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Georis I, Ronsmans A, Vierendeels F, Dubois E. Differing SAGA module requirements for NCR-sensitive gene transcription in yeast. Yeast 2024; 41:207-221. [PMID: 37357465 DOI: 10.1002/yea.3885] [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: 10/02/2022] [Revised: 04/24/2023] [Accepted: 05/25/2023] [Indexed: 06/27/2023] Open
Abstract
Nitrogen catabolite repression (NCR) is a means for yeast to adapt its transcriptome to changing nitrogen sources in its environment. In conditions of derepression (under poor nitrogen conditions, upon rapamycin treatment, or when glutamine production is inhibited), two transcriptional activators of the GATA family are recruited to NCR-sensitive promoters and activate transcription of NCR-sensitive genes. Earlier observations have involved the Spt-Ada-Gcn5 acetyltransferase (SAGA) chromatin remodeling complex in these transcriptional regulations. In this report, we provide an illustration of the varying NCR-sensitive responses and question whether differing SAGA recruitment could explain this diversity of responses.
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Affiliation(s)
| | | | | | - Evelyne Dubois
- Labiris, Brussels, Belgium
- Université Libre de Bruxelles, Brussels, Belgium
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2
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Wu Q, Zheng Q, Yuan L, Gao D, Hu Y, Jiang X, Zhai Q, Liu M, Xu L, Xu H, Ye J, Zhang F. Repression of YEATS2 induces cellular senescence in hepatocellular carcinoma and inhibits tumor growth. Cell Cycle 2024; 23:478-494. [PMID: 38619971 PMCID: PMC11174065 DOI: 10.1080/15384101.2024.2342714] [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: 11/29/2023] [Accepted: 03/21/2024] [Indexed: 04/17/2024] Open
Abstract
Hepatocellular carcinoma (HCC) stands as the third leading cause of cancer-related fatalities globally. In this study, we observed a significant increase in the expression level of the YEATS2 gene in HCC patients, and it is negatively correlated with the patients' survival rate. While we have previously identified the association between YEATS2 and the survival of pancreatic cancer cells, the regulatory mechanisms and significance in HCC are still to be fully elucidated. Our study shows that knockdown (KD) of YEATS2 expression leads to DNA damage, which in turn results in an upregulation of γ-H2A.X expression and activation of the canonical senescence-related pathway p53/p21Cip1. Moreover, our transcriptomic analysis reveals that YEATS2 KD cells can enhance the expression of p21Cip1 via the c-Myc/miR-93-5p pathway, consequently fostering the senescence of HCC cells. The initiation of cellular senescence through dual-channel activation suggests that YEATS2 plays a pivotal regulatory role in the process of cell proliferation. Ultimately, our in vivo research utilizing a nude mouse tumor model revealed a notable decrease in both tumor volume and weight after the suppression of YEATS2 expression. This phenomenon is likely attributable to the attenuation of proliferative cell activity, coupled with a concurrent augmentation in the population of natural killer (NK) cells. In summary, our research results have supplemented the understanding of the regulatory mechanisms of HCC cell proliferation and indicated that targeting YEATS2 may potentially inhibit liver tumor growth.
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Affiliation(s)
- Qi Wu
- Department of Hepatobiliary Surgery, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Quan Zheng
- Department of Hepatobiliary Surgery, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Lei Yuan
- Department of Hepatobiliary Surgery, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Dandan Gao
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yabing Hu
- School of Basic Medical Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xinqing Jiang
- The Joint Innovation Center for Engineering in Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qiaocheng Zhai
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Ming Liu
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Lifeng Xu
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Heng Xu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jinlin Ye
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Feng Zhang
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
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3
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Fierling N, Billard P, Bauda P, Blaudez D. Global deletome profile of Saccharomyces cerevisiae exposed to lithium. Metallomics 2024; 16:mfad073. [PMID: 38142127 DOI: 10.1093/mtomcs/mfad073] [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: 10/06/2023] [Accepted: 12/22/2023] [Indexed: 12/25/2023]
Abstract
The increasing use of lithium (Li) in new technologies raises the question of its impact on living microorganisms. In the present study, we aimed to identify putative Li targets and resistance mechanisms in the yeast model Saccharomyces cerevisiae using a deletomic approach based on the screening of a collection of 4733 knockout mutants under Li exposure. This screening highlighted 60 mutants resistant to Li and 124 mutants sensitive to Li. Through functional enrichment analyses, transport systems were identified as playing a central role in cell resistance to toxic concentrations of Li. In contrast, the AKT/protein kinase B family, signal transduction or cell communication were identified as potential toxic targets of Li. The majority of the mutants with a Li-sensitive phenotype were also sensitive to other alkali and alkaline earth metals, whereas the Li-resistance phenotype was mostly resistant to Na but poorly resistant to other metals. A comparison with the results of deletomics studies carried out in the presence of other metals highlighted Li-specific phenotypes. Three genes (NAM7, NMD2, UPF3) of the nonsense-mediated decay pathway were specifically involved in resistance to Li. In contrast, mutants with the NCA2, SPT20, GCN5, YOR376W, YPK3, and DCW1 genes deleted were specifically resistant to Li. These genes encode various functions from putative mannosidase to constitution of the Spt-Ada-Gcn5 acetyltransferase complex. This work provides a better understanding of potential specific resistance mechanisms and cellular targets of Li in yeast.
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Maeshima K, Iida S, Shimazoe MA, Tamura S, Ide S. Is euchromatin really open in the cell? Trends Cell Biol 2024; 34:7-17. [PMID: 37385880 DOI: 10.1016/j.tcb.2023.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 07/01/2023]
Abstract
Genomic DNA is wrapped around a core histone octamer and forms a nucleosome. In higher eukaryotic cells, strings of nucleosomes are irregularly folded as chromatin domains that act as functional genome units. According to a typical textbook model, chromatin can be categorized into two types, euchromatin and heterochromatin, based on its degree of compaction. Euchromatin is open, while heterochromatin is closed and condensed. However, is euchromatin really open in the cell? New evidence from genomics and advanced imaging studies has revealed that euchromatin consists of condensed liquid-like domains. Condensed chromatin seems to be the default chromatin state in higher eukaryotic cells. We discuss this novel view of euchromatin in the cell and how the revealed organization is relevant to genome functions.
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Affiliation(s)
- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Masa A Shimazoe
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
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5
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Zhang X, Fawwal DV, Spangle JM, Corbett AH, Jones CY. Exploring the Molecular Underpinnings of Cancer-Causing Oncohistone Mutants Using Yeast as a Model. J Fungi (Basel) 2023; 9:1187. [PMID: 38132788 PMCID: PMC10744705 DOI: 10.3390/jof9121187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Understanding the molecular basis of cancer initiation and progression is critical in developing effective treatment strategies. Recently, mutations in genes encoding histone proteins that drive oncogenesis have been identified, converting these essential proteins into "oncohistones". Understanding how oncohistone mutants, which are commonly single missense mutations, subvert the normal function of histones to drive oncogenesis requires defining the functional consequences of such changes. Histones genes are present in multiple copies in the human genome with 15 genes encoding histone H3 isoforms, the histone for which the majority of oncohistone variants have been analyzed thus far. With so many wildtype histone proteins being expressed simultaneously within the oncohistone, it can be difficult to decipher the precise mechanistic consequences of the mutant protein. In contrast to humans, budding and fission yeast contain only two or three histone H3 genes, respectively. Furthermore, yeast histones share ~90% sequence identity with human H3 protein. Its genetic simplicity and evolutionary conservation make yeast an excellent model for characterizing oncohistones. The power of genetic approaches can also be exploited in yeast models to define cellular signaling pathways that could serve as actionable therapeutic targets. In this review, we focus on the value of yeast models to serve as a discovery tool that can provide mechanistic insights and inform subsequent translational studies in humans.
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Affiliation(s)
- Xinran Zhang
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
| | - Dorelle V. Fawwal
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Jennifer M. Spangle
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Anita H. Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Celina Y. Jones
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
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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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Yan K, Ji Q, Zhao D, Li M, Sun X, Wang Z, Liu X, Liu Z, Li H, Ding Y, Wang S, Belmonte JCI, Qu J, Zhang W, Liu GH. SGF29 nuclear condensates reinforce cellular aging. Cell Discov 2023; 9:110. [PMID: 37935676 PMCID: PMC10630320 DOI: 10.1038/s41421-023-00602-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/07/2023] [Indexed: 11/09/2023] Open
Abstract
Phase separation, a biophysical segregation of subcellular milieus referred as condensates, is known to regulate transcription, but its impacts on physiological processes are less clear. Here, we demonstrate the formation of liquid-like nuclear condensates by SGF29, a component of the SAGA transcriptional coactivator complex, during cellular senescence in human mesenchymal progenitor cells (hMPCs) and fibroblasts. The Arg 207 within the intrinsically disordered region is identified as the key amino acid residue for SGF29 to form phase separation. Through epigenomic and transcriptomic analysis, our data indicated that both condensate formation and H3K4me3 binding of SGF29 are essential for establishing its precise chromatin location, recruiting transcriptional factors and co-activators to target specific genomic loci, and initiating the expression of genes associated with senescence, such as CDKN1A. The formation of SGF29 condensates alone, however, may not be sufficient to drive H3K4me3 binding or achieve transactivation functions. Our study establishes a link between phase separation and aging regulation, highlighting nuclear condensates as a functional unit that facilitate shaping transcriptional landscapes in aging.
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Affiliation(s)
- Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dongxin Zhao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Mingheng Li
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyan Sun
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Zehua Wang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoqian Liu
- University of Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zunpeng Liu
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongyu Li
- University of Chinese Academy of Sciences, Beijing, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yingjie Ding
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, China
| | | | - Jing Qu
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Weiqi Zhang
- University of Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, China.
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, China.
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Sun K, Li Y, Gai Y, Wang J, Jian Y, Liu X, Wu L, Shim WB, Lee YW, Ma Z, Haas H, Yin Y. HapX-mediated H2B deub1 and SreA-mediated H2A.Z deposition coordinate in fungal iron resistance. Nucleic Acids Res 2023; 51:10238-10260. [PMID: 37650633 PMCID: PMC10602907 DOI: 10.1093/nar/gkad708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 07/26/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023] Open
Abstract
Plant pathogens are challenged by host-derived iron starvation or excess during infection, but the mechanism through which pathogens counteract iron stress is unclear. Here, we found that Fusarium graminearum encounters iron excess during the colonization of wheat heads. Deletion of heme activator protein X (FgHapX), siderophore transcription factor A (FgSreA) or both attenuated virulence. Further, we found that FgHapX activates iron storage under iron excess by promoting histone H2B deubiquitination (H2B deub1) at the promoter of the responsible gene. Meanwhile, FgSreA is shown to inhibit genes mediating iron acquisition during iron excess by facilitating the deposition of histone variant H2A.Z and histone 3 lysine 27 trimethylation (H3K27 me3) at the first nucleosome after the transcription start site. In addition, the monothiol glutaredoxin FgGrx4 is responsible for iron sensing and control of the transcriptional activity of FgHapX and FgSreA via modulation of their enrichment at target genes and recruitment of epigenetic regulators, respectively. Taken together, our findings elucidated the molecular mechanisms for adaptation to iron excess mediated by FgHapX and FgSreA during infection in F. graminearum and provide novel insights into regulation of iron homeostasis at the chromatin level in eukaryotes.
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Affiliation(s)
- Kewei Sun
- State Key Laboratory of Rice Biology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yiqing Li
- State Key Laboratory of Rice Biology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yunpeng Gai
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Jingrui Wang
- State Key Laboratory of Rice Biology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yunqing Jian
- State Key Laboratory of Rice Biology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xin Liu
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Liang Wu
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Won-Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, USA
| | - Yin-Won Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Hubertus Haas
- Instiute of Molecular Biology, Biocenter, Medical University Innsbruck, Innsbruck A-6020, Austria
| | - Yanni Yin
- State Key Laboratory of Rice Biology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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Li K, Mocciaro G, Griffin JL, Zhang N. The Saccharomyces cerevisiae acetyltransferase Gcn5 exerts antagonistic pleiotropic effects on chronological ageing. Aging (Albany NY) 2023; 15:10915-10937. [PMID: 37874684 PMCID: PMC10637828 DOI: 10.18632/aging.205109] [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: 04/07/2023] [Accepted: 09/18/2023] [Indexed: 10/26/2023]
Abstract
Compared to replicative lifespan, epigenetic regulation of chronological lifespan (CLS) is less well understood in yeast. Here, by screening all the viable mutants of histone acetyltransferase (HAT) and histone deacetylase (HDAC), we demonstrate that Gcn5, functioning in the HAT module of the SAGA/SLIK complex, exhibits an epistatic relationship with the HDAC Hda1 to control the expression of starvation-induced stress response and respiratory cell growth. Surprisingly, the gcn5Δ mutants lose their colony-forming potential early in the stationary phase but display a longer maximum CLS than their WT counterparts, suggesting the contradictory roles of Gcn5 in lifespan regulation. Integrative analyses of the transcriptome, metabolome and ChIP assays reveal that Gcn5 is necessary for the activation of two regulons upon glucose starvation: the Msn2/4-/Gis1-dependent stress response and the Cat8-/Adr1-mediated metabolic reprogramming, to enable pro-longevity characteristics, including redox homeostasis, stress resistance and maximal storage of carbohydrates. The activation of Cat8-/Adr1-dependent regulon also promotes the pyruvate dehydrogenase (PDH) bypass, leading to acetyl-CoA synthesis, global and targeted H3K9 acetylation. Global H3K9 acetylation levels mediated by Gcn5 and Hda1 during the transition into stationary phase are positively correlated with senescent cell populations accumulated in the aged cell cultures. These data suggest that Gcn5 lies in the centre of a feed-forward loop between histone acetylation and starvation-induced gene expression, enabling stress resistance and homeostasis but also promoting chronological ageing concomitantly.
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Affiliation(s)
- Kaiqiang Li
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Gabriele Mocciaro
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Jules L. Griffin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
- The Rowett Institute, University of Aberdeen, Foresterhill Campus, Aberdeen AB25 2ZD, UK
| | - Nianshu Zhang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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10
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Zhou WH, Luo Y, Li RX, Degrace P, Jourdan T, Qiao F, Chen LQ, Zhang ML, Du ZY. Inhibition of mitochondrial fatty acid β-oxidation activates mTORC1 pathway and protein synthesis via Gcn5-dependent acetylation of Raptor in zebrafish. J Biol Chem 2023; 299:105220. [PMID: 37660921 PMCID: PMC10540046 DOI: 10.1016/j.jbc.2023.105220] [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: 05/08/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
Pharmacological inhibition of mitochondrial fatty acid oxidation (FAO) has been clinically used to alleviate certain metabolic diseases by remodeling cellular metabolism. However, mitochondrial FAO inhibition also leads to mechanistic target of rapamycin complex 1 (mTORC1) activation-related protein synthesis and tissue hypertrophy, but the mechanism remains unclear. Here, by using a mitochondrial FAO inhibitor (mildronate or etomoxir) or knocking out carnitine palmitoyltransferase-1, we revealed that mitochondrial FAO inhibition activated the mTORC1 pathway through general control nondepressible 5-dependent Raptor acetylation. Mitochondrial FAO inhibition significantly promoted glucose catabolism and increased intracellular acetyl-CoA levels. In response to the increased intracellular acetyl-CoA, acetyltransferase general control nondepressible 5 activated mTORC1 by catalyzing Raptor acetylation through direct interaction. Further investigation also screened Raptor deacetylase histone deacetylase class II and identified histone deacetylase 7 as a potential regulator of Raptor. These results provide a possible mechanistic explanation for the mTORC1 activation after mitochondrial FAO inhibition and also bring light to reveal the roles of nutrient metabolic remodeling in regulating protein acetylation by affecting acetyl-CoA production.
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Affiliation(s)
- Wen-Hao Zhou
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China
| | - Yuan Luo
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China
| | - Rui-Xin Li
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China
| | - Pascal Degrace
- Pathophysiology of Dyslipidemia Research Group, INSERM UMR1231 CTM (Center for Translational and Molecular Medicine) Ex-Lipids, Nutrition, Cancer, Université de Bourgogne Franche-Comté, Dijon, France
| | - Tony Jourdan
- Pathophysiology of Dyslipidemia Research Group, INSERM UMR1231 CTM (Center for Translational and Molecular Medicine) Ex-Lipids, Nutrition, Cancer, Université de Bourgogne Franche-Comté, Dijon, France
| | - Fang Qiao
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China
| | - Li-Qiao Chen
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China
| | - Mei-Ling Zhang
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China
| | - Zhen-Yu Du
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China.
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11
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Yayli G, Bernardini A, Mendoza Sanchez PK, Scheer E, Damilot M, Essabri K, Morlet B, Negroni L, Vincent SD, Timmers HTM, Tora L. ATAC and SAGA co-activator complexes utilize co-translational assembly, but their cellular localization properties and functions are distinct. Cell Rep 2023; 42:113099. [PMID: 37682711 PMCID: PMC10591836 DOI: 10.1016/j.celrep.2023.113099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/19/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
To understand the function of multisubunit complexes, it is of key importance to uncover the precise mechanisms that guide their assembly. Nascent proteins can find and bind their interaction partners during their translation, leading to co-translational assembly. Here, we demonstrate that the core modules of ATAC (ADA-two-A-containing) and SAGA (Spt-Ada-Gcn5-acetyltransferase), two lysine acetyl transferase-containing transcription co-activator complexes, assemble co-translationally in the cytoplasm of mammalian cells. In addition, a SAGA complex containing all of its modules forms in the cytoplasm and acetylates non-histone proteins. In contrast, ATAC complex subunits cannot be detected in the cytoplasm of mammalian cells. However, an endogenous ATAC complex containing two functional modules forms and functions in the nucleus. Thus, the two related co-activators, ATAC and SAGA, assemble using co-translational pathways, but their subcellular localization, cytoplasmic abundance, and functions are distinct.
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Affiliation(s)
- Gizem Yayli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Mylène Damilot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Karim Essabri
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - H T Marc Timmers
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France.
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12
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Yayli G, Bernardini A, Sanchez PKM, Scheer E, Damilot M, Essabri K, Morlet B, Negroni L, Vincent SD, Timmers HTM, Tora L. ATAC and SAGA coactivator complexes utilize co-translational assembly, but their cellular localization properties and functions are distinct. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551787. [PMID: 37577620 PMCID: PMC10418265 DOI: 10.1101/2023.08.03.551787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
To understand the function of multisubunit complexes it is of key importance to uncover the precise mechanisms that guide their assembly. Nascent proteins can find and bind their interaction partners during their translation, leading to co-translational assembly. Here we demonstrate that the core modules of ATAC (ADA-Two-A-Containing) and SAGA (Spt-Ada-Gcn5-acetyltransferase), two lysine acetyl transferase-containing transcription coactivator complexes, assemble co-translationally in the cytoplasm of mammalian cells. In addition, SAGA complex containing all of its modules forms in the cytoplasm and acetylates non-histones proteins. In contrast, fully assembled ATAC complex cannot be detected in the cytoplasm of mammalian cells. However, endogenous ATAC complex containing two functional modules forms and functions in the nucleus. Thus, the two related coactivators, ATAC and SAGA, assemble by using co-translational pathways, but their subcellular localization, cytoplasmic abundance and functions are distinct.
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Affiliation(s)
- Gizem Yayli
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Andrea Bernardini
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research, Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Mylène Damilot
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Karim Essabri
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Stéphane D. Vincent
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - HT Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research, Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
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13
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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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14
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Wu CJ, Yuan DY, Liu ZZ, Xu X, Wei L, Cai XW, Su YN, Li L, Chen S, He XJ. Conserved and plant-specific histone acetyltransferase complexes cooperate to regulate gene transcription and plant development. NATURE PLANTS 2023; 9:442-459. [PMID: 36879016 DOI: 10.1038/s41477-023-01359-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 01/30/2023] [Indexed: 05/18/2023]
Abstract
Although a conserved SAGA complex containing the histone acetyltransferase GCN5 is known to mediate histone acetylation and transcriptional activation in eukaryotes, how to maintain different levels of histone acetylation and transcription at the whole-genome level remains to be determined. Here we identify and characterize a plant-specific GCN5-containing complex, which we term PAGA, in Arabidopsis thaliana and Oryza sativa. In Arabidopsis, the PAGA complex consists of two conserved subunits (GCN5 and ADA2A) and four plant-specific subunits (SPC, ING1, SDRL and EAF6). We find that PAGA and SAGA can independently mediate moderate and high levels of histone acetylation, respectively, thereby promoting transcriptional activation. Moreover, PAGA and SAGA can also repress gene transcription via the antagonistic effect between PAGA and SAGA. Unlike SAGA, which regulates multiple biological processes, PAGA is specifically involved in plant height and branch growth by regulating the transcription of hormone biosynthesis and response related genes. These results reveal how PAGA and SAGA cooperate to regulate histone acetylation, transcription and development. Given that the PAGA mutants show semi-dwarf and increased branching phenotypes without reduction in seed yield, the PAGA mutations could potentially be used for crop improvement.
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Affiliation(s)
- Chan-Juan Wu
- National Institute of Biological Sciences, Beijing, China
| | - Dan-Yang Yuan
- National Institute of Biological Sciences, Beijing, China
| | - Zhen-Zhen Liu
- National Institute of Biological Sciences, Beijing, China
| | - Xin Xu
- National Institute of Biological Sciences, Beijing, China
| | - Long Wei
- National Institute of Biological Sciences, Beijing, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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15
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An C, Deng L, Zhai H, You Y, Wu F, Zhai Q, Goossens A, Li C. Regulation of jasmonate signaling by reversible acetylation of TOPLESS in Arabidopsis. MOLECULAR PLANT 2022; 15:1329-1346. [PMID: 35780296 DOI: 10.1016/j.molp.2022.06.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
The plant hormone jasmonate (JA) regulates plant immunity and adaptive growth by orchestrating a genome-wide transcriptional program. Key regulators of JA-responsive gene expression include the master transcription factor MYC2, which is repressed by the conserved Groucho/Tup1-like corepressor TOPLESS (TPL) in the resting state. However, the mechanisms underlying TPL-mediated transcriptional repression of MYC2 activity and hormone-dependent switching between repression and de-repression remain enigmatic. Here, we report the regulation of TPL activity and JA signaling by reversible acetylation of TPL. We found that the histone acetyltransferase GCN5 could mediate TPL acetylation, which enhances its interaction with the NOVEL-INTERACTOR-OF-JAZ (NINJA) adaptor and promotes its recruitment to MYC2 target promoters, facilitating transcriptional repression. Conversely, TPL deacetylation by the histone deacetylase HDA6 weakens TPL-NINJA interaction and inhibits TPL recruitment to MYC2 target promoters, facilitating transcriptional activation. In the resting state, the opposing activities of GCN5 and HDA6 maintain TPL acetylation homeostasis, promoting transcriptional repression activity of TPL. In response to JA elicitation, HDA6 expression is transiently induced, resulted in decreased TPL acetylation and repressor activity, thereby transcriptional activation of MYC2 target genes. Thus, the GCN5-TPL-HDA6 module maintains the homeostasis of acetylated TPL, thereby determining the transcriptional state of JA-responsive genes. Our findings uncovered a mechanism by which the TPL corepressor activity in JA signaling is actively tuned in a rapid and reversible manner.
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Affiliation(s)
- Chunpeng An
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Deng
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huawei Zhai
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Yanrong You
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangming Wu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingzhe Zhai
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China.
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16
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Fischer V, Hisler V, Scheer E, Lata E, Morlet B, Plassard D, Helmlinger D, Devys D, Tora L, Vincent S. SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells. Nucleic Acids Res 2022; 50:7972-7990. [PMID: 35871303 PMCID: PMC9371916 DOI: 10.1093/nar/gkac637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/05/2022] [Accepted: 07/12/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Coactivator complexes regulate chromatin accessibility and transcription. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved coactivator complex. The core module scaffolds the entire SAGA complex and adopts a histone octamer-like structure, which consists of six histone-fold domain (HFD)-containing proteins forming three histone-fold (HF) pairs, to which the double HFD-containing SUPT3H adds one HF pair. Spt3, the yeast ortholog of SUPT3H, interacts genetically and biochemically with the TATA binding protein (TBP) and contributes to global RNA polymerase II (Pol II) transcription. Here we demonstrate that (i) SAGA purified from human U2OS or mouse embryonic stem cells (mESC) can assemble without SUPT3H, (ii) SUPT3H is not essential for mESC survival, but required for their growth and self-renewal, and (iii) the loss of SUPT3H from mammalian cells affects the transcription of only a specific subset of genes. Accordingly, in the absence of SUPT3H no major change in TBP accumulation at gene promoters was observed. Thus, SUPT3H is not required for the assembly of SAGA, TBP recruitment, or overall Pol II transcription, but plays a role in mESC growth and self-renewal. Our data further suggest that yeast and mammalian SAGA complexes contribute to transcription regulation by distinct mechanisms.
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Affiliation(s)
- Veronique Fischer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Vincent Hisler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Elisabeth Lata
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Damien Plassard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- Plateforme GenomEast, infrastructure France Génomique, 67404 Illkirch, France
| | | | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
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17
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Pezza A, Tavernelli LE, Alonso VL, Perdomo V, Gabarro R, Prinjha R, Rodríguez Araya E, Rioja I, Docampo R, Calderón F, Martin J, Serra E. Essential Bromodomain TcBDF2 as a Drug Target against Chagas Disease. ACS Infect Dis 2022; 8:1062-1074. [PMID: 35482332 DOI: 10.1021/acsinfecdis.2c00057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Trypanosoma cruzi is a unicellular parasite that causes Chagas disease, which is endemic in the American continent but also worldwide, distributed by migratory movements. A striking feature of trypanosomatids is the polycistronic transcription associated with post-transcriptional mechanisms that regulate the levels of translatable mRNA. In this context, epigenetic regulatory mechanisms have been revealed to be of great importance, since they are the only ones that would control the access of RNA polymerases to chromatin. Bromodomains are epigenetic protein readers that recognize and specifically bind to acetylated lysine residues, mostly at histone proteins. There are seven coding sequences for BD-containing proteins in trypanosomatids, named TcBDF1 to TcBDF7, and a putative new protein containing a bromodomain was recently described. Using the Tet-regulated overexpression plasmid pTcINDEX-GW and CRISPR/Cas9 genome editing, we were able to demonstrate the essentiality of TcBDF2 in T. cruzi. This bromodomain is located in the nucleus, through a bipartite nuclear localization signal. TcBDF2 was shown to be important for host cell invasion, amastigote replication, and differentiation from amastigotes to trypomastigotes. Overexpression of TcBDF2 diminished epimastigote replication. Also, some processes involved in pathogenesis were altered in these parasites, such as infection of mammalian cells, replication of amastigotes, and the number of trypomastigotes released from host cells. In in vitro studies, TcBDF2 was also able to bind inhibitors showing a specificity profile different from that of the previously characterized TcBDF3. These results point to TcBDF2 as a druggable target against T. cruzi.
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Affiliation(s)
- Alejandro Pezza
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
| | - Luis E. Tavernelli
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
| | - Victoria L. Alonso
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Virginia Perdomo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Raquel Gabarro
- GlaxoSmithKline Global Health, Tres Cantos, 28760 Madrid, Spain
| | - Rab Prinjha
- Immunology Research Unit, Research, R&D GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Elvio Rodríguez Araya
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Inmaculada Rioja
- Immunology Research Unit, Research, R&D GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Roberto Docampo
- Department of Cellular Biology and Center for Tropical and Global Emerging Diseases, University of Georgia, Athens, Georgia30602, United States
| | - Felix Calderón
- GlaxoSmithKline Global Health, Tres Cantos, 28760 Madrid, Spain
| | - Julio Martin
- GlaxoSmithKline Global Health, Tres Cantos, 28760 Madrid, Spain
| | - Esteban Serra
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
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18
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Pan J, Kwon JJ, Talamas JA, Borah AA, Vazquez F, Boehm JS, Tsherniak A, Zitnik M, McFarland JM, Hahn WC. Sparse dictionary learning recovers pleiotropy from human cell fitness screens. Cell Syst 2022; 13:286-303.e10. [PMID: 35085500 PMCID: PMC9035054 DOI: 10.1016/j.cels.2021.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/30/2021] [Accepted: 12/21/2021] [Indexed: 12/28/2022]
Abstract
In high-throughput functional genomic screens, each gene product is commonly assumed to exhibit a singular biological function within a defined protein complex or pathway. In practice, a single gene perturbation may induce multiple cascading functional outcomes, a genetic principle known as pleiotropy. Here, we model pleiotropy in fitness screen collections by representing each gene perturbation as the sum of multiple perturbations of biological functions, each harboring independent fitness effects inferred empirically from the data. Our approach (Webster) recovered pleiotropic functions for DNA damage proteins from genotoxic fitness screens, untangled distinct signaling pathways upstream of shared effector proteins from cancer cell fitness screens, and predicted the stoichiometry of an unknown protein complex subunit from fitness data alone. Modeling compound sensitivity profiles in terms of genetic functions recovered compound mechanisms of action. Our approach establishes a sparse approximation mechanism for unraveling complex genetic architectures underlying high-dimensional gene perturbation readouts.
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Affiliation(s)
- Joshua Pan
- Dana-Farber Cancer Institute, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Jason J Kwon
- Dana-Farber Cancer Institute, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Jessica A Talamas
- Dana-Farber Cancer Institute, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Ashir A Borah
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Jesse S Boehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviad Tsherniak
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marinka Zitnik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Department of Biomedical Informatics, Boston, MA 02215, USA; Harvard University, Data Science Initiative, Cambridge, MA 02138, USA
| | | | - William C Hahn
- Dana-Farber Cancer Institute, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Brigham and Women's Hospital and Harvard Medical School, Department of Medicine, Boston, MA 02215, USA.
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19
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Huang J, Dai W, Xiao D, Xiong Q, Liu C, Hu J, Ge F, Yu X, Li S. Acetylation-dependent SAGA complex dimerization promotes nucleosome acetylation and gene transcription. Nat Struct Mol Biol 2022; 29:261-273. [PMID: 35301489 DOI: 10.1038/s41594-022-00736-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/30/2021] [Accepted: 02/02/2022] [Indexed: 11/09/2022]
Abstract
Cells reprogram their transcriptomes to adapt to external conditions. The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is a highly conserved transcriptional coactivator that plays essential roles in cell growth and development, in part by acetylating histones. Here, we uncover an autoregulatory mechanism of the Saccharomyces cerevisiae SAGA complex in response to environmental changes. Specifically, the SAGA complex acetylates its Ada3 subunit at three sites (lysines 8, 14 and 182) that are dynamically deacetylated by Rpd3. The acetylated Ada3 lysine residues are bound by bromodomains within SAGA subunits Gcn5 and Spt7 that synergistically facilitate formation of SAGA homo-dimers. Ada3-mediated dimerization is enhanced when cells are grown under sucrose or under phosphate-starvation conditions. Once dimerized, SAGA efficiently acetylates nucleosomes, promotes gene transcription and enhances cell resistance to stress. Collectively, our work reveals a mechanism for regulation of SAGA structure and activity and provides insights into how cells adapt to environmental conditions.
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Affiliation(s)
- Junhua Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Wenjing Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Duncheng Xiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Qian Xiong
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jie Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China.
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China.
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20
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Abstract
Transcription factors (TFs) interact with several other proteins in the process of transcriptional regulation. Here, we identify 6703 and 1536 protein–protein interactions for 109 different human TFs through proximity-dependent biotinylation (BioID) and affinity purification mass spectrometry (AP-MS), respectively. The BioID analysis identifies more high-confidence interactions, highlighting the transient and dynamic nature of many of the TF interactions. By performing clustering and correlation analyses, we identify subgroups of TFs associated with specific biological functions, such as RNA splicing or chromatin remodeling. We also observe 202 TF-TF interactions, of which 118 are interactions with nuclear factor 1 (NFI) family members, indicating uncharacterized cross-talk between NFI signaling and other TF signaling pathways. Moreover, TF interactions with basal transcription machinery are mainly observed through TFIID and SAGA complexes. This study provides a rich resource of human TF interactions and also act as a starting point for future studies aimed at understanding TF-mediated transcription. Transcription factors (TFs) interact with several other proteins in the process of transcriptional regulation. Here the authors identify 6703 and 1536 protein–protein interactions for 109 different human TFs through BioID and AP-MS analyses, respectively.
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21
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Hawar A, Xiong S, Yang Z, Sun B. Histone Acetyltransferase SlGCN5 Regulates Shoot Meristem and Flower Development in Solanum lycopersicum. FRONTIERS IN PLANT SCIENCE 2022; 12:805879. [PMID: 35126431 PMCID: PMC8814577 DOI: 10.3389/fpls.2021.805879] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/21/2021] [Indexed: 06/02/2023]
Abstract
The histone acetyltransferase (HAT) general control non-repressed protein 5 (GCN5) plays important roles in plant development via epigenetic regulation of its target genes. However, the role of GCN5 in tomato, especially in the regulation of tomato shoot meristem and flower development, has not been well-understood. In this study, we found that silencing of Solanum lycopersicum GCN5 (SlGCN5, Solyc10g045400.1.1) by virus-induced gene silencing (VIGS) and RNA interference (RNAi) resulted in the loss of shoot apical dominance, reduced shoot apical meristem (SAM) size, and dwarf and bushy plant phenotype. Besides, we occasionally observed extra carpelloid stamens and carpels fused with stamens at the late stages of flower development. Through gene expression analysis, we noticed that SlGCN5 could enhance SlWUS transcript levels in both SAM and floral meristem (FM). Similar to the known function of GCN5 in Arabidopsis, we demonstrated that SIGCN5 may form a HAT unit with S. lycopersicum alteration/deficiency in activation 2a (SlADA2a) and SlADA2b proteins in tomato. Therefore, our results provide insights in the SlGCN5-mediated regulation of SAM maintenance and floral development in tomato.
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22
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Li X, Liu S, Li X, Li XD. YEATS Domains as Novel Epigenetic Readers: Structures, Functions, and Inhibitor Development. ACS Chem Biol 2022; 18:994-1013. [PMID: 35041380 DOI: 10.1021/acschembio.1c00945] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Interpretation of the histone posttranslational modifications (PTMs) by effector proteins, or readers, is an important epigenetic mechanism to regulate gene function. YEATS domains have been recently identified as novel readers of histone lysine acetylation and a variety of nonacetyl acylation marks. Accumulating evidence has revealed the association of dysregulated interactions between YEATS domains and histone PTMs with human diseases, suggesting the therapeutic potential of YEATS domain inhibition. Here, we discuss the molecular mechanisms adopted by YEATS domains in recognizing their preferred histone marks and the biological significance of such recognitions in normal cell physiology and pathogenesis of human diseases. Recent progress in the development of YEATS domain inhibitors is also discussed.
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Affiliation(s)
- Xin Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong G01, China
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Sha Liu
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong G01, China
| | - Xiang Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong G01, China
| | - Xiang David Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong G01, China
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23
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Arede L, Foerner E, Wind S, Kulkarni R, Domingues AF, Giotopoulos G, Kleinwaechter S, Mollenhauer-Starkl M, Davison H, Chandru A, Asby R, Samarista R, Gupta S, Forte D, Curti A, Scheer E, Huntly BJP, Tora L, Pina C. KAT2A complexes ATAC and SAGA play unique roles in cell maintenance and identity in hematopoiesis and leukemia. Blood Adv 2022; 6:165-180. [PMID: 34654054 PMCID: PMC8753207 DOI: 10.1182/bloodadvances.2020002842] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/20/2021] [Indexed: 12/03/2022] Open
Abstract
Epigenetic histone modifiers are key regulators of cell fate decisions in normal and malignant hematopoiesis. Their enzymatic activities are of particular significance as putative therapeutic targets in leukemia. In contrast, less is known about the contextual role in which those enzymatic activities are exercised and specifically how different macromolecular complexes configure the same enzymatic activity with distinct molecular and cellular consequences. We focus on KAT2A, a lysine acetyltransferase responsible for histone H3 lysine 9 acetylation, which we recently identified as a dependence in acute myeloid leukemia stem cells and that participates in 2 distinct macromolecular complexes: Ada two-A-containing (ATAC) and Spt-Ada-Gcn5-Acetyltransferase (SAGA). Through analysis of human cord blood hematopoietic stem cells and progenitors, and of myeloid leukemia cells, we identify unique respective contributions of the ATAC complex to regulation of biosynthetic activity in undifferentiated self-renewing cells and of the SAGA complex to stabilization or correct progression of cell type-specific programs with putative preservation of cell identity. Cell type and stage-specific dependencies on ATAC and SAGA-regulated programs explain multilevel KAT2A requirements in leukemia and in erythroid lineage specification and development. Importantly, they set a paradigm against which lineage specification and identity can be explored across developmental stem cell systems.
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Affiliation(s)
- Liliana Arede
- Department of Haematology
- Department of Genetics, and
| | | | | | | | | | - George Giotopoulos
- Department of Haematology
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | | | - Holly Davison
- College of Health, Medicine and Life Sciences, Division of Biosciences, Brunel University London, Uxbridge, UK
| | | | - Ryan Asby
- Department of Haematology
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Ralph Samarista
- College of Health, Medicine and Life Sciences, Division of Biosciences, Brunel University London, Uxbridge, UK
| | - Shikha Gupta
- Department of Haematology
- Department of Genetics, and
| | - Dorian Forte
- Department of Haematology
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Institute of Hematology “Seràgnoli”, Bologna, Italy
| | - Antonio Curti
- IRCCS Azienda ospedaliero-universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, Bologna, Italy
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France; and
| | - Brian J. P. Huntly
- Department of Haematology
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Laszlo Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France; and
| | - Cristina Pina
- College of Health, Medicine and Life Sciences, Division of Biosciences, Brunel University London, Uxbridge, UK
- Centre for Genome Engineering and Maintenance (CenGEM), Brunel University London, Uxbridge, UK
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24
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McCarthy A, Sarkar K, Martin ET, Upadhyay M, Jang S, Williams ND, Forni PE, Buszczak M, Rangan P. Msl3 promotes germline stem cell differentiation in female Drosophila. Development 2022; 149:dev199625. [PMID: 34878097 PMCID: PMC8783043 DOI: 10.1242/dev.199625] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/19/2021] [Indexed: 01/07/2023]
Abstract
Gamete formation from germline stem cells (GSCs) is essential for sexual reproduction. However, the regulation of GSC differentiation is incompletely understood. Set2, which deposits H3K36me3 modifications, is required for GSC differentiation during Drosophila oogenesis. We discovered that the H3K36me3 reader Male-specific lethal 3 (Msl3) and histone acetyltransferase complex Ada2a-containing (ATAC) cooperate with Set2 to regulate GSC differentiation in female Drosophila. Msl3, acting independently of the rest of the male-specific lethal complex, promotes transcription of genes, including a germline-enriched ribosomal protein S19 paralog RpS19b. RpS19b upregulation is required for translation of RNA-binding Fox protein 1 (Rbfox1), a known meiotic cell cycle entry factor. Thus, Msl3 regulates GSC differentiation by modulating translation of a key factor that promotes transition to an oocyte fate.
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Affiliation(s)
- Alicia McCarthy
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12202, USA
| | - Kahini Sarkar
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12202, USA
| | - Elliot T. Martin
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12202, USA
| | - Maitreyi Upadhyay
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12202, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Seoyeon Jang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nathan D. Williams
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Paolo E. Forni
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12202, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12202, USA
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25
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Nikolenko JV, Vdovina YA, Fefelova EI, Glukhova AA, Nabirochkina EN, Kopytova DV. The SAGA Deubiquitinilation (DUB) Module Participates in Pol III-Dependent Transcription. Mol Biol 2021. [DOI: 10.1134/s0026893321020278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Shahin T, Kuehn HS, Shoeb MR, Gawriyski L, Giuliani S, Repiscak P, Hoeger B, Yüce Petronczki Ö, Bal SK, Zoghi S, Dmytrus J, Seruggia D, Castanon I, Rezaei N, Varjosalo M, Halbritter F, Rosenzweig SD, Boztug K. Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity. Sci Immunol 2021; 6:eabe3981. [PMID: 34826259 DOI: 10.1126/sciimmunol.abe3981] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Tala Shahin
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20814, USA
| | - Mohamed R Shoeb
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Lisa Gawriyski
- Institute of Biotechnology, Helsinki Institute of Life Science, Proteomics Unit, University of Helsinki, Helsinki, Finland
| | - Sarah Giuliani
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Peter Repiscak
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Birgit Hoeger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Özlem Yüce Petronczki
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Sevgi Köstel Bal
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Samaneh Zoghi
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Jasmin Dmytrus
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Davide Seruggia
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Irinka Castanon
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science, Proteomics Unit, University of Helsinki, Helsinki, Finland
| | | | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20814, USA
| | - Kaan Boztug
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.,St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
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27
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Osadchuk K, Cheng CL, Irish EE. The integration of leaf-derived signals sets the timing of vegetative phase change in maize, a process coordinated by epigenetic remodeling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 312:111035. [PMID: 34620439 DOI: 10.1016/j.plantsci.2021.111035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/02/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
After germination, the maize shoot proceeds through a series of developmental stages before flowering. The first transition occurs during the vegetative phase where the shoot matures from the juvenile to the adult phase, called vegetative phase change (VPC). In maize, both phases exhibit easily-scored morphological characteristics, facilitating the elucidation of molecular mechanisms directing the characteristic gene expression patterns and resulting physiological features of each phase. miR156 expression is high during the juvenile phase, suppressing expression of squamosa promoter binding proteins/SBP-like transcription factors and miR172. The decline in miR156 and subsequent increase in miR172 expression marks the transition into the adult phase, where miR172 represses transcripts that confer juvenile traits. Leaf-derived signals attenuate miR156 expression and thus the duration of the juvenile phase. As found in other species, VPC in maize utilizes signals that consist of hormones, stress, and sugar to direct epigenetic modifiers. In this review we identify the intersection of leaf-derived signaling with components that contribute to the epigenetic changes which may, in turn, manage the distinct global gene expression patterns of each phase. In maize, published research regarding chromatin remodeling during VPC is minimal. Therefore, we identified epigenetic regulators in the maize genome and, using published gene expression data and research from other plant species, identify VPC candidates.
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Affiliation(s)
- Krista Osadchuk
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Chi-Lien Cheng
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Erin E Irish
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA.
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28
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Lütkenhaus R, Breuer J, Nowrousian M. Functional characterization of the developmental genes asm2, asm3, and spt3 required for fruiting body formation in the filamentous ascomycete Sordaria macrospora. Genetics 2021; 219:iyab103. [PMID: 34849873 PMCID: PMC8633134 DOI: 10.1093/genetics/iyab103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/30/2021] [Indexed: 01/10/2023] Open
Abstract
The formation of fruiting bodies is one of the most complex developmental processes in filamentous ascomycetes. It requires the development of sexual structures that give rise to meiosporangia (asci) and meiotic spores (ascospores) as well as surrounding structures for protection and dispersal of the spores. Previous studies have shown that these developmental processes are accompanied by significant changes of the transcriptome, and comparative transcriptomics of different fungi as well as the analysis of transcriptome changes in developmental mutants have aided in the identification of differentially regulated genes that are themselves involved in regulating fruiting body development. In previous analyses, we used transcriptomics to identify the genes asm2 and spt3, which result in developmental phenotypes when deleted in Sordaria macrospora. In this study, we identified another gene, asm3, required for fruiting body formation, and performed transcriptomics analyses of Δasm2, Δasm3, and Δspt3. Deletion of spt3, which encodes a subunit of the SAGA complex, results in a block at an early stage of development and drastic changes in the transcriptome. Deletion mutants of asm2 and asm3 are able to form fruiting bodies, but have defects in ascospore maturation. Transcriptomics analysis of fruiting bodies revealed a large overlap in differentially regulated genes in Δasm2 and Δasm3 compared to the wild type. Analysis of nuclear distribution during ascus development showed that both mutants undergo meiosis and postmeiotic divisions, suggesting that the transcriptomic and morphological changes might be related to defects in the morphogenesis of structural features of the developing asci and ascospores.
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Affiliation(s)
- Ramona Lütkenhaus
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum 44801, Germany
| | - Jan Breuer
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum 44801, Germany
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum 44801, Germany
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29
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Fischer V, Plassard D, Ye T, Reina-San-Martin B, Stierle M, Tora L, Devys D. The related coactivator complexes SAGA and ATAC control embryonic stem cell self-renewal through acetyltransferase-independent mechanisms. Cell Rep 2021; 36:109598. [PMID: 34433046 PMCID: PMC8430043 DOI: 10.1016/j.celrep.2021.109598] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/17/2021] [Accepted: 08/03/2021] [Indexed: 01/10/2023] Open
Abstract
SAGA (Spt-Ada-Gcn5 acetyltransferase) and ATAC (Ada-two-A-containing) are two related coactivator complexes, sharing the same histone acetyltransferase (HAT) subunit. The HAT activities of SAGA and ATAC are required for metazoan development, but the role of these complexes in RNA polymerase II transcription is less understood. To determine whether SAGA and ATAC have redundant or specific functions, we compare the effects of HAT inactivation in each complex with that of inactivation of either SAGA or ATAC core subunits in mouse embryonic stem cells (ESCs). We show that core subunits of SAGA or ATAC are required for complex assembly and mouse ESC growth and self-renewal. Surprisingly, depletion of HAT module subunits causes a global decrease in histone H3K9 acetylation, but does not result in significant phenotypic or transcriptional defects. Thus, our results indicate that SAGA and ATAC are differentially required for self-renewal of mouse ESCs by regulating transcription through different pathways in a HAT-independent manner.
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Affiliation(s)
- Veronique Fischer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Damien Plassard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France; Plateforme GenomEast, infrastructure France Génomique, Illkirch, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France; Plateforme GenomEast, infrastructure France Génomique, Illkirch, France
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Matthieu Stierle
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Laszlo Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France.
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Miao J, Wang C, Lucky AB, Liang X, Min H, Adapa SR, Jiang R, Kim K, Cui L. A unique GCN5 histone acetyltransferase complex controls erythrocyte invasion and virulence in the malaria parasite Plasmodium falciparum. PLoS Pathog 2021; 17:e1009351. [PMID: 34403450 PMCID: PMC8396726 DOI: 10.1371/journal.ppat.1009351] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 08/27/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
The histone acetyltransferase GCN5-associated SAGA complex is evolutionarily conserved from yeast to human and functions as a general transcription co-activator in global gene regulation. In this study, we identified a divergent GCN5 complex in Plasmodium falciparum, which contains two plant homeodomain (PHD) proteins (PfPHD1 and PfPHD2) and a plant apetela2 (AP2)-domain transcription factor (PfAP2-LT). To dissect the functions of the PfGCN5 complex, we generated parasite lines with either the bromodomain in PfGCN5 or the PHD domain in PfPHD1 deleted. The two deletion mutants closely phenocopied each other, exhibiting significantly reduced merozoite invasion of erythrocytes and elevated sexual conversion. These domain deletions caused dramatic decreases not only in histone H3K9 acetylation but also in H3K4 trimethylation, indicating synergistic crosstalk between the two euchromatin marks. Domain deletion in either PfGCN5 or PfPHD1 profoundly disturbed the global transcription pattern, causing altered expression of more than 60% of the genes. At the schizont stage, these domain deletions were linked to specific down-regulation of merozoite genes involved in erythrocyte invasion, many of which contain the AP2-LT binding motif and are also regulated by AP2-I and BDP1, suggesting targeted recruitment of the PfGCN5 complex to the invasion genes by these specific factors. Conversely, at the ring stage, PfGCN5 or PfPHD1 domain deletions disrupted the mutually exclusive expression pattern of the entire var gene family, which encodes the virulent factor PfEMP1. Correlation analysis between the chromatin state and alteration of gene expression demonstrated that up- and down-regulated genes in these mutants are highly correlated with the silent and active chromatin states in the wild-type parasite, respectively. Collectively, the PfGCN5 complex represents a novel HAT complex with a unique subunit composition including an AP2 transcription factor, which signifies a new paradigm for targeting the co-activator complex to regulate general and parasite-specific cellular processes in this low-branching parasitic protist. Epigenetic regulation of gene expression plays essential roles in orchestrating the general and parasite-specific cellular pathways in the malaria parasite Plasmodium falciparum. To better understand the epigenetic mechanisms in this parasite, we characterized the histone acetyltransferase GCN5-mediated transcription regulation during intraerythrocytic development of the parasite. Using tandem affinity purification and proteomic characterization, we identified that the PfGCN5-associated complex contains nine core components, including two PHD domain proteins (PfPHD1 and PfPHD2) and an AP2-domain transcription factor, which is divergent from the canonical GCN5 complexes evolutionarily conserved from yeast to human. To understand the functions of the PfGCN5 complex, we performed domain deletions in two subunits of this complex, PfGCN5 and PfPHD1. We found that the two deletion mutants displayed very similar growth phenotypes, including significantly reduced merozoite invasion rates and elevated sexual conversion. These two mutants were associated with dramatic decreases in histone H3K9 acetylation and H3K4 trimethylation, which led to global changes in chromatin states and gene expression. Consistent with the phenotypes, genes significantly affected by the PfGCN5 and PfPHD1 gene disruption include those participating in parasite-specific pathways such as invasion, virulence, and sexual development. In conclusion, this study presents a new model of the PfGCN5 complex for targeting the co-activator complex to regulate general and parasite-specific cellular processes in this low-branching parasitic protist.
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Affiliation(s)
- Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- * E-mail: (JM); (LC)
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Amuza Byaruhanga Lucky
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Xiaoying Liang
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Hui Min
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Swamy Rakesh Adapa
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Rays Jiang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Kami Kim
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- * E-mail: (JM); (LC)
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Wu CJ, Liu ZZ, Wei L, Zhou JX, Cai XW, Su YN, Li L, Chen S, He XJ. Three functionally redundant plant-specific paralogs are core subunits of the SAGA histone acetyltransferase complex in Arabidopsis. MOLECULAR PLANT 2021; 14:1071-1087. [PMID: 33737195 DOI: 10.1016/j.molp.2021.03.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/25/2021] [Accepted: 03/12/2021] [Indexed: 05/29/2023]
Abstract
The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is an evolutionarily conserved histone acetyltransferase complex that has a critical role in histone acetylation, gene expression, and various developmental processes in eukaryotes. However, little is known about the composition and function of the SAGA complex in plants. In this study, we found that the SAGA complex in Arabidopsis thaliana contains not only conserved subunits but also four plant-specific subunits: three functionally redundant paralogs, SCS1, SCS2A, and SCS2B (SCS1/2A/2B), and a TAF-like subunit, TAFL. Mutations in SCS1/2A/2B lead to defective phenotypes similar to those caused by mutations in the genes encoding conserved SAGA subunits HAG1 and ADA2B, including delayed juvenile-to-adult phase transition, late flowering, and increased trichome density. Furthermore, we demonstrated that SCS1/2A/2B are required for the function of the SAGA complex in histone acetylation, thereby promoting the transcription of development-related genes. These results together suggest that SCS1/2A/2B are core subunits of the SAGA complex in Arabidopsis. Compared with SAGA complexes in other eukaryotes, the SAGA complexes in plants have evolved unique features that are necessary for normal growth and development.
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Affiliation(s)
- Chan-Juan Wu
- College of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Zhen-Zhen Liu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Long Wei
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jin-Xing Zhou
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- College of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 10084, China
| | - Xin-Jian He
- College of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 10084, China.
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32
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Dong J, LeBlanc C, Poulet A, Mermaz B, Villarino G, Webb KM, Joly V, Mendez J, Voigt P, Jacob Y. H3.1K27me1 maintains transcriptional silencing and genome stability by preventing GCN5-mediated histone acetylation. THE PLANT CELL 2021; 33:961-979. [PMID: 33793815 PMCID: PMC8226292 DOI: 10.1093/plcell/koaa027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/25/2020] [Indexed: 05/17/2023]
Abstract
Epigenetic mechanisms play diverse roles in the regulation of genome stability in eukaryotes. In Arabidopsis thaliana, genome stability is maintained during DNA replication by the H3.1K27 methyltransferases ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) and ATXR6, which catalyze the deposition of K27me1 on replication-dependent H3.1 variants. The loss of H3.1K27me1 in atxr5 atxr6 double mutants leads to heterochromatin defects, including transcriptional de-repression and genomic instability, but the molecular mechanisms involved remain largely unknown. In this study, we identified the transcriptional co-activator and conserved histone acetyltransferase GCN5 as a mediator of transcriptional de-repression and genomic instability in the absence of H3.1K27me1. GCN5 is part of a SAGA-like complex in plants that requires the GCN5-interacting protein ADA2b and the chromatin remodeler CHR6 to mediate the heterochromatic defects in atxr5 atxr6 mutants. Our results also indicate that Arabidopsis GCN5 acetylates multiple lysine residues on H3.1 variants, but H3.1K27 and H3.1K36 play essential functions in inducing genomic instability in the absence of H3.1K27me1. Finally, we show that H3.1K36 acetylation by GCN5 is negatively regulated by H3.1K27me1 in vitro. Overall, this work reveals a key molecular role for H3.1K27me1 in maintaining transcriptional silencing and genome stability in heterochromatin by restricting GCN5-mediated histone acetylation in plants.
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Affiliation(s)
- Jie Dong
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Chantal LeBlanc
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Axel Poulet
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Benoit Mermaz
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Gonzalo Villarino
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Kimberly M Webb
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF
| | - Valentin Joly
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Josefina Mendez
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF
| | - Yannick Jacob
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
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Kohli S, Gulati P, Narang A, Maini J, Shamsudheen KV, Pandey R, Scaria V, Sivasubbu S, Brahmachari V. Genome and transcriptome analysis of the mealybug Maconellicoccus hirsutus: Correlation with its unique phenotypes. Genomics 2021; 113:2483-2494. [PMID: 34022346 DOI: 10.1016/j.ygeno.2021.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 04/02/2021] [Accepted: 05/17/2021] [Indexed: 11/27/2022]
Abstract
Mealybugs are aggressive pests with world-wide distribution and are suitable for the study of different phenomena like genomic imprinting and epigenetics. Genomic approaches facilitate these studies in absence of robust genetics in this system. We sequenced, de novo assembled, annotated Maconellicoccus hirsutus genome. We carried out comparative genomics it with four mealybug and eight other insect species, to identify expanded, specific and contracted gene classes that relate to pesticide and desiccation resistance. We identified horizontally transferred genes adding to the mutualism between the mealybug and its endosymbionts. Male and female transcriptome analysis indicates differential expression of metabolic pathway genes correlating with their physiology and the genes for sexual dimorphism. The significantly lower expression of endosymbiont genes in males relates to the depletion of endosymbionts in males during development.
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Affiliation(s)
- Surbhi Kohli
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Parul Gulati
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Ankita Narang
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India.
| | - Jayant Maini
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - K V Shamsudheen
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Vani Brahmachari
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India.
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Interplay between transcriptional regulators and the SAGA chromatin modifying complex fine-tune iron homeostasis. J Biol Chem 2021; 297:100727. [PMID: 33933457 PMCID: PMC8217685 DOI: 10.1016/j.jbc.2021.100727] [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: 03/02/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 11/20/2022] Open
Abstract
The human fungal pathogen Candida albicans responds to iron deprivation by a global transcriptome reconfiguration known to be controlled by the transcriptional regulators Hap43 (also known as Cap2), Sef1, and the trimeric Hap2-Hap3-Hap5 complex. However, the relative roles of these regulators are not known. To dissect this system, we focused on the FRP1 and ACO1 genes, which are induced and repressed, respectively, under iron deprivation conditions. Chromatin immunoprecipitation assays showed that the trimeric HAP complex and Sef1 are recruited to both FRP1 and ACO1 promoters. While the HAP complex occupancy at the FRP1 promoter was Sef1-dependent, occupancy of Sef1 was not dependent on the HAP complex. Furthermore, iron deprivation elicited histone H3-Lys9 hyperacetylation and Pol II recruitment mediated by the trimeric HAP complex and Sef1 at the FRP1 promoter. In contrast, at the ACO1 promoter, the HAP trimeric complex and Hap43 promoted histone deacetylation and also limited Pol II recruitment under iron deprivation conditions. Mutational analysis showed that the SAGA subunits Gcn5, Spt7, and Spt20 are required for C. albicans growth in iron-deficient medium and for H3-K9 acetylation and transcription from the FRP1 promoter. Thus, the trimeric HAP complex promotes FRP1 transcription by stimulating H3K9Ac and Pol II recruitment and, along with Hap43, functions as a repressor of ACO1 by maintaining a deacetylated promoter under iron-deficient conditions. Thus, a regulatory network involving iron-responsive transcriptional regulators and the SAGA histone modifying complex functions as a molecular switch to fine-tune tight control of iron homeostasis gene expression in C. albicans.
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Fang Z, Wang X, Sun X, Hu W, Miao QR. The Role of Histone Protein Acetylation in Regulating Endothelial Function. Front Cell Dev Biol 2021; 9:672447. [PMID: 33996829 PMCID: PMC8113824 DOI: 10.3389/fcell.2021.672447] [Citation(s) in RCA: 16] [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: 02/25/2021] [Accepted: 04/06/2021] [Indexed: 12/16/2022] Open
Abstract
Endothelial cell (EC), consisting of the innermost cellular layer of all types of vessels, is not only a barrier composer but also performing multiple functions in physiological processes. It actively controls the vascular tone and the extravasation of water, solutes, and macromolecules; modulates circulating immune cells as well as platelet and leukocyte recruitment/adhesion and activation. In addition, EC also tightly keeps coagulation/fibrinolysis balance and plays a major role in angiogenesis. Therefore, endothelial dysfunction contributes to the pathogenesis of many diseases. Growing pieces of evidence suggest that histone protein acetylation, an epigenetic mark, is altered in ECs under different conditions, and the acetylation status change at different lysine sites on histone protein plays a key role in endothelial dysfunction and involved in hyperglycemia, hypertension, inflammatory disease, cancer and so on. In this review, we highlight the importance of histone acetylation in regulating endothelial functions and discuss the roles of histone acetylation across the transcriptional unit of protein-coding genes in ECs under different disease-related pathophysiological processes. Since histone acetylation changes are conserved and reversible, the knowledge of histone acetylation in endothelial function regulation could provide insights to develop epigenetic interventions in preventing or treating endothelial dysfunction-related diseases.
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Affiliation(s)
- Zhi Fang
- Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, NY, United States
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Xiang Wang
- Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, NY, United States
| | - Xiaoran Sun
- Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, NY, United States
| | - Wenquan Hu
- Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, NY, United States
| | - Qing R. Miao
- Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, NY, United States
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36
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Mark KG, Rape M. Ubiquitin-dependent regulation of transcription in development and disease. EMBO Rep 2021; 22:e51078. [PMID: 33779035 DOI: 10.15252/embr.202051078] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/29/2020] [Accepted: 03/01/2021] [Indexed: 12/19/2022] Open
Abstract
Transcription is an elaborate process that is required to establish and maintain the identity of the more than two hundred cell types of a metazoan organism. Strict regulation of gene expression is therefore vital for tissue formation and homeostasis. An accumulating body of work found that ubiquitylation of histones, transcription factors, or RNA polymerase II is crucial for ensuring that transcription occurs at the right time and place during development. Here, we will review principles of ubiquitin-dependent control of gene expression and discuss how breakdown of these regulatory circuits leads to a wide array of human diseases.
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Affiliation(s)
- Kevin G Mark
- Department of Molecular Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Michael Rape
- Department of Molecular Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
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Vlachonasios K, Poulios S, Mougiou N. The Histone Acetyltransferase GCN5 and the Associated Coactivators ADA2: From Evolution of the SAGA Complex to the Biological Roles in Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:308. [PMID: 33562796 PMCID: PMC7915528 DOI: 10.3390/plants10020308] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 01/08/2023]
Abstract
Transcription of protein-encoding genes starts with forming a pre-initiation complex comprised of RNA polymerase II and several general transcription factors. To activate gene expression, transcription factors must overcome repressive chromatin structure, which is accomplished with multiprotein complexes. One such complex, SAGA, modifies the nucleosomal histones through acetylation and other histone modifications. A prototypical histone acetyltransferase (HAT) known as general control non-repressed protein 5 (GCN5), was defined biochemically as the first transcription-linked HAT with specificity for histone H3 lysine 14. In this review, we analyze the components of the putative plant SAGA complex during plant evolution, and current knowledge on the biological role of the key components of the HAT module, GCN5 and ADA2b in plants, will be summarized.
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Affiliation(s)
- Konstantinos Vlachonasios
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.P.); (N.M.)
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Culbertson SJ, Shogren-Knaak MA. Mechanisms of stimulation of SAGA-mediated nucleosome acetylation by a transcriptional activator. Biochem Biophys Rep 2021; 25:100884. [PMID: 33437882 PMCID: PMC7786029 DOI: 10.1016/j.bbrep.2020.100884] [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: 01/07/2020] [Revised: 11/06/2020] [Accepted: 12/18/2020] [Indexed: 12/02/2022] Open
Abstract
Eukaryotic gene expression requires the coordination of multiple factors to overcome the repressive nature of chromatin. However, the mechanistic details of this coordination are not well understood. The SAGA family of transcriptional coactivators interacts with DNA-binding activators to establish regions of hyperacetylation. We have previously shown that, contrary to the prevailing model in which activator protein increases SAGA affinity for nucleosome substrate, the Gal4-VP16 activator model system augments the rate of acetylation turnover for the SAGA complex from budding yeast. To better understand how this stimulation occurs, we have identified necessary components using both kinetics assays and binding interactions studies. We find that Gal4-VP16-mediated stimulation requires activator binding to DNA flanking the nucleosome, as it cannot be reproduced in trans by activator protein alone or by exogenous DNA containing the activator binding site in combination with the activator protein. Further, activator-mediated stimulation requires subunits outside of the histone acetylation (HAT) module, with the Tra1 subunit being responsible for the majority of the stimulation. Interestingly, for the HAT module alone, nucleosome acetylation is inhibited by activator proteins due to non-specific binding of the activator to the nucleosomes. This inhibition is not observed for the yeast ADA complex, a small complex comprised mostly of the HAT module, suggesting that subunits outside of the HAT module in both it and SAGA can overcome non-specific activator binding to nucleosomes. However, this activity appears distinct from activator-mediated stimulation, as ADA complex acetylation is not stimulated by Gal4-VP16. Stimulation of nucleosome acetylation by SAGA requires activator in cis Tra1 mediates the majority of activator stimulation The core HAT complex of SAGA is inhibited by activator due to non-specific binding The related ADA complex is neither stimulated nor inhibited by activator
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Affiliation(s)
- Sannie J Culbertson
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, United States
| | - Michael A Shogren-Knaak
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, United States
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Nuño-Cabanes C, García-Molinero V, Martín-Expósito M, Gas ME, Oliete-Calvo P, García-Oliver E, de la Iglesia-Vayá M, Rodríguez-Navarro S. SAGA-CORE subunit Spt7 is required for correct Ubp8 localization, chromatin association and deubiquitinase activity. Epigenetics Chromatin 2020; 13:46. [PMID: 33115507 PMCID: PMC7594455 DOI: 10.1186/s13072-020-00367-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023] Open
Abstract
Background Histone H2B deubiquitination is performed by numerous deubiquitinases in eukaryotic cells including Ubp8, the catalytic subunit of the tetrameric deubiquitination module (DUBm: Ubp8; Sus1; Sgf11; Sgf73) of the Spt-Ada-Gcn5 acetyltransferase (SAGA). Ubp8 is linked to the rest of SAGA through Sgf73 and is activated by the adaptors Sus1 and Sgf11. It is unknown if DUBm/Ubp8 might also work in a SAGA-independent manner. Results Here we report that a tetrameric DUBm is assembled independently of the SAGA–CORE components SPT7, ADA1 and SPT20. In the absence of SPT7, i.e., independent of the SAGA complex, Ubp8 and Sus1 are poorly recruited to SAGA-dependent genes and to chromatin. Notably, cells lacking Spt7 or Ada1, but not Spt20, show lower levels of nuclear Ubp8 than wild-type cells, suggesting a possible role for SAGA–CORE subunits in Ubp8 localization. Last, deletion of SPT7 leads to defects in Ubp8 deubiquitinase activity in in vivo and in vitro assays. Conclusions Collectively, our studies show that the DUBm tetrameric structure can form without a complete intact SAGA–CORE complex and that it includes full-length Sgf73. However, subunits of this SAGA–CORE influence DUBm association with chromatin, its localization and its activity.
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Affiliation(s)
- Carme Nuño-Cabanes
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), C/Jaume Roig 11, 46010, Valencia, Spain.,Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), C/E. Primo Yúfera 3, 46012, Valencia, Spain
| | - Varinia García-Molinero
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), C/E. Primo Yúfera 3, 46012, Valencia, Spain
| | - Manuel Martín-Expósito
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), C/Jaume Roig 11, 46010, Valencia, Spain.,Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), C/E. Primo Yúfera 3, 46012, Valencia, Spain
| | - María-Eugenia Gas
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), C/E. Primo Yúfera 3, 46012, Valencia, Spain
| | - Paula Oliete-Calvo
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), C/E. Primo Yúfera 3, 46012, Valencia, Spain
| | - Encar García-Oliver
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), C/E. Primo Yúfera 3, 46012, Valencia, Spain
| | - María de la Iglesia-Vayá
- Brain Connectivity Lab. Joint Unit FISABIO & Centro de Investigación Príncipe Felipe (CIPF), C/E. Primo Yúfera 3, 46012, Valencia, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), C/Jaume Roig 11, 46010, Valencia, Spain. .,Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), C/E. Primo Yúfera 3, 46012, Valencia, Spain.
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Arede L, Pina C. Buffering noise: KAT2A modular contributions to stabilization of transcription and cell identity in cancer and development. Exp Hematol 2020; 93:25-37. [PMID: 33223444 DOI: 10.1016/j.exphem.2020.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023]
Abstract
KAT2A is a histone acetyltransferase recently identified as a vulnerability in at least some forms of Acute Myeloid Leukemia (AML). Its loss or inhibition prompts leukemia stem cells out of self-renewal and into differentiation with ultimate exhaustion of the leukemia pool. We have recently linked the Kat2a requirement in AML to control of transcriptional noise, reflecting an evolutionary-conserved role of Kat2a in promoting burst-like promoter activity and stabilizing gene expression. We suggest that through this role, Kat2a contributes to preservation of cell identity. KAT2A exerts its acetyltransferase activity in the context of two macromolecular complexes, Spt-Ada-Gcn5-Acetyltransferase (SAGA) and Ada-Two-A-Containing (ATAC), but the specific contribution of each complex to stabilization of gene expression is currently unknown. By reviewing specific gene targets and requirements of the two complexes in cancer and development, we suggest that SAGA regulates lineage-specific programs, and ATAC maintains biosynthetic activity through control of ribosomal protein and translation-associated genes, on which cells may be differentially dependent. While our data suggest that KAT2A-mediated regulation of transcriptional noise in AML may be exerted through ATAC, we discuss potential caveats and probe general vs. complex-specific contributions of KAT2A to transcriptional stability, with implications for control and perturbation of cell identity.
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Affiliation(s)
- Liliana Arede
- Departments of Haematology; Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Cristina Pina
- College of Health, Medicine and Life Sciences - Life Sciences, Division of Biosciences, Brunel University London, Uxbridge, UB8 3PH, United Kingdom.
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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease. Nat Genet 2020; 52:1024-1035. [PMID: 32989324 PMCID: PMC8098004 DOI: 10.1038/s41588-020-0696-0] [Citation(s) in RCA: 186] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 08/20/2020] [Indexed: 12/19/2022]
Abstract
Protein aggregation is the hallmark of neurodegeneration but the molecular mechanisms underlying late-onset Alzheimer’s disease (AD) remain unclear. Here we integrated transcriptomic, proteomic and epigenomic analyses of post-mortem human brains to identify molecular pathways involved in AD. RNA-seq analysis revealed upregulation of transcription- and chromatin-related genes, including the histone acetyltransferases for H3K27ac and H3K9ac. An unbiased proteomic screening singled out H3K27ac and H3K9ac as main enrichments specific to AD. In turn, epigenomic profiling revealed gains of H3K27ac and H3K9ac linked to transcription, chromatin, and disease pathways in AD. Increasing genome-wide H3K27ac and H3K9ac in a fly model of AD exacerbated amyloid-β42-driven neurodegeneration. Together, these findings suggest that AD involves a reconfiguration of the epigenome, where H3K27ac and H3K9ac impact disease pathways by dysregulating transcription- and chromatin-gene feedback loops. The identification of this process highlights potential epigenetic strategies for early-stage disease treatment.
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42
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What do the structures of GCN5-containing complexes teach us about their function? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194614. [PMID: 32739556 DOI: 10.1016/j.bbagrm.2020.194614] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
Abstract
Transcription initiation is a major regulatory step in eukaryotic gene expression. It involves the assembly of general transcription factors and RNA polymerase II into a functional pre-initiation complex at core promoters. The degree of chromatin compaction controls the accessibility of the transcription machinery to template DNA. Co-activators have critical roles in this process by actively regulating chromatin accessibility. Many transcriptional coactivators are multisubunit complexes, organized into distinct structural and functional modules and carrying multiple regulatory activities. The first nuclear histone acetyltransferase (HAT) characterized was General Control Non-derepressible 5 (Gcn5). Gcn5 was subsequently identified as a subunit of the HAT module of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex, which is an experimental paradigm for multifunctional co-activators. We know today that Gcn5 is the catalytic subunit of multiple distinct co-activator complexes with specific functions. In this review, we summarize recent advances in the structure of Gcn5-containing co-activator complexes, most notably SAGA, and discuss how these new structural insights contribute to better understand their functions.
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43
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Grasser KD, Rubio V, Barneche F. Multifaceted activities of the plant SAGA complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194613. [PMID: 32745625 DOI: 10.1016/j.bbagrm.2020.194613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022]
Abstract
From yeast to human, the Spt-Ada-GCN5-acetyltransferase (SAGA) gigantic complex modifies chromatin during RNA polymerase II initiation and elongation steps to facilitate transcription. Its enzymatic activity involves a histone acetyltransferase module (HATm) that acetylates multiple lysine residues on the N-terminal tails of histones H2B and H3 and a deubiquitination module (DUBm) that triggers co-transcriptional deubiquitination of histone H2B. With a few notable exceptions described in this review, most SAGA subunits identified in yeast and metazoa are present in plants. Studies from the last 20 years have unveiled that different SAGA subunits are involved in gene expression regulation during the plant life cycle and in response to various types of stress or environmental cues. Their functional analysis in the Arabidopsis thaliana model species is increasingly shedding light on their intrinsic properties and how they can themselves be regulated during plant adaptive responses. Recent biochemical studies have also uncovered multiple associations between plant SAGA and chromatin machineries linked to RNA Pol II transcription. Still, considerably less is known about the molecular links between SAGA or SAGA-like complexes and chromatin dynamics during transcription in Arabidopsis and other plant species. We summarize the emerging knowledge on plant SAGA complex composition and activity, with a particular focus on the best-characterized subunits from its HAT (such as GCN5) and DUB (such as UBP22) modules, and implication of these ensembles in plant development and adaptive responses.
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Affiliation(s)
- Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany.
| | - Vicente Rubio
- Plant Molecular Genetics Dept., Centro Nacional de Biotecnología (CNB-CSIC), Darwin, 3, 28049 Madrid, Spain.
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
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Torres-Zelada EF, Weake VM. The Gcn5 complexes in Drosophila as a model for metazoa. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194610. [PMID: 32735945 DOI: 10.1016/j.bbagrm.2020.194610] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 01/14/2023]
Abstract
The histone acetyltransferase Gcn5 is conserved throughout eukaryotes where it functions as part of large multi-subunit transcriptional coactivator complexes that stimulate gene expression. Here, we describe how studies in the model insect Drosophila melanogaster have provided insight into the essential roles played by Gcn5 in the development of multicellular organisms. We outline the composition and activity of the four different Gcn5 complexes in Drosophila: the Spt-Ada-Gcn5 Acetyltransferase (SAGA), Ada2a-containing (ATAC), Ada2/Gcn5/Ada3 transcription activator (ADA), and Chiffon Histone Acetyltransferase (CHAT) complexes. Whereas the SAGA and ADA complexes are also present in the yeast Saccharomyces cerevisiae, ATAC has only been identified in other metazoa such as humans, and the CHAT complex appears to be unique to insects. Each of these Gcn5 complexes is nucleated by unique Ada2 homologs or splice isoforms that share conserved N-terminal domains, and differ only in their C-terminal domains. We describe the common and specialized developmental functions of each Gcn5 complex based on phenotypic analysis of mutant flies. In addition, we outline how gene expression studies in mutant flies have shed light on the different biological roles of each complex. Together, these studies highlight the key role that Drosophila has played in understanding the expanded biological function of Gcn5 in multicellular eukaryotes.
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Affiliation(s)
| | - Vikki M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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45
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Non-histone protein acetylation by the evolutionarily conserved GCN5 and PCAF acetyltransferases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194608. [PMID: 32711095 DOI: 10.1016/j.bbagrm.2020.194608] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/08/2023]
Abstract
GCN5, conserved from yeast to humans, and the vertebrate specific PCAF, are lysine acetyltransferase enzymes found in large protein complexes. Both enzymes have well documented roles in the histone acetylation and the concomitant regulation of transcription. However, these enzymes also acetylate non-histone substrates to impact diverse aspects of cell physiology. Here, I review our current understanding of non-histone acetylation by GCN5 and PCAF across eukaryotes, from target identification to molecular mechanism and regulation. I focus mainly on budding yeast, where Gcn5 was first discovered, and mammalian systems, where the bulk of non-histone substrates have been characterized. I end the review by defining critical caveats and open questions that apply to all models.
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46
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Timmers HTM. SAGA and TFIID: Friends of TBP drifting apart. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194604. [PMID: 32673655 DOI: 10.1016/j.bbagrm.2020.194604] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/24/2023]
Abstract
Transcription initiation constitutes a major checkpoint in gene regulation across all living organisms. Control of chromatin function is tightly linked to this checkpoint, which is best illustrated by the SAGA coactivator. This evolutionary conserved complex of 18-20 subunits was first discovered as a Gcn5p-containing histone acetyltransferase, but it also integrates a histone H2B deubiquitinase. The SAGA subunits are organized in a modular fashion around its central core. Strikingly, this central module of SAGA shares a number of proteins with the central core of the basal transcription factor TFIID. In this review I will compare the SAGA and TFIID complexes with respect to their shared subunits, structural organization, enzymatic activities and chromatin binding. I will place a special emphasis on the ancestry of SAGA and TFIID subunits, which suggests that these complexes evolved to control the activity of TBP (TATA-binding protein) in directing the assembly of transcription initiation complexes.
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Affiliation(s)
- H Th Marc Timmers
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK) partner site Freiburg, 79106 Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Breisacher Straße 66, 79106 Freiburg, Germany.
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47
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Cheon Y, Kim H, Park K, Kim M, Lee D. Dynamic modules of the coactivator SAGA in eukaryotic transcription. Exp Mol Med 2020; 52:991-1003. [PMID: 32616828 PMCID: PMC8080568 DOI: 10.1038/s12276-020-0463-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 02/08/2023] Open
Abstract
SAGA (Spt-Ada-Gcn5 acetyltransferase) is a highly conserved transcriptional coactivator that consists of four functionally independent modules. Its two distinct enzymatic activities, histone acetylation and deubiquitylation, establish specific epigenetic patterns on chromatin and thereby regulate gene expression. Whereas earlier studies emphasized the importance of SAGA in regulating global transcription, more recent reports have indicated that SAGA is involved in other aspects of gene expression and thus plays a more comprehensive role in regulating the overall process. Here, we discuss recent structural and functional studies of each SAGA module and compare the subunit compositions of SAGA with related complexes in yeast and metazoans. We discuss the regulatory role of the SAGA deubiquitylating module (DUBm) in mRNA surveillance and export, and in transcription initiation and elongation. The findings suggest that SAGA plays numerous roles in multiple stages of transcription. Further, we describe how SAGA is related to human disease. Overall, in this report, we illustrate the newly revealed understanding of SAGA in transcription regulation and disease implications for fine-tuning gene expression. A protein that helps add epigenetic information to genome, SAGA, controls many aspects of gene activation, potentially making it a target for cancer therapies. To fit inside the tiny cell nucleus, the genome is tightly packaged, and genes must be unpacked before they can be activated. Known to be important in genome opening, SAGA has now been shown to also play many roles in gene activation. Daeyoup Lee at the KAIST, Daejeon, South Korea, and co-workers have reviewed recent discoveries about SAGA’s structure, function, and roles in disease. They report that SAGA’s complex (19 subunits organized into four modules) allows it to play so many roles, genome opening, initiating transcription, and efficiently exporting mRNAs. Its master role means that malfunction of SAGA may be linked to many diseases.
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Affiliation(s)
- Youngseo Cheon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Harim Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Kyubin Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Minhoo Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea.
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Niewiadomska-Cimicka A, Hache A, Trottier Y. Gene Deregulation and Underlying Mechanisms in Spinocerebellar Ataxias With Polyglutamine Expansion. Front Neurosci 2020; 14:571. [PMID: 32581696 PMCID: PMC7296114 DOI: 10.3389/fnins.2020.00571] [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: 04/07/2020] [Accepted: 05/11/2020] [Indexed: 12/14/2022] Open
Abstract
Polyglutamine spinocerebellar ataxias (polyQ SCAs) include SCA1, SCA2, SCA3, SCA6, SCA7, and SCA17 and constitute a group of adult onset neurodegenerative disorders caused by the expansion of a CAG repeat sequence located within the coding region of specific genes, which translates into polyglutamine tract in the corresponding proteins. PolyQ SCAs are characterized by degeneration of the cerebellum and its associated structures and lead to progressive ataxia and other diverse symptoms. In recent years, gene and epigenetic deregulations have been shown to play a critical role in the pathogenesis of polyQ SCAs. Here, we provide an overview of the functions of wild type and pathogenic polyQ SCA proteins in gene regulation, describe the extent and nature of gene expression changes and their pathological consequences in diseases, and discuss potential avenues to further investigate converging and distinct disease pathways and to develop therapeutic strategies.
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Affiliation(s)
- Anna Niewiadomska-Cimicka
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Antoine Hache
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Yvon Trottier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
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Iwami R, Takai N, Kokubo T. The function of Spt3, a subunit of the SAGA complex, in <i>PGK1</i> transcription is restored only partially when reintroduced by plasmid into <i>taf1 spt3</i> double mutant yeast strains. Genes Genet Syst 2020; 95:151-163. [DOI: 10.1266/ggs.20-00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Ryo Iwami
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University
| | - Naoki Takai
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University
| | - Tetsuro Kokubo
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University
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50
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The deubiquitinating enzyme MoUbp8 is required for infection-related development, pathogenicity, and carbon catabolite repression in Magnaporthe oryzae. Appl Microbiol Biotechnol 2020; 104:5081-5094. [PMID: 32274561 DOI: 10.1007/s00253-020-10572-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/29/2020] [Accepted: 03/22/2020] [Indexed: 12/22/2022]
Abstract
Deubiquitination is an essential regulatory step in the Ub-dependent pathway. Deubiquitinating enzymes (DUBs) mediate the removal of ubiquitin moieties from substrate proteins, which are involved in many regulatory mechanisms. As a component of the DUB module (Ubp8/Sgf11/Sus1/Sgf73) in the SAGA (Spt-Ada-Gcn5-acetyltransferase) complex, Ubp8 plays a crucial role in both Saccharomyces cerevisiae and humans. In S. cerevisiae, Ubp8-mediated deubiquitination regulates transcriptional activation processes. To investigate the contributions of Ubp8 to physiological and pathological development of filamentous fungi, we generated the deletion mutant of ortholog MoUBP8 (MGG-03527) in Magnaporthe oryzae (syn. Pyricularia oryzae). The ΔMoubp8 strain showed reduced sporulation, pathogenicity, and resistance to distinct stresses. Even though the conidia of the ΔMoubp8 mutant were delayed in appressorium formation, the normal and abnormal (none-septum or one-septum) conidia could finally form appressoria. Reduced melanin in the ΔMoubp8 mutant is highly responsible for the attenuated pathogenicity since the appressoria of the ΔMoubp8 mutant was much more fragile than those of the wild type, due to the defective turgidity. The weakened ability to detoxify or scavenge host-derived reactive oxygen species (ROS) further restricted the invasion of the pathogen. We also showed that carbon derepression, on the one hand, rendered the ΔMoubp8 strain highly sensitive to allyl alcohol, on the other hand, it enhances the resistance of the MoUBP8 defective strain to deoxyglucose. Overall, we suggest that MoUbp8 is not only required for sporulation, melanin formation, appressoria development, and pathogenicity but also involved in carbon catabolite repression of M. oryzae.
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