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Fetian T, Grover A, Arndt KM. Histone H2B ubiquitylation: Connections to transcription and effects on chromatin structure. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195018. [PMID: 38331024 PMCID: PMC11098702 DOI: 10.1016/j.bbagrm.2024.195018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
Nucleosomes are major determinants of eukaryotic genome organization and regulation. Many studies, incorporating a diversity of experimental approaches, have been focused on identifying and discerning the contributions of histone post-translational modifications to DNA-centered processes. Among these, monoubiquitylation of H2B (H2Bub) on K120 in humans or K123 in budding yeast is a critical histone modification that has been implicated in a wide array of DNA transactions. H2B is co-transcriptionally ubiquitylated and deubiquitylated via the concerted action of an extensive network of proteins. In addition to altering the chemical and physical properties of the nucleosome, H2Bub is important for the proper control of gene expression and for the deposition of other histone modifications. In this review, we discuss the molecular mechanisms underlying the ubiquitylation cycle of H2B and how it connects to the regulation of transcription and chromatin structure.
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Affiliation(s)
- Tasniem Fetian
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Aakash Grover
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States of America.
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2
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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] [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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3
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Qin B, Lu G, Chen X, Zheng C, Lin H, Liu Q, Shang J, Feng G. H2B oncohistones cause homologous recombination defect and genomic instability through reducing H2B monoubiquitination in Schizosaccharomyces pombe. J Biol Chem 2024; 300:107345. [PMID: 38718864 PMCID: PMC11167522 DOI: 10.1016/j.jbc.2024.107345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 06/02/2024] Open
Abstract
Canonical oncohistones are histone H3 mutations in the N-terminal tail associated with tumors and affect gene expression by altering H3 post-translational modifications (PTMs) and the epigenetic landscape. Noncanonical oncohistone mutations occur in both tails and globular domains of all four core histones and alter gene expression by perturbing chromatin remodeling. However, the effects and mechanisms of noncanonical oncohistones remain largely unknown. Here we characterized 16 noncanonical H2B oncohistones in the fission yeast Schizosaccharomyces pombe. We found that seven of them exhibited temperature sensitivities and 11 exhibited genotoxic sensitivities. A detailed study of two of these onco-mutants H2BG52D and H2BP102L revealed that they were defective in homologous recombination (HR) repair with compromised histone eviction and Rad51 recruitment. Interestingly, their genotoxic sensitivities and HR defects were rescued by the inactivation of the H2BK119 deubiquitination function of Ubp8 in the Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex. The levels of H2BK119 monoubiquitination (H2Bub) in the H2BG52D and H2BP102L mutants are reduced in global genome and at local DNA break sites presumably due to enhanced recruitment of Ubp8 onto nucleosomes and are recovered upon loss of H2B deubiquitination function of the SAGA complex. Moreover, H2BG52D and H2BP102L heterozygotes exhibit genotoxic sensitivities and reduced H2Bub in cis. We therefore conclude that H2BG52D and H2BP102L oncohistones affect HR repair and genome stability via the reduction of H2Bub and propose that other noncanonical oncohistones may also affect histone PTMs to cause diseases.
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Affiliation(s)
- Bingxin Qin
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guangchun Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuejin Chen
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Chenhua Zheng
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Huanteng Lin
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qi Liu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jinjie Shang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Gang Feng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China; School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
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4
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Lu Q, Shi W, Zhang F, Ding Y. ATX1 and HUB1/2 promote recruitment of the transcription elongation factor VIP2 to modulate the floral transition in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1760-1773. [PMID: 38446797 DOI: 10.1111/tpj.16707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/14/2024] [Accepted: 01/27/2024] [Indexed: 03/08/2024]
Abstract
Histone 2B ubiquitination (H2Bub) and trimethylation of H3 at lysine 4 (H3K4me3) are associated with transcription activation. However, the function of these modifications in transcription in plants remains largely unknown. Here, we report that coordination of H2Bub and H3K4me3 deposition with the binding of the RNA polymerase-associated factor VERNALIZATION INDEPENDENCE2 (VIP2) to FLOWERING LOCUS C (FLC) modulates flowering time in Arabidopsis. We found that RING domain protein HISTONE MONOUBIQUITINATION1 (HUB1) and HUB2 (we refer as HUB1/2), which are responsible for H2Bub, interact with ARABIDOPSIS TRITHORAX1 (ATX1), which is required for H3K4me3 deposition, to promote the transcription of FLC and repress the flowering time. The atx1-2 hub1-10 hub2-2 triple mutant in FRIGIDIA (FRI) background displayed early flowering like FRI hub1-10 hub2-2 and overexpression of ATX1 failed to rescue the early flowering phenotype of hub1-10 hub2-2. Mutations in HUB1 and HUB2 reduced the ATX1 enrichment at FLC, indicating that HUB1 and HUB2 are required for ATX1 recruitment and H3K4me3 deposition at FLC. We also found that the VIP2 directly binds to HUB1, HUB2, and ATX1 and that loss of VIP2 in FRI hub1-10 hub2-2 and FRI atx1-2 plants resulted in early flowering like that observed in FRI vip2-10. Loss of function of HUB2 and ATX1 impaired VIP2 enrichment at FLC, and reduced the transcription initiation and elongation of FLC. In addition, mutations in VIP2 reduced HUB1 and ATX1 enrichment and H2Bub and H3K4me3 levels at FLC. Together, our findings revealed that HUB1/2, ATX1, and VIP2 coordinately modulate H2Bub and H3K4me3 deposition, FLC transcription, and flowering time.
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Affiliation(s)
- Qianqian Lu
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Wenwen Shi
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Fei Zhang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Yong Ding
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
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5
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Verma P, Sánchez Alvarado A, Duncan EM. Chromatin remodeling protein BPTF regulates transcriptional stability in planarian stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595819. [PMID: 38826365 PMCID: PMC11142235 DOI: 10.1101/2024.05.24.595819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Trimethylation of histone H3 lysine 4 (H3K4me3) correlates strongly with gene expression in many different organisms, yet the question of whether it plays a causal role in transcriptional activity remains unresolved. Although H3K4me3 does not directly affect chromatin accessibility, it can indirectly affect genome accessibility by recruiting the ATP-dependent chromatin remodeling complex NuRF (Nucleosome Remodeling Factor). The largest subunit of NuRF, BPTF/NURF301, binds H3K4me3 specifically and recruits the NuRF complex to loci marked by this modification. Studies have shown that the strength and duration of BPTF binding likely also depends on additional chromatin features at these loci, such as lysine acetylation and variant histone proteins. However, the exact details of this recruitment mechanism vary between studies and have largely been tested in vitro. Here, we use stem cells isolated directly from live planarian animals to investigate the role of BPTF in regulating chromatin accessibility in vivo. We find that BPTF operates at gene promoters and is most effective at facilitating transcription at genes marked by Set1-dependent H3K4me3 peaks, which are significantly broader than those added by the lysine methyltransferase MLL1/2. Moreover, BPTF is essential for planarian stem cell biology and its loss of function phenotype mimics that of Set1 knockdown. Together, these data suggest that BPTF and H3K4me3 are important mediators of both transcription and in vivo stem cell function.
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Liu H, Marayati BF, de la Cerda D, Lemezis BM, Gao J, Song Q, Chen M, Reid KZ. The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe. PLoS Genet 2024; 20:e1011107. [PMID: 38181050 PMCID: PMC10795994 DOI: 10.1371/journal.pgen.1011107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/18/2024] [Accepted: 12/12/2023] [Indexed: 01/07/2024] Open
Abstract
Eukaryotic chromatin is organized into either silenced heterochromatin or relaxed euchromatin regions, which controls the accessibility of transcriptional machinery and thus regulates gene expression. In fission yeast, Schizosaccharomyces pombe, Set1 is the sole H3K4 methyltransferase and is mainly enriched at the promoters of actively transcribed genes. In contrast, Clr4 methyltransferase initiates H3K9 methylation, which has long been regarded as a hallmark of heterochromatic silencing. Lsd1 and Lsd2 are two highly conserved H3K4 and H3K9 demethylases. As these histone-modifying enzymes perform critical roles in maintaining histone methylation patterns and, consequently, gene expression profiles, cross-regulations among these enzymes are part of the complex regulatory networks. Thus, elucidating the mechanisms that govern their signaling and mutual regulations remains crucial. Here, we demonstrated that C-terminal truncation mutants, lsd1-ΔHMG and lsd2-ΔC, do not compromise the integrity of the Lsd1/2 complex but impair their chromatin-binding capacity at the promoter region of target genomic loci. We identified protein-protein interactions between Lsd1/2 and Raf2 or Swd2, which are the subunits of the Clr4 complex (CLRC) and Set1-associated complex (COMPASS), respectively. We showed that Clr4 and Set1 modulate the protein levels of Lsd1 and Lsd2 in opposite ways through the ubiquitin-proteasome-dependent pathway. During heat stress, the protein levels of Lsd1 and Lsd2 are upregulated in a Set1-dependent manner. The increase in protein levels is crucial for differential gene expression under stress conditions. Together, our results support a cross-regulatory model by which Set1 and Clr4 methyltransferases control the protein levels of Lsd1/2 demethylases to shape the dynamic chromatin landscape.
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Affiliation(s)
- Haoran Liu
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Bahjat Fadi Marayati
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - David de la Cerda
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Brendan Matthew Lemezis
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Jieyu Gao
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Qianqian Song
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, Florida, United States of America
| | - Minghan Chen
- Department of Computer Science, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Ke Zhang Reid
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
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7
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Barman P, Chakraborty P, Bhaumik R, Bhaumik SR. UPS writes a new saga of SAGA. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194981. [PMID: 37657588 PMCID: PMC10843445 DOI: 10.1016/j.bbagrm.2023.194981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023]
Abstract
SAGA (Spt-Ada-Gcn5-Acetyltransferase), an evolutionarily conserved transcriptional co-activator among eukaryotes, is a large multi-subunit protein complex with two distinct enzymatic activities, namely HAT (Histone acetyltransferase) and DUB (De-ubiquitinase), and is targeted to the promoter by the gene-specific activator proteins for histone covalent modifications and PIC (Pre-initiation complex) formation in enhancing transcription (or gene activation). Targeting of SAGA to the gene promoter is further facilitated by the 19S RP (Regulatory particle) of the 26S proteasome (that is involved in targeted degradation of protein via ubiquitylation) in a proteolysis-independent manner. Moreover, SAGA is also recently found to be regulated by the 26S proteasome in a proteolysis-dependent manner via the ubiquitylation of its Sgf73/ataxin-7 component that is required for SAGA's integrity and DUB activity (and hence transcription), and is linked to various diseases including neurodegenerative disorders and cancer. Thus, SAGA itself and its targeting to the active gene are regulated by the UPS (Ubiquitin-proteasome system) with implications in diseases.
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Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA
| | - Pritam Chakraborty
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA
| | - Rhea Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA.
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Barman P, Kaja A, Chakraborty P, Guha S, Roy A, Ferdoush J, Bhaumik SR. A novel ubiquitin-proteasome system regulation of Sgf73/ataxin-7 that maintains the integrity of the coactivator SAGA in orchestrating transcription. Genetics 2023; 224:iyad071. [PMID: 37075097 PMCID: PMC10324951 DOI: 10.1093/genetics/iyad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 01/31/2023] [Accepted: 03/15/2023] [Indexed: 04/20/2023] Open
Abstract
Ataxin-7 maintains the integrity of Spt-Ada-Gcn5-Acetyltransferase (SAGA), an evolutionarily conserved coactivator in stimulating preinitiation complex (PIC) formation for transcription initiation, and thus, its upregulation or downregulation is associated with various diseases. However, it remains unknown how ataxin-7 is regulated that could provide new insights into disease pathogenesis and therapeutic interventions. Here, we show that ataxin-7's yeast homologue, Sgf73, undergoes ubiquitylation and proteasomal degradation. Impairment of such regulation increases Sgf73's abundance, which enhances recruitment of TATA box-binding protein (TBP) (that nucleates PIC formation) to the promoter but impairs transcription elongation. Further, decreased Sgf73 level reduces PIC formation and transcription. Thus, Sgf73 is fine-tuned by ubiquitin-proteasome system (UPS) in orchestrating transcription. Likewise, ataxin-7 undergoes ubiquitylation and proteasomal degradation, alteration of which changes ataxin-7's abundance that is associated with altered transcription and cellular pathologies/diseases. Collectively, our results unveil a novel UPS regulation of Sgf73/ataxin-7 for normal cellular health and implicate alteration of such regulation in diseases.
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Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Amala Kaja
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX-77030, USA
| | - Pritam Chakraborty
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Shalini Guha
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Arpan Roy
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Jannatul Ferdoush
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
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9
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Shukla PK, Bissell JE, Kumar S, Pokhrel S, Palani S, Radmall K, Obidi O, Parnell TJ, Brasch J, Shrieve D, Chandrasekharan M. Structure and functional determinants of Rad6-Bre1 subunits in the histone H2B ubiquitin-conjugating complex. Nucleic Acids Res 2023; 51:2117-2136. [PMID: 36715322 PMCID: PMC10018343 DOI: 10.1093/nar/gkad012] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a crystal structure of Rad6 and the non-RING domain N-terminal region of Bre1, which shows an asymmetric homodimer of Bre1 contacting a conserved loop on the Rad6 'backside'. This contact is distant from the Rad6 catalytic site and is the location of mutations that impair telomeric silencing in yeast. Mutational analyses validated the importance of this contact for the Rad6-Bre1 interaction, chromatin-binding dynamics, H2Bub1 formation and gene expression. Moreover, the non-RING N-terminal region of Bre1 is sufficient to confer nucleosome binding ability to Rad6 in vitro. Interestingly, Rad6 P43L protein, an interaction interface mutant and equivalent to a cancer mutation in the human homolog, bound Bre1 5-fold more tightly than native Rad6 in vitro, but showed reduced chromatin association of Bre1 and reduced levels of H2Bub1 in vivo. These surprising observations imply conformational transitions of the Rad6-Bre1 complex during its chromatin-associated functional cycle, and reveal the differential effects of specific disease-relevant mutations on the chromatin-bound and unbound states. Overall, our study provides structural insights into Rad6-Bre1 interaction through a novel interface that is important for their biochemical and biological responses.
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Affiliation(s)
- Prakash K Shukla
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jesse E Bissell
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Sanjit Kumar
- Centre for Bioseparation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Srijana Pokhrel
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Sowmiya Palani
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kaitlin S Radmall
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Onyeka Obidi
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Timothy J Parnell
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Julia Brasch
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Dennis C Shrieve
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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10
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Zhu X, Ricci-Tam C, Hager ER, Sgro AE. Self-cleaving peptides for expression of multiple genes in Dictyostelium discoideum. PLoS One 2023; 18:e0281211. [PMID: 36862626 PMCID: PMC9980757 DOI: 10.1371/journal.pone.0281211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 01/18/2023] [Indexed: 03/03/2023] Open
Abstract
The social amoeba Dictyostelium discoideum is a model for a wide range of biological processes including chemotaxis, cell-cell communication, phagocytosis, and development. Interrogating these processes with modern genetic tools often requires the expression of multiple transgenes. While it is possible to transfect multiple transcriptional units, the use of separate promoters and terminators for each gene leads to large plasmid sizes and possible interference between units. In many eukaryotic systems this challenge has been addressed through polycistronic expression mediated by 2A viral peptides, permitting efficient, co-regulated gene expression. Here, we screen the most commonly used 2A peptides, porcine teschovirus-1 2A (P2A), Thosea asigna virus 2A (T2A), equine rhinitis A virus 2A (E2A), and foot-and-mouth disease virus 2A (F2A), for activity in D. discoideum and find that all the screened 2A sequences are effective. However, combining the coding sequences of two proteins into a single transcript leads to notable strain-dependent decreases in expression level, suggesting additional factors regulate gene expression in D. discoideum that merit further investigation. Our results show that P2A is the optimal sequence for polycistronic expression in D. discoideum, opening up new possibilities for genetic engineering in this model system.
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Affiliation(s)
- Xinwen Zhu
- Department of Biomedical Engineering, Boston University, Boston, MA, United States of America
- Biological Design Center, Boston University, Boston, MA, United States of America
| | - Chiara Ricci-Tam
- Department of Biomedical Engineering, Boston University, Boston, MA, United States of America
- Biological Design Center, Boston University, Boston, MA, United States of America
| | - Emily R. Hager
- Department of Biomedical Engineering, Boston University, Boston, MA, United States of America
- Biological Design Center, Boston University, Boston, MA, United States of America
| | - Allyson E. Sgro
- Department of Biomedical Engineering, Boston University, Boston, MA, United States of America
- Biological Design Center, Boston University, Boston, MA, United States of America
- * E-mail:
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11
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Fanourgakis S, Synacheri AC, Lavigne MD, Konstantopoulos D, Fousteri M. Histone H2Bub dynamics in the 5' region of active genes are tightly linked to the UV-induced transcriptional response. Comput Struct Biotechnol J 2022; 21:614-629. [PMID: 36659919 PMCID: PMC9823127 DOI: 10.1016/j.csbj.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/22/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
The timing and location of writing and erasing of histone modifications determine gene expression programs and are tightly controlled processes. One such modification is the monoubiquitination of histone H2B (H2Bub), whose precise level during transcription elongation is dynamically regulated by the synergistic action of RNF20/40 ubiquitin-ligase and the de-ubiquitinase (DUB) of the ATXN7L3-containing DUB modules. Here, we characterize the dynamics of H2Bub in transcription and explore its role in perspective with the recently updated model of UV damage-induced transcription reorganization. Employing integrative analysis of genome-wide high-throughput approaches, transcription inhibitors and ATXN7L3-DUB knockdown cells, we find that H2Bub levels and patterns depend on intron-exon architecture both in steady state and upon UV. Importantly, our analysis reveals a widespread redistribution of this histone mark, rather than a uniform loss as previously suggested, which closely mirrors the post-UV dynamics of elongating RNA Polymerase II (RNAPII) at transcribed loci. The observed effects are due to a direct inter-dependence on RNAPII local concentration and speed, and we show that deficient ATXN7L3-mediated DUB activity leads to increased elongation rates in both non-irradiated and irradiated conditions. Our data and the implementation of a high-resolution computational framework reveal that the H2Bub pattern follows that of RNAPII, both in the ATXNL3 knockdown and in response to UV guaranteeing faithful elongation speed, especially in the context of the transcription-driven DNA damage response.
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12
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Korenfeld HT, Avram-Shperling A, Zukerman Y, Iluz A, Boocholez H, Ben-Shimon L, Ben-Aroya S. Reversal of histone H2B mono-ubiquitination is required for replication stress recovery. DNA Repair (Amst) 2022; 119:103387. [DOI: 10.1016/j.dnarep.2022.103387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 07/11/2022] [Accepted: 08/09/2022] [Indexed: 11/15/2022]
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13
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Characterizing and exploiting the many roles of aberrant H2B monoubiquitination in cancer pathogenesis. Semin Cancer Biol 2022; 86:782-798. [PMID: 34953650 DOI: 10.1016/j.semcancer.2021.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/08/2021] [Accepted: 12/19/2021] [Indexed: 01/27/2023]
Abstract
Monoubiquitination of histone H2B on lysine 120 (H2Bub1) is implicated in the control of multiple essential processes, including transcription, DNA damage repair and mitotic chromosome segregation. Accordingly, aberrant regulation of H2Bub1 can induce transcriptional reprogramming and genome instability that may promote oncogenesis. Remarkably, alterations of the ubiquitin ligases and deubiquitinating enzymes regulating H2Bub1 are emerging as ubiquitous features in cancer, further supporting the possibility that the misregulation of H2Bub1 is an underlying mechanism contributing to cancer pathogenesis. To date, aberrant H2Bub1 dynamics have been reported in multiple cancer types and are associated with transcriptional changes that promote oncogenesis in a cancer type-specific manner. Owing to the multi-functional nature of H2Bub1, misregulation of its writers and erasers may drive disease initiation and progression through additional synergistic processes. Accordingly, understanding the molecular determinants and pathogenic impacts associated with aberrant H2Bub1 regulation may reveal novel drug targets and therapeutic vulnerabilities that can be exploited to develop innovative precision medicine strategies that better combat cancer. In this review, we present the normal functions of H2Bub1 in the control of DNA-associated processes and describe the pathogenic implications associated with its misregulation in cancer. We further discuss the challenges coupled with the development of therapeutic strategies targeting H2Bub1 misregulation and expose the potential benefits of designing treatments that synergistically exploit the multiple functionalities of H2Bub1 to improve treatment selectivity and efficacy.
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14
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Esquivel-Chávez A, Maki T, Tsubouchi H, Handa T, Kimura H, Haber JE, Thon G, Iwasaki H. Euchromatin factors HULC and Set1C affect heterochromatin organization and mating-type switching in fission yeast Schizosaccharomyces pombe. Genes Genet Syst 2022; 97:123-138. [PMID: 35908934 DOI: 10.1266/ggs.22-00012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mating-type (P or M) of fission yeast Schizosaccharomyces pombe is determined by the transcriptionally active mat1 cassette and is switched by gene conversion using a donor, either mat2 or mat3, located in an adjacent heterochromatin region (mating-type switching; MTS). In the switching process, heterochromatic donors of genetic information are selected based on the P or M cell type and on the action of two recombination enhancers, SRE2 promoting the use of mat2-P and SRE3 promoting the use of mat3-M, leading to replacement of the content of the expressed mat1 cassette. Recently, we found that the histone H3K4 methyltransferase complex Set1C participates in donor selection, raising the question of how a complex best known for its effects in euchromatin controls recombination in heterochromatin. Here, we report that the histone H2BK119 ubiquitin ligase complex HULC functions with Set1C in MTS, as mutants in the shf1, brl1, brl2 and rad6 genes showed defects similar to Set1C mutants and belonged to the same epistasis group as set1Δ. Moreover, using H3K4R and H2BK119R histone mutants and a Set1-Y897A catalytic mutant, we found that ubiquitylation of histone H2BK119 by HULC and methylation of histone H3K4 by Set1C are functionally coupled in MTS. Cell-type biases in MTS in these mutants suggested that HULC and Set1C inhibit the use of the SRE3 recombination enhancer in M cells, thus favoring SRE2 and mat2-P. Consistent with this, imbalanced switching in the mutants was traced to compromised association of the directionality factor Swi6 with the recombination enhancers in M cells. Based on their known effects at other chromosomal locations, we speculate that HULC and Set1C control nucleosome mobility and strand invasion near the SRE elements. In addition, we uncovered distinct effects of HULC and Set1C on histone H3K9 methylation and gene silencing, consistent with additional functions in the heterochromatic domain.
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Affiliation(s)
- Alfredo Esquivel-Chávez
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology
- Institute of Innovative Research, Tokyo Institute of Technology
| | - Takahisa Maki
- Institute of Innovative Research, Tokyo Institute of Technology
| | - Hideo Tsubouchi
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology
- Institute of Innovative Research, Tokyo Institute of Technology
| | - Testuya Handa
- Institute of Innovative Research, Tokyo Institute of Technology
| | - Hiroshi Kimura
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology
- Institute of Innovative Research, Tokyo Institute of Technology
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University
| | | | - Hiroshi Iwasaki
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology
- Institute of Innovative Research, Tokyo Institute of Technology
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15
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Quantitative Assessment of Histone H2B Monoubiquitination in Yeast Using Immunoblotting. Methods Protoc 2022; 5:mps5050074. [PMID: 36287046 PMCID: PMC9609377 DOI: 10.3390/mps5050074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 02/07/2023] Open
Abstract
Studies in Saccharomyces cerevisiae and Schizosaccharomyces pombe have enhanced our understanding of the regulation and functions of histone H2B monoubiquitination (H2Bub1), a key epigenetic marker with important roles in transcription and other processes. The detection of H2Bub1 in yeasts using immunoblotting has been greatly facilitated by the commercial availability of antibodies against yeast histone H2B and the cross-reactivity of an antibody raised against monoubiquitinated human H2BK120. These antibodies have obviated the need to express epitope-tagged histone H2B to detect H2Bub1 in yeasts. Here, we provide a step-by-step protocol and best practices for the quantification of H2Bub1 in yeast systems, from cell extract preparation to immunoblotting using the commercially available antibodies. We demonstrate that the commercial antibodies can effectively and accurately detect H2Bub1 in S. cerevisiae and S. pombe. Further, we show that the C-terminal epitope-tagging of histone H2B alters the steady-state levels of H2Bub1 in yeast systems. We report a sectioned blot probing approach combined with the serial dilution of protein lysates and the use of reversibly stained proteins as loading controls that together provide a cost-effective and sensitive method for the quantitative evaluation of H2Bub1 in yeast.
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16
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Chen JJ, Stermer D, Tanny JC. Decoding histone ubiquitylation. Front Cell Dev Biol 2022; 10:968398. [PMID: 36105353 PMCID: PMC9464978 DOI: 10.3389/fcell.2022.968398] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
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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17
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Chatfield-Reed K, Marno Jones K, Shah F, Chua G. Genetic-interaction screens uncover novel biological roles and regulators of transcription factors in fission yeast. G3 GENES|GENOMES|GENETICS 2022; 12:6655692. [PMID: 35924983 PMCID: PMC9434175 DOI: 10.1093/g3journal/jkac194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022]
Abstract
In Schizosaccharomyces pombe, systematic analyses of single transcription factor deletion or overexpression strains have made substantial advances in determining the biological roles and target genes of transcription factors, yet these characteristics are still relatively unknown for over a quarter of them. Moreover, the comprehensive list of proteins that regulate transcription factors remains incomplete. To further characterize Schizosaccharomyces pombe transcription factors, we performed synthetic sick/lethality and synthetic dosage lethality screens by synthetic genetic array. Examination of 2,672 transcription factor double deletion strains revealed a sick/lethality interaction frequency of 1.72%. Phenotypic analysis of these sick/lethality strains revealed potential cell cycle roles for several poorly characterized transcription factors, including SPBC56F2.05, SPCC320.03, and SPAC3C7.04. In addition, we examined synthetic dosage lethality interactions between 14 transcription factors and a miniarray of 279 deletion strains, observing a synthetic dosage lethality frequency of 4.99%, which consisted of known and novel transcription factor regulators. The miniarray contained deletions of genes that encode primarily posttranslational-modifying enzymes to identify putative upstream regulators of the transcription factor query strains. We discovered that ubiquitin ligase Ubr1 and its E2/E3-interacting protein, Mub1, degrade the glucose-responsive transcriptional repressor Scr1. Loss of ubr1+ or mub1+ increased Scr1 protein expression, which resulted in enhanced repression of flocculation through Scr1. The synthetic dosage lethality screen also captured interactions between Scr1 and 2 of its known repressors, Sds23 and Amk2, each affecting flocculation through Scr1 by influencing its nuclear localization. Our study demonstrates that sick/lethality and synthetic dosage lethality screens can be effective in uncovering novel functions and regulators of Schizosaccharomyces pombe transcription factors.
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Affiliation(s)
- Kate Chatfield-Reed
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Kurtis Marno Jones
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Farah Shah
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
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18
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Etier A, Dumetz F, Chéreau S, Ponts N. Post-Translational Modifications of Histones Are Versatile Regulators of Fungal Development and Secondary Metabolism. Toxins (Basel) 2022; 14:toxins14050317. [PMID: 35622565 PMCID: PMC9145779 DOI: 10.3390/toxins14050317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 02/04/2023] Open
Abstract
Chromatin structure is a major regulator of DNA-associated processes, such as transcription, DNA repair, and replication. Histone post-translational modifications, or PTMs, play a key role on chromatin dynamics. PTMs are involved in a wide range of biological processes in eukaryotes, including fungal species. Their deposition/removal and their underlying functions have been extensively investigated in yeasts but much less in other fungi. Nonetheless, the major role of histone PTMs in regulating primary and secondary metabolisms of filamentous fungi, including human and plant pathogens, has been pinpointed. In this review, an overview of major identified PTMs and their respective functions in fungi is provided, with a focus on filamentous fungi when knowledge is available. To date, most of these studies investigated histone acetylations and methylations, but the development of new methodologies and technologies increasingly allows the wider exploration of other PTMs, such as phosphorylation, ubiquitylation, sumoylation, and acylation. Considering the increasing number of known PTMs and the full range of their possible interactions, investigations of the subsequent Histone Code, i.e., the biological consequence of the combinatorial language of all histone PTMs, from a functional point of view, are exponentially complex. Better knowledge about histone PTMs would make it possible to efficiently fight plant or human contamination, avoid the production of toxic secondary metabolites, or optimize the industrial biosynthesis of certain beneficial compounds.
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19
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Parween S, Alawathugoda TT, Prabakaran AD, Dheen ST, Morse RH, Emerald BS, Ansari SA. Nutrient sensitive protein O-GlcNAcylation modulates the transcriptome through epigenetic mechanisms during embryonic neurogenesis. Life Sci Alliance 2022; 5:5/8/e202201385. [PMID: 35470239 PMCID: PMC9039347 DOI: 10.26508/lsa.202201385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 01/02/2023] Open
Abstract
Protein O-GlcNAcylation is a dynamic, nutrient-sensitive mono-glycosylation deposited on numerous nucleo-cytoplasmic and mitochondrial proteins, including transcription factors, epigenetic regulators, and histones. However, the role of protein O-GlcNAcylation on epigenome regulation in response to nutrient perturbations during development is not well understood. Herein we recapitulated early human embryonic neurogenesis in cell culture and found that pharmacological up-regulation of O-GlcNAc levels during human embryonic stem cells' neuronal differentiation leads to up-regulation of key neurogenic transcription factor genes. This transcriptional de-repression is associated with reduced H3K27me3 and increased H3K4me3 levels on the promoters of these genes, perturbing promoter bivalency possibly through increased EZH2-Thr311 phosphorylation. Elevated O-GlcNAc levels also lead to increased Pol II-Ser5 phosphorylation and affect H2BS112O-GlcNAc and H2BK120Ub1 on promoters. Using an in vivo rat model of maternal hyperglycemia, we show similarly elevated O-GlcNAc levels and epigenetic dysregulations in the developing embryo brains because of hyperglycemia, whereas pharmacological inhibition of O-GlcNAc transferase (OGT) restored these molecular changes. Together, our results demonstrate O-GlcNAc mediated sensitivity of chromatin to nutrient status, and indicate how metabolic perturbations could affect gene expression during neurodevelopment.
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Affiliation(s)
- Shama Parween
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Thilina T Alawathugoda
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ashok D Prabakaran
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - S Thameem Dheen
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Randall H Morse
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Suraiya A Ansari
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates .,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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20
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Trans-tail regulation-mediated suppression of cryptic transcription. Exp Mol Med 2021; 53:1683-1688. [PMID: 34845331 PMCID: PMC8639711 DOI: 10.1038/s12276-021-00711-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 01/08/2023] Open
Abstract
Crosstalk between post-translational modifications of histone proteins influences the regulation of chromatin structure and gene expression. Among such crosstalk pathways, the best-characterized example is H2B monoubiquitination-mediated H3K4 and H3K79 methylation, which is referred to as trans-tail regulation. Although many studies have investigated the fragmentary effects of this pathway on silencing and transcription, its ultimate contribution to transcriptional control has remained unclear. Recent advances in molecular techniques and genomics have, however, revealed that the trans-tail crosstalk is linked to a more diverse cascade of histone modifications and has various functions in cotranscriptional processes. Furthermore, H2B monoubiquitination sequentially facilitates H3K4 dimethylation and histone sumoylation, thereby providing a binding platform for recruiting Set3 complex proteins, including two histone deacetylases, to restrict cryptic transcription from gene bodies. The removal of both ubiquitin and SUMO, small ubiquitin-like modifier, modifications from histones also facilitates a change in the phosphorylation pattern of the RNA polymerase II C-terminal domain that is required for subsequent transcriptional elongation. Therefore, this review describes recent findings regarding trans-tail regulation-driven processes to elaborate on their contribution to maintaining transcriptional fidelity. Crosstalk between different DNA-winding proteins, or histones, is a mechanism of molecular fidelity that helps prevent the initiation of aberrant gene expression, which may contribute to cancer and neurodegenerative disease. A team from South Korea, led by Jungmin Choi from the Korea University College of Medicine in Seoul and Hong-Yeoul Ryu from Kyungpook National University in Daegu, review the ways in which different histone proteins chemically modify parts of each other’s structure to regulate their functions. These modifications affect how histones interact with DNA, which in turn alters the dynamics of other factors implicated in gene expression. The correct interaction of histones is necessary to prevent the gene expression machinery from starting RNA synthesis from the wrong sites. Accurate control of these mechanisms is essential for cellular wellbeing
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21
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Adamowicz M, Hailstone R, Demin AA, Komulainen E, Hanzlikova H, Brazina J, Gautam A, Wells SE, Caldecott KW. XRCC1 protects transcription from toxic PARP1 activity during DNA base excision repair. Nat Cell Biol 2021; 23:1287-1298. [PMID: 34811483 PMCID: PMC8683375 DOI: 10.1038/s41556-021-00792-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022]
Abstract
Genetic defects in the repair of DNA single-strand breaks (SSBs) can result in neurological disease triggered by toxic activity of the single-strand-break sensor protein PARP1. However, the mechanism(s) by which this toxic PARP1 activity triggers cellular dysfunction are unclear. Here we show that human cells lacking XRCC1 fail to rapidly recover transcription following DNA base damage, a phenotype also observed in patient-derived fibroblasts with XRCC1 mutations and Xrcc1−/− mouse neurons. This defect is caused by excessive/aberrant PARP1 activity during DNA base excision repair, resulting from the loss of PARP1 regulation by XRCC1. We show that aberrant PARP1 activity suppresses transcriptional recovery during base excision repair by promoting excessive recruitment and activity of the ubiquitin protease USP3, which as a result reduces the level of monoubiquitinated histones important for normal transcriptional regulation. Importantly, inhibition and/or deletion of PARP1 or USP3 restores transcriptional recovery in XRCC1−/− cells, highlighting PARP1 and USP3 as possible therapeutic targets in neurological disease. Adamowicz et al. report that toxic PARP1 activity, induced by ataxia-associated mutations in XRCC1, impairs the recovery of global transcription during DNA base excision repair by promoting aberrant recruitment and activity of the histone ubiquitin protease USP3.
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Affiliation(s)
- Marek Adamowicz
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Richard Hailstone
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Annie A Demin
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Emilia Komulainen
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Hana Hanzlikova
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK.,Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Science, Prague, Czech Republic
| | - Jan Brazina
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Amit Gautam
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Sophie E Wells
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Keith W Caldecott
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK. .,Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Science, Prague, Czech Republic.
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22
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Subtelomeric Chromatin in the Fission Yeast S. pombe. Microorganisms 2021; 9:microorganisms9091977. [PMID: 34576871 PMCID: PMC8466458 DOI: 10.3390/microorganisms9091977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/06/2021] [Accepted: 09/14/2021] [Indexed: 01/15/2023] Open
Abstract
Telomeres play important roles in safeguarding the genome. The specialized repressive chromatin that assembles at telomeres and subtelomeric domains is key to this protective role. However, in many organisms, the repetitive nature of telomeric and subtelomeric sequences has hindered research efforts. The fission yeast S. pombe has provided an important model system for dissection of chromatin biology due to the relative ease of genetic manipulation and strong conservation of important regulatory proteins with higher eukaryotes. Telomeres and the telomere-binding shelterin complex are highly conserved with mammals, as is the assembly of constitutive heterochromatin at subtelomeres. In this review, we seek to summarize recent work detailing the assembly of distinct chromatin structures within subtelomeric domains in fission yeast. These include the heterochromatic SH subtelomeric domains, the telomere-associated sequences (TAS), and ST chromatin domains that assemble highly condensed chromatin clusters called knobs. Specifically, we review new insights into the sequence of subtelomeric domains, the distinct types of chromatin that assemble on these sequences and how histone H3 K36 modifications influence these chromatin structures. We address the interplay between the subdomains of chromatin structure and how subtelomeric chromatin is influenced by both the telomere-bound shelterin complexes and by euchromatic chromatin regulators internal to the subtelomeric domain. Finally, we demonstrate that telomere clustering, which is mediated via the condensed ST chromatin knob domains, does not depend on knob assembly within these domains but on Set2, which mediates H3K36 methylation.
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23
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Stanek TJ, Gennaro VJ, Tracewell MA, Di Marcantonio D, Pauley KL, Butt S, McNair C, Wang F, Kossenkov AV, Knudsen KE, Butt T, Sykes SM, McMahon SB. The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22. EMBO J 2021; 40:e102509. [PMID: 34155658 PMCID: PMC8365265 DOI: 10.15252/embj.2019102509] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 04/10/2021] [Accepted: 04/26/2021] [Indexed: 12/12/2022] Open
Abstract
The SAGA coactivator complex is essential for eukaryotic transcription and comprises four distinct modules, one of which contains the ubiquitin hydrolase USP22. In yeast, the USP22 ortholog deubiquitylates H2B, resulting in Pol II Ser2 phosphorylation and subsequent transcriptional elongation. In contrast to this H2B-associated role in transcription, we report here that human USP22 contributes to the early stages of stimulus-responsive transcription, where USP22 is required for pre-initiation complex (PIC) stability. Specifically, USP22 maintains long-range enhancer-promoter contacts and controls loading of Mediator tail and general transcription factors (GTFs) onto promoters, with Mediator core recruitment being USP22-independent. In addition, we identify Mediator tail subunits MED16 and MED24 and the Pol II subunit RBP1 as potential non-histone substrates of USP22. Overall, these findings define a role for human SAGA within the earliest steps of transcription.
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Affiliation(s)
- Timothy J Stanek
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Victoria J Gennaro
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Mason A Tracewell
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | | | - Kristen L Pauley
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Sabrina Butt
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Christopher McNair
- Department of Cancer BiologySidney Kimmel Medical College and Sidney Kimmel Cancer CenterThomas Jefferson UniversityPhiladelphiaPAUSA
| | | | | | - Karen E Knudsen
- Department of Cancer BiologySidney Kimmel Medical College and Sidney Kimmel Cancer CenterThomas Jefferson UniversityPhiladelphiaPAUSA
| | | | - Stephen M Sykes
- Blood Cell Development and Function ProgramFox Chase Cancer CenterPhiladelphiaPAUSA
| | - Steven B McMahon
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
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24
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Yuan W, Al-Hadid Q, Wang Z, Shen L, Cho H, Wu X, Yang Y. TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution. Nucleic Acids Res 2021; 49:8573-8591. [PMID: 34329467 PMCID: PMC8421139 DOI: 10.1093/nar/gkab642] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 06/14/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022] Open
Abstract
R-loops, which consist of a DNA/RNA hybrid and a displaced single-stranded DNA (ssDNA), are increasingly recognized as critical regulators of chromatin biology. R-loops are particularly enriched at gene promoters, where they play important roles in regulating gene expression. However, the molecular mechanisms that control promoter-associated R-loops remain unclear. The epigenetic ‘reader’ Tudor domain-containing protein 3 (TDRD3), which recognizes methylarginine marks on histones and on the C-terminal domain of RNA polymerase II, was previously shown to recruit DNA topoisomerase 3B (TOP3B) to relax negatively supercoiled DNA and prevent R-loop formation. Here, we further characterize the function of TDRD3 in R-loop metabolism and introduce the DExH-box helicase 9 (DHX9) as a novel interaction partner of the TDRD3/TOP3B complex. TDRD3 directly interacts with DHX9 via its Tudor domain. This interaction is important for recruiting DHX9 to target gene promoters, where it resolves R-loops in a helicase activity-dependent manner to facilitate gene expression. Additionally, TDRD3 also stimulates the helicase activity of DHX9. This stimulation relies on the OB-fold of TDRD3, which likely binds the ssDNA in the R-loop structure. Thus, DHX9 functions together with TOP3B to suppress promoter-associated R-loops. Collectively, these findings reveal new functions of TDRD3 and provide important mechanistic insights into the regulation of R-loop metabolism.
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Affiliation(s)
- Wei Yuan
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Qais Al-Hadid
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Zhihao Wang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Lei Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Hyejin Cho
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Xiwei Wu
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Yanzhong Yang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
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Jian Y, Liu Z, Wang H, Chen Y, Yin Y, Zhao Y, Ma Z. Interplay of two transcription factors for recruitment of the chromatin remodeling complex modulates fungal nitrosative stress response. Nat Commun 2021; 12:2576. [PMID: 33958593 PMCID: PMC8102577 DOI: 10.1038/s41467-021-22831-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 03/25/2021] [Indexed: 02/03/2023] Open
Abstract
Nitric oxide (NO) is a diffusible signaling molecule that modulates animal and plant immune responses. In addition, reactive nitrogen species derived from NO can display antimicrobial activities by reacting with microbial cellular components, leading to nitrosative stress (NS) in pathogens. Here, we identify FgAreB as a regulator of the NS response in Fusarium graminearum, a fungal pathogen of cereal crops. FgAreB serves as a pioneer transcription factor for recruitment of the chromatin-remodeling complex SWI/SNF at the promoters of genes involved in the NS response, thus promoting their transcription. FgAreB plays important roles in fungal infection and growth. Furthermore, we show that a transcription repressor (FgIxr1) competes with the SWI/SNF complex for FgAreB binding, and negatively regulates the NS response. NS, in turn, promotes the degradation of FgIxr1, thus enhancing the recruitment of the SWI/SNF complex by FgAreB.
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Affiliation(s)
- Yunqing Jian
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China
| | - Zunyong Liu
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Haixia Wang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China
| | - Yun Chen
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yanni Yin
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China.
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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26
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Grant PA, Winston F, Berger SL. The biochemical and genetic discovery of the SAGA complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194669. [PMID: 33338653 DOI: 10.1016/j.bbagrm.2020.194669] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
One of the major advances in our understanding of gene regulation in eukaryotes was the discovery of factors that regulate transcription by controlling chromatin structure. Prominent among these discoveries was the demonstration that Gcn5 is a histone acetyltransferase, establishing a direct connection between transcriptional activation and histone acetylation. This breakthrough was soon followed by the purification of a protein complex that contains Gcn5, the SAGA complex. In this article, we review the early genetic and biochemical experiments that led to the discovery of SAGA and the elucidation of its multiple activities.
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Affiliation(s)
- Patrick A Grant
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, United States of America
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States of America.
| | - Shelley L Berger
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Department of Biology, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
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27
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Wang D, Wang Y, Wu X, Kong X, Li J, Dong C. RNF20 Is Critical for Snail-Mediated E-Cadherin Repression in Human Breast Cancer. Front Oncol 2020; 10:613470. [PMID: 33364200 PMCID: PMC7753216 DOI: 10.3389/fonc.2020.613470] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/09/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND E-cadherin, a hallmark of epithelial-mesenchymal transition (EMT), is often repressed due to Snail-mediated epigenetic modification; however, the exact mechanism remains unclear. There is an urgent need to understand the determinants of tumor aggressiveness and identify potential therapeutic targets in breast cancer. EXPERIMENTAL DESIGN We studied the association of RNF20 with Snail and G9a by co-immunoprecipitation. We employed quantitative real-time PCR, ChIP, transwell assay, colony formation assay, and mammosphere assay to dissect the molecular events associated with the repression of E-cadherin in human breast cancer. We used a proteogenomic dataset that contains 105 breast tumor samples to determine the clinical relevance of RNF20 by Kaplan-Meier analyses. RESULTS In this study, we identified that Snail interacted with RNF20, an E3 ubiquitin-protein ligase responsible for monoubiquitination of H2BK120, and G9a, a methyltransferase for H3K9me2. RNF20 expression led to the inhibition of E-cadherin expression in the human breast cancer cells. Mechanically, we showed that RNF20 and H3K9m2 were enriched on the promoter of E-cadherin and knockdown of Snail reduced the enrichment of RNF20, showing a Snail-dependent manner. RNF20 expression enhanced breast cancer cell migration, invasion, tumorsphere and colony formation. Clinically, patients with high RNF20 expression had shorter overall survival. CONCLUSION RNF20 expression contributes to EMT induction and breast cancer progression through Snail-mediated epigenetic suppression of E-cadherin expression, suggesting the importance of RNF20 in breast cancer.
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Affiliation(s)
- Danping Wang
- Department of Pathology and Pathophysiology, and Department of Surgical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifan Wang
- Department of Pathology and Pathophysiology, and Department of Surgical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Institute of Integrative Medicine, Zhejiang Academy of Traditional Chinese Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Xuebiao Wu
- Department of Pathophysiology, Zunyi Medical University, Zunyi, China
| | - Xiangxing Kong
- Department of Pathology and Pathophysiology, and Department of Surgical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Li
- Department of Pathology and Pathophysiology, and Department of Surgical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chenfang Dong
- Department of Pathology and Pathophysiology, and Department of Surgical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
- Department of Pathophysiology, Zunyi Medical University, Zunyi, China
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28
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Zhu W, Fan X, Zhao Q, Xu Y, Wang X, Chen J. Bre1 and Ubp8 regulate H2B mono-ubiquitination and the reversible yeast-hyphae transition in Candida albicans. Mol Microbiol 2020; 115:332-343. [PMID: 33010070 DOI: 10.1111/mmi.14619] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 02/06/2023]
Abstract
The reversible yeast-hyphae transition of the human fungal pathogen Candida albicans is tightly linked to its pathogenicity. In this study, we show that histone H2B mono-ubiquitination (H2Bub) at lysine 123 was maintained at a low level in the yeast state, whereas it increased significantly during yeast-to-hyphae transition and decreased when hyphae converted to yeast. The increased H2Bub level is correlated with activation of the hyphal program. H2B ubiquitination and deubiquitination are dynamically regulated by the E3 ligase Bre1 and the deubiquitinase Ubp8 during the reversible yeast-hyphae transition. The functions of Bre1 and Ubp8 in hypha-specific gene (HSG) regulation appears to be direct because both are recruited to the coding regions of HSGs during hyphal induction. The sequential recruitment of Bre1 and Ubp8 to HSGs coding regions is important for the initiation and maintenance of HSG expression. Additionally, Ubp8 contributes to the pathogenicity of C. albicans during early infection in a mouse model. Our study is the first to link H2B ubiquitination to the morphological plasticity and pathogenicity of the human fungal pathogen C. albicans and shed light on potential antifungal treatments.
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Affiliation(s)
- Wencheng Zhu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xueyi Fan
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qun Zhao
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yinxing Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiongjun Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiangye Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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29
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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] [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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30
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Spt5 Phosphorylation and the Rtf1 Plus3 Domain Promote Rtf1 Function through Distinct Mechanisms. Mol Cell Biol 2020; 40:MCB.00150-20. [PMID: 32366382 DOI: 10.1128/mcb.00150-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/28/2020] [Indexed: 11/20/2022] Open
Abstract
Rtf1 is a conserved RNA polymerase II (RNAPII) elongation factor that promotes cotranscriptional histone modification, RNAPII transcript elongation, and mRNA processing. Rtf1 function requires the phosphorylation of Spt5, an essential RNAPII processivity factor. Spt5 is phosphorylated within its C-terminal domain (CTD) by cyclin-dependent kinase 9 (Cdk9), the catalytic component of positive transcription elongation factor b (P-TEFb). Rtf1 recognizes phosphorylated Spt5 (pSpt5) through its Plus3 domain. Since Spt5 is a unique target of Cdk9 and Rtf1 is the only known pSpt5-binding factor, the Plus3/pSpt5 interaction is thought to be a key Cdk9-dependent event regulating RNAPII elongation. Here, we dissect Rtf1 regulation by pSpt5 in the fission yeast Schizosaccharomyces pombe We demonstrate that the Plus3 domain of Rtf1 (Prf1 in S. pombe) and pSpt5 are functionally distinct and that they act in parallel to promote Prf1 function. This alternate Plus3 domain function involves an interface that overlaps the pSpt5-binding site and that can interact with single-stranded nucleic acid or with the polymerase-associated factor (PAF) complex in vitro We further show that the C-terminal region of Prf1, which also interacts with PAF, has a similar parallel function with pSpt5. Our results elucidate unexpected complexity underlying Cdk9-dependent pathways that regulate transcription elongation.
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31
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Keren I, Lacroix B, Kohrman A, Citovsky V. Histone Deubiquitinase OTU1 Epigenetically Regulates DA1 and DA2, Which Control Arabidopsis Seed and Organ Size. iScience 2020; 23:100948. [PMID: 32169818 PMCID: PMC7068640 DOI: 10.1016/j.isci.2020.100948] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 01/05/2020] [Accepted: 02/24/2020] [Indexed: 12/31/2022] Open
Abstract
Seeds are central to plant life cycle and to human nutrition, functioning as the major supplier of human population energy intake. To understand better the roles of enzymic writers and erasers of the epigenetic marks, in particular, histone ubiquitylation and the corresponding histone modifiers, involved in control of seed development, we identified the otubain-like cysteine protease OTU1 as a histone deubiquitinase involved in transcriptional repression of the DA1 and DA2 genes known to regulate seed and organ size in Arabidopsis. Loss-of-function mutants of OTU1 accumulate H2B monoubiquitylation and such euchromatic marks as H3 trimethylation and hyperacetylation in the DA1 and DA2 chromatin. These data advance our knowledge about epigenetic regulation of the DA1 and DA2 genes by recognizing OTU1 as a member of a putative repressor complex that negatively regulates their transcription. Histone ubiquitylation regulates transcription of DA1/DA2 that control seed/organ size OTU1 deubiquitinase is involved in deubiquitylation of the DA1/DA2 chromatin OTU1 acts as an epigenetic transcriptional repressor of the DA1/DA2 genes OTU1 is nucleocytoplasmic, indicating involvement in nuclear and cytoplasmic processes
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Affiliation(s)
- Ido Keren
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA.
| | - Benoît Lacroix
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
| | - Abraham Kohrman
- Graduate Program in Genetics, State University of New York, Stony Brook, NY 11794-5222, USA
| | - Vitaly Citovsky
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
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32
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Murawska M, Schauer T, Matsuda A, Wilson MD, Pysik T, Wojcik F, Muir TW, Hiraoka Y, Straub T, Ladurner AG. The Chaperone FACT and Histone H2B Ubiquitination Maintain S. pombe Genome Architecture through Genic and Subtelomeric Functions. Mol Cell 2020; 77:501-513.e7. [PMID: 31837996 PMCID: PMC7007867 DOI: 10.1016/j.molcel.2019.11.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 10/01/2019] [Accepted: 11/15/2019] [Indexed: 12/31/2022]
Abstract
The histone chaperone FACT and histone H2B ubiquitination (H2Bub) facilitate RNA polymerase II (Pol II) passage through chromatin, yet it is not clear how they cooperate mechanistically. We used genomics, genetic, biochemical, and microscopic approaches to dissect their interplay in Schizosaccharomyces pombe. We show that FACT and H2Bub globally repress antisense transcripts near the 5' end of genes and inside gene bodies, respectively. The accumulation of these transcripts is accompanied by changes at genic nucleosomes and Pol II redistribution. H2Bub is required for FACT activity in genic regions. In the H2Bub mutant, FACT binding to chromatin is altered and its association with histones is stabilized, which leads to the reduction of genic nucleosomes. Interestingly, FACT depletion globally restores nucleosomes in the H2Bub mutant. Moreover, in the absence of Pob3, the FACT Spt16 subunit controls the 3' end of genes. Furthermore, FACT maintains nucleosomes in subtelomeric regions, which is crucial for their compaction.
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Affiliation(s)
- Magdalena Murawska
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Tamas Schauer
- Biomedical Center, Bioinformatics Unit, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Atsushi Matsuda
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan; Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Thomas Pysik
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Felix Wojcik
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan; Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Tobias Straub
- Biomedical Center, Bioinformatics Unit, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Andreas G Ladurner
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany.
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33
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Cucinotta CE, Hildreth AE, McShane BM, Shirra MK, Arndt KM. The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo. Nucleic Acids Res 2019; 47:8410-8423. [PMID: 31226204 PMCID: PMC6895269 DOI: 10.1093/nar/gkz549] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
The nucleosome core regulates DNA-templated processes through the highly conserved nucleosome acidic patch. While structural and biochemical studies have shown that the acidic patch controls chromatin factor binding and activity, few studies have elucidated its functions in vivo. We employed site-specific crosslinking to identify proteins that directly bind the acidic patch in Saccharomyces cerevisiae and demonstrated crosslinking of histone H2A to Paf1 complex subunit Rtf1 and FACT subunit Spt16. Rtf1 bound to nucleosomes through its histone modification domain, supporting its role as a cofactor in H2B K123 ubiquitylation. An acidic patch mutant showed defects in nucleosome positioning and occupancy genome-wide. Our results provide new information on the chromatin engagement of two central players in transcription elongation and emphasize the importance of the nucleosome core as a hub for proteins that regulate chromatin during transcription.
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Affiliation(s)
- Christine E Cucinotta
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - A Elizabeth Hildreth
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Brendan M McShane
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Margaret K Shirra
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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34
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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: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [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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Chen FX, Smith ER, Shilatifard A. Born to run: control of transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 2019; 19:464-478. [PMID: 29740129 DOI: 10.1038/s41580-018-0010-5] [Citation(s) in RCA: 262] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The dynamic regulation of transcription elongation by RNA polymerase II (Pol II) is an integral part of the implementation of gene expression programmes during development. In most metazoans, the majority of transcribed genes exhibit transient pausing of Pol II at promoter-proximal regions, and the release of Pol II into gene bodies is controlled by many regulatory factors that respond to environmental and developmental cues. Misregulation of the elongation stage of transcription is implicated in cancer and other human diseases, suggesting that mechanistic understanding of transcription elongation control is therapeutically relevant. In this Review, we discuss the features, establishment and maintenance of Pol II pausing, the transition into productive elongation, the control of transcription elongation by enhancers and by factors of other cellular processes, such as topoisomerases and poly(ADP-ribose) polymerases (PARPs), and the potential of therapeutic targeting of the elongation stage of transcription by Pol II.
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Affiliation(s)
- Fei Xavier Chen
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Edwin R Smith
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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Suzuki H, Okamoto-Katsuyama M, Suwa T, Maeda R, Tamura TA, Yamaguchi Y. TLP-mediated global transcriptional repression after double-strand DNA breaks slows down DNA repair and induces apoptosis. Sci Rep 2019; 9:4868. [PMID: 30890736 PMCID: PMC6425004 DOI: 10.1038/s41598-019-41057-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/18/2019] [Indexed: 11/16/2022] Open
Abstract
Transcription and DNA damage repair act in a coordinated manner. Recent studies have shown that double-strand DNA breaks (DSBs) are repaired in a transcription-coupled manner. Active transcription results in a faster recruitment of DSB repair factors and expedites DNA repair. On the other hand, transcription is repressed by DNA damage through multiple mechanisms. We previously reported that TLP, a TATA box-binding protein (TBP) family member that functions as a transcriptional regulator, is also involved in DNA damage-induced apoptosis. However, the mechanism by which TLP affects DNA damage response was largely unknown. Here we show that TLP-mediated global transcriptional repression after DSBs is crucial for apoptosis induction by DNA-damaging agents such as etoposide and doxorubicin. Compared to control cells, TLP-knockdown cells were resistant to etoposide-induced apoptosis and exhibited an elevated level of global transcription after etoposide exposure. DSBs were efficiently removed in transcriptionally hyperactive TLP-knockdown cells. However, forced transcriptional shutdown using transcriptional inhibitors α-amanitin and 5,6-dichloro-1-ß-D-ribofuranosylbenzimidazole (DRB) slowed down DSB repair and resensitized TLP-knockdown cells to etoposide. Taken together, these results indicate that TLP is a critical determinant as to how cells respond to DSBs and triggers apoptosis to cells that have sustained DNA damage.
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Affiliation(s)
- Hidefumi Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226-8501, Japan
| | - Mayumi Okamoto-Katsuyama
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226-8501, Japan
| | - Tetsufumi Suwa
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226-8501, Japan
| | - Ryo Maeda
- Graduate School of Science, Chiba University, 1-33 Yayoicho, Chiba, 263-8522, Japan
| | - Taka-Aki Tamura
- Graduate School of Science, Chiba University, 1-33 Yayoicho, Chiba, 263-8522, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226-8501, Japan.
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Nune M, Morgan MT, Connell Z, McCullough L, Jbara M, Sun H, Brik A, Formosa T, Wolberger C. FACT and Ubp10 collaborate to modulate H2B deubiquitination and nucleosome dynamics. eLife 2019; 8:40988. [PMID: 30681413 PMCID: PMC6372288 DOI: 10.7554/elife.40988] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/24/2019] [Indexed: 12/21/2022] Open
Abstract
Monoubiquitination of histone H2B (H2B-Ub) plays a role in transcription and DNA replication, and is required for normal localization of the histone chaperone, FACT. In yeast, H2B-Ub is deubiquitinated by Ubp8, a subunit of SAGA, and Ubp10. Although they target the same substrate, loss of Ubp8 and Ubp10 cause different phenotypes and alter the transcription of different genes. We show that Ubp10 has poor activity on yeast nucleosomes, but that the addition of FACT stimulates Ubp10 activity on nucleosomes and not on other substrates. Consistent with a role for FACT in deubiquitinating H2B in vivo, a FACT mutant strain shows elevated levels of H2B-Ub. Combination of FACT mutants with deletion of Ubp10, but not Ubp8, confers increased sensitivity to hydroxyurea and activates a cryptic transcription reporter, suggesting that FACT and Ubp10 may coordinate nucleosome assembly during DNA replication and transcription. Our findings reveal unexpected interplay between H2B deubiquitination and nucleosome dynamics.
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Affiliation(s)
- Melesse Nune
- Program in Molecular Biophysics, Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Michael T Morgan
- Program in Molecular Biophysics, Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Zaily Connell
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Laura McCullough
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Muhammad Jbara
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hao Sun
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Tim Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Cynthia Wolberger
- Program in Molecular Biophysics, Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
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Zhao W, Neyt P, Van Lijsebettens M, Shen WH, Berr A. Interactive and noninteractive roles of histone H2B monoubiquitination and H3K36 methylation in the regulation of active gene transcription and control of plant growth and development. THE NEW PHYTOLOGIST 2019; 221:1101-1116. [PMID: 30156703 DOI: 10.1111/nph.15418] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/27/2018] [Indexed: 05/23/2023]
Abstract
Covalent modifications of histones are essential to control a wide range of processes during development and adaptation to environmental changes. With the establishment of reference epigenomes, patterns of histone modifications were correlated with transcriptionally active or silenced genes. These patterns imply the need for the precise and dynamic coordination of different histone-modifying enzymes to control transcription at a given gene. Classically, the influence of these enzymes on gene expression is examined separately and their interplays rarely established. In Arabidopsis, HISTONE MONOUBIQUITINATION2 (HUB2) mediates H2B monoubiquitination (H2Bub1), whereas SET DOMAIN GROUP8 (SDG8) catalyzes H3 lysine 36 trimethylation (H3K36me3). In this work, we crossed hub2 with sdg8 mutants to elucidate their functional relationships. Despite similar phenotypic defects, sdg8 and hub2 mutations broadly affect genome transcription and plant growth and development synergistically. Also, whereas H3K4 methylation appears largely dependent on H2Bub1, H3K36me3 and H2Bub1 modifications mutually reinforce each other at some flowering time genes. In addition, SDG8 and HUB2 jointly antagonize the increase of the H3K27me3 repressive mark. Collectively, our data provide an important insight into the interplay between histone marks and highlight their interactive complexity in regulating chromatin landscape which might be necessary to fine-tune transcription and ensure plant developmental plasticity.
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Affiliation(s)
- Wei Zhao
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Pia Neyt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
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Role of RNF20 in cancer development and progression - a comprehensive review. Biosci Rep 2018; 38:BSR20171287. [PMID: 29934362 PMCID: PMC6043722 DOI: 10.1042/bsr20171287] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/20/2018] [Accepted: 06/22/2018] [Indexed: 02/06/2023] Open
Abstract
Evolving strategies to counter cancer initiation and progression rely on the identification of novel therapeutic targets that exploit the aberrant genetic changes driving oncogenesis. Several chromatin associated enzymes have been shown to influence post-translational modification (PTM) in DNA, histones, and non-histone proteins. Any deregulation of this core group of enzymes often leads to cancer development. Ubiquitylation of histone H2B in mammalian cells was identified over three decades ago. An exciting really interesting new gene (RING) family of E3 ubiquitin ligases, known as RNF20 and RNF40, monoubiquitinates histone H2A at K119 or H2B at K120, is known to function in transcriptional elongation, DNA double-strand break (DSB) repair processes, maintenance of chromatin differentiation, and exerting tumor suppressor activity. RNF20 is somatically altered in breast, lung, prostate cancer, clear cell renal cell carcinoma (ccRCC), and mixed lineage leukemia, and its reduced expression is a key factor in initiating genome instability; and it also functions as one of the significant driving factors of oncogenesis. Loss of RNF20/40 and H2B monoubiquitination (H2Bub1) is found in several cancers and is linked to an aggressive phenotype, and is also an indicator of poor prognosis. In this review, we summarized the current knowledge of RNF20 in chronic inflammation-driven cancers, DNA DSBs, and apoptosis, and its impact on chromatin structure beyond the single nucleosome level.
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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: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [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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New insights into donor directionality of mating-type switching in Schizosaccharomyces pombe. PLoS Genet 2018; 14:e1007424. [PMID: 29852001 PMCID: PMC6007933 DOI: 10.1371/journal.pgen.1007424] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/19/2018] [Accepted: 05/17/2018] [Indexed: 11/29/2022] Open
Abstract
Mating-type switching in Schizosaccharomyces pombe entails programmed gene conversion events regulated by DNA replication, heterochromatin, and the HP1-like chromodomain protein Swi6. The whole mechanism remains to be fully understood. Using a gene deletion library, we screened ~ 3400 mutants for defects in the donor selection step where a heterochromatic locus, mat2-P or mat3-M, is chosen to convert the expressed mat1 locus. By measuring the biases in mat1 content that result from faulty directionality, we identified in total 20 factors required for donor selection. Unexpectedly, these included the histone H3 lysine 4 (H3K4) methyltransferase complex subunits Set1, Swd1, Swd2, Swd3, Spf1 and Ash2, the BRE1-like ubiquitin ligase Brl2 and the Elongator complex subunit Elp6. The mutant defects were investigated in strains with reversed donor loci (mat2-M mat3-P) or when the SRE2 and SRE3 recombination enhancers, adjacent to the donors, were deleted or transposed. Mutants in Set1C, Brl2 or Elp6 altered balanced donor usage away from mat2 and the SRE2 enhancer, towards mat3 and the SRE3 enhancer. The defects in these mutants were qualitatively similar to heterochromatin mutants lacking Swi6, the NAD+-dependent histone deacetylase Sir2, or the Clr4, Raf1 or Rik1 subunits of the histone H3 lysine 9 (H3K9) methyltransferase complex, albeit not as extreme. Other mutants showed clonal biases in switching. This was the case for mutants in the NAD+-independent deacetylase complex subunits Clr1, Clr2 and Clr3, the casein kinase CK2 subunit Ckb1, the ubiquitin ligase component Pof3, and the CENP-B homologue Cbp1, as well as for double mutants lacking Swi6 and Brl2, Pof3, or Cbp1. Thus, we propose that Set1C cooperates with Swi6 and heterochromatin to direct donor choice to mat2-P in M cells, perhaps by inhibiting the SRE3 recombination enhancer, and that in the absence of Swi6 other factors are still capable of imposing biases to donor choice. Effects of chromatin structure on recombination can be studied in the fission yeast S. pombe where two heterochromatic loci, mat2 and mat3, are chosen in a cell-type specific manner to convert the expressed mat1 locus and switch the yeast mating-type. The system has previously revealed the determining role of heterochromatin, histone H3K9 methylation and HP1 family protein Swi6, in donor selection. Here, we find that other chromatin modifiers and protein complexes, including components of the histone H3K4 methyltransferase complex Set1C, the histone H2B ubiquitin ligase HULC and Elongator, also participate in donor selection. Our findings open up new research paths to study mating-type switching in fission yeast and the roles of these complexes in recombination.
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Zukowski A, Johnson AM. The interplay of histone H2B ubiquitination with budding and fission yeast heterochromatin. Curr Genet 2018; 64:799-806. [PMID: 29464330 DOI: 10.1007/s00294-018-0812-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 02/13/2018] [Accepted: 02/14/2018] [Indexed: 12/12/2022]
Abstract
Mono-ubiquitinated histone H2B (H2B-Ub) is important for chromatin regulation of transcription, chromatin assembly, and also influences heterochromatin. In this review, we discuss the effects of H2B-Ub from nucleosome to higher-order chromatin structure. We then assess what is currently known of the role of H2B-Ub in heterochromatic silencing in budding and fission yeasts (S. cerevisiae and S. pombe), which have distinct silencing mechanisms. In budding yeast, the SIR complex initiates heterochromatin assembly with the aid of a H2B-Ub deubiquitinase, Ubp10. In fission yeast, the RNAi-dependent pathway initiates heterochromatin in the context of low H2B-Ub. We examine how the different silencing machineries overcome the challenge of H2B-Ub chromatin and highlight the importance of using these microorganisms to further our understanding of H2B-Ub in heterochromatic silencing pathways.
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Affiliation(s)
- Alexis Zukowski
- Department of Biochemistry and Molecular Genetics, University of Colorado, Denver - School of Medicine, 12801 E. 17th Ave., Aurora, CO, 80045, USA
| | - Aaron M Johnson
- Department of Biochemistry and Molecular Genetics, University of Colorado, Denver - School of Medicine, 12801 E. 17th Ave., Aurora, CO, 80045, USA.
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Flury V, Georgescu PR, Iesmantavicius V, Shimada Y, Kuzdere T, Braun S, Bühler M. The Histone Acetyltransferase Mst2 Protects Active Chromatin from Epigenetic Silencing by Acetylating the Ubiquitin Ligase Brl1. Mol Cell 2017. [PMID: 28648780 PMCID: PMC5526834 DOI: 10.1016/j.molcel.2017.05.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Faithful propagation of functionally distinct chromatin states is crucial for maintaining cellular identity, and its breakdown can lead to diseases such as cancer. Whereas mechanisms that sustain repressed states have been intensely studied, regulatory circuits that protect active chromatin from inactivating signals are not well understood. Here we report a positive feedback loop that preserves the transcription-competent state of RNA polymerase II-transcribed genes. We found that Pdp3 recruits the histone acetyltransferase Mst2 to H3K36me3-marked chromatin. Thereby, Mst2 binds to all transcriptionally active regions genome-wide. Besides acetylating histone H3K14, Mst2 also acetylates Brl1, a component of the histone H2B ubiquitin ligase complex. Brl1 acetylation increases histone H2B ubiquitination, which positively feeds back on transcription and prevents ectopic heterochromatin assembly. Our work uncovers a molecular pathway that secures epigenome integrity and highlights the importance of opposing feedback loops for the partitioning of chromatin into transcriptionally active and inactive states.
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Affiliation(s)
- Valentin Flury
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Paula Raluca Georgescu
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Vytautas Iesmantavicius
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Yukiko Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Tahsin Kuzdere
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Sigurd Braun
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany.
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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Keren I, Citovsky V. The histone deubiquitinase OTLD1 targets euchromatin to regulate plant growth. Sci Signal 2016; 9:ra125. [DOI: 10.1126/scisignal.aaf6767] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ido Keren
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794–5215, USA
| | - Vitaly Citovsky
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794–5215, USA
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45
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Materne P, Vázquez E, Sánchez M, Yague-Sanz C, Anandhakumar J, Migeot V, Antequera F, Hermand D. Histone H2B ubiquitylation represses gametogenesis by opposing RSC-dependent chromatin remodeling at the ste11 master regulator locus. eLife 2016; 5. [PMID: 27171419 PMCID: PMC4865366 DOI: 10.7554/elife.13500] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/30/2016] [Indexed: 11/13/2022] Open
Abstract
In fission yeast, the ste11 gene encodes the master regulator initiating the switch from vegetative growth to gametogenesis. In a previous paper, we showed that the methylation of H3K4 and consequent promoter nucleosome deacetylation repress ste11 induction and cell differentiation (Materne et al., 2015) but the regulatory steps remain poorly understood. Here we report a genetic screen that highlighted H2B deubiquitylation and the RSC remodeling complex as activators of ste11 expression. Mechanistic analyses revealed more complex, opposite roles of H2Bubi at the promoter where it represses expression, and over the transcribed region where it sustains it. By promoting H3K4 methylation at the promoter, H2Bubi initiates the deacetylation process, which decreases chromatin remodeling by RSC. Upon induction, this process is reversed and efficient NDR (nucleosome depleted region) formation leads to high expression. Therefore, H2Bubi represses gametogenesis by opposing the recruitment of RSC at the promoter of the master regulator ste11 gene. DOI:http://dx.doi.org/10.7554/eLife.13500.001
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Affiliation(s)
- Philippe Materne
- URPHYM-GEMO, Namur Research College, University of Namur, Namur, Belgium
| | - Enrique Vázquez
- Instituto de Biología Funcional y Genómica, Salamanca, Spain
| | - Mar Sánchez
- Instituto de Biología Funcional y Genómica, Salamanca, Spain
| | - Carlo Yague-Sanz
- URPHYM-GEMO, Namur Research College, University of Namur, Namur, Belgium
| | | | - Valerie Migeot
- URPHYM-GEMO, Namur Research College, University of Namur, Namur, Belgium
| | | | - Damien Hermand
- URPHYM-GEMO, Namur Research College, University of Namur, Namur, Belgium
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Barati MT, Gould JC, Salyer SA, Isaacs S, Wilkey DW, Merchant ML. Influence of Acute High Glucose on Protein Abundance Changes in Murine Glomerular Mesangial Cells. J Diabetes Res 2015; 2016:3537863. [PMID: 26839892 PMCID: PMC4709621 DOI: 10.1155/2016/3537863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 11/22/2015] [Accepted: 11/30/2015] [Indexed: 01/30/2023] Open
Abstract
The effects of acute exposure to high glucose levels as experienced by glomerular mesangial cells in postprandial conditions and states such as in prediabetes were investigated using proteomic methods. Two-dimensional gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry methods were used to identify protein expression patterns in immortalized rat mesangial cells altered by 2 h high glucose (HG) growth conditions as compared to isoosmotic/normal glucose control (NG(⁎)) conditions. Unique protein expression changes at 2 h HG treatment were measured for 51 protein spots. These proteins could be broadly grouped into two categories: (1) proteins involved in cell survival/cell signaling and (2) proteins involved in stress response. Immunoblot experiments for a protein belonging to both categories, prohibitin (PHB), supported a trend for increased total expression as well as significant increases in an acidic PHB isoform. Additional studies confirmed the regulation of proteasomal subunit alpha-type 2 and the endoplasmic reticulum chaperone and oxidoreductase PDI (protein disulfide isomerase), suggesting altered ER protein folding capacity and proteasomal function in response to acute HG. We conclude that short term high glucose induces subtle changes in protein abundances suggesting posttranslational modifications and regulation of pathways involved in proteostasis.
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Affiliation(s)
- Michelle T. Barati
- Kidney Disease Program, Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - James C. Gould
- Kidney Disease Program, Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Sarah A. Salyer
- Kidney Disease Program, Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Tuskegee University School of Veterinary Medicine, Tuskegee, AL 36088, USA
| | - Susan Isaacs
- Kidney Disease Program, Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Daniel W. Wilkey
- Kidney Disease Program, Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Michael L. Merchant
- Kidney Disease Program, Department of Medicine, University of Louisville, Louisville, KY 40202, USA
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Set1 and MLL1/2 Target Distinct Sets of Functionally Different Genomic Loci In Vivo. Cell Rep 2015; 13:2741-55. [PMID: 26711341 DOI: 10.1016/j.celrep.2015.11.059] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 10/14/2015] [Accepted: 11/17/2015] [Indexed: 12/24/2022] Open
Abstract
Histone H3 lysine 4 trimethylation (H3K4me3) is known to correlate with both active and poised genomic loci, yet many questions remain regarding its functional roles in vivo. We identify functional genomic targets of two H3K4 methyltransferases, Set1 and MLL1/2, in both the stem cells and differentiated tissue of the planarian flatworm Schmidtea mediterranea. We show that, despite their common substrate, these enzymes target distinct genomic loci in vivo, which are distinguishable by the pattern each enzyme leaves on the chromatin template, i.e., the breadth of the H3K4me3 peak. Whereas Set1 targets are largely associated with the maintenance of the stem cell population, MLL1/2 targets are specifically enriched for genes involved in ciliogenesis. These data not only confirm that chromatin regulation is fundamental to planarian stem cell function but also provide evidence for post-embryonic functional specificity of H3K4me3 methyltransferases in vivo.
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Bitton DA, Schubert F, Dey S, Okoniewski M, Smith GC, Khadayate S, Pancaldi V, Wood V, Bähler J. AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast. Front Genet 2015; 6:330. [PMID: 26635866 PMCID: PMC4644808 DOI: 10.3389/fgene.2015.00330] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/30/2015] [Indexed: 01/08/2023] Open
Abstract
Genome-wide assays and screens typically result in large lists of genes or proteins. Enrichments of functional or other biological properties within such lists can provide valuable insights and testable hypotheses. To systematically detect these enrichments can be challenging and time-consuming, because relevant data to compare against query gene lists are spread over many different sources. We have developed AnGeLi (Analysis of Gene Lists), an intuitive, integrated web-tool for comprehensive and customized interrogation of gene lists from the fission yeast, Schizosaccharomyces pombe. AnGeLi searches for significant enrichments among multiple qualitative and quantitative information sources, including gene and phenotype ontologies, genetic and protein interactions, numerous features of genes, transcripts, translation, and proteins such as copy numbers, chromosomal positions, genetic diversity, RNA polymerase II and ribosome occupancy, localization, conservation, half-lives, domains, and molecular weight among others, as well as diverse sets of genes that are co-regulated or lead to the same phenotypes when mutated. AnGeLi uses robust statistics which can be tailored to specific needs. It also provides the option to upload user-defined gene sets to compare against the query list. Through an integrated data submission form, AnGeLi encourages the community to contribute additional curated gene lists to further increase the usefulness of this resource and to get the most from the ever increasing large-scale experiments. AnGeLi offers a rigorous yet flexible statistical analysis platform for rich insights into functional enrichments and biological context for query gene lists, thus providing a powerful exploratory tool through which S. pombe researchers can uncover fresh perspectives and unexpected connections from genomic data. AnGeLi is freely available at: www.bahlerlab.info/AnGeLi.
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Affiliation(s)
- Danny A. Bitton
- Research Department of Genetics, Evolution and Environment – UCL Genetics Institute, University College LondonLondon, UK
| | - Falk Schubert
- Research Department of Genetics, Evolution and Environment – UCL Genetics Institute, University College LondonLondon, UK
| | - Shoumit Dey
- Research Department of Genetics, Evolution and Environment – UCL Genetics Institute, University College LondonLondon, UK
| | | | - Graeme C. Smith
- Research Department of Genetics, Evolution and Environment – UCL Genetics Institute, University College LondonLondon, UK
| | - Sanjay Khadayate
- Research Department of Genetics, Evolution and Environment – UCL Genetics Institute, University College LondonLondon, UK
| | - Vera Pancaldi
- Research Department of Genetics, Evolution and Environment – UCL Genetics Institute, University College LondonLondon, UK
| | - Valerie Wood
- Cambridge Systems Biology and Department of Biochemistry, University of CambridgeCambridge, UK
| | - Jürg Bähler
- Research Department of Genetics, Evolution and Environment – UCL Genetics Institute, University College LondonLondon, UK
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Sadeghi L, Prasad P, Ekwall K, Cohen A, Svensson JP. The Paf1 complex factors Leo1 and Paf1 promote local histone turnover to modulate chromatin states in fission yeast. EMBO Rep 2015; 16:1673-87. [PMID: 26518661 PMCID: PMC4687421 DOI: 10.15252/embr.201541214] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/05/2015] [Indexed: 11/21/2022] Open
Abstract
The maintenance of open and repressed chromatin states is crucial for the regulation of gene expression. To study the genes involved in maintaining chromatin states, we generated a random mutant library in Schizosaccharomyces pombe and monitored the silencing of reporter genes inserted into the euchromatic region adjacent to the heterochromatic mating type locus. We show that Leo1–Paf1 [a subcomplex of the RNA polymerase II‐associated factor 1 complex (Paf1C)] is required to prevent the spreading of heterochromatin into euchromatin by mapping the heterochromatin mark H3K9me2 using high‐resolution genomewide ChIP (ChIP–exo). Loss of Leo1–Paf1 increases heterochromatin stability at several facultative heterochromatin loci in an RNAi‐independent manner. Instead, deletion of Leo1 decreases nucleosome turnover, leading to heterochromatin stabilization. Our data reveal that Leo1–Paf1 promotes chromatin state fluctuations by enhancing histone turnover.
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Affiliation(s)
- Laia Sadeghi
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Punit Prasad
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Amikam Cohen
- Department of Microbiology and Molecular Genetics, IMRIC The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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50
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Yao X, Tang Z, Fu X, Yin J, Liang Y, Li C, Li H, Tian Q, Roeder RG, Wang G. The Mediator subunit MED23 couples H2B mono-ubiquitination to transcriptional control and cell fate determination. EMBO J 2015; 34:2885-902. [PMID: 26330467 DOI: 10.15252/embj.201591279] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/10/2015] [Indexed: 01/18/2023] Open
Abstract
The Mediator complex orchestrates multiple transcription factors with the Pol II apparatus for precise transcriptional control. However, its interplay with the surrounding chromatin remains poorly understood. Here, we analyze differential histone modifications between WT and MED23(-/-) (KO) cells and identify H2B mono-ubiquitination at lysine 120 (H2Bub) as a MED23-dependent histone modification. Using tandem affinity purification and mass spectrometry, we find that MED23 associates with the RNF20/40 complex, the enzyme for H2Bub, and show that this association is critical for the recruitment of RNF20/40 to chromatin. In a cell-free system, Mediator directly and substantially increases H2Bub on recombinant chromatin through its cooperation with RNF20/40 and the PAF complex. Integrative genome-wide analyses show that MED23 depletion specifically reduces H2Bub on a subset of MED23-controlled genes. Importantly, MED23-coupled H2Bub levels are oppositely regulated during myogenesis and lung carcinogenesis. In sum, these results establish a mechanistic link between the Mediator complex and a critical chromatin modification in coordinating transcription with cell growth and differentiation.
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Affiliation(s)
- Xiao Yao
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Jingwen Yin
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Yan Liang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Chonghui Li
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Huayun Li
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Qing Tian
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Gang Wang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
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