1
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Chen JJ, Moy C, Pagé V, Monnin C, El-Hajj ZW, Avizonis DZ, Reyes-Lamothe R, Tanny JC. The Rtf1/Prf1-dependent histone modification axis counteracts multi-drug resistance in fission yeast. Life Sci Alliance 2024; 7:e202302494. [PMID: 38514187 PMCID: PMC10958104 DOI: 10.26508/lsa.202302494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
RNA polymerase II transcription elongation directs an intricate pattern of histone modifications. This pattern includes a regulatory cascade initiated by the elongation factor Rtf1, leading to monoubiquitylation of histone H2B, and subsequent methylation of histone H3 on lysine 4. Previous studies have defined the molecular basis for these regulatory relationships, but it remains unclear how they regulate gene expression. To address this question, we investigated a drug resistance phenotype that characterizes defects in this axis in the model eukaryote Schizosaccharomyces pombe (fission yeast). The mutations caused resistance to the ribonucleotide reductase inhibitor hydroxyurea (HU) that correlated with a reduced effect of HU on dNTP pools, reduced requirement for the S-phase checkpoint, and blunting of the transcriptional response to HU treatment. Mutations in the C-terminal repeat domain of the RNA polymerase II large subunit Rpb1 led to similar phenotypes. Moreover, all the HU-resistant mutants also exhibited resistance to several azole-class antifungal agents. Our results suggest a novel, shared gene regulatory function of the Rtf1-H2Bub1-H3K4me axis and the Rpb1 C-terminal repeat domain in controlling fungal drug tolerance.
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Affiliation(s)
- Jennifer J Chen
- https://ror.org/01pxwe438 Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Calvin Moy
- https://ror.org/01pxwe438 Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Viviane Pagé
- https://ror.org/01pxwe438 Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Cian Monnin
- https://ror.org/01pxwe438 Metabolomics Innovation Resource, Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Ziad W El-Hajj
- https://ror.org/01pxwe438 Department of Biology, McGill University, Montreal, Canada
| | - Daina Z Avizonis
- https://ror.org/01pxwe438 Metabolomics Innovation Resource, Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Rodrigo Reyes-Lamothe
- https://ror.org/01pxwe438 Department of Biology, McGill University, Montreal, Canada
| | - Jason C Tanny
- https://ror.org/01pxwe438 Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
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2
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MacKinnon S, Pagé V, Chen JJ, Shariat-Panahi A, Martin RD, Hébert TE, Tanny JC. Spt5 C-terminal repeat domain phosphorylation and length negatively regulate heterochromatin through distinct mechanisms. PLoS Genet 2023; 19:e1010492. [PMID: 37939109 PMCID: PMC10659198 DOI: 10.1371/journal.pgen.1010492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/20/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023] Open
Abstract
Heterochromatin is a condensed chromatin structure that represses transcription of repetitive DNA elements and developmental genes, and is required for genome stability. Paradoxically, transcription of heterochromatic sequences is required for establishment of heterochromatin in diverse eukaryotic species. As such, components of the transcriptional machinery can play important roles in establishing heterochromatin. How these factors coordinate with heterochromatin proteins at nascent heterochromatic transcripts remains poorly understood. In the model eukaryote Schizosaccharomyces pombe (S. pombe), heterochromatin nucleation can be coupled to processing of nascent transcripts by the RNA interference (RNAi) pathway, or to other post-transcriptional mechanisms that are RNAi-independent. Here we show that the RNA polymerase II processivity factor Spt5 negatively regulates heterochromatin in S. pombe through its C-terminal domain (CTD). The Spt5 CTD is analogous to the CTD of the RNA polymerase II large subunit, and is comprised of multiple repeats of an amino acid motif that is phosphorylated by Cdk9. We provide evidence that genetic ablation of Spt5 CTD phosphorylation results in aberrant RNAi-dependent nucleation of heterochromatin at an ectopic location, as well as inappropriate spread of heterochromatin proximal to centromeres. In contrast, truncation of Spt5 CTD repeat number enhanced RNAi-independent heterochromatin formation and bypassed the requirement for RNAi. We relate these phenotypes to the known Spt5 CTD-binding factor Prf1/Rtf1. This separation of function argues that Spt5 CTD phosphorylation and CTD length restrict heterochromatin through unique mechanisms. More broadly, our findings argue that length and phosphorylation of the Spt5 CTD repeat array have distinct regulatory effects on transcription.
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Affiliation(s)
- Sarah MacKinnon
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Jennifer J. Chen
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Ali Shariat-Panahi
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Ryan D. Martin
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Terence E. Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Jason C. Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
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3
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Bourque K, Jones-Tabah J, Pétrin D, Martin RD, Tanny JC, Hébert TE. Comparing the signaling and transcriptome profiling landscapes of human iPSC-derived and primary rat neonatal cardiomyocytes. Sci Rep 2023; 13:12248. [PMID: 37507481 PMCID: PMC10382583 DOI: 10.1038/s41598-023-39525-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023] Open
Abstract
The inaccessibility of human cardiomyocytes significantly hindered years of cardiovascular research efforts. To overcome these limitations, non-human cell sources were used as proxies to study heart function and associated diseases. Rodent models became increasingly acceptable surrogates to model the human heart either in vivo or through in vitro cultures. More recently, due to concerns regarding animal to human translation, including cross-species differences, the use of human iPSC-derived cardiomyocytes presented a renewed opportunity. Here, we conducted a comparative study, assessing cellular signaling through cardiac G protein-coupled receptors (GPCRs) in rat neonatal cardiomyocytes (RNCMs) and human induced pluripotent stem cell-derived cardiomyocytes. Genetically encoded biosensors were used to explore GPCR-mediated nuclear protein kinase A (PKA) and extracellular signal-regulated kinase 1/ 2 (ERK1/2) activities in both cardiomyocyte populations. To increase data granularity, a single-cell analytical approach was conducted. Using automated high content microscopy, our analyses of nuclear PKA and ERK1/2 signaling revealed distinct response clusters in rat and human cardiomyocytes. In line with this, bulk RNA-seq revealed key differences in the expression patterns of GPCRs, G proteins and downstream effector expression levels. Our study demonstrates that human stem cell-derived models of the cardiomyocyte offer distinct advantages for understanding cellular signaling in the heart.
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Affiliation(s)
- Kyla Bourque
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Jace Jones-Tabah
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Darlaine Pétrin
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Ryan D Martin
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada.
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4
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Khan SM, Martin RD, Bayne A, Pétrin D, Bourque K, Jones-Tabah J, Bouazza C, Blaney J, Lau J, Martins-Cannavino K, Gora S, Zhang A, MacKinnon S, Trieu P, Clarke PBS, Trempe JF, Tanny JC, Hébert TE. Gβγ subunits colocalize with RNA polymerase II and regulate transcription in cardiac fibroblasts. J Biol Chem 2023; 299:103064. [PMID: 36841480 PMCID: PMC10060754 DOI: 10.1016/j.jbc.2023.103064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/26/2023] Open
Abstract
Gβγ subunits mediate many different signaling processes in various compartments of the cell, including the nucleus. To gain insight into the functions of nuclear Gβγ signaling, we investigated the functional role of Gβγ signaling in the regulation of GPCR-mediated gene expression in primary rat neonatal cardiac fibroblasts. We identified a novel, negative, regulatory role for the Gβ1γ dimer in the fibrotic response. Depletion of Gβ1 led to derepression of the fibrotic response at the mRNA and protein levels under basal conditions and an enhanced fibrotic response after sustained stimulation of the angiotensin II type I receptor. Our genome-wide chromatin immunoprecipitation experiments revealed that Gβ1 colocalized and interacted with RNA polymerase II on fibrotic genes in an angiotensin II-dependent manner. Additionally, blocking transcription with inhibitors of Cdk9 prevented association of Gβγ with transcription complexes. Together, our findings suggest that Gβ1γ is a novel transcriptional regulator of the fibrotic response that may act to restrict fibrosis to conditions of sustained fibrotic signaling. Our work expands the role for Gβγ signaling in cardiac fibrosis and may have broad implications for the role of nuclear Gβγ signaling in other cell types.
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Affiliation(s)
- Shahriar M Khan
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Ryan D Martin
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Andrew Bayne
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada; Centre de Recherche en Biologie Structurale, McGill University, Montréal, Québec, Canada
| | - Darlaine Pétrin
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Kyla Bourque
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Jace Jones-Tabah
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Celia Bouazza
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Jacob Blaney
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Jenny Lau
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | | | - Sarah Gora
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Andy Zhang
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Sarah MacKinnon
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Phan Trieu
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Paul B S Clarke
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Jean-François Trempe
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, Québec, Canada
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada.
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada.
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5
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Abstract
Histone ubiquitylation is a critical part of both active and repressed transcriptional states, and lies at the heart of DNA damage repair signaling. The histone residues targeted for ubiquitylation are often highly conserved through evolution, and extensive functional studies of the enzymes that catalyze the ubiquitylation and de-ubiquitylation of histones have revealed key roles linked to cell growth and division, development, and disease in model systems ranging from yeast to human cells. Nonetheless, the downstream consequences of these modifications have only recently begun to be appreciated on a molecular level. Here we review the structure and function of proteins that act as effectors or “readers” of histone ubiquitylation. We highlight lessons learned about how ubiquitin recognition lends specificity and function to intermolecular interactions in the context of transcription and DNA repair, as well as what this might mean for how we think about histone modifications more broadly.
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6
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Jones-Tabah J, Martin RD, Chen JJ, Tanny JC, Clarke PBS, Hébert TE. A role for BET proteins in regulating basal, dopamine-induced and cAMP/PKA-dependent transcription in rat striatal neurons. Cell Signal 2021; 91:110226. [PMID: 34974082 DOI: 10.1016/j.cellsig.2021.110226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/01/2023]
Abstract
The activity of striatal medium-spiny projection neurons is regulated by D1 and D2 dopamine receptors. The D1 receptor (D1R) is a Gαs/olf-coupled GPCR which activates a cAMP/PKA/DARPP-32 signalling cascade that increases excitability and facilitates plasticity, partly through the regulation of transcription. Upon activation via D1R, PKA can translocate to the nucleus to regulate transcription through the phosphorylation of various targets. One candidate effector of PKA-dependent transcriptional regulation is the BET protein Brd4. It is known that when Brd4 is activated by phosphorylation, it binds more readily to acetylated histones at promoters and enhancers; moreover, in non-neuronal cells, PKA signalling has been shown to increase recruitment of Brd4 to chromatin. However, it is unknown whether BET proteins, or Brd4 specifically, are involved in transcriptional activation by cAMP/PKA in neurons. Here, we demonstrate that in adult rats, inhibition of BET proteins with the bromodomain inhibitor JQ1 suppressed the expression of ~25% of D1R-upregulated genes, while also increasing the expression of a subset of immediate-early genes. We further found that cAMP/PKA signalling promotes Brd4 recruitment to dopamine-induced genes in striatal neurons, and that knockdown of Brd4 attenuates D1R-induced gene expression. Finally, we report that JQ1 treatment downregulated expression of many GPCRs and also impaired ERK1/2 signalling in striatal neurons. Our findings identify the BET protein family, and Brd4 in particular, as novel regulators of basal and D1R-dependent transcription in rat striatal neurons, and delineate complex bi-directional effects of bromodomain inhibitors on neuronal transcription.
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Affiliation(s)
- Jace Jones-Tabah
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Ryan D Martin
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Jennifer J Chen
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Paul B S Clarke
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada.
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada.
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7
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Jones-Tabah J, Martin RD, Tanny JC, Clarke PBS, Hébert TE. High-Content Single-Cell Förster Resonance Energy Transfer Imaging of Cultured Striatal Neurons Reveals Novel Cross-Talk in the Regulation of Nuclear Signaling by Protein Kinase A and Extracellular Signal-Regulated Kinase 1/2. Mol Pharmacol 2021; 100:526-539. [PMID: 34503973 DOI: 10.1124/molpharm.121.000290] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/07/2021] [Indexed: 11/22/2022] Open
Abstract
Genetically encoded biosensors can be used to track signaling events in living cells by measuring changes in fluorescence emitted by one or more fluorescent proteins. Here, we describe the use of genetically encoded biosensors based on Förster resonance energy transfer (FRET), combined with high-content microscopy, to image dynamic signaling events simultaneously in thousands of neurons in response to drug treatments. We first applied this approach to examine intercellular variation in signaling responses among cultured striatal neurons stimulated with multiple drugs. Using high-content FRET imaging and immunofluorescence, we identified neuronal subpopulations with unique responses to pharmacological manipulation and used nuclear morphology to identify medium spiny neurons within these heterogeneous striatal cultures. Focusing on protein kinase A (PKA) and extracellular signal-regulated kinase 1/2 (ERK1/2) signaling in the cytoplasm and nucleus, we noted pronounced intercellular differences among putative medium spiny neurons, in both the magnitude and kinetics of signaling responses to drug application. Importantly, a conventional "bulk" analysis that pooled all cells in culture yielded a different rank order of drug potency than that revealed by single-cell analysis. Using a single-cell analytical approach, we dissected the relative contributions of PKA and ERK1/2 signaling in striatal neurons and unexpectedly identified a novel role for ERK1/2 in promoting nuclear activation of PKA in striatal neurons. This finding adds a new dimension of signaling crosstalk between PKA and ERK1/2 with relevance to dopamine D1 receptor signaling in striatal neurons. In conclusion, high-content single-cell imaging can complement and extend traditional population-level analyses and provides a novel vantage point from which to study cellular signaling. SIGNIFICANCE STATEMENT: High-content imaging revealed substantial intercellular variation in the magnitude and pattern of intracellular signaling events driven by receptor stimulation. Since individual neurons within the same population can respond differently to a given agonist, interpreting measures of intracellular signaling derived from the averaged response of entire neuronal populations may not always reflect what happened at the single-cell level. This study uses this approach to identify a new form of cross-talk between PKA and ERK1/2 signaling in the nucleus of striatal neurons.
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Affiliation(s)
- Jace Jones-Tabah
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Ryan D Martin
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Paul B S Clarke
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
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8
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Nassour H, Hoang TA, Martin RD, Dallagnol JCC, Billard É, Létourneau M, Novellino E, Carotenuto A, Allen BG, Tanny JC, Fournier A, Hébert TE, Chatenet D. Lipidated peptides derived from intracellular loops 2 and 3 of the urotensin II receptor act as biased allosteric ligands. J Biol Chem 2021; 297:101057. [PMID: 34389356 PMCID: PMC8424217 DOI: 10.1016/j.jbc.2021.101057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 07/23/2021] [Accepted: 08/05/2021] [Indexed: 01/14/2023] Open
Abstract
Over the last decade, the urotensinergic system, composed of one G protein-coupled receptor and two endogenous ligands, has garnered significant attention as a promising new target for the treatment of various cardiovascular diseases. Indeed, this system is associated with various biomarkers of cardiovascular dysfunctions and is involved in changes in cardiac contractility, fibrosis and hypertrophy contributing, like the angiotensinergic system, to the pathogenesis and progression of heart failure. Significant investment has been made toward the development of clinically relevant UT ligands for therapeutic intervention, but with little or no success to date. This system therefore remains to be therapeutically exploited. Pepducins and other lipidated peptides have been used as both mechanistic probes and potential therapeutics; therefore, pepducins derived from the human urotensin II receptor might represent unique tools to generate signaling bias and study hUT signaling networks. Two hUT-derived pepducins, derived from the second and the third intracellular loop of the receptor (hUT-Pep2 and [Trp1, Leu2]hUT-Pep3, respectively) were synthesized and pharmacologically characterized. Our results demonstrated that hUT-Pep2 and [Trp1, Leu2]hUT-Pep3 acted as biased ago-allosteric modulators, triggered ERK1/2 phosphorylation and to a lesser extent, IP1 production and stimulated cell proliferation yet were devoid of contractile activity. Interestingly, both hUT-derived pepducins were able to modulate human urotensin II (hUII)- and urotensin II-related peptide (URP)-mediated contraction albeit to different extents. These new derivatives represent unique tools to reveal the intricacies of hUT signaling and also a novel avenue for the design of allosteric ligands selectively targeting hUT signaling potentially.
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Affiliation(s)
- Hassan Nassour
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Groupe de Recherche en Ingénierie des Peptides et en Pharmacothérapie (GRIPP), Université du Québec, Ville de Laval, Québec, Canada
| | - Tuan Anh Hoang
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Groupe de Recherche en Ingénierie des Peptides et en Pharmacothérapie (GRIPP), Université du Québec, Ville de Laval, Québec, Canada
| | - Ryan D Martin
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Québec, Canada
| | - Juliana C C Dallagnol
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Groupe de Recherche en Ingénierie des Peptides et en Pharmacothérapie (GRIPP), Université du Québec, Ville de Laval, Québec, Canada; Department of Pharmacology and Therapeutics, McGill University, Montreal, Québec, Canada; Department of Medicine, Université de Montreal, Montreal Heart Institute, Montreal, Québec, Canada
| | - Étienne Billard
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Groupe de Recherche en Ingénierie des Peptides et en Pharmacothérapie (GRIPP), Université du Québec, Ville de Laval, Québec, Canada; Department of Pharmacology and Therapeutics, McGill University, Montreal, Québec, Canada
| | - Myriam Létourneau
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Groupe de Recherche en Ingénierie des Peptides et en Pharmacothérapie (GRIPP), Université du Québec, Ville de Laval, Québec, Canada
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy
| | - Alfonso Carotenuto
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy
| | - Bruce G Allen
- Department of Medicine, Université de Montreal, Montreal Heart Institute, Montreal, Québec, Canada
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Québec, Canada
| | - Alain Fournier
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Groupe de Recherche en Ingénierie des Peptides et en Pharmacothérapie (GRIPP), Université du Québec, Ville de Laval, Québec, Canada
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Québec, Canada
| | - David Chatenet
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Groupe de Recherche en Ingénierie des Peptides et en Pharmacothérapie (GRIPP), Université du Québec, Ville de Laval, Québec, Canada.
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9
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Pinto D, Pagé V, Fisher RP, Tanny JC. New connections between ubiquitylation and methylation in the co-transcriptional histone modification network. Curr Genet 2021; 67:695-705. [PMID: 34089069 DOI: 10.1007/s00294-021-01196-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 01/01/2023]
Abstract
Co-transcriptional histone modifications are a ubiquitous feature of RNA polymerase II (RNAPII) transcription, with profound but incompletely understood effects on gene expression. Unlike the covalent marks found at promoters, which are thought to be instructive for transcriptional activation, these modifications occur in gene bodies as a result of transcription, which has made elucidation of their functions challenging. Here we review recent insights into the regulation and roles of two such modifications: monoubiquitylation of histone H2B at lysine 120 (H2Bub1) and methylation of histone H3 at lysine 36 (H3K36me). Both H2Bub1 and H3K36me are enriched in the coding regions of transcribed genes, with highly overlapping distributions, but they were thought to work largely independently. We highlight our recent demonstration that, as was previously shown for H3K36me, H2Bub1 signals to the histone deacetylase (HDAC) complex Rpd3S/Clr6-CII, and that Rpd3S/Clr6-CII and H2Bub1 function in the same pathway to repress aberrant antisense transcription initiating within gene coding regions. Moreover, both of these histone modification pathways are influenced by protein phosphorylation catalyzed by the cyclin-dependent kinases (CDKs) that regulate RNAPII elongation, chiefly Cdk9. Therefore, H2Bub1 and H3K36me are more tightly linked than previously thought, sharing both upstream regulatory inputs and downstream effectors. Moreover, these newfound connections suggest extensive, bidirectional signaling between RNAPII elongation complexes and chromatin-modifying enzymes, which helps to determine transcriptional outputs and should be a focus for future investigation.
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Affiliation(s)
- Daniel Pinto
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Vivane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada.
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10
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Sansó M, Parua PK, Pinto D, Svensson JP, Pagé V, Bitton DA, MacKinnon S, Garcia P, Hidalgo E, Bähler J, Tanny JC, Fisher RP. Cdk9 and H2Bub1 signal to Clr6-CII/Rpd3S to suppress aberrant antisense transcription. Nucleic Acids Res 2020; 48:7154-7168. [PMID: 32496538 PMCID: PMC7367204 DOI: 10.1093/nar/gkaa474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 04/01/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022] Open
Abstract
Mono-ubiquitylation of histone H2B (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. It remained unclear whether Cdk9 and H2Bub1 cooperate to regulate the expression of individual genes. Here, we show that Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of ∼10% of fission yeast genes, with each perturbation affecting largely distinct subsets; ablation of both pathways de-represses antisense transcription of over half the genome. H2Bub1 and phospho-Spt5 have similar genome-wide distributions; both modifications are enriched, and directly proportional to each other, in coding regions, and decrease abruptly around the cleavage and polyadenylation signal (CPS). Cdk9-dependence of antisense suppression at specific genes correlates with high H2Bub1 occupancy, and with promoter-proximal RNAPII pausing. Genetic interactions link Cdk9, H2Bub1 and the histone deacetylase Clr6-CII, while combined Cdk9 inhibition and H2Bub1 loss impair Clr6-CII recruitment to chromatin and lead to decreased occupancy and increased acetylation of histones within gene coding regions. These results uncover novel interactions between co-transcriptional histone modification pathways, which link regulation of RNAPII transcription elongation to suppression of aberrant initiation.
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Affiliation(s)
- Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Pinto
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Danny A Bitton
- Research Department of Genetics, Evolution & Environment, University College, London, UK
| | - Sarah MacKinnon
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Patricia Garcia
- Departament de Ciènces Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Hidalgo
- Departament de Ciènces Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jürg Bähler
- Research Department of Genetics, Evolution & Environment, University College, London, UK
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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11
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Jones-Tabah J, Mohammad H, Hadj-Youssef S, Kim LEH, Martin RD, Benaliouad F, Tanny JC, Clarke PBS, Hébert TE. Dopamine D1 receptor signalling in dyskinetic Parkinsonian rats revealed by fiber photometry using FRET-based biosensors. Sci Rep 2020; 10:14426. [PMID: 32879346 PMCID: PMC7468292 DOI: 10.1038/s41598-020-71121-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
As with many G protein-coupled receptors (GPCRs), the signalling pathways regulated by the dopamine D1 receptor (D1R) are dynamic, cell type-specific, and can change in the face of disease or drug exposures. In striatal neurons, the D1R activates cAMP/protein kinase A (PKA) signalling. However, in Parkinson's disease (PD), alterations in this pathway lead to functional upregulation of extracellular regulated kinases 1/2 (ERK1/2), contributing to L-DOPA-induced dyskinesia (LID). In order to detect D1R activation in vivo and to study the progressive dysregulation of D1R signalling in PD and LID, we developed ratiometric fiber-photometry with Förster resonance energy transfer (FRET) biosensors and optically detected PKA and ERK1/2 signalling in freely moving rats. We show that in Parkinsonian animals, D1R signalling through PKA and ERK1/2 is sensitized, but that following chronic treatment with L-DOPA, these pathways become partially desensitized while concurrently D1R activation leads to greater induction of dyskinesia.
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Affiliation(s)
- Jace Jones-Tabah
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Room 1325, Montreal, QC, H3G 1Y6, Canada
| | - Hanan Mohammad
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Room 1325, Montreal, QC, H3G 1Y6, Canada
| | - Shadi Hadj-Youssef
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Room 1325, Montreal, QC, H3G 1Y6, Canada
| | - Lucy E H Kim
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Room 1325, Montreal, QC, H3G 1Y6, Canada
| | - Ryan D Martin
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Room 1325, Montreal, QC, H3G 1Y6, Canada
| | - Faïza Benaliouad
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Room 1325, Montreal, QC, H3G 1Y6, Canada
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Room 1325, Montreal, QC, H3G 1Y6, Canada
| | - Paul B S Clarke
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Room 1325, Montreal, QC, H3G 1Y6, Canada.
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Room 1325, Montreal, QC, H3G 1Y6, Canada.
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12
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Pagé V, Chen JJ, Durand-Dubief M, Grabowski D, Oya E, Sansô M, Martin RD, Hébert TE, Fisher RP, Ekwall K, Tanny JC. Histone H2B Ubiquitylation Regulates Histone Gene Expression by Suppressing Antisense Transcription in Fission Yeast. Genetics 2019; 213:161-172. [PMID: 31345994 PMCID: PMC6727805 DOI: 10.1534/genetics.119.302499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/23/2019] [Indexed: 02/08/2023] Open
Abstract
Histone H2B monoubiquitylation (H2Bub1) is tightly linked to RNA polymerase II transcription elongation, and is also directly implicated in DNA replication and repair. Loss of H2Bub1 is associated with defects in cell cycle progression, but how these are related to its various functions, and the underlying mechanisms involved, is not understood. Here we describe a role for H2Bub1 in the regulation of replication-dependent histone genes in the fission yeast Schizosaccharomyces pombe H2Bub1 activates histone genes indirectly by suppressing antisense transcription of ams2+ -a gene encoding a GATA-type transcription factor that activates histone genes and is required for assembly of centromeric chromatin. Mutants lacking the ubiquitylation site in H2B or the H2B-specific E3 ubiquitin ligase Brl2 had elevated levels of ams2+ antisense transcripts and reduced Ams2 protein levels. These defects were reversed upon inhibition of Cdk9-an ortholog of the kinase component of positive transcription elongation factor b (P-TEFb)-indicating that they likely resulted from aberrant transcription elongation. Reduced Cdk9 activity also partially rescued chromosome segregation phenotypes of H2Bub1 mutants. In a genome-wide analysis, loss of H2Bub1 led to increased antisense transcripts at over 500 protein-coding genes in H2Bub1 mutants; for a subset of these, including several genes involved in chromosome segregation and chromatin assembly, antisense derepression was Cdk9-dependent. Our results highlight antisense suppression as a key feature of cell cycle-dependent gene regulation by H2Bub1, and suggest that aberrant transcription elongation may underlie the effects of H2Bub1 loss on cell cycle progression.
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Affiliation(s)
- Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Jennifer J Chen
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Mickael Durand-Dubief
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm 17177, Sweden
| | - David Grabowski
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Eriko Oya
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm 17177, Sweden
| | - Miriam Sansô
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, Mount Sinai School of Medicine, New York, New York 10029
| | - Ryan D Martin
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, Mount Sinai School of Medicine, New York, New York 10029
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm 17177, Sweden
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
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13
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Parua PK, Booth GT, Sansó M, Benjamin B, Tanny JC, Lis JT, Fisher RP. A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II. Nature 2018; 558:460-464. [PMID: 29899453 PMCID: PMC6021199 DOI: 10.1038/s41586-018-0214-z] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [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: 08/09/2017] [Accepted: 04/17/2018] [Indexed: 11/09/2022]
Abstract
The end of the RNA polymerase II (Pol II) transcription cycle is strictly regulated to prevent interference between neighbouring genes and to safeguard transcriptome integrity 1 . The accumulation of Pol II downstream of the cleavage and polyadenylation signal can facilitate the recruitment of factors involved in mRNA 3'-end formation and termination 2 , but how this sequence is initiated remains unclear. In a chemical-genetic screen, human protein phosphatase 1 (PP1) isoforms were identified as substrates of positive transcription elongation factor b (P-TEFb), also known as the cyclin-dependent kinase 9 (Cdk9)-cyclin T1 (CycT1) complex 3 . Here we show that Cdk9 and PP1 govern phosphorylation of the conserved elongation factor Spt5 in the fission yeast Schizosaccharomyces pombe. Cdk9 phosphorylates both Spt5 and a negative regulatory site on the PP1 isoform Dis2 4 . Sites targeted by Cdk9 in the Spt5 carboxy-terminal domain can be dephosphorylated by Dis2 in vitro, and dis2 mutations retard Spt5 dephosphorylation after inhibition of Cdk9 in vivo. Chromatin immunoprecipitation and sequencing analysis indicates that Spt5 is dephosphorylated as transcription complexes traverse the cleavage and polyadenylation signal, concomitant with the accumulation of Pol II phosphorylated at residue Ser2 of the carboxy-terminal domain consensus heptad repeat 5 . A conditionally lethal Dis2-inactivating mutation attenuates the drop in Spt5 phosphorylation on chromatin, promotes transcription beyond the normal termination zone (as detected by precision run-on transcription and sequencing 6 ) and is genetically suppressed by the ablation of Cdk9 target sites in Spt5. These results suggest that the transition of Pol II from elongation to termination coincides with a Dis2-dependent reversal of Cdk9 signalling-a switch that is analogous to a Cdk1-PP1 circuit that controls mitotic progression 4 .
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Affiliation(s)
- Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Bradley Benjamin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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14
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Abstract
Chromatin immunoprecipitation (ChIP) is a sensitive, accurate, and reliable technique widely used to analyze protein-DNA interactions at specific binding sites in vivo. It has been a particularly powerful technique for mapping of histone modification patterns both at individual loci and genome-wide. Here we provide a detailed protocol for ChIP of histone modifications associated with active transcription in fission yeast (Schizosaccharomyces pombe).
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Affiliation(s)
- Jean Mbogning
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada.
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15
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Martin RD, Sun Y, Bourque K, Audet N, Inoue A, Tanny JC, Hébert TE. Receptor- and cellular compartment-specific activation of the cAMP/PKA pathway by α 1-adrenergic and ETA endothelin receptors. Cell Signal 2018; 44:43-50. [PMID: 29329779 DOI: 10.1016/j.cellsig.2018.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/11/2017] [Accepted: 01/07/2018] [Indexed: 10/18/2022]
Abstract
The signalling functions of many G protein-coupled receptors (GPCRs) expressed in the myocardium are incompletely understood. Among these are the endothelin receptor (ETR) family and α1-adrenergic receptor (α1-AR), which are thought to couple to the G protein Gαq. In this study, we used transcriptome analysis to compare the signalling networks downstream of these receptors in primary neonatal rat cardiomyocytes. This analysis indicated increased expression of target genes of cAMP responsive element modulator (CREM) after 24 h treatment with the α1-AR agonist phenylephrine, but not the ETR agonist endothelin-1, suggesting a specific role for the α1-AR in promoting cAMP production in cardiomyocytes. To validate the difference observed between these two GPCRs, we used heterologous expression of the receptors and genetically encoded biosensors in HEK 293 cell lines. We validated that both α1A- and α1B-AR subtypes were able to lead to the accumulation of cAMP in response to phenylephrine in both the nucleus and cytoplasm in a Gαs-dependent manner. However, the ETR subtype ETA did not affect cAMP levels in either compartment. All three receptors were coupled to Gαq signalling as expected. Further, we showed that activation of PKA in different compartments was α1-AR subtype specific, with α1B-AR able to activate PKA in the cytoplasm and nucleus and α1A-AR only able to in the nucleus. We provide evidence for a pathway downstream of the α1-AR, and show that distinct pools of a receptor lead to differential activation of downstream effector proteins dependent on their cellular compartment.
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Affiliation(s)
- Ryan D Martin
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Yalin Sun
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Kyla Bourque
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Nicolas Audet
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada.
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada.
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16
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Mbogning J, Pagé V, Burston J, Schwenger E, Fisher RP, Schwer B, Shuman S, Tanny JC. Functional interaction of Rpb1 and Spt5 C-terminal domains in co-transcriptional histone modification. Nucleic Acids Res 2015; 43:9766-75. [PMID: 26275777 PMCID: PMC4787787 DOI: 10.1093/nar/gkv837] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 03/20/2015] [Accepted: 08/09/2015] [Indexed: 12/11/2022] Open
Abstract
Transcription by RNA polymerase II (RNAPII) is accompanied by a conserved pattern of histone modifications that plays important roles in regulating gene expression. The establishment of this pattern requires phosphorylation of both Rpb1 (the largest RNAPII subunit) and the elongation factor Spt5 on their respective C-terminal domains (CTDs). Here we interrogated the roles of individual Rpb1 and Spt5 CTD phospho-sites in directing co-transcriptional histone modifications in the fission yeast Schizosaccharomyces pombe. Steady-state levels of methylation at histone H3 lysines 4 (H3K4me) and 36 (H3K36me) were sensitive to multiple mutations of the Rpb1 CTD repeat motif (Y1S2P3T4S5P6S7). Ablation of the Spt5 CTD phospho-site Thr1 reduced H3K4me levels but had minimal effects on H3K36me. Nonetheless, Spt5 CTD mutations potentiated the effects of Rpb1 CTD mutations on H3K36me, suggesting overlapping functions. Phosphorylation of Rpb1 Ser2 by the Cdk12 orthologue Lsk1 positively regulated H3K36me but negatively regulated H3K4me. H3K36me and histone H2B monoubiquitylation required Rpb1 Ser5 but were maintained upon inactivation of Mcs6/Cdk7, the major kinase for Rpb1 Ser5 in vivo, implicating another Ser5 kinase in these regulatory pathways. Our results elaborate the CTD ‘code’ for co-transcriptional histone modifications.
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Affiliation(s)
- Jean Mbogning
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Jillian Burston
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Emily Schwenger
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
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17
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Svensson JP, Shukla M, Menendez-Benito V, Norman-Axelsson U, Audergon P, Sinha I, Tanny JC, Allshire RC, Ekwall K. A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin. Genome Res 2015; 25:872-83. [PMID: 25778913 PMCID: PMC4448683 DOI: 10.1101/gr.188870.114] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/12/2015] [Indexed: 12/16/2022]
Abstract
Nucleosome composition actively contributes to chromatin structure and accessibility. Cells have developed mechanisms to remove or recycle histones, generating a landscape of differentially aged nucleosomes. This study aimed to create a high-resolution, genome-wide map of nucleosome turnover in Schizosaccharomyces pombe. The recombination-induced tag exchange (RITE) method was used to study replication-independent nucleosome turnover through the appearance of new histone H3 and the disappearance or preservation of old histone H3. The genome-wide location of histones was determined by chromatin immunoprecipitation-exonuclease methodology (ChIP-exo). The findings were compared with diverse chromatin marks, including histone variant H2A.Z, post-translational histone modifications, and Pol II binding. Finally, genome-wide mapping of the methylation states of H4K20 was performed to determine the relationship between methylation (mono, di, and tri) of this residue and nucleosome turnover. Our analysis showed that histone recycling resulted in low nucleosome turnover in the coding regions of active genes, stably expressed at intermediate levels. High levels of transcription resulted in the incorporation of new histones primarily at the end of transcribed units. H4K20 was methylated in low-turnover nucleosomes in euchromatic regions, notably in the coding regions of long genes that were expressed at low levels. This transcription-dependent accumulation of histone methylation was dependent on the histone chaperone complex FACT. Our data showed that nucleosome turnover is highly dynamic in the genome and that several mechanisms are at play to either maintain or suppress stability. In particular, we found that FACT-associated transcription conserves histones by recycling them and is required for progressive H4K20 methylation.
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Affiliation(s)
- J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 57 Huddinge, Sweden
| | - Manu Shukla
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
| | | | - Ulrika Norman-Axelsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 57 Huddinge, Sweden
| | - Pauline Audergon
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Indranil Sinha
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 57 Huddinge, Sweden
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Robin C Allshire
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 57 Huddinge, Sweden
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18
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Abstract
Transcription elongation by RNA polymerase II (RNAP II) involves the coordinated action of numerous regulatory factors. Among these are chromatin-modifying enzymes, which generate a stereotypic and conserved pattern of histone modifications along transcribed genes. This pattern implies a precise coordination between regulators of histone modification and the RNAP II elongation complex. Here I review the pathways and molecular events that regulate co-transcriptional histone modifications. Insight into these events will illuminate the assembly of functional RNAP II elongation complexes and how the chromatin landscape influences their composition and function.
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Affiliation(s)
- Jason C Tanny
- a Department of Pharmacology and Therapeutics ; McGill University ; Montreal , Canada
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19
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Mbogning J, Nagy S, Pagé V, Schwer B, Shuman S, Fisher RP, Tanny JC. The PAF complex and Prf1/Rtf1 delineate distinct Cdk9-dependent pathways regulating transcription elongation in fission yeast. PLoS Genet 2013; 9:e1004029. [PMID: 24385927 PMCID: PMC3873232 DOI: 10.1371/journal.pgen.1004029] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 10/31/2013] [Indexed: 11/19/2022] Open
Abstract
Cyclin-dependent kinase 9 (Cdk9) promotes elongation by RNA polymerase II (RNAPII), mRNA processing, and co-transcriptional histone modification. Cdk9 phosphorylates multiple targets, including the conserved RNAPII elongation factor Spt5 and RNAPII itself, but how these different modifications mediate Cdk9 functions is not known. Here we describe two Cdk9-dependent pathways in the fission yeast Schizosaccharomyces pombe that involve distinct targets and elicit distinct biological outcomes. Phosphorylation of Spt5 by Cdk9 creates a direct binding site for Prf1/Rtf1, a transcription regulator with functional and physical links to the Polymerase Associated Factor (PAF) complex. PAF association with chromatin is also dependent on Cdk9 but involves alternate phosphoacceptor targets. Prf1 and PAF are biochemically separate in cell extracts, and genetic analyses show that Prf1 and PAF are functionally distinct and exert opposing effects on the RNAPII elongation complex. We propose that this opposition constitutes a Cdk9 auto-regulatory mechanism, such that a positive effect on elongation, driven by the PAF pathway, is kept in check by a negative effect of Prf1/Rtf1 and downstream mono-ubiquitylation of histone H2B. Thus, optimal RNAPII elongation may require balanced action of functionally distinct Cdk9 pathways.
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Affiliation(s)
- Jean Mbogning
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Stephen Nagy
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Robert P. Fisher
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jason C. Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
- * E-mail:
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20
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Sansó M, Lee KM, Viladevall L, Jacques PÉ, Pagé V, Nagy S, Racine A, St. Amour CV, Zhang C, Shokat KM, Schwer B, Robert F, Fisher RP, Tanny JC. A positive feedback loop links opposing functions of P-TEFb/Cdk9 and histone H2B ubiquitylation to regulate transcript elongation in fission yeast. PLoS Genet 2012; 8:e1002822. [PMID: 22876190 PMCID: PMC3410854 DOI: 10.1371/journal.pgen.1002822] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 05/24/2012] [Indexed: 11/25/2022] Open
Abstract
Transcript elongation by RNA polymerase II (RNAPII) is accompanied by conserved patterns of histone modification. Whereas histone modifications have established roles in transcription initiation, their functions during elongation are not understood. Mono-ubiquitylation of histone H2B (H2Bub1) plays a key role in coordinating co-transcriptional histone modification by promoting site-specific methylation of histone H3. H2Bub1 also regulates gene expression through an unidentified, methylation-independent mechanism. Here we reveal bidirectional communication between H2Bub1 and Cdk9, the ortholog of metazoan positive transcription elongation factor b (P-TEFb), in the fission yeast Schizosaccharomyces pombe. Chemical and classical genetic analyses indicate that lowering Cdk9 activity or preventing phosphorylation of its substrate, the transcription processivity factor Spt5, reduces H2Bub1 in vivo. Conversely, mutations in the H2Bub1 pathway impair Cdk9 recruitment to chromatin and decrease Spt5 phosphorylation. Moreover, an Spt5 phosphorylation-site mutation, combined with deletion of the histone H3 Lys4 methyltransferase Set1, phenocopies morphologic and growth defects due to H2Bub1 loss, suggesting independent, partially redundant roles for Cdk9 and Set1 downstream of H2Bub1. Surprisingly, mutation of the histone H2B ubiquitin-acceptor residue relaxes the Cdk9 activity requirement in vivo, and cdk9 mutations suppress cell-morphology defects in H2Bub1-deficient strains. Genome-wide analyses by chromatin immunoprecipitation also demonstrate opposing effects of Cdk9 and H2Bub1 on distribution of transcribing RNAPII. Therefore, whereas mutual dependence of H2Bub1 and Spt5 phosphorylation indicates positive feedback, mutual suppression by cdk9 and H2Bub1-pathway mutations suggests antagonistic functions that must be kept in balance to regulate elongation. Loss of H2Bub1 disrupts that balance and leads to deranged gene expression and aberrant cell morphologies, revealing a novel function of a conserved, co-transcriptional histone modification. Modification of histone proteins is an important transcriptional regulatory mechanism in eukaryotic cells. Although various histone modifications are found primarily within the coding regions of transcribed genes, how they influence transcription elongation remains unclear. Among these modifications is mono-ubiquitylation of histone H2B (H2Bub1), which is needed for co-transcriptional methylation of histone H3 at specific sites. Here we show that H2Bub1 and Cdk9, the kinase component of positive transcription elongation factor b (P-TEFb), are jointly regulated by a positive feedback loop: Cdk9 activity is needed for co-transcriptional H2Bub1, and H2Bub1 in turn stimulates Cdk9 activity toward one of its major substrates, the conserved elongation factor Spt5. We provide genetic evidence that the combined action of H2Bub1 on Spt5 phosphorylation and histone methylation accounts for the gene-regulatory effects of this modification. Surprisingly, our genetic and genome-wide studies indicate that P-TEFb and H2Bub1 act in opposition on elongating RNA polymerase. We suggest that the positive feedback linking P-TEFb and H2Bub1 helps to maintain a balance between their opposing actions. These results highlight a novel regulatory role for a conserved histone modification during transcription elongation.
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Affiliation(s)
- Miriam Sansó
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Karen M. Lee
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Laia Viladevall
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | | | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Canada
| | - Stephen Nagy
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Canada
| | - Ariane Racine
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Canada
| | - Courtney V. St. Amour
- Programs in Biochemistry, Cell and Molecular Biology, Weill Cornell Medical College, New York, New York, United States of America
| | - Chao Zhang
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Kevan M. Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - François Robert
- Institut de Recherches Cliniques de Montréal, Montréal, Canada
| | - Robert P. Fisher
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
- * E-mail: (RPF); (JCT)
| | - Jason C. Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Canada
- * E-mail: (RPF); (JCT)
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Racine A, Pagé V, Nagy S, Grabowski D, Tanny JC. Histone H2B ubiquitylation promotes activity of the intact Set1 histone methyltransferase complex in fission yeast. J Biol Chem 2012; 287:19040-7. [PMID: 22505722 DOI: 10.1074/jbc.m112.356253] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The methylation of histone H3 at lysine 4 (H3K4me) is critical for the formation of transcriptionally active chromatin in eukaryotes. In yeast, Drosophila, and some human cell lines, H3K4me is globally stimulated by the monoubiquitylation of histone H2B (H2Bub1), another histone modification associated with transcription. The mechanism of this "trans-histone" modification pathway remains uncertain, and studies carried out in different experimental systems have suggested that H2Bub1 could either influence the subunit composition of methyltransferase complexes or directly stimulate methyltransferase activity. We have reconstituted this pathway in vitro using the native H3K4-specific methyltransferase complex Set1C purified from the fission yeast Schizosaccharomyces pombe and chromatin substrates that contain semisynthetic H2Bub1. We found that the activity of S. pombe Set1C toward nucleosomal histone H3 is directly enhanced by H2Bub1 in vitro. Importantly, Set1C purified from cells lacking H2Bub1 retained activity on free histone substrates, suggesting that Set1C remains intact in the absence of H2Bub1. Chromatin immunoprecipitation assays revealed a defect in recruitment of intact Set1C to transcribed chromatin in H2Bub1-deficient mutants. Our data argue that trans-histone crosstalk in S. pombe involves direct enhancement of Set1C methyltransferase activity by H2Bub1 and suggest that this represents a conserved aspect of H2Bub1-H3K4me crosstalk in eukaryotes.
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Affiliation(s)
- Ariane Racine
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
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22
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Moazed D, Rudner AD, Huang J, Hoppe GJ, Tanny JC. A Model for Step-Wise Assembly of Heterochromatin in Yeast. Reversible Protein Acetylation 2008. [DOI: 10.1002/0470862637.ch4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Tanny JC, Erdjument-Bromage H, Tempst P, Allis CD. Ubiquitylation of histone H2B controls RNA polymerase II transcription elongation independently of histone H3 methylation. Genes Dev 2007; 21:835-47. [PMID: 17374714 PMCID: PMC1838534 DOI: 10.1101/gad.1516207] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transcription by RNA polymerase II (polII) is accompanied by dramatic changes in chromatin structure. Numerous enzymatic activities contribute to these changes, including ATP-dependent nucleosome remodeling enzymes and histone modifying enzymes. Recent studies in budding yeast document a histone modification pathway associated with polII transcription, whereby ubiquitylation of histone H2B leads to methylation of histone H3 on specific lysine residues. Although this series of events appears to be highly conserved among eukaryotes, its mechanistic function in transcription is unknown. Here we document a significant functional divergence between ubiquitylation of H2B and methylation of Lys 4 on histone H3 in the fission yeast Schizosaccharomyces pombe. Loss of H2B ubiquitylation results in defects in cell growth, septation, and nuclear structure, phenotypes not observed in cells lacking H3 Lys 4 methylation. Consistent with these results, gene expression microarray analysis reveals a greater role for H2B ubiquitylation in gene regulation than for H3 Lys 4 methylation. Chromatin immunoprecipitation (ChIP) experiments demonstrate that loss of H2B ubiquitylation alters the distribution of polII and histones in gene coding regions. We propose that ubiquitylation of H2B impacts transcription elongation and nuclear architecture through its effects on chromatin dynamics.
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Affiliation(s)
- Jason C. Tanny
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
| | - Hediye Erdjument-Bromage
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Paul Tempst
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - C. David Allis
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
- Corresponding author.E-MAIL ; FAX (212) 327-7849
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24
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Taverna SD, Ilin S, Rogers RS, Tanny JC, Lavender H, Li H, Baker L, Boyle J, Blair LP, Chait BT, Patel DJ, Aitchison JD, Tackett AJ, Allis CD. Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol Cell 2007; 24:785-796. [PMID: 17157260 PMCID: PMC4690528 DOI: 10.1016/j.molcel.2006.10.026] [Citation(s) in RCA: 233] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 08/22/2006] [Accepted: 10/19/2006] [Indexed: 12/31/2022]
Abstract
Posttranslational histone modifications participate in modulating the structure and function of chromatin. Promoters of transcribed genes are enriched with K4 trimethylation and hyperacetylation on the N-terminal tail of histone H3. Recently, PHD finger proteins, like Yng1 in the NuA3 HAT complex, were shown to interact with H3K4me3, indicating a biochemical link between K4 methylation and hyperacetylation. By using a combination of mass spectrometry, biochemistry, and NMR, we detail the Yng1 PHD-H3K4me3 interaction and the importance of NuA3-dependent acetylation at K14. Furthermore, genome-wide ChIP-Chip analysis demonstrates colocalization of Yng1 and H3K4me3 in vivo. Disrupting the K4me3 binding of Yng1 altered K14ac and transcription at certain genes, thereby demonstrating direct in vivo evidence of sequential trimethyl binding, acetyltransferase activity, and gene regulation by NuA3. Our data support a general mechanism of transcriptional control through which histone acetylation upstream of gene activation is promoted partially through availability of H3K4me3, "read" by binding modules in select subunits.
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Affiliation(s)
- Sean D Taverna
- Laboratory of Chromatin Biology, The Rockefeller University
| | - Serge Ilin
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | | | - Jason C Tanny
- Laboratory of Chromatin Biology, The Rockefeller University
| | - Heather Lavender
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Haitao Li
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | - Lindsey Baker
- Laboratory of Chromatin Biology, The Rockefeller University
| | - John Boyle
- Institute for Systems Biology, Seattle, Washington 98103
| | - Lauren P Blair
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | | | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205.
| | - C David Allis
- Laboratory of Chromatin Biology, The Rockefeller University.
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25
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Rothfels K, Tanny JC, Molnar E, Friesen H, Commisso C, Segall J. Components of the ESCRT pathway, DFG16, and YGR122w are required for Rim101 to act as a corepressor with Nrg1 at the negative regulatory element of the DIT1 gene of Saccharomyces cerevisiae. Mol Cell Biol 2005; 25:6772-88. [PMID: 16024810 PMCID: PMC1190364 DOI: 10.1128/mcb.25.15.6772-6788.2005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The divergently transcribed DIT1 and DIT2 genes of Saccharomyces cerevisiae, which belong to the mid-late class of sporulation-specific genes, are subject to Ssn6-Tup1-mediated repression in mitotic cells. The Ssn6-Tup1 complex, which is required for repression of diverse sets of coordinately regulated genes, is known to be recruited to target genes by promoter-specific DNA-binding proteins. In this study, we show that a 42-bp negative regulatory element (NRE) present in the DIT1-DIT2 intergenic region consists of two distinct subsites and that a multimer of each subsite supports efficient Ssn6-Tup1-dependent repression of a CYC1-lacZ reporter gene. By genetic screening procedures, we identified DFG16, YGR122w, VPS36, and the DNA-binding proteins Rim101 and Nrg1 as potential mediators of NRE-directed repression. We show that Nrg1 and Rim101 bind simultaneously to adjacent target sites within the NRE in vitro and act as corepressors in vivo. We have found that the ability of Rim101 to be proteolytically processed to its active form and mediate NRE-directed repression not only depends on the previously characterized RIM signaling pathway but also requires Dfg16, Ygr122w, and components of the ESCRT trafficking pathway. Interestingly, Rim101 was processed in bro1 and doa4 strains but was unable to mediate efficient repression.
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Affiliation(s)
- Karen Rothfels
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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26
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Liou GG, Tanny JC, Kruger RG, Walz T, Moazed D. Assembly of the SIR complex and its regulation by O-acetyl-ADP-ribose, a product of NAD-dependent histone deacetylation. Cell 2005; 121:515-527. [PMID: 15907466 DOI: 10.1016/j.cell.2005.03.035] [Citation(s) in RCA: 209] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2005] [Revised: 03/25/2005] [Accepted: 03/31/2005] [Indexed: 10/25/2022]
Abstract
Assembly of silent chromatin domains in budding yeast involves the deacetylation of histone tails by Sir2 and the association of the Sir3 and Sir4 proteins with hypoacetylated histone tails. Sir2 couples deacetylation to NAD hydrolysis and the synthesis of a metabolite, O-acetyl-ADP-ribose (AAR), but the functional significance of NAD hydrolysis or AAR, if any, is unknown. Here we examine the association of the Sir2, Sir3, and Sir4 proteins with each other and histone tails. Our analysis reveals that deacetylation of histone H4-lysine 16 (K16), which is critical for silencing in vivo, is also critical for the binding of Sir3 and Sir4 to histone H4 peptides in vitro. Moreover, AAR itself promotes the association of multiple copies of Sir3 with Sir2/Sir4 and induces a dramatic structural rearrangement in the SIR complex. These results suggest that Sir2 activity modulates the assembly of the SIR complex through both histone deacetylation and AAR synthesis.
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Affiliation(s)
- Gunn-Guang Liou
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Jason C Tanny
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Ryan G Kruger
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Danesh Moazed
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115.
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27
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Tanny JC, Kirkpatrick DS, Gerber SA, Gygi SP, Moazed D. Budding yeast silencing complexes and regulation of Sir2 activity by protein-protein interactions. Mol Cell Biol 2004; 24:6931-46. [PMID: 15282295 PMCID: PMC479720 DOI: 10.1128/mcb.24.16.6931-6946.2004] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gene silencing in the budding yeast Saccharomyces cerevisiae requires the enzymatic activity of the Sir2 protein, a highly conserved NAD-dependent deacetylase. In order to study the activity of native Sir2, we purified and characterized two budding yeast Sir2 complexes: the Sir2/Sir4 complex, which mediates silencing at mating-type loci and at telomeres, and the RENT complex, which mediates silencing at the ribosomal DNA repeats. Analyses of the protein compositions of these complexes confirmed previously described interactions. We show that the assembly of Sir2 into native silencing complexes does not alter its selectivity for acetylated substrates, nor does it allow the deacetylation of nucleosomal histones. The inability of Sir2 complexes to deacetylate nucleosomes suggests that additional factors influence Sir2 activity in vivo. In contrast, Sir2 complexes show significant enhancement in their affinities for acetylated substrates and their sensitivities to the physiological inhibitor nicotinamide relative to recombinant Sir2. Reconstitution experiments showed that, for the Sir2/Sir4 complex, these differences stem from the physical interaction of Sir2 with Sir4. Finally, we provide evidence that the different nicotinamide sensitivities of Sir2/Sir4 and RENT in vitro could contribute to locus-specific differences in how Sir2 activity is regulated in vivo.
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Affiliation(s)
- Jason C Tanny
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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Chang JF, Hall BE, Tanny JC, Moazed D, Filman D, Ellenberger T. Structure of the Coiled-Coil Dimerization Motif of Sir4 and Its Interaction with Sir3. Structure 2004. [DOI: 10.1016/j.str.2004.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Moazed D, Rudner AD, Huang J, Hoppe GJ, Tanny JC. A model for step-wise assembly of heterochromatin in yeast. Novartis Found Symp 2004; 259:48-56; discussion 56-62, 163-9. [PMID: 15171246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Gene silencing involves the assembly of DNA into specialized chromatin domains that are inaccessible to trans-acting factors and are epigenetically inherited. In the budding yeast Saccharomyces cerevisiae, silent heterochromatic DNA domains occur at telomeres, the silent mating type loci, and the rDNA repeats. At telomeres and the mating type loci, silencing requires the Sir2, Sir3 and Sir4 proteins, the conserved N-termini of histones H3 and H4, and a number of chromatin assembly factors. The Sir proteins form a multimeric complex that binds preferentially to deacetylated nucleosomes through the Sir3 and Sir4 subunits. The Sir2 subunit possesses an unusual NAD-dependent deacetylase activity that is required for silencing at each of the above loci. Recent studies have shown that silent chromatin domains are assembled in a step-wise manner involving sequential cycles of deacetylation and SIR complex binding. Sir2-dependent deacetylation is specifically required for the spreading of the complex to regions beyond nucleation sites but not for its initial binding to DNA at the mating type loci and telomeres. A distinct Sir2 complex called RENT is required for silencing at rDNA. In contrast to telomeres and the mating type loci, Sir2 activity is not required for association of RENT with rDNA.
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Affiliation(s)
- Danesh Moazed
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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Abstract
The yeast silent information regulators Sir2, Sir3, and Sir4 physically interact with one another to establish a transcriptionally silent state by forming repressive chromatin structures. The Sir4 protein contains binding sites for both Sir2 and Sir3, and these protein-protein interactions are required for gene silencing. Here, we report the X-ray structure of the coiled-coil dimerization motif within the C-terminus of Sir4 and show that it forms a stable 1:1 complex with a dimeric fragment of Sir3 (residues 464-978). We have identified a cluster of residues on the surface of the Sir4 coiled coil required for specific interactions with Sir3. The histone deacetylase Sir2 can also bind to this complex, forming a ternary complex with the truncated Sir3 and Sir4 proteins. The dual interactions of Sir4 with Sir3 and Sir2 suggest a physical basis for recruiting Sir3 to chromatin by virtue of its interactions with Sir4 and with deacetylated histones in chromatin.
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Affiliation(s)
- Ju-Fang Chang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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31
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Abstract
The structure of a Sir2-like enzyme in complex with an acetylated peptide substrate has been solved, and provides the first glimpse into the mechanism of substrate recognition by this highly conserved family of enzymes.
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Affiliation(s)
- Jason C Tanny
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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Hoppe GJ, Tanny JC, Rudner AD, Gerber SA, Danaie S, Gygi SP, Moazed D. Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Mol Cell Biol 2002; 22:4167-80. [PMID: 12024030 PMCID: PMC133845 DOI: 10.1128/mcb.22.12.4167-4180.2002] [Citation(s) in RCA: 228] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional silencing at the budding yeast silent mating type (HM) loci and telomeric DNA regions requires Sir2, a conserved NAD-dependent histone deacetylase, Sir3, Sir4, histones H3 and H4, and several DNA-binding proteins. Silencing at the yeast ribosomal DNA (rDNA) repeats requires a complex containing Sir2, Net1, and Cdc14. Here we show that the native Sir2/Sir4 complex is composed solely of Sir2 and Sir4 and that native Sir3 is not associated with other proteins. We further show that the initial binding of the Sir2/Sir4 complex to DNA sites that nucleate silencing, accompanied by partial Sir2-dependent histone deacetylation, occurs independently of Sir3 and is likely to be the first step in assembly of silent chromatin at the HM loci and telomeres. The enzymatic activity of Sir2 is not required for this initial binding, but is required for the association of silencing proteins with regions distal from nucleation sites. At the rDNA repeats, we show that histone H3 and H4 tails are required for silencing and rDNA-associated H4 is hypoacetylated in a Sir2-dependent manner. However, the binding of Sir2 to rDNA is independent of its histone deacetylase activity. Together, these results support a stepwise model for the assembly of silent chromatin domains in Saccharomyces cerevisiae.
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Affiliation(s)
- Georg J Hoppe
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Tanny JC, Moazed D. Coupling of histone deacetylation to NAD breakdown by the yeast silencing protein Sir2: Evidence for acetyl transfer from substrate to an NAD breakdown product. Proc Natl Acad Sci U S A 2001; 98:415-20. [PMID: 11134535 PMCID: PMC14600 DOI: 10.1073/pnas.98.2.415] [Citation(s) in RCA: 175] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Saccharomyces cerevisiae silencing protein Sir2 is the founding member of a universally conserved family of proteins that have been shown to possess NAD-dependent histone deacetylation and ADP-ribosylation activities. Here we show that histone deacetylation by Sir2 is coupled to cleavage of the high-energy bond that links the ADP-ribose moiety of NAD to nicotinamide. Analysis of the NAD cleavage products revealed the presence of nicotinamide, ADP-ribose, and a third product that appeared to be related to ADP-ribose. With the use of label transfer experiments, we show that the acetyl group in the histone substrate is transferred to this NAD breakdown product during deacetylation, forming a product that we conclude to be O-acetyl-ADP-ribose. Detection of this species strongly argues for obligate coupling of histone deacetylation to NAD breakdown by Sir2. We propose reaction mechanisms that could account for this coupling via acetyl-ADP-ribose formation. The unprecedented coupling of amide bond cleavage to cleavage of a high-energy bond raises the possibility that NAD breakdown by Sir2 plays an important role in silencing that is independent of its requirement for deacetylation.
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Affiliation(s)
- J C Tanny
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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Abstract
Despite its conservation in organisms from bacteria to human and its general requirement for transcriptional silencing in yeast, the function of the Sir2 protein is unknown. Here we show that Sir2 can transfer labeled phosphate from nicotinamide adenine dinucleotide to itself and histones in vitro. A modified form of Sir2, which results from its automodification activity, is specifically recognized by anti-mono-ADP-ribose antibodies, suggesting that Sir2 is an ADP-ribosyltransferase. Mutation of a phylogenetically invariant histidine residue in Sir2 abolishes both its enzymatic activity in vitro and its silencing functions in vivo. However, the mutant protein is associated with chromatin and other silencing factors in a manner similar to wild-type Sir2. These findings suggest that Sir2 contains an ADP-ribosyltransferase activity that is essential for its silencing function.
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Affiliation(s)
- J C Tanny
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Friesen H, Tanny JC, Segall J. Spe3, which encodes spermidine synthase, is required for full repression through NRE(DIT) in Saccharomyces cerevisiae. Genetics 1998; 150:59-73. [PMID: 9725830 PMCID: PMC1460323 DOI: 10.1093/genetics/150.1.59] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We previously identified a transcriptional regulatory element, which we call NRE(DIT), that is required for repression of the sporulation-specific genes, DIT1 and DIT2, during vegetative growth of Saccharomyces cerevisiae. Repression through this element is dependent on the Ssn6-Tup1 corepressor. In this study, we show that SIN4 contributes to NRE(DIT)-mediated repression, suggesting that changes in chromatin structure are, at least in part, responsible for regulation of DIT gene expression. In a screen for additional genes that function in repression of DIT (FRD genes), we recovered alleles of TUP1, SSN6, SIN4, and ROX3 and identified mutations comprising eight complementation groups of FRD genes. Four of these FRD genes appeared to act specifically in NRE(DIT)mediated repression, and four appeared to be general regulators of gene expression. We cloned the gene complementing the frd3-1 phenotype and found that it was identical to SPE3, which encodes spermidine synthase. Mutant spe3 cells not only failed to support complete repression through NRE(DIT) but also had modest defects in repression of some other genes. Addition of spermidine to the medium partially restored repression to spe3 cells, indicating that spermidine may play a role in vivo as a modulator of gene expression. We suggest various mechanisms by which spermidine could act to repress gene expression.
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Affiliation(s)
- H Friesen
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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