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Schneider MF, Müller V, Müller SA, Lichtenthaler SF, Becker PB, Scheuermann JC. LncRNA RUS shapes the gene expression program towards neurogenesis. Life Sci Alliance 2022; 5:5/10/e202201504. [PMID: 35688487 PMCID: PMC9187872 DOI: 10.26508/lsa.202201504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022] Open
Abstract
The chromatin-associated lncRNA RUS binds in the vicinity to neural differentiation-associated genes and regulates them in a context-dependent manner to enable proper neuron development. The evolution of brain complexity correlates with an increased expression of long, noncoding (lnc) RNAs in neural tissues. Although prominent examples illustrate the potential of lncRNAs to scaffold and target epigenetic regulators to chromatin loci, only few cases have been described to function during brain development. We present a first functional characterization of the lncRNA LINC01322, which we term RUS for “RNA upstream of Slitrk3.” The RUS gene is well conserved in mammals by sequence and synteny next to the neurodevelopmental gene Slitrk3. RUS is exclusively expressed in neural cells and its expression increases during neuronal differentiation of mouse embryonic cortical neural stem cells. Depletion of RUS locks neuronal precursors in an intermediate state towards neuronal differentiation resulting in arrested cell cycle and increased apoptosis. RUS associates with chromatin in the vicinity of genes involved in neurogenesis, most of which change their expression upon RUS depletion. The identification of a range of epigenetic regulators as specific RUS interactors suggests that the lncRNA may mediate gene activation and repression in a highly context-dependent manner.
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Affiliation(s)
- Marius F Schneider
- Division of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians-University, Munich, Germany.,Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center Munich (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Veronika Müller
- Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center Munich (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stephan A Müller
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE) Munich and Neuroproteomics Unit, Technical University, Munich, Germany
| | - Stefan F Lichtenthaler
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE) Munich and Neuroproteomics Unit, Technical University, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Peter B Becker
- Division of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Johanna C Scheuermann
- Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center Munich (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
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Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S, Abo R, Tabebordbar M, Lee RT, Burge CB, Boyer LA. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 2013; 152:570-83. [PMID: 23352431 DOI: 10.1016/j.cell.2013.01.003] [Citation(s) in RCA: 714] [Impact Index Per Article: 64.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/09/2012] [Accepted: 12/20/2012] [Indexed: 11/26/2022]
Abstract
Long noncoding RNAs (lncRNAs) are often expressed in a development-specific manner, yet little is known about their roles in lineage commitment. Here, we identified Braveheart (Bvht), a heart-associated lncRNA in mouse. Using multiple embryonic stem cell (ESC) differentiation strategies, we show that Bvht is required for progression of nascent mesoderm toward a cardiac fate. We find that Bvht is necessary for activation of a core cardiovascular gene network and functions upstream of mesoderm posterior 1 (MesP1), a master regulator of a common multipotent cardiovascular progenitor. We also show that Bvht interacts with SUZ12, a component of polycomb-repressive complex 2 (PRC2), during cardiomyocyte differentiation, suggesting that Bvht mediates epigenetic regulation of cardiac commitment. Finally, we demonstrate a role for Bvht in maintaining cardiac fate in neonatal cardiomyocytes. Together, our work provides evidence for a long noncoding RNA with critical roles in the establishment of the cardiovascular lineage during mammalian development.
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Affiliation(s)
- Carla A Klattenhoff
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Abstract
Polycomb group (PcG) proteins were originally identified as negative regulators of HOX genes in Drosophila but have since emerged as a widely used transcriptional repression system that controls a variety of developmental processes in animals and plants. PcG proteins exist in multi-protein complexes that comprise specific chromatin-modifying enzymatic activities. Genome-wide binding studies in Drosophila and in mammalian cells revealed that these complexes co-localize at a large set of genes encoding developmental regulators. Recent analyses in Drosophila have begun to explore how the different chromatin-modifying activities of PcG protein complexes contribute to the repression of individual target genes. These studies suggest that monoubiquitination of histone H2A (H2Aub) by the PcG protein Sce is only essential for repression of a subset of PcG target genes but is not required for the Polycomb-mediated repression of other targets. Calypso/dBap1, a major deubiquitinase for H2Aub is also critically needed for repression of a subset of PcG target genes. Here, we review our current understanding of the role of H2A monoubiquitination and deubiquitination in Polycomb repression in Drosophila. We discuss unresolved issues concerning the immunological detection of H2Aub and critically evaluate experiments that used Sce and Ring1B point mutants with impaired H2A ubiquitinase activity to study H2Aub-dependent and -independent functions of these proteins in transcriptional repression.
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Affiliation(s)
- Johanna C Scheuermann
- Department of Chromatin and Chromosome Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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Gutiérrez L, Oktaba K, Scheuermann JC, Gambetta MC, Ly-Hartig N, Müller J. The role of the histone H2A ubiquitinase Sce in Polycomb repression. Development 2011; 139:117-27. [PMID: 22096074 PMCID: PMC3253035 DOI: 10.1242/dev.074450] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Polycomb group (PcG) proteins exist in multiprotein complexes that modify chromatin to repress transcription. Drosophila PcG proteins Sex combs extra (Sce; dRing) and Posterior sex combs (Psc) are core subunits of PRC1-type complexes. The Sce:Psc module acts as an E3 ligase for monoubiquitylation of histone H2A, an activity thought to be crucial for repression by PRC1-type complexes. Here, we created an Sce knockout allele and show that depletion of Sce results in loss of H2A monoubiquitylation in developing Drosophila. Genome-wide profiling identified a set of target genes co-bound by Sce and all other PRC1 subunits. Analyses in mutants lacking individual PRC1 subunits reveals that these target genes comprise two distinct classes. Class I genes are misexpressed in mutants lacking any of the PRC1 subunits. Class II genes are only misexpressed in animals lacking the Psc-Su(z)2 and Polyhomeotic (Ph) subunits but remain stably repressed in the absence of the Sce and Polycomb (Pc) subunits. Repression of class II target genes therefore does not require Sce and H2A monoubiquitylation but might rely on the ability of Psc-Su(z)2 and Ph to inhibit nucleosome remodeling or to compact chromatin. Similarly, Sce does not provide tumor suppressor activity in larval tissues under conditions in which Psc-Su(z)2, Ph and Pc show such activity. Sce and H2A monoubiquitylation are therefore only crucial for repression of a subset of genes and processes regulated by PRC1-type complexes. Sce synergizes with the Polycomb repressive deubiquitinase (PR-DUB) complex to repress transcription at class I genes, suggesting that H2A monoubiquitylation must be appropriately balanced for their transcriptional repression.
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Affiliation(s)
- Luis Gutiérrez
- EMBL, Gene Expression Programme, Meyerhofstr. 1, 69117 Heidelberg, Germany
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Scheuermann JC, de Ayala Alonso AG, Oktaba K, Ly-Hartig N, McGinty RK, Fraterman S, Wilm M, Muir TW, Müller J. Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Nature 2010; 465:243-7. [PMID: 20436459 DOI: 10.1038/nature08966] [Citation(s) in RCA: 576] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 02/25/2010] [Indexed: 12/23/2022]
Abstract
Polycomb group (PcG) proteins are transcriptional repressors that control processes ranging from the maintenance of cell fate decisions and stem cell pluripotency in animals to the control of flowering time in plants. In Drosophila, genetic studies identified more than 15 different PcG proteins that are required to repress homeotic (HOX) and other developmental regulator genes in cells where they must stay inactive. Biochemical analyses established that these PcG proteins exist in distinct multiprotein complexes that bind to and modify chromatin of target genes. Among those, Polycomb repressive complex 1 (PRC1) and the related dRing-associated factors (dRAF) complex contain an E3 ligase activity for monoubiquitination of histone H2A (refs 1-4). Here we show that the uncharacterized Drosophila PcG gene calypso encodes the ubiquitin carboxy-terminal hydrolase BAP1. Biochemically purified Calypso exists in a complex with the PcG protein ASX, and this complex, named Polycomb repressive deubiquitinase (PR-DUB), is bound at PcG target genes in Drosophila. Reconstituted recombinant Drosophila and human PR-DUB complexes remove monoubiquitin from H2A but not from H2B in nucleosomes. Drosophila mutants lacking PR-DUB show a strong increase in the levels of monoubiquitinated H2A. A mutation that disrupts the catalytic activity of Calypso, or absence of the ASX subunit abolishes H2A deubiquitination in vitro and HOX gene repression in vivo. Polycomb gene silencing may thus entail a dynamic balance between H2A ubiquitination by PRC1 and dRAF, and H2A deubiquitination by PR-DUB.
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