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Andjus S, Szachnowski U, Vogt N, Gioftsidi S, Hatin I, Cornu D, Papadopoulos C, Lopes A, Namy O, Wery M, Morillon A. Pervasive translation of Xrn1-sensitive unstable long noncoding RNAs in yeast. RNA (NEW YORK, N.Y.) 2024; 30:662-679. [PMID: 38443115 PMCID: PMC11098462 DOI: 10.1261/rna.079903.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024]
Abstract
Despite being predicted to lack coding potential, cytoplasmic long noncoding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNA translation remain poorly studied. In yeast, cytoplasmic Xrn1-sensitive unstable transcripts (XUTs) are targeted by nonsense-mediated mRNA decay (NMD), suggesting a translation-dependent degradation process. Here, we report that XUTs are pervasively translated, which impacts their decay. We show that XUTs globally accumulate upon translation elongation inhibition, but not when initial ribosome loading is impaired. Ribo-seq confirmed ribosomes binding to XUTs and identified ribosome-associated 5'-proximal small ORFs. Mechanistically, the NMD-sensitivity of XUTs mainly depends on the 3'-untranslated region length. Finally, we show that the peptide resulting from the translation of an NMD-sensitive XUT reporter exists in NMD-competent cells. Our work highlights the role of translation in the posttranscriptional metabolism of XUTs. We propose that XUT-derived peptides could be exposed to natural selection, while NMD restricts XUT levels.
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Affiliation(s)
- Sara Andjus
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL University, Sorbonne Université, CNRS UMR3244, F-75248 Paris Cedex 05, France
| | - Ugo Szachnowski
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, F-75248 Paris Cedex 05, France
| | - Nicolas Vogt
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, F-75248 Paris Cedex 05, France
| | - Stamatia Gioftsidi
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, F-75248 Paris Cedex 05, France
| | - Isabelle Hatin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - David Cornu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Chris Papadopoulos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Anne Lopes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Olivier Namy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, F-75248 Paris Cedex 05, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, F-75248 Paris Cedex 05, France
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Ghimire P, Motamedi M, Joh R. Mathematical model for the role of multiple pericentromeric repeats on heterochromatin assembly. PLoS Comput Biol 2024; 20:e1012027. [PMID: 38598558 PMCID: PMC11034663 DOI: 10.1371/journal.pcbi.1012027] [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: 08/04/2023] [Revised: 04/22/2024] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
Although the length and constituting sequences for pericentromeric repeats are highly variable across eukaryotes, the presence of multiple pericentromeric repeats is one of the conserved features of the eukaryotic chromosomes. Pericentromeric heterochromatin is often misregulated in human diseases, with the expansion of pericentromeric repeats in human solid cancers. In this article, we have developed a mathematical model of the RNAi-dependent methylation of H3K9 in the pericentromeric region of fission yeast. Our model, which takes copy number as an explicit parameter, predicts that the pericentromere is silenced only if there are many copies of repeats. It becomes bistable or desilenced if the copy number of repeats is reduced. This suggests that the copy number of pericentromeric repeats alone can determine the fate of heterochromatin silencing in fission yeast. Through sensitivity analysis, we identified parameters that favor bistability and desilencing. Stochastic simulation shows that faster cell division and noise favor the desilenced state. These results show the unexpected role of pericentromeric repeat copy number in gene silencing and provide a quantitative basis for how the copy number allows or protects repetitive and unique parts of the genome from heterochromatin silencing, respectively.
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Affiliation(s)
- Puranjan Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Mo Motamedi
- Massachusetts General Hospital Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, Boston, Massachusetts, United States of America
| | - Richard Joh
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Massey Cancer Center, Virginia Commonwealth University, Richmond Virginia, United States of America
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3
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Dhillon VS, Shahid M, Deo P, Fenech M. Reduced SIRT1 and SIRT3 and Lower Antioxidant Capacity of Seminal Plasma Is Associated with Shorter Sperm Telomere Length in Oligospermic Men. Int J Mol Sci 2024; 25:718. [PMID: 38255792 PMCID: PMC10815409 DOI: 10.3390/ijms25020718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Infertility affects millions of couples worldwide and has a profound impact not only on their families, but also on communities. Telomere attrition has been associated with infertility, DNA damage and fragmentation. Oxidative stress has been shown to affect sperm DNA integrity and telomere length. Sirtuins such as SIRT1 and SIRT3 are involved in aging and oxidative stress response. The aim of the present study is to determine the role of SIRT1 and SIRT3 in regulating oxidative stress, telomere shortening, and their association with oligospermia. Therefore, we assessed the protein levels of SIRT1 and SIRT3, total antioxidant capacity (TAC), superoxide dismutase (SOD), malondialdehyde (MDA) and catalase activity (CAT) in the seminal plasma of 272 patients with oligospermia and 251 fertile men. We also measured sperm telomere length (STL) and leukocyte telomere length (LTL) using a standard real-time quantitative PCR assay. Sperm chromatin and protamine deficiency were also measured as per standard methods. Our results for oligospermic patients demonstrate significant reductions in semen parameters, shorter STL and LTL, lower levels of SOD, TAC, CAT, SIRT1 and SIRT3 levels, and also significant protamine deficiency and higher levels of MDA and DNA fragmentation. We conclude that a shorter TL in sperms and leukocytes is associated with increased oxidative stress that also accounts for high levels of DNA fragmentation in sperms. Our results support the hypothesis that various sperm parameters in the state of oligospermia are associated with or caused by reduced levels of SIRT1 and SIRT3 proteins.
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Affiliation(s)
- Varinderpal S. Dhillon
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (P.D.); (M.F.)
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Permal Deo
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (P.D.); (M.F.)
| | - Michael Fenech
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (P.D.); (M.F.)
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4
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Tian X, Wang T, Shen H, Wang S. Tumor microenvironment, histone modifications, and myeloid-derived suppressor cells. Cytokine Growth Factor Rev 2023; 74:108-121. [PMID: 37598011 DOI: 10.1016/j.cytogfr.2023.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023]
Abstract
Myeloid-derived suppressor cells (MDSCs) are important components of the tumor microenvironment (TME), which drive the tumor immune escape by inducing immunosuppression. The expansion and function of MDSCs are tightly associated with signaling pathways induced by molecules from tumor cells, stromal cells, and activated immune cells in the TME. Although these pathways have been well-characterized, the understanding of the epigenetic regulators involved is incomplete. Since histone modifications are the most studied epigenetic changes in MDSCs, we summarize current knowledge on the role of histone modifications in MDSCs within this review. We first discuss the influence of the TME on histone modifications in MDSCs, with an emphasis on histone modifications and modifiers that direct MDSC differentiation and function. Furthermore, we highlight current epigenetic interventions that can reverse MDSC-induced immunosuppression by modulating histone modifications and discuss future research directions to fully appreciate the role of histone modifications in MDSCs.
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Affiliation(s)
- Xinyu Tian
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Ting Wang
- Department of Laboratory Medicine, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China.
| | - Shengjun Wang
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China; Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.
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5
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Wery M, Szachnowski U, Andjus S, de Andres-Pablo A, Morillon A. The RNA helicases Dbp2 and Mtr4 regulate the expression of Xrn1-sensitive long non-coding RNAs in yeast. FRONTIERS IN RNA RESEARCH 2023; 1:1244554. [PMID: 37667796 PMCID: PMC7615016 DOI: 10.3389/frnar.2023.1244554] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The expression of yeast long non-coding (lnc)RNAs is restricted by RNA surveillance machineries, including the cytoplasmic 5'-3' exonuclease Xrn1 which targets a conserved family of lncRNAs defined as XUTs, and that are mainly antisense to protein-coding genes. However, the co-factors involved in the degradation of these transcripts and the underlying molecular mechanisms remain largely unknown. Here, we show that two RNA helicases, Dbp2 and Mtr4, act as global regulators of XUTs expression. Using RNA-Seq, we found that most of them accumulate upon Dbp2 inactivation or Mtr4 depletion. Mutants of the cytoplasmic RNA helicases Ecm32, Ski2, Slh1, Dbp1, and Dhh1 did not recapitulate this global stabilization of XUTs, suggesting that XUTs decay is specifically controlled by Dbp2 and Mtr4. Notably, Dbp2 and Mtr4 affect XUTs independently of their configuration relative to their paired-sense mRNAs. Finally, we show that the effect of Dbp2 on XUTs depends on a cytoplasmic localization. Overall, our data indicate that Dbp2 and Mtr4 are global regulators of lncRNAs expression and contribute to shape the non-coding transcriptome together with RNA decay machineries.
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Affiliation(s)
- Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne
Université, CNRS UMR3244, Paris Cedex, France
| | - Ugo Szachnowski
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne
Université, CNRS UMR3244, Paris Cedex, France
| | - Sara Andjus
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL
University, Sorbonne Université, CNRS UMR3244, Paris Cedex, France
| | - Alvaro de Andres-Pablo
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne
Université, CNRS UMR3244, Paris Cedex, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne
Université, CNRS UMR3244, Paris Cedex, France
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Nuckolls NL, Nidamangala Srinivasa A, Mok AC, Helston RM, Bravo Núñez MA, Lange JJ, Gallagher TJ, Seidel CW, Zanders SE. S. pombe wtf drivers use dual transcriptional regulation and selective protein exclusion from spores to cause meiotic drive. PLoS Genet 2022; 18:e1009847. [PMID: 36477651 PMCID: PMC9762604 DOI: 10.1371/journal.pgen.1009847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/19/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
Meiotic drivers bias gametogenesis to ensure their transmission into more than half the offspring of a heterozygote. In Schizosaccharomyces pombe, wtf meiotic drivers destroy the meiotic products (spores) that do not inherit the driver from a heterozygote, thereby reducing fertility. wtf drivers encode both a Wtfpoison protein and a Wtfantidote protein using alternative transcriptional start sites. Here, we analyze how the expression and localization of the Wtf proteins are regulated to achieve drive. We show that transcriptional timing and selective protein exclusion from developing spores ensure that all spores are exposed to Wtf4poison, but only the spores that inherit wtf4 receive a dose of Wtf4antidote sufficient for survival. In addition, we show that the Mei4 transcription factor, a master regulator of meiosis, controls the expression of the wtf4poison transcript. This transcriptional regulation, which includes the use of a critical meiotic transcription factor, likely complicates the universal suppression of wtf genes without concomitantly disrupting spore viability. We propose that these features contribute to the evolutionary success of the wtf drivers.
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Affiliation(s)
- Nicole L. Nuckolls
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Ananya Nidamangala Srinivasa
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Anthony C. Mok
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- University of Missouri—Kansas City, Kansas City, Missouri, United States of America
| | - Rachel M. Helston
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | | | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Todd J. Gallagher
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Chris W. Seidel
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Sarah E. Zanders
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
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7
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Li L, Xie W. LncRNA HDAC11-AS1 Suppresses Atherosclerosis by Inhibiting HDAC11-Mediated Adropin Histone Deacetylation. J Cardiovasc Transl Res 2022; 15:1256-1269. [PMID: 35505157 DOI: 10.1007/s12265-022-10248-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/31/2022] [Indexed: 12/16/2022]
Abstract
LncRNA HDAC11-AS1 (HDAC11-AS1) is the natural antisense transcript of HDAC11, a key enzyme for DNA histone deacetylation. We evaluated the role of HDAC11-AS1 in atherosclerosis. In this research, we found that HDAC11-AS1 ameliorated blood lipid levels and atherosclerosis in high fat-dieted apoE-/- mice by regulating HDAC11 negatively. The change in blood lipid levels is related to the expression of LPL, which is enhanced by HDAC11-AS1 through regulating adropin histone deacetylation in vitro and in vivo. In conclusion, HDAC11-AS1 plays an anti-atherogenic role through adropin to induce LPL expressions, thereby enhancing TG metabolism. The results are valuable for the further development of HDAC11-AS1 and its clinical applications. It provides a new clinical therapeutic target for cardiovascular disease treatment.
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Affiliation(s)
- Liang Li
- Department of Physiology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Wei Xie
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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8
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Sun Z, Zhao S, Suo X, Dou Y. Sirt1 protects against hippocampal atrophy and its induced cognitive impairment in middle-aged mice. BMC Neurosci 2022; 23:33. [PMID: 35668361 PMCID: PMC9169381 DOI: 10.1186/s12868-022-00718-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sirtuin 1 (Sirt1) is a recognized longevity gene and has been shown to be associated with aging and its related diseases. Hippocampal volume is considered to be the most sensitive brain imaging phenotype for cognition, but the effect of Sirt1 on hippocampal morphology during aging has not been reported. RESULTS Herein, we investigated the effect of conditional Sirt1 knockdown on hippocampal volume in middle-aged mice, as well as its cognitive function and the underlying molecular mechanisms. Brain structural magnetic resonance imaging (MRI) showed that adeno-associated virus (AAV) mediated hippocampal Sirt1 knockdown caused hippocampal atrophy in 8-month-old mice. Open field test (OFT) and Morris Water Maze (MWM) test revealed that hippocampal Sirt1 knockdown significantly weakened spatial learning and memory of mice without effect on anxiety and exploratory behavior. Western blotting analysis showed that P-tau levels at serine 396 epitope were significantly increased with slightly decreased T-tau levels, while PSD95 and NMDAR2B levels were obviously reduced, indicating that hippocampal Sirt1 knockdown could activate tau hyperphosphorylation and synaptic damage. CONCLUSIONS This work revealed that Sirt1 is an important protective gene against hippocampal atrophy and its induced cognitive impairment during aging, providing potential therapeutic targets for the prevention and intervention of aging-related neuropsychic diseases.
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Affiliation(s)
- Zuhao Sun
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, People's Republic of China.,School of Medical Technology, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Shuang Zhao
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, People's Republic of China
| | - Xinjun Suo
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, People's Republic of China.,School of Medical Technology, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Yan Dou
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, People's Republic of China.
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10
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Transcription and chromatin-based surveillance mechanism controls suppression of cryptic antisense transcription. Cell Rep 2021; 36:109671. [PMID: 34496258 PMCID: PMC8441049 DOI: 10.1016/j.celrep.2021.109671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/26/2020] [Accepted: 08/13/2021] [Indexed: 12/25/2022] Open
Abstract
Phosphorylation of the RNA polymerase II C-terminal domain Y1S2P3T4S5P6S7 consensus sequence coordinates key events during transcription, and its deregulation leads to defects in transcription and RNA processing. Here, we report that the histone deacetylase activity of the fission yeast Hos2/Set3 complex plays an important role in suppressing cryptic initiation of antisense transcription when RNA polymerase II phosphorylation is dysregulated due to the loss of Ssu72 phosphatase. Interestingly, although single Hos2 and Set3 mutants have little effect, loss of Hos2 or Set3 combined with ssu72Δ results in a synergistic increase in antisense transcription globally and correlates with elevated sensitivity to genotoxic agents. We demonstrate a key role for the Ssu72/Hos2/Set3 mechanism in the suppression of cryptic antisense transcription at the 3' end of convergent genes that are most susceptible to these defects, ensuring the fidelity of gene expression within dense genomes of simple eukaryotes.
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11
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Breakers and amplifiers in chromatin circuitry: acetylation and ubiquitination control the heterochromatin machinery. Curr Opin Struct Biol 2021; 71:156-163. [PMID: 34303934 PMCID: PMC8667873 DOI: 10.1016/j.sbi.2021.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/06/2021] [Accepted: 06/13/2021] [Indexed: 11/30/2022]
Abstract
Eukaryotic genomes are segregated into active euchromatic and repressed heterochromatic compartments. Gene regulatory networks, chromosomal structures, and genome integrity rely on the timely and locus-specific establishment of active and silent states to protect the genome and provide the basis for cell division and specification of cellular identity. Here, we focus on the mechanisms and molecular machinery that establish heterochromatin in Schizosaccharomyces pombe and compare it with Saccharomyces cerevisiae and the mammalian polycomb system. We present recent structural and mechanistic evidence, which suggests that histone acetylation protects active transcription by disrupting the positive feedback loops used by the heterochromatin machinery and that H2A and H3 monoubiquitination actively drives heterochromatin, whereas H2B monoubiquitination mobilizes the defenses to quench heterochromatin. Heterochromatin-associated complexes are attracted and repelled by histone marks. Acetylation of specific lysine residues protects euchromatin from silencing. Methylation of histone H3 lysine 9 and 27 amplifies heterochromatin. Nucleosome ubiquitination licences and enforces feedback loops.
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12
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Satterwhite ER, Mansfield KD. RNA methyltransferase METTL16: Targets and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1681. [PMID: 34227247 PMCID: PMC9286414 DOI: 10.1002/wrna.1681] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/12/2022]
Abstract
The N6-methyladenosine (m6A) RNA methyltransferase METTL16 is an emerging player in the RNA modification landscape of the human cell. Originally thought to be a ribosomal RNA methyltransferase, it has now been shown to bind and methylate the MAT2A messenger RNA (mRNA) and U6 small nuclear RNA (snRNA). It has also been shown to bind the MALAT1 long noncoding RNA and several other RNAs. METTL16's methyltransferase domain contains the Rossmann-like fold of class I methyltransferases and uses S-adenosylmethionine (SAM) as the methyl donor. It has an RNA methylation consensus sequence of UACAGARAA (modified A underlined), and structural requirements for its known RNA interactors. In addition to the methyltransferase domain, METTL16 protein has two other RNA binding domains, one of which resides in a vertebrate conserved region, and a putative nuclear localization signal. The role of METTL16 in the cell is still being explored, however evidence suggests it is essential for most cells. This is currently hypothesized to be due to its role in regulating the splicing of MAT2A mRNA in response to cellular SAM levels. However, one of the more pressing questions remaining is what role METTL16's methylation of U6 snRNA plays in splicing and potentially cellular survival. METTL16 also has several other putative coding and noncoding RNA interactors but the definitive methylation status of those RNAs and the role METTL16 plays in their life cycle is yet to be determined. Overall, METTL16 is an intriguing RNA binding protein and methyltransferase whose important functions in the cell are just beginning to be understood. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Emily R Satterwhite
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Kyle D Mansfield
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
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13
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Ma X, Chen T, Peng Z, Wang Z, Liu J, Yang T, Wu L, Liu G, Zhou M, Tong M, Guan Y, Zhang X, Lin Y, Tang X, Li L, Tang Z, Pan T, Zhang H. Histone chaperone CAF-1 promotes HIV-1 latency by leading the formation of phase-separated suppressive nuclear bodies. EMBO J 2021; 40:e106632. [PMID: 33739466 PMCID: PMC8126954 DOI: 10.15252/embj.2020106632] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 01/08/2023] Open
Abstract
HIV-1 latency is a major obstacle to achieving a functional cure for AIDS. Reactivation of HIV-1-infected cells followed by their elimination via immune surveillance is one proposed strategy for eradicating the viral reservoir. However, current latency-reversing agents (LRAs) show high toxicity and low efficiency, and new targets are needed to develop more promising LRAs. Here, we found that the histone chaperone CAF-1 (chromatin assembly factor 1) is enriched on the HIV-1 long terminal repeat (LTR) and forms nuclear bodies with liquid-liquid phase separation (LLPS) properties. CAF-1 recruits epigenetic modifiers and histone chaperones to the nuclear bodies to establish and maintain HIV-1 latency in different latency models and primary CD4+ T cells. Three disordered regions of the CHAF1A subunit are important for phase-separated CAF-1 nuclear body formation and play a key role in maintaining HIV-1 latency. Disruption of phase-separated CAF-1 bodies could be a potential strategy to reactivate latent HIV-1.
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Affiliation(s)
- Xiancai Ma
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Tao Chen
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Zhilin Peng
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ziwen Wang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Jun Liu
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Tao Yang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Liyang Wu
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Guangyan Liu
- College of Basic Medical SciencesShenyang Medical CollegeShenyangLiaoningChina
| | - Mo Zhou
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Muye Tong
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yuanjun Guan
- Core Laboratory Platform for Medical ScienceZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Xu Zhang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yingtong Lin
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Xiaoping Tang
- Department of Infectious DiseasesGuangzhou 8th People’s HospitalGuangzhouGuangdongChina
| | - Linghua Li
- Department of Infectious DiseasesGuangzhou 8th People’s HospitalGuangzhouGuangdongChina
| | - Zhonghui Tang
- Department of BioinformaticsZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ting Pan
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Center for Infection and Immunity StudySchool of MedicineSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Hui Zhang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
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14
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Mugat B, Nicot S, Varela-Chavez C, Jourdan C, Sato K, Basyuk E, Juge F, Siomi MC, Pélisson A, Chambeyron S. The Mi-2 nucleosome remodeler and the Rpd3 histone deacetylase are involved in piRNA-guided heterochromatin formation. Nat Commun 2020; 11:2818. [PMID: 32499524 PMCID: PMC7272611 DOI: 10.1038/s41467-020-16635-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
In eukaryotes, trimethylation of lysine 9 on histone H3 (H3K9) is associated with transcriptional silencing of transposable elements (TEs). In drosophila ovaries, this heterochromatic repressive mark is thought to be deposited by SetDB1 on TE genomic loci after the initial recognition of nascent transcripts by PIWI-interacting RNAs (piRNAs) loaded on the Piwi protein. Here, we show that the nucleosome remodeler Mi-2, in complex with its partner MEP-1, forms a subunit that is transiently associated, in a MEP-1 C-terminus-dependent manner, with known Piwi interactors, including a recently reported SUMO ligase, Su(var)2-10. Together with the histone deacetylase Rpd3, this module is involved in the piRNA-dependent TE silencing, correlated with H3K9 deacetylation and trimethylation. Therefore, drosophila piRNA-mediated transcriptional silencing involves three epigenetic effectors, a remodeler, Mi-2, an eraser, Rpd3 and a writer, SetDB1, in addition to the Su(var)2-10 SUMO ligase.
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Affiliation(s)
- Bruno Mugat
- Institute of Human Genetics, UMR9002, CNRS and Univ. Montpellier, Montpellier, France
| | - Simon Nicot
- Institute of Human Genetics, UMR9002, CNRS and Univ. Montpellier, Montpellier, France
| | | | - Christophe Jourdan
- Institute of Human Genetics, UMR9002, CNRS and Univ. Montpellier, Montpellier, France
| | - Kaoru Sato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Eugenia Basyuk
- Institute of Human Genetics, UMR9002, CNRS and Univ. Montpellier, Montpellier, France
| | - François Juge
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Alain Pélisson
- Institute of Human Genetics, UMR9002, CNRS and Univ. Montpellier, Montpellier, France
| | - Séverine Chambeyron
- Institute of Human Genetics, UMR9002, CNRS and Univ. Montpellier, Montpellier, France.
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15
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Thillainadesan G, Xiao H, Holla S, Dhakshnamoorthy J, Jenkins LMM, Wheeler D, Grewal SIS. Conserved protein Pir2 ARS2 mediates gene repression through cryptic introns in lncRNAs. Nat Commun 2020; 11:2412. [PMID: 32415063 PMCID: PMC7229227 DOI: 10.1038/s41467-020-16280-y] [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: 09/03/2019] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are components of epigenetic control mechanisms that ensure appropriate and timely gene expression. The functions of lncRNAs are often mediated through associated gene regulatory activities, but how lncRNAs are distinguished from other RNAs and recruit effector complexes is unclear. Here, we utilize the fission yeast Schizosaccharomyces pombe to investigate how lncRNAs engage silencing activities to regulate gene expression in cis. We find that invasion of lncRNA transcription into the downstream gene body incorporates a cryptic intron required for repression of that gene. Our analyses show that lncRNAs containing cryptic introns are targeted by the conserved Pir2ARS2 protein in association with splicing factors, which recruit RNA processing and chromatin-modifying activities involved in gene silencing. Pir2 and splicing machinery are broadly required for gene repression. Our finding that human ARS2 also interacts with splicing factors suggests a conserved mechanism mediates gene repression through cryptic introns within lncRNAs. In fission yeast, several lncRNAs act in cis to regulate expression of adjacent genes. Here, the authors show that the conserved Pir2ARS2 protein is targeted, along with splicing factors, to cryptic introns in lncRNAs and recruits effectors, including RNAi machinery, for gene repression.
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Affiliation(s)
- Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lisa M Miller Jenkins
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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16
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Marayati BF, Tucker JF, De La Cerda DA, Hou TC, Chen R, Sugiyama T, Pease JB, Zhang K. The Catalytic-Dependent and -Independent Roles of Lsd1 and Lsd2 Lysine Demethylases in Heterochromatin Formation in Schizosaccharomyces pombe. Cells 2020; 9:E955. [PMID: 32295063 PMCID: PMC7226997 DOI: 10.3390/cells9040955] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 12/30/2022] Open
Abstract
In eukaryotes, heterochromatin plays a critical role in organismal development and cell fate acquisition, through regulating gene expression. The evolutionarily conserved lysine-specific demethylases, Lsd1 and Lsd2, remove mono- and dimethylation on histone H3, serving complex roles in gene expression. In the fission yeast Schizosaccharomyces pombe, null mutations of Lsd1 and Lsd2 result in either severe growth defects or inviability, while catalytic inactivation causes minimal defects, indicating that Lsd1 and Lsd2 have essential functions beyond their known demethylase activity. Here, we show that catalytic mutants of Lsd1 or Lsd2 partially assemble functional heterochromatin at centromeres in RNAi-deficient cells, while the C-terminal truncated alleles of Lsd1 or Lsd2 exacerbate heterochromatin formation at all major heterochromatic regions, suggesting that Lsd1 and Lsd2 repress heterochromatic transcripts through mechanisms both dependent on and independent of their catalytic activities. Lsd1 and Lsd2 are also involved in the establishment and maintenance of heterochromatin. At constitutive heterochromatic regions, Lsd1 and Lsd2 regulate one another and cooperate with other histone modifiers, including the class II HDAC Clr3 and the Sirtuin family protein Sir2 for gene silencing, but not with the class I HDAC Clr6. Our findings explore the roles of lysine-specific demethylases in epigenetic gene silencing at heterochromatic regions.
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Affiliation(s)
- Bahjat F. Marayati
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC 27109, USA; (B.F.M.); (J.F.T.); (D.A.D.L.C.); (T.-C.H.); (J.B.P.)
| | - James F. Tucker
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC 27109, USA; (B.F.M.); (J.F.T.); (D.A.D.L.C.); (T.-C.H.); (J.B.P.)
| | - David A. De La Cerda
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC 27109, USA; (B.F.M.); (J.F.T.); (D.A.D.L.C.); (T.-C.H.); (J.B.P.)
| | - Tien-Chi Hou
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC 27109, USA; (B.F.M.); (J.F.T.); (D.A.D.L.C.); (T.-C.H.); (J.B.P.)
| | - Rong Chen
- Physiology and pharmacology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA;
| | - Tomoyasu Sugiyama
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China;
| | - James B. Pease
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC 27109, USA; (B.F.M.); (J.F.T.); (D.A.D.L.C.); (T.-C.H.); (J.B.P.)
| | - Ke Zhang
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC 27109, USA; (B.F.M.); (J.F.T.); (D.A.D.L.C.); (T.-C.H.); (J.B.P.)
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17
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Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin. Sci Rep 2020; 10:6055. [PMID: 32269268 PMCID: PMC7142091 DOI: 10.1038/s41598-020-63209-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 03/26/2020] [Indexed: 01/24/2023] Open
Abstract
Heterochromatin regulation is critical for genomic stability. Different H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fission yeast. We identified several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin.
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18
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Walther M, Schrahn S, Krauss V, Lein S, Kessler J, Jenuwein T, Reuter G. Heterochromatin formation in Drosophila requires genome-wide histone deacetylation in cleavage chromatin before mid-blastula transition in early embryogenesis. Chromosoma 2020; 129:83-98. [PMID: 31950239 PMCID: PMC7021753 DOI: 10.1007/s00412-020-00732-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/13/2019] [Accepted: 01/02/2020] [Indexed: 02/05/2023]
Abstract
Su(var) mutations define epigenetic factors controlling heterochromatin formation and gene silencing in Drosophila. Here, we identify SU(VAR)2-1 as a novel chromatin regulator that directs global histone deacetylation during the transition of cleavage chromatin into somatic blastoderm chromatin in early embryogenesis. SU(VAR)2-1 is heterochromatin-associated in blastoderm nuclei but not in later stages of development. In larval polytene chromosomes, SU(VAR)2-1 is a band-specific protein. SU(VAR)2-1 directs global histone deacetylation by recruiting the histone deacetylase RPD3. In Su(var)2-1 mutants H3K9, H3K27, H4K8 and H4K16 acetylation shows elevated levels genome-wide and heterochromatin displays aberrant histone hyper-acetylation. Whereas H3K9me2- and HP1a-binding appears unaltered, the heterochromatin-specific H3K9me2S10ph composite mark is impaired in heterochromatic chromocenters of larval salivary polytene chromosomes. SU(VAR)2-1 contains an NRF1/EWG domain and a C2HC zinc-finger motif. Our study identifies SU(VAR)2-1 as a dosage-dependent, heterochromatin-initiating SU(VAR) factor, where the SU(VAR)2-1-mediated control of genome-wide histone deacetylation after cleavage and before mid-blastula transition (pre-MBT) is required to enable heterochromatin formation.
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Affiliation(s)
- Matthias Walther
- Developmental Genetics, Institute of Biology, Martin Luther University Halle, Weinbergweg 10, 06120, Halle/S., Germany
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Sandy Schrahn
- Developmental Genetics, Institute of Biology, Martin Luther University Halle, Weinbergweg 10, 06120, Halle/S., Germany
| | - Veiko Krauss
- Cluster of Excellence in Plant Science (CEPLAS), University of Cologne, Biocenter, 50674, Cologne, Germany
| | - Sandro Lein
- Developmental Genetics, Institute of Biology, Martin Luther University Halle, Weinbergweg 10, 06120, Halle/S., Germany
| | - Jeannette Kessler
- Developmental Genetics, Institute of Biology, Martin Luther University Halle, Weinbergweg 10, 06120, Halle/S., Germany
| | - Thomas Jenuwein
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Gunter Reuter
- Developmental Genetics, Institute of Biology, Martin Luther University Halle, Weinbergweg 10, 06120, Halle/S., Germany.
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19
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Targeted Forward Genetics: Population-Scale Analyses of Allele Replacements Spanning Thousands of Base Pairs in Fission Yeast. G3-GENES GENOMES GENETICS 2019; 9:4097-4106. [PMID: 31597677 PMCID: PMC6893178 DOI: 10.1534/g3.119.400805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Precise allele replacement (genome editing), without unwanted changes to the genome, provides a powerful tool to define the functions of DNA elements and encoded factors in their normal biological context. While CRISPR is now used extensively for gene targeting, its utility for precise allele replacement at population scale is limited because: (A) there is a strict requirement for a correctly positioned PAM motif to introduce recombinogenic dsDNA breaks (DSBs); (B) efficient replacements only occur very close to the DSBs; and (C) indels and off-target changes are frequently generated. Here we show, using a saturated mutation library with about 15,000 alleles of the ade6 gene of Schizosaccharomyces pombe, that pop-in, pop-out allele replacement circumvents these problems. Two rounds of selection ensure that clones arise by homologous recombination with the target locus. Moreover, the exceptionally high efficiency allows one to carry out the process in bulk, then screen individual clones for phenotypes and genotypes. Alleles were introduced successfully throughout the region targeted, up to 1,956 base pairs from the DSB. About 11% of mutant alleles were hypomorphic, demonstrating utility for analyses of essential genes and genetic elements. This process of “targeted forward genetics” can be used to analyze comprehensively, across thousands of base pairs within a specific target region, a variety of allelic changes, such as scanning amino acid substitutions, deletions, and epitope tags. The overall approach and optimized workflow are extensible to other organisms that support gene targeting.
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20
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Wu T, Sun XY, Yang X, Liu L, Tong K, Gao Y, Hao JR, Cao J, Gao C. Histone H3K9 Trimethylation Downregulates the Expression of Brain-Derived Neurotrophic Factor in the Dorsal Hippocampus and Impairs Memory Formation During Anaesthesia and Surgery. Front Mol Neurosci 2019; 12:246. [PMID: 31708739 PMCID: PMC6823536 DOI: 10.3389/fnmol.2019.00246] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/24/2019] [Indexed: 01/01/2023] Open
Abstract
Brain-derived neurotrophic factor (BDNF) is essential for cognitive and memory functions. Abnormal BDNF expression in the central nervous system may impair these functions. Anaesthesia and surgery can induce perioperative neurocognitive disorders (PND). Clinical studies show that BDNF expression is decreased in patients presenting with cognitive impairment after anaesthesia and surgery. However, the molecular mechanism is still unclear. Epigenetic regulation plays an important role in cognition. The hypermethylation of H3K9 is crucial for transcriptional silencing and the onset of cognitive disorders. Here, we hypothesised that H3K9 trimethylation repressed BDNF expression and impaired memory formation or recall during anaesthesia and surgery. Laparotomy under isoflurane inhalation anaesthesia, behavioural tests, Western blotting, quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR), chromatin immunoprecipitation (ChIP), and immunohistochemistry were used in this study. BDNF expression was decreased in the hippocampus after anaesthesia and surgery. Cognitive impairment affected memory formation but not recall. The trimethylation of H3K9 downregulated BDNF expression. The overexpression of BDNF or use of exogenous BDNF improved the impairment of memory formation caused by anaesthesia and surgery. Therefore, inhibiting H3K9 trimethylation and increasing the expression of BDNF may help prevent PND in the clinical setting.
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Affiliation(s)
- Tong Wu
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China.,Department of Anesthesia, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Xiao-Yu Sun
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
| | - Xiu Yang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
| | - Le Liu
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
| | - Kun Tong
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
| | - Ya Gao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
| | - Jing-Ru Hao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
| | - Jing Cao
- Department of Anesthesia, Xuzhou Central Hospital, The Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
| | - Can Gao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
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21
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Sorida M, Murakami Y. Unprogrammed epigenetic variation mediated by stochastic formation of ectopic heterochromatin. Curr Genet 2019; 66:319-325. [PMID: 31598751 DOI: 10.1007/s00294-019-01031-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 01/09/2023]
Abstract
Changes in gene expression via chromatin-mediated mechanisms are important for reprogramming and differentiation, but uncontrolled changes can potentially lead to harmful or adaptive phenotypic alteration. Thus, diversification of the genome-wide chromatin state must be strictly limited, but the underlying mechanism of this regulation is largely unknown. In this review, we focused on distribution of heterochromatin, a tight chromatin structure that negatively regulates gene expression. Heterochromatin is characterized by methylation of histone H3 at lysine 9, and its formation and spreading are controlled by H3K9-specific methyltransferases and reversal factors such as histone demethylases. We summarize recent findings and discuss how variability in the heterochromatin distribution is controlled in the unicellular eukaryote fission yeast. In this context, we recently found that the anti-silencing factor Epe1 plays a key role in the formation of the individual-specific heterochromatin distribution. In conclusion, recent studies revealed that there are many potential heterochromatin formation sites in the fission yeast genome, and several proteins contribute to suppression of spreading and genome-wide dispersal of heterochromatin; knowledge from fission yeast studies may provide insights into the mechanisms regulating epigenetic diversification in multicellular eukaryotes.
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Affiliation(s)
- Masato Sorida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yota Murakami
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan. .,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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22
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Szachnowski U, Andjus S, Foretek D, Morillon A, Wery M. Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome. Life Sci Alliance 2019; 2:2/5/e201900407. [PMID: 31462400 PMCID: PMC6713810 DOI: 10.26508/lsa.201900407] [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: 04/26/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 12/19/2022] Open
Abstract
A genome-wide comparative analysis of “cryptic” aslncRNAs decay in RNAi-capable and RNAi-deficient budding yeasts suggests an evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome. Antisense long noncoding (aslnc)RNAs are extensively degraded by the nuclear exosome and the cytoplasmic exoribonuclease Xrn1 in the budding yeast Saccharomyces cerevisiae, lacking RNAi. Whether the ribonuclease III Dicer affects aslncRNAs in close RNAi-capable relatives remains unknown. Using genome-wide RNA profiling, here we show that aslncRNAs are primarily targeted by the exosome and Xrn1 in the RNAi-capable budding yeast Naumovozyma castellii, Dicer only affecting Xrn1-sensitive aslncRNAs levels in Xrn1-deficient cells. The dcr1 and xrn1 mutants display synergic growth defects, indicating that Dicer becomes critical in the absence of Xrn1. Small RNA sequencing showed that Dicer processes aslncRNAs into small RNAs, with a preference for Xrn1-sensitive aslncRNAs. Consistently, Dicer localizes into the cytoplasm. Finally, we observed an expansion of the exosome-sensitive antisense transcriptome in N. castellii compared with S. cerevisiae, suggesting that the presence of cytoplasmic RNAi has reinforced the nuclear RNA surveillance machinery to temper aslncRNAs expression. Our data provide fundamental insights into aslncRNAs metabolism and open perspectives into the possible evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.
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Affiliation(s)
- Ugo Szachnowski
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR 3244, Paris, France
| | - Sara Andjus
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR 3244, Paris, France
| | - Dominika Foretek
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR 3244, Paris, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR 3244, Paris, France
| | - Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR 3244, Paris, France
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23
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Xie G, Vo TV, Thillainadesan G, Holla S, Zhang B, Jiang Y, Lv M, Xu Z, Wang C, Balachandran V, Shi Y, Li F, Grewal SIS. A conserved dimer interface connects ERH and YTH family proteins to promote gene silencing. Nat Commun 2019; 10:251. [PMID: 30651569 PMCID: PMC6335422 DOI: 10.1038/s41467-018-08273-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/21/2018] [Indexed: 12/18/2022] Open
Abstract
Gene regulatory mechanisms rely on a complex network of RNA processing factors to prevent untimely gene expression. In fission yeast, the highly conserved ortholog of human ERH, called Erh1, interacts with the YTH family RNA binding protein Mmi1 to form the Erh1-Mmi1 complex (EMC) implicated in gametogenic gene silencing. However, the structural basis of EMC assembly and its functions are poorly understood. Here, we present the co-crystal structure of the EMC that consists of Erh1 homodimers interacting with Mmi1 in a 2:2 stoichiometry via a conserved molecular interface. Structure-guided mutation of the Mmi1Trp112 residue, which is required for Erh1 binding, causes defects in facultative heterochromatin assembly and gene silencing while leaving Mmi1-mediated transcription termination intact. Indeed, EMC targets masked in mmi1∆ due to termination defects are revealed in mmi1W112A. Our study delineates EMC requirements in gene silencing and identifies an ERH interface required for interaction with an RNA binding protein.
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Affiliation(s)
- Guodong Xie
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Tommy V Vo
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Beibei Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Mengqi Lv
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Zheng Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Chongyuan Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China.
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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