Zhu
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Yong Yu
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Lu Yu
- The Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Jyoti Choudhary
- The Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Mana M Parast
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Boris Greber
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Pelin Sahlén
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA; Bioinformatics Program, Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
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Villanueva-Chimal E, Salinas LS, Fernández-Cardenas LP, Huelgas-Morales G, Cabrera-Wrooman A, Navarro RE. DPFF-1 transcription factor deficiency causes the aberrant activation of MPK-1 and meiotic defects in the Caenorhabditis elegans germline. Genesis 2017; 55. [PMID: 28940692 DOI: 10.1002/dvg.23072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 09/15/2017] [Accepted: 09/20/2017] [Indexed: 12/19/2022]
Abstract
The d4 family of transcription factors consists of three members in mammals. DPF1/neuro-d4 is expressed mainly in neurons and the peripheral nervous system, and is important for brain development. DPF2/requiem/ubi-d4 is expressed ubiquitously and presumably functions as an apoptotic factor, especially during the deprivation of trophic factors. DPF3/cer-d4 is expressed in neurons and in the heart, and is important for heart development and function in zebrafish. In Drosophila, there is only one member, dd4, whose function is still unknown, but it is expressed in many tissues and is particularly abundant in the brain of developing embryos and in adults. Here, we present DPFF-1, the only member of this family of proteins in the nematode C. elegans. DPFF-1 is similar to its mammalian homolog DPF2/requiem/ubi-d4 because it is ubiquitously expressed during embryogenesis and in adult tissues, and because it is important for the induction of germ cell apoptosis during stress. Here, we show that dpff-1 null mutant animals produce less progeny than wild-type nematodes, presumably due to meiotic defects. Gonads of dpff-1 deficient animals showed more germ cells in pachytene and overexpressed the P-MPK-1 signal. Additionally, these animals presented higher levels of p53-induced germ cell apoptosis than wild-type animals. Furthermore, we observed that dpff-1 deficient animals are more sensitive to heat shock. This is the first report showing that the d4 family of transcription factors could be involved in meiosis and stress protection.
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Affiliation(s)
- Emmanuel Villanueva-Chimal
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., México
| | - Laura S Salinas
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., México
| | - Laura P Fernández-Cardenas
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., México
| | - Gabriela Huelgas-Morales
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., México
| | - Alejandro Cabrera-Wrooman
- Laboratorio de Tejido Conjuntivo, Centro Nacional de Investigación y Atención de Quemados, Instituto Nacional de Rehabilitación "Luis Guillermo Ibarra Ibarra,", México, D.F, México
| | - Rosa E Navarro
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., México
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Abstract
Requiem, a hypothesized transcription factor with apoptosis-related activity, was previously shown to be a potential cell engineering gene target for improving recombinant protein production. Requiem suppression has resulted in improved viable cell density and extended culture viability, leading to an overall improvement in recombinant protein productivity. However, not much is known about the function of requiem. We found that requiem is highly conserved at both nucleotide and amino acid levels in Chinese hamster ovary (CHO) cells when compared to human and mouse sequences, suggesting that requiem's functional role is evolutionary well conserved. Upon inducing requiem over-expression, proliferation rates of CHO cells were significantly decreased with doubling times increased by 26%. Interestingly, the over-expression of requiem did not decrease cell viability and could not induce apoptosis. However, requiem sensitized the cells to increased caspase-9 activities under staurosporine-induced apoptosis, suggesting that it has a role to play in mitochondria-mediated apoptosis under staurosporine treatment. The nuclear localization of REQUIEM in CHO cells and its conserved plant homeodomain (PHD) zinc fingers seem to further support the hypothesis that requiem encodes for a potential transcription factor. Upon requiem over-expression, we found that the differentially expressed genes involved in transcriptional regulation and cell proliferation and growth were associated both upstream and downstream of p53.
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Lange M, Kaynak B, Forster UB, Tönjes M, Fischer JJ, Grimm C, Schlesinger J, Just S, Dunkel I, Krueger T, Mebus S, Lehrach H, Lurz R, Gobom J, Rottbauer W, Abdelilah-Seyfried S, Sperling S. Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex. Genes Dev 2008; 22:2370-84. [PMID: 18765789 DOI: 10.1101/gad.471408] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chromatin remodeling and histone modifications facilitate access of transcription factors to DNA by promoting the unwinding and destabilization of histone-DNA interactions. We present DPF3, a new epigenetic key factor for heart and muscle development characterized by a double PHD finger. DPF3 is associated with the BAF chromatin remodeling complex and binds methylated and acetylated lysine residues of histone 3 and 4. Thus, DPF3 may represent the first plant homeodomains that bind acetylated lysines, a feature previously only shown for the bromodomain. During development Dpf3 is expressed in the heart and somites of mouse, chicken, and zebrafish. Morpholino knockdown of dpf3 in zebrafish leads to incomplete cardiac looping and severely reduced ventricular contractility, with disassembled muscular fibers caused by transcriptional deregulation of structural and regulatory proteins. Promoter analysis identified Dpf3 as a novel downstream target of Mef2a. Taken together, DPF3 adds a further layer of complexity to the BAF complex by representing a tissue-specific anchor between histone acetylations as well as methylations and chromatin remodeling. Furthermore, this shows that plant homeodomain proteins play a yet unexplored role in recruiting chromatin remodeling complexes to acetylated histones.
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Affiliation(s)
- Martin Lange
- Group Cardiovascular Genetics, Department Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
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Buchman VL, Luke C, Borthwick EB, Gout I, Ninkina N. Organization of the mouse Ruk locus and expression of isoforms in mouse tissues. Gene 2003; 295:13-17. [PMID: 12242006 DOI: 10.1016/s0378-1119(02)00821-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ruk is a recently identified gene with a complex pattern of expression in mammalian cells and tissues. Multiple Ruk transcripts and several protein isoforms have been detected in various types of cells. Ruk proteins have multidomain organization characteristic of adapter proteins involved in regulation of signal transduction. Interaction of some Ruk isoforms with several signalling proteins, including the p85 regulatory subunit of the Class IA PI 3-kinase, c-Cbl and Grb2, has been demonstrated. Ruk(l), an isoform with three SH3 domains, inhibits lipid kinase activity of the PI 3-kinase in vitro; overexpression of this protein induces apoptotic cell death of primary neurons in culture and changes in membrane trafficking in other cultured cells. However, shorter isoforms of Ruk block pro-apoptotic effect of Ruk(l), suggesting that expression of different combinations of Ruk proteins in cells could be involved in the regulation of their survival and other intracellular processes. To understand the mechanism of differential expression of Ruk proteins we studied organization of the mouse Ruk gene and its transcripts. Twenty-four exons of the Ruk gene span over 320 kb of the mouse chromosome X. Analysis of cDNA clones, ESTs and products of RT-PCR amplifications with different combinations of primers revealed how alternative splicing and promoter usage generate a variety of Ruk transcripts and encoded protein isoforms in different mouse tissues.
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Affiliation(s)
- Vladimir L Buchman
- Department of Preclinical Veterinary Sciences, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, Scotland, UK.
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Nabirochkina E, Simonova OB, Mertsalov IB, Kulikova DA, Ladigina NG, Korochkin LI, Buchman VL. Expression pattern of dd4, a sole member of the d4 family of transcription factors in Drosophila melanogaster. Mech Dev 2002; 114:119-23. [PMID: 12175496 DOI: 10.1016/s0925-4773(02)00035-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In vertebrates, three members of the d4 gene family code for proteins, which are believed to function as transcription factors and involved in regulation of various intracellular processes. One member of the family, ubi-d4/requiem is ubiquitously expressed gene and two other, neuro-d4 and cer-d4, are expressed predominantly in the neural tissues (Nucleic Acids Res. 20 (1992) 5579; Biochim. Biophys. Acta 14 (1992) 172; Mamm. Genome 11 (2000) 72; Mamm. Genome 12 (2001) 862). Typically, d4 proteins show distinct domain organisation with domain 2/3 in the N-terminal, Krüppel-type zinc finger in the central and two adjacent PHD-fingers (d4-domain) in the C-terminal part of the molecule. However, alternative splicing, which is responsible for complex expression patterns of both neurospecific members of the family, generates multiple protein isoforms lacking certain domains (Nucleic Acids Res. 20 (1992) 5579; Genomics 36 (1996) 174; Mamm. Genome 11 (2000) 72; Mamm. Genome 12 (2001) 862). Exact function of d4 proteins is unclear but their involvement in regulation of differentiation and apoptotic cell death has been proposed (J. Biol. Chem. 269 (1994) 29515; Mamm. Genome 11 (2000) 72; Mamm. Genome 12 (2001) 862). Here we identified a single gene, dd4, in the genome of Drosophila melanogaster, the protein product of which could be assigned to the d4 family. Expression of dd4 is regulated during Drosophila development, and is most prominent in syncytial embryos and later in the embryonic nervous and reproductive systems. In flies dd4 mRNA is found in most tissues but the highest level of expression is detected in ovaries.
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Affiliation(s)
- Elena Nabirochkina
- Institute of Gene Biology, Russian Academy of Sciences, 34/5, Vavilov Street, 117334 Moscow, Russia
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