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Dhillon N, Kamakaka RT. Transcriptional silencing in Saccharomyces cerevisiae: known unknowns. Epigenetics Chromatin 2024; 17:28. [PMID: 39272151 PMCID: PMC11401328 DOI: 10.1186/s13072-024-00553-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024] Open
Abstract
Transcriptional silencing in Saccharomyces cerevisiae is a persistent and highly stable form of gene repression. It involves DNA silencers and repressor proteins that bind nucleosomes. The silenced state is influenced by numerous factors including the concentration of repressors, nature of activators, architecture of regulatory elements, modifying enzymes and the dynamics of chromatin.Silencers function to increase the residence time of repressor Sir proteins at silenced domains while clustering of silenced domains enables increased concentrations of repressors and helps facilitate long-range interactions. The presence of an accessible NDR at the regulatory regions of silenced genes, the cycling of chromatin configurations at regulatory sites, the mobility of Sir proteins, and the non-uniform distribution of the Sir proteins across the silenced domain, all result in silenced chromatin that only stably silences weak promoters and enhancers via changes in transcription burst duration and frequency.These data collectively suggest that silencing is probabilistic and the robustness of silencing is achieved through sub-optimization of many different nodes of action such that a stable expression state is generated and maintained even though individual constituents are in constant flux.
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Affiliation(s)
- Namrita Dhillon
- Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Rohinton T Kamakaka
- Department of MCD Biology, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA.
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2
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Liu Y, Zhou Z, Su H, Wu S, Ni G, Zhang A, Tsimring LS, Hasty J, Hao N. Enhanced cellular longevity arising from environmental fluctuations. Cell Syst 2024; 15:738-752.e5. [PMID: 39173586 PMCID: PMC11380573 DOI: 10.1016/j.cels.2024.07.007] [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: 07/01/2023] [Revised: 05/07/2024] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Cellular longevity is regulated by both genetic and environmental factors. However, the interactions of these factors in the context of aging remain largely unclear. Here, we formulate a mathematical model for dynamic glucose modulation of a core gene circuit in yeast aging, which not only guided the design of pro-longevity interventions but also revealed the theoretical principles underlying these interventions. We introduce the dynamical systems theory to capture two general means for promoting longevity-the creation of a stable fixed point in the "healthy" state of the cell and the "dynamic stabilization" of the system around this healthy state through environmental oscillations. Guided by the model, we investigate how both of these can be experimentally realized by dynamically modulating environmental glucose levels. The results establish a paradigm for theoretically analyzing the trajectories and perturbations of aging that can be generalized to aging processes in diverse cell types and organisms.
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Affiliation(s)
- Yuting Liu
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhen Zhou
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Hetian Su
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Songlin Wu
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gavin Ni
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alex Zhang
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lev S Tsimring
- Synthetic Biology Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Synthetic Biology Institute, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nan Hao
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Synthetic Biology Institute, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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3
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Bhunjun C, Chen Y, Phukhamsakda C, Boekhout T, Groenewald J, McKenzie E, Francisco E, Frisvad J, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie C, Bai F, Błaszkowski J, Braun U, de Souza F, de Queiroz M, Dutta A, Gonkhom D, Goto B, Guarnaccia V, Hagen F, Houbraken J, Lachance M, Li J, Luo K, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe D, Wang D, Wei D, Zhao C, Aiphuk W, Ajayi-Oyetunde O, Arantes T, Araujo J, Begerow D, Bakhshi M, Barbosa R, Behrens F, Bensch K, Bezerra J, Bilański P, Bradley C, Bubner B, Burgess T, Buyck B, Čadež N, Cai L, Calaça F, Campbell L, Chaverri P, Chen Y, Chethana K, Coetzee B, Costa M, Chen Q, Custódio F, Dai Y, Damm U, Santiago A, De Miccolis Angelini R, Dijksterhuis J, Dissanayake A, Doilom M, Dong W, Álvarez-Duarte E, Fischer M, Gajanayake A, Gené J, Gomdola D, Gomes A, Hausner G, He M, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena R, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin C, Liu J, Liu X, Loizides M, Luangharn T, Maharachchikumbura S, Mkhwanazi GM, Manawasinghe I, Marin-Felix Y, McTaggart A, Moreau P, Morozova O, Mostert L, Osiewacz H, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips A, Phonemany M, Promputtha I, Rathnayaka A, Rodrigues A, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe S, Scholler M, Scott P, Shivas R, Silar P, Silva-Filho A, Souza-Motta C, Spies C, Stchigel A, Sterflinger K, Summerbell R, Svetasheva T, Takamatsu S, Theelen B, Theodoro R, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang X, Wartchow F, Welti S, Wijesinghe S, Wu F, Xu R, Yang Z, Yilmaz N, Yurkov A, Zhao L, Zhao R, Zhou N, Hyde K, Crous P. What are the 100 most cited fungal genera? Stud Mycol 2024; 108:1-411. [PMID: 39100921 PMCID: PMC11293126 DOI: 10.3114/sim.2024.108.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/17/2024] [Indexed: 08/06/2024] Open
Abstract
The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research. Citation: Bhunjun CS, Chen YJ, Phukhamsakda C, Boekhout T, Groenewald JZ, McKenzie EHC, Francisco EC, Frisvad JC, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie CM, Bai FY, Błaszkowski J, Braun U, de Souza FA, de Queiroz MB, Dutta AK, Gonkhom D, Goto BT, Guarnaccia V, Hagen F, Houbraken J, Lachance MA, Li JJ, Luo KY, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe DN, Wang DQ, Wei DP, Zhao CL, Aiphuk W, Ajayi-Oyetunde O, Arantes TD, Araujo JC, Begerow D, Bakhshi M, Barbosa RN, Behrens FH, Bensch K, Bezerra JDP, Bilański P, Bradley CA, Bubner B, Burgess TI, Buyck B, Čadež N, Cai L, Calaça FJS, Campbell LJ, Chaverri P, Chen YY, Chethana KWT, Coetzee B, Costa MM, Chen Q, Custódio FA, Dai YC, Damm U, de Azevedo Santiago ALCM, De Miccolis Angelini RM, Dijksterhuis J, Dissanayake AJ, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake AJ, Gené J, Gomdola D, Gomes AAM, Hausner G, He MQ, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena RS, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin CG, Liu JK, Liu XB, Loizides M, Luangharn T, Maharachchikumbura SSN, Makhathini Mkhwanazi GJ, Manawasinghe IS, Marin-Felix Y, McTaggart AR, Moreau PA, Morozova OV, Mostert L, Osiewacz HD, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips AJL, Phonemany M, Promputtha I, Rathnayaka AR, Rodrigues AM, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe SJ, Scholler M, Scott P, Shivas RG, Silar P, Souza-Motta CM, Silva-Filho AGS, Spies CFJ, Stchigel AM, Sterflinger K, Summerbell RC, Svetasheva TY, Takamatsu S, Theelen B, Theodoro RC, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang XW, Wartchow F, Welti S, Wijesinghe SN, Wu F, Xu R, Yang ZL, Yilmaz N, Yurkov A, Zhao L, Zhao RL, Zhou N, Hyde KD, Crous PW (2024). What are the 100 most cited fungal genera? Studies in Mycology 108: 1-411. doi: 10.3114/sim.2024.108.01.
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Affiliation(s)
- C.S. Bhunjun
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Y.J. Chen
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - C. Phukhamsakda
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - T. Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- The Yeasts Foundation, Amsterdam, the Netherlands
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - E.H.C. McKenzie
- Landcare Research Manaaki Whenua, Private Bag 92170, Auckland, New Zealand
| | - E.C. Francisco
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Laboratório Especial de Micologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - V. G. Hurdeal
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - J. Luangsa-ard
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - G. Perrone
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), Via G. Amendola 122/O, 70126 Bari, Italy
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - F.Y. Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - J. Błaszkowski
- Laboratory of Plant Protection, Department of Shaping of Environment, West Pomeranian University of Technology in Szczecin, Słowackiego 17, PL-71434 Szczecin, Poland
| | - U. Braun
- Martin Luther University, Institute of Biology, Department of Geobotany and Botanical Garden, Neuwerk 21, 06099 Halle (Saale), Germany
| | - F.A. de Souza
- Núcleo de Biologia Aplicada, Embrapa Milho e Sorgo, Empresa Brasileira de Pesquisa Agropecuária, Rodovia MG 424 km 45, 35701–970, Sete Lagoas, MG, Brazil
| | - M.B. de Queiroz
- Programa de Pós-graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal-RN, 59078-970, Brazil
| | - A.K. Dutta
- Molecular & Applied Mycology Laboratory, Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati - 781014, Assam, India
| | - D. Gonkhom
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - B.T. Goto
- Programa de Pós-graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal-RN, 59078-970, Brazil
| | - V. Guarnaccia
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Braccini 2, 10095 Grugliasco, TO, Italy
| | - F. Hagen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - M.A. Lachance
- Department of Biology, University of Western Ontario London, Ontario, Canada N6A 5B7
| | - J.J. Li
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - K.Y. Luo
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - F. Magurno
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland
| | - S. Mongkolsamrit
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - V. Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - N. Roy
- Molecular & Applied Mycology Laboratory, Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati - 781014, Assam, India
| | - S. Tibpromma
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, P.R. China
| | - D.N. Wanasinghe
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, China
| | - D.Q. Wang
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - D.P. Wei
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China
| | - C.L. Zhao
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - W. Aiphuk
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - O. Ajayi-Oyetunde
- Syngenta Crop Protection, 410 S Swing Rd, Greensboro, NC. 27409, USA
| | - T.D. Arantes
- Laboratório de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, 74605-050, Goiânia, GO, Brazil
| | - J.C. Araujo
- Mykocosmos - Mycology and Science Communication, Rua JP 11 Qd. 18 Lote 13, Jd. Primavera 1ª etapa, Post Code 75.090-260, Anápolis, Goiás, Brazil
- Secretaria de Estado da Educação de Goiás (SEDUC/ GO), Quinta Avenida, Quadra 71, número 212, Setor Leste Vila Nova, Goiânia, Goiás, 74643-030, Brazil
| | - D. Begerow
- Organismic Botany and Mycology, Institute of Plant Sciences and Microbiology, Ohnhorststraße 18, 22609 Hamburg, Germany
| | - M. Bakhshi
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - R.N. Barbosa
- Micoteca URM-Department of Mycology Prof. Chaves Batista, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Center for Biosciences, University City, Recife, Pernambuco, Zip Code: 50670-901, Brazil
| | - F.H. Behrens
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - J.D.P. Bezerra
- Laboratório de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, 74605-050, Goiânia, GO, Brazil
| | - P. Bilański
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - C.A. Bradley
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445, USA
| | - B. Bubner
- Johan Heinrich von Thünen-Institut, Bundesforschungsinstitut für Ländliche Räume, Wald und Fischerei, Institut für Forstgenetik, Eberswalder Chaussee 3a, 15377 Waldsieversdorf, Germany
| | - T.I. Burgess
- Harry Butler Institute, Murdoch University, Murdoch, 6150, Australia
| | - B. Buyck
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 39, 75231, Paris cedex 05, France
| | - N. Čadež
- University of Ljubljana, Biotechnical Faculty, Food Science and Technology Department Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F.J.S. Calaça
- Mykocosmos - Mycology and Science Communication, Rua JP 11 Qd. 18 Lote 13, Jd. Primavera 1ª etapa, Post Code 75.090-260, Anápolis, Goiás, Brazil
- Secretaria de Estado da Educação de Goiás (SEDUC/ GO), Quinta Avenida, Quadra 71, número 212, Setor Leste Vila Nova, Goiânia, Goiás, 74643-030, Brazil
- Laboratório de Pesquisa em Ensino de Ciências (LabPEC), Centro de Pesquisas e Educação Científica, Universidade Estadual de Goiás, Campus Central (CEPEC/UEG), Anápolis, GO, 75132-903, Brazil
| | - L.J. Campbell
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - P. Chaverri
- Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, U.S.A
| | - Y.Y. Chen
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - K.W.T. Chethana
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - B. Coetzee
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- School for Data Sciences and Computational Thinking, University of Stellenbosch, South Africa
| | - M.M. Costa
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Q. Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F.A. Custódio
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - Y.C. Dai
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - U. Damm
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - A.L.C.M.A. Santiago
- Post-graduate course in the Biology of Fungi, Department of Mycology, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, 50740-465, Recife, PE, Brazil
| | | | - J. Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - A.J. Dissanayake
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - M. Doilom
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - W. Dong
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - E. Álvarez-Duarte
- Mycology Unit, Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile, Chile
| | - M. Fischer
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany
| | - A.J. Gajanayake
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - J. Gené
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
| | - D. Gomdola
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - A.A.M. Gomes
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife-PE, Brazil
| | - G. Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 5N6
| | - M.Q. He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - L. Hou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - I. Iturrieta-González
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
- Department of Preclinic Sciences, Medicine Faculty, Laboratory of Infectology and Clinical Immunology, Center of Excellence in Translational Medicine-Scientific and Technological Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile
| | - F. Jami
- Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa
| | - R. Jankowiak
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - R.S. Jayawardena
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, South Korea
| | - H. Kandemir
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - L. Kiss
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, QLD 4350 Toowoomba, Australia
- Centre for Research and Development, Eszterházy Károly Catholic University, H-3300 Eger, Hungary
| | - N. Kobmoo
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - T. Kowalski
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - L. Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - C.G. Lin
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - J.K. Liu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - X.B. Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Temesvári krt. 62, Szeged H-6726, Hungary
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | | | - T. Luangharn
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - S.S.N. Maharachchikumbura
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - G.J. Makhathini Mkhwanazi
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - I.S. Manawasinghe
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - Y. Marin-Felix
- Department Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - A.R. McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park 4102, Queensland, Australia
| | - P.A. Moreau
- Univ. Lille, ULR 4515 - LGCgE, Laboratoire de Génie Civil et géo-Environnement, F-59000 Lille, France
| | - O.V. Morozova
- Komarov Botanical Institute of the Russian Academy of Sciences, 2, Prof. Popov Str., 197376 Saint Petersburg, Russia
- Tula State Lev Tolstoy Pedagogical University, 125, Lenin av., 300026 Tula, Russia
| | - L. Mostert
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - H.D. Osiewacz
- Faculty for Biosciences, Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - D. Pem
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - R. Phookamsak
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, China
| | - S. Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - A. Pordel
- Plant Protection Research Department, Baluchestan Agricultural and Natural Resources Research and Education Center, AREEO, Iranshahr, Iran
| | - C. Poyntner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - A.J.L. Phillips
- Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| | - M. Phonemany
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - I. Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - A.R. Rathnayaka
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - G. Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - L. Rothmann
- Plant Pathology, Department of Plant Sciences, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa
| | - C. Salgado-Salazar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), 10300 Baltimore Avenue, Beltsville MD, 20705, USA
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - S.J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS Université de Bordeaux, 1 rue Camille Saint Saëns, 33077 Bordeaux cedex, France
| | - M. Scholler
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstraße 13, 76133 Karlsruhe, Germany
| | - P. Scott
- Harry Butler Institute, Murdoch University, Murdoch, 6150, Australia
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, Perth WA 6000, Australia
| | - R.G. Shivas
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, QLD 4350 Toowoomba, Australia
| | - P. Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université de Paris Cité, 75205 Paris Cedex, France
| | - A.G.S. Silva-Filho
- IFungiLab, Departamento de Ciências e Matemática (DCM), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), São Paulo, BraziI
| | - C.M. Souza-Motta
- Micoteca URM-Department of Mycology Prof. Chaves Batista, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Center for Biosciences, University City, Recife, Pernambuco, Zip Code: 50670-901, Brazil
| | - C.F.J. Spies
- Agricultural Research Council - Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, South Africa
| | - A.M. Stchigel
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
| | - K. Sterflinger
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Augasse 2–6, 1090, Vienna, Austria
| | - R.C. Summerbell
- Sporometrics, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - T.Y. Svetasheva
- Tula State Lev Tolstoy Pedagogical University, 125, Lenin av., 300026 Tula, Russia
| | - S. Takamatsu
- Mie University, Graduate School, Department of Bioresources, 1577 Kurima-Machiya, Tsu 514-8507, Japan
| | - B. Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - R.C. Theodoro
- Laboratório de Micologia Médica, Instituto de Medicina Tropical do RN, Universidade Federal do Rio Grande do Norte, 59078-900, Natal, RN, Brazil
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt Am Main, Germany
| | - N. Thongklang
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - R. Torres
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Agrobiotech de Lleida, Parc de Gardeny, 25003, Lleida, Catalonia, Spain
| | - B. Turchetti
- Department of Agricultural, Food and Environmental Sciences and DBVPG Industrial Yeasts Collection, University of Perugia, Italy
| | - T. van den Brule
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- TIFN, P.O. Box 557, 6700 AN Wageningen, the Netherlands
| | - X.W. Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F. Wartchow
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Paraiba, João Pessoa, Brazil
| | - S. Welti
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - S.N. Wijesinghe
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - F. Wu
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - R. Xu
- School of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China
| | - Z.L. Yang
- Syngenta Crop Protection, 410 S Swing Rd, Greensboro, NC. 27409, USA
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - L. Zhao
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - R.L. Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - N. Zhou
- Department of Biological Sciences and Biotechnology, Botswana University of Science and Technology, Private Bag, 16, Palapye, Botswana
| | - K.D. Hyde
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
- Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht
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4
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Wu K, Dhillon N, Bajor A, Abrahamsson S, Kamakaka RT. Yeast heterochromatin stably silences only weak regulatory elements by altering burst duration. Cell Rep 2024; 43:113983. [PMID: 38517895 PMCID: PMC11141299 DOI: 10.1016/j.celrep.2024.113983] [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: 08/24/2023] [Revised: 12/25/2023] [Accepted: 03/06/2024] [Indexed: 03/24/2024] Open
Abstract
Transcriptional silencing in Saccharomyces cerevisiae involves the generation of a chromatin state that stably represses transcription. Using multiple reporter assays, a diverse set of upstream activating sequence enhancers and core promoters were investigated for their susceptibility to silencing. We show that heterochromatin stably silences only weak and stress-induced regulatory elements but is unable to stably repress housekeeping gene regulatory elements, and the partial repression of these elements did not result in bistable expression states. Permutation analysis of enhancers and promoters indicates that both elements are targets of repression. Chromatin remodelers help specific regulatory elements to resist repression, most probably by altering nucleosome mobility and changing transcription burst duration. The strong enhancers/promoters can be repressed if silencer-bound Sir1 is increased. Together, our data suggest that the heterochromatic locus has been optimized to stably silence the weak mating-type gene regulatory elements but not strong housekeeping gene regulatory sequences.
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Affiliation(s)
- Kenneth Wu
- Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Namrita Dhillon
- Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Antone Bajor
- Electrical Engineering Department, Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Sara Abrahamsson
- Electrical Engineering Department, Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Rohinton T Kamakaka
- Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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5
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Ayano T, Yokosawa T, Oki M. GTP-dependent regulation of heterochromatin fluctuations at subtelomeric regions in Saccharomyces cerevisiae. Genes Cells 2024; 29:217-230. [PMID: 38229233 DOI: 10.1111/gtc.13094] [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: 10/13/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 01/18/2024]
Abstract
In eukaryotes, single cells in a population display different transcriptional profiles. One of the factors regulating this heterogeneity is the chromatin state in each cell. However, the mechanisms of epigenetic chromatin regulation of specific chromosomal regions remain unclear. Therefore, we used single-cell tracking system to analyze IMD2. IMD2 is located at the subtelomeric region of budding yeast, and its expression is epigenetically regulated by heterochromatin fluctuations. Treatment with mycophenolic acid, an inhibitor of de novo GTP biosynthesis, triggered a decrease in GTP, which caused heterochromatin fluctuations at the IMD2 locus. Interestingly, within individually tracked cells, IMD2 expression state underwent repeated switches even though IMD2 is positioned within the heterochromatin region. We also found that 30% of the cells in a population always expressed IMD2. Furthermore, the addition of nicotinamide, a histone deacetylase inhibitor, or guanine, the GTP biosynthesis factor in salvage pathway of GTP biosynthesis, regulated heterogeneity, resulting in IMD2 expression being uniformly induced or suppressed in the population. These results suggest that gene expression heterogeneity in the IMD2 region is regulated by changes in chromatin structure triggered by slight decreases in GTP.
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Affiliation(s)
- Takahito Ayano
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
- Research Fellowships of Japan Society for the Promotion of Science for Young Scientists (JSPS), Tokyo, Japan
| | - Takuma Yokosawa
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
| | - Masaya Oki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
- Life Science Innovation Center, University of Fukui, Fukui, Japan
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6
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Yeom S, Oh J, Kim D, Lee JS. The 80 th Threonine Residue of Histone H3 Is Important for Maintaining HM Silencing in Saccharomyces cerevisiae. J Microbiol Biotechnol 2024; 34:39-46. [PMID: 37957109 PMCID: PMC10840469 DOI: 10.4014/jmb.2310.10031] [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: 10/23/2023] [Revised: 11/02/2023] [Accepted: 11/08/2023] [Indexed: 11/15/2023]
Abstract
Gene expression in eukaryotic cells is intricately regulated by chromatin structure and various factors, including histone proteins. In Saccharomyces cerevisiae, transcriptionally silenced regions, such as telomeres and homothallic mating (HM) loci, are essential for genome stability and proper cellular function. We firstly observed the defective HM silencing in alanine substitution mutant of 80th threonine residue of histone H3 (H3T80A). To identify which properties in the H3T80 residue are important for the HM silencing, we created several substitution mutants of H3T80 residue by considering the changed states of charge, polarity, and structural similarity. This study reveals that the structural similarity of the 80th position of H3 to the threonine residue, not the polarity and charges, is the most important thing for the transcriptional silencing in the HM loci.
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Affiliation(s)
- Soojin Yeom
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Institute of Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Institute of Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Donghyun Kim
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Institute of Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
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7
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Shaban K, Dolson A, Fisher A, Lessard E, Sauty SM, Yankulov K. TOF1 and RRM3 reveal a link between gene silencing and the pausing of replication forks. Curr Genet 2023; 69:235-249. [PMID: 37347284 DOI: 10.1007/s00294-023-01273-3] [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: 02/16/2023] [Revised: 06/01/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023]
Abstract
Eukaryotic DNA replication is accompanied by the disassembly and reassembly of nucleosomes and the transmission of epigenetic marks to the newly assembled chromatids. Several histone chaperones, including CAF-1 and Asf1p, are central to these processes. On the other hand, replication forks pause at numerous positions throughout the genome, but it is not known if and how this pausing affects the reassembly and maintenance of chromatin structures. Here, we applied drug-free gene silencing assays to analyze the genetic interactions between CAC1, ASF1, and two genes that regulate the stability of the paused replisome (TOF1) and the resumption of elongation (RRM3). Our results show that TOF1 and RRM3 differentially interact with CAF-1 and ASF1 and that the deletions of TOF1 and RRM3 lead to reduced silencing and increased frequency of epigenetic conversions at three loci in the genome of S. cerevisiae. Our study adds details to the known activities of CAF-1 and Asf1p and suggests that the pausing of the replication fork can lead to epigenetic instability.
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Affiliation(s)
- Kholoud Shaban
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Andrew Dolson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Ashley Fisher
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Emma Lessard
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Safia Mahabub Sauty
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G2W1, Canada.
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8
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Ivessa AS, Singh S. The increase in cell death rates in caloric restricted cells of the yeast helicase mutant rrm3 is Sir complex dependent. Sci Rep 2023; 13:17832. [PMID: 37857740 PMCID: PMC10587150 DOI: 10.1038/s41598-023-45125-z] [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: 11/29/2022] [Accepted: 10/16/2023] [Indexed: 10/21/2023] Open
Abstract
Calorie restriction (CR), which is a reduction in calorie intake without malnutrition, usually extends lifespan and improves tissue integrity. This report focuses on the relationship between nuclear genomic instability and dietary-restriction and its effect on cell survival. We demonstrate that the cell survival rates of the genomic instability yeast mutant rrm3 change under metabolic restricted conditions. Rrm3 is a DNA helicase, chromosomal replication slows (and potentially stalls) in its absence with increased rates at over 1400 natural pause sites including sites within ribosomal DNA and tRNA genes. Whereas rrm3 mutant cells have lower cell death rates compared to wild type (WT) in growth medium containing normal glucose levels (i.e., 2%), under CR growth conditions cell death rates increase in the rrm3 mutant to levels, which are higher than WT. The silent-information-regulatory (Sir) protein complex and mitochondrial oxidative stress are required for the increase in cell death rates in the rrm3 mutant when cells are transferred from growth medium containing 2% glucose to CR-medium. The Rad53 checkpoint protein is highly phosphorylated in the rrm3 mutant in response to genomic instability in growth medium containing 2% glucose. Under CR, Rad53 phosphorylation is largely reduced in the rrm3 mutant in a Sir-complex dependent manner. Since CR is an adjuvant treatment during chemotherapy, which may target genomic instability in cancer cells, our studies may gain further insight into how these therapy strategies can be improved.
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Affiliation(s)
- Andreas S Ivessa
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07101-1709, USA.
| | - Sukhwinder Singh
- Pathology and Laboratory Medicine/Flow Cytometry and Immunology Core Laboratory, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07101-1709, USA
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9
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Wu K, Dhillon N, Bajor A, Abrahamson S, Kamakaka RT. Yeast Heterochromatin Only Stably Silences Weak Regulatory Elements by Altering Burst Duration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.05.561072. [PMID: 37873261 PMCID: PMC10592971 DOI: 10.1101/2023.10.05.561072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The interplay between nucleosomes and transcription factors leads to programs of gene expression. Transcriptional silencing involves the generation of a chromatin state that represses transcription and is faithfully propagated through DNA replication and cell division. Using multiple reporter assays, including directly visualizing transcription in single cells, we investigated a diverse set of UAS enhancers and core promoters for their susceptibility to heterochromatic gene silencing. These results show that heterochromatin only stably silences weak and stress induced regulatory elements but is unable to stably repress housekeeping gene regulatory elements and the partial repression did not result in bistable expression states. Permutation analysis of different UAS enhancers and core promoters indicate that both elements function together to determine the susceptibility of regulatory sequences to repression. Specific histone modifiers and chromatin remodellers function in an enhancer specific manner to aid these elements to resist repression suggesting that Sir proteins likely function in part by reducing nucleosome mobility. We also show that the strong housekeeping regulatory elements can be repressed if silencer bound Sir1 is increased, suggesting that Sir1 is a limiting component in silencing. Together, our data suggest that the heterochromatic locus has been optimized to stably silence the weak mating type gene regulatory elements but not strong housekeeping gene regulatory sequences which could help explain why these genes are often found at the boundaries of silenced domains.
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Affiliation(s)
- Kenneth Wu
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Namrita Dhillon
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Antone Bajor
- Electrical Engineering Department, Baskin School of Engineering, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Sara Abrahamson
- Electrical Engineering Department, Baskin School of Engineering, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Rohinton T. Kamakaka
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
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10
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Bondra ER, Rine J. Context-dependent function of the transcriptional regulator Rap1 in gene silencing and activation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2023; 120:e2304343120. [PMID: 37769255 PMCID: PMC10556627 DOI: 10.1073/pnas.2304343120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/04/2023] [Indexed: 09/30/2023] Open
Abstract
In Saccharomyces cerevisiae, heterochromatin is formed through interactions between site-specific DNA-binding factors, including the transcriptional activator Repressor Activator Protein (Rap1), and Sir proteins. Despite an understanding of the establishment and maintenance of Sir-silenced chromatin, the mechanism of gene silencing by Sir proteins has remained a mystery. Utilizing high-resolution chromatin immunoprecipitation, we found that Rap1, the native activator of the bidirectional HMLα promoter, bound its recognition sequence in silenced chromatin, and its binding was enhanced by the presence of Sir proteins. In contrast to prior results, various components of transcription machinery were not able to access HMLα in the silenced state. These findings disproved the long-standing model of indiscriminate steric occlusion by Sir proteins and led to investigation of the role of the transcriptional activator Rap1 in Sir-silenced chromatin. Using a highly sensitive assay that monitors loss-of-silencing events, we identified a role for promoter-bound Rap1 in the maintenance of silent chromatin through interactions with the Sir complex. We also found that promoter-bound Rap1 activated HMLα when in an expressed state, and aided in the transition from transcription initiation to elongation. Highlighting the importance of epigenetic context in transcription factor function, these results point toward a model in which the duality of Rap1 function was mediated by local chromatin environment rather than binding-site availability.
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Affiliation(s)
- Eliana R. Bondra
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
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11
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Brickner JH. The nuclear pore complex as a platform for epigenetic regulation. J Cell Biol 2023; 222:e202307078. [PMID: 37603083 PMCID: PMC10439725 DOI: 10.1083/jcb.202307078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023] Open
Abstract
The nuclear pore complex (NPC) both mediates exchange of proteins and RNA between the nucleus and the cytoplasm and physically interacts with chromatin to regulate transcription. In this issue of JCB, Kumar et al. (2023. J. Cell Biol.https://doi.org/10.1083/jcb.202207060) provide new insight into the molecular basis for NPC-mediated epigenetic silencing through loading of the replication processivity factor PCNA.
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Affiliation(s)
- Jason H. Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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12
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Abbiati F, Garagnani SA, Orlandi I, Vai M. Sir2 and Glycerol Underlie the Pro-Longevity Effect of Quercetin during Yeast Chronological Aging. Int J Mol Sci 2023; 24:12223. [PMID: 37569599 PMCID: PMC10419316 DOI: 10.3390/ijms241512223] [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: 07/06/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
Quercetin (QUER) is a natural polyphenolic compound endowed with beneficial properties for human health, with anti-aging effects. However, although this flavonoid is commercially available as a nutraceutical, target molecules/pathways underlying its pro-longevity potential have yet to be fully clarified. Here, we investigated QUER activity in yeast chronological aging, the established model for simulating the aging of postmitotic quiescent mammalian cells. We found that QUER supplementation at the onset of chronological aging, namely at the diauxic shift, significantly increases chronological lifespan (CLS). Consistent with the antioxidant properties of QUER, this extension takes place in concert with a decrease in oxidative stress. In addition, QUER triggers substantial changes in carbon metabolism. Specifically, it promotes an enhancement of a pro-longevity anabolic metabolism toward gluconeogenesis due to improved catabolism of C2 by-products of yeast fermentation and glycerol. The former is attributable to the Sir2-dependent activity of phosphoenolpyruvate carboxykinase and the latter to the L-glycerol 3-phosphate pathway. Such a combined increased supply of gluconeogenesis leads to an increase in the reserve carbohydrate trehalose, ensuring CLS extension. Moreover, QUER supplementation to chronologically aging cells in water alone amplifies their long-lived phenotype. This is associated with intracellular glycerol catabolism and trehalose increase, further indicating a QUER-specific influence on carbon metabolism that results in CLS extension.
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Affiliation(s)
- Francesco Abbiati
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (F.A.); (S.A.G.); (I.O.)
| | - Stefano Angelo Garagnani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (F.A.); (S.A.G.); (I.O.)
| | - Ivan Orlandi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (F.A.); (S.A.G.); (I.O.)
- SYSBIO Centre for Systems Biology, 20126 Milano, Italy
| | - Marina Vai
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (F.A.); (S.A.G.); (I.O.)
- SYSBIO Centre for Systems Biology, 20126 Milano, Italy
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13
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Liu Y, Zhou Z, Wu S, Ni G, Zhang A, Tsimring LS, Hasty J, Hao N. Enhanced cellular longevity arising from environmental fluctuations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547867. [PMID: 37461504 PMCID: PMC10350066 DOI: 10.1101/2023.07.05.547867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Cellular longevity is regulated by both genetic and environmental factors. However, the interactions of these factors in the context of aging remain largely unclear. Here, we formulate a mathematical model for dynamic glucose modulation of a core gene circuit in yeast aging, which not only guided the design of pro-longevity interventions, but also revealed the theoretical principles underlying these interventions. We introduce the dynamical systems theory to capture two general means for promoting longevity - the creation of a stable fixed point in the "healthy" state of the cell and the dynamic stabilization of the system around this healthy state through environmental oscillations. Guided by the model, we investigate how both of these can be experimentally realized by dynamically modulating environmental glucose levels. The results establish a paradigm for theoretically analyzing the trajectories and perturbations of aging that can be generalized to aging processes in diverse cell types and organisms.
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Affiliation(s)
- Yuting Liu
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Zhen Zhou
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Songlin Wu
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gavin Ni
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Alex Zhang
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Lev S. Tsimring
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Nan Hao
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
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14
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Bondra ER, Rine J. Context dependent function of the transcriptional regulator Rap1 in gene silencing and activation in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539937. [PMID: 37214837 PMCID: PMC10197613 DOI: 10.1101/2023.05.08.539937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In Saccharomyces cerevisiae, heterochromatin is formed through interactions between site-specific DNA-binding factors, including the transcriptional activator Rap1, and Sir proteins. Despite a vast understanding of the establishment and maintenance of Sir-silenced chromatin, the mechanism of gene silencing by Sir proteins has remained a mystery. Utilizing high resolution chromatin immunoprecipitation, we found that Rap1, the native activator of the bi-directional HML α promoter, bound its recognition sequence in silenced chromatin and its binding was enhanced by the presence of Sir proteins. In contrast to prior results, various components of transcription machinery were not able to access HML α in the silenced state. These findings disproved the long-standing model of indiscriminate steric occlusion by Sir proteins and led to investigation of the transcriptional activator Rap1 in Sir-silenced chromatin. Using a highly sensitive assay that monitors loss-of-silencing events, we identified a novel role for promoter-bound Rap1 in the maintenance of silent chromatin through interactions with the Sir complex. We also found that promoter-bound Rap1 activated HML α when in an expressed state, and aided in the transition from transcription initiation to elongation. Highlighting the importance of epigenetic context in transcription factor function, these results point toward a model in which the duality of Rap1 function was mediated by local chromatin environment rather than binding-site availability. Significance Statement The coarse partitioning of the genome into regions of active euchromatin and repressed heterochromatin is an important, and conserved, level gene expression regulation in eukaryotes. Repressor Activator Protein (Rap1) is a transcription factor that promotes the activation of genes when recruited to promoters, and aids in the establishment of heterochromatin through interactions with silencer elements. Here, we investigate the role of Rap1 when bound to a promoter in silent chromatin and dissect the context-specific epigenetic cues that regulate the dual properties of this transcription factor. Together, our data highlight the importance of protein-protein interactions and local chromatin state on transcription factor function.
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Affiliation(s)
- Eliana R Bondra
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
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15
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Zhou Z, Liu Y, Feng Y, Klepin S, Tsimring LS, Pillus L, Hasty J, Hao N. Engineering longevity-design of a synthetic gene oscillator to slow cellular aging. Science 2023; 380:376-381. [PMID: 37104589 PMCID: PMC10249776 DOI: 10.1126/science.add7631] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 03/03/2023] [Indexed: 04/29/2023]
Abstract
Synthetic biology enables the design of gene networks to confer specific biological functions, yet it remains a challenge to rationally engineer a biological trait as complex as longevity. A naturally occurring toggle switch underlies fate decisions toward either nucleolar or mitochondrial decline during the aging of yeast cells. We rewired this endogenous toggle to engineer an autonomous genetic clock that generates sustained oscillations between the nucleolar and mitochondrial aging processes in individual cells. These oscillations increased cellular life span through the delay of the commitment to aging that resulted from either the loss of chromatin silencing or the depletion of heme. Our results establish a connection between gene network architecture and cellular longevity that could lead to rationally designed gene circuits that slow aging.
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Affiliation(s)
- Zhen Zhou
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yuting Liu
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yushen Feng
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Stephen Klepin
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Lev S. Tsimring
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Lorraine Pillus
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Nan Hao
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
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16
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Gnügge R, Reginato G, Cejka P, Symington LS. Sequence and chromatin features guide DNA double-strand break resection initiation. Mol Cell 2023; 83:1237-1250.e15. [PMID: 36917982 PMCID: PMC10131398 DOI: 10.1016/j.molcel.2023.02.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 01/09/2023] [Accepted: 02/09/2023] [Indexed: 03/14/2023]
Abstract
DNA double-strand breaks (DSBs) are cytotoxic genome lesions that must be accurately and efficiently repaired to ensure genome integrity. In yeast, the Mre11-Rad50-Xrs2 (MRX) complex nicks 5'-terminated DSB ends to initiate nucleolytic processing of DSBs for repair by homologous recombination. How MRX-DNA interactions support 5' strand-specific nicking and how nicking is influenced by the chromatin context have remained elusive. Using a deep sequencing-based assay, we mapped MRX nicks at single-nucleotide resolution next to multiple DSBs in the yeast genome. We observed that the DNA end-binding Ku70-Ku80 complex directed DSB-proximal nicks and that repetitive MRX cleavage extended the length of resection tracts. We identified a sequence motif and a DNA meltability profile that is preferentially nicked by MRX. Furthermore, we found that nucleosomes as well as transcription impeded MRX incisions. Our findings suggest that local DNA sequence and chromatin features shape the activity of this central DSB repair complex.
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Affiliation(s)
- Robert Gnügge
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Giordano Reginato
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland; Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Petr Cejka
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland; Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA.
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17
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Kamata K, Ayano T, Oki M. Spt3 and Spt8 Are Involved in the Formation of a Silencing Boundary by Interacting with TATA-Binding Protein. Biomolecules 2023; 13:biom13040619. [PMID: 37189367 DOI: 10.3390/biom13040619] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
In Saccharomyces cerevisiae, a heterochromatin-like chromatin structure called the silencing region is present at the telomere as a complex of Sir2, Sir3, and Sir4. Although spreading of the silencing region is blocked by histone acetylase-mediated boundary formation, the details of the factors and mechanisms involved in the spread and formation of the boundary at each telomere are unknown. Here, we show that Spt3 and Spt8 block the spread of the silencing regions. Spt3 and Spt8 are members of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex, which has histone acetyltransferase activity. We performed microarray analysis of the transcriptome of spt3Δ and spt8Δ strains and RT-qPCR analysis of the transcript levels of genes from the subtelomeric region in mutants in which the interaction of Spt3 with TATA-binding protein (TBP) is altered. The results not only indicated that both Spt3 and Spt8 are involved in TBP-mediated boundary formation on the right arm of chromosome III, but also that boundary formation in this region is DNA sequence independent. Although both Spt3 and Spt8 interact with TBP, Spt3 had a greater effect on genome-wide transcription. Mutant analysis showed that the interaction between Spt3 and TBP plays an important role in the boundary formation.
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18
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Cabrera A, Edelstein HI, Glykofrydis F, Love KS, Palacios S, Tycko J, Zhang M, Lensch S, Shields CE, Livingston M, Weiss R, Zhao H, Haynes KA, Morsut L, Chen YY, Khalil AS, Wong WW, Collins JJ, Rosser SJ, Polizzi K, Elowitz MB, Fussenegger M, Hilton IB, Leonard JN, Bintu L, Galloway KE, Deans TL. The sound of silence: Transgene silencing in mammalian cell engineering. Cell Syst 2022; 13:950-973. [PMID: 36549273 PMCID: PMC9880859 DOI: 10.1016/j.cels.2022.11.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/22/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022]
Abstract
To elucidate principles operating in native biological systems and to develop novel biotechnologies, synthetic biology aims to build and integrate synthetic gene circuits within native transcriptional networks. The utility of synthetic gene circuits for cell engineering relies on the ability to control the expression of all constituent transgene components. Transgene silencing, defined as the loss of expression over time, persists as an obstacle for engineering primary cells and stem cells with transgenic cargos. In this review, we highlight the challenge that transgene silencing poses to the robust engineering of mammalian cells, outline potential molecular mechanisms of silencing, and present approaches for preventing transgene silencing. We conclude with a perspective identifying future research directions for improving the performance of synthetic gene circuits.
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Affiliation(s)
- Alan Cabrera
- Department of Bioengineering, Rice University, Houston, TX 77005, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hailey I Edelstein
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; The Eli and Edythe Broad CIRM Center, Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Fokion Glykofrydis
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033-9080, USA
| | - Kasey S Love
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sebastian Palacios
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Meng Zhang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, Urbana, IL 61801, USA
| | - Sarah Lensch
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Cara E Shields
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | - Mark Livingston
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, Urbana, IL 61801, USA
| | - Karmella A Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | - Leonardo Morsut
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033-9080, USA
| | - Yvonne Y Chen
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA; Parker Institute for Cancer Immunotherapy Center at UCLA, Los Angeles, CA 90095, USA
| | - Ahmad S Khalil
- Biological Design Center and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Wilson W Wong
- Biological Design Center and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - James J Collins
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033-9080, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Susan J Rosser
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Karen Polizzi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland; Faculty of Science, University of Basel, Mattenstrasse 26, Basel 4058, Switzerland
| | - Isaac B Hilton
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Joshua N Leonard
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; The Eli and Edythe Broad CIRM Center, Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kate E Galloway
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tara L Deans
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA.
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19
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Paxman J, Zhou Z, O'Laughlin R, Liu Y, Li Y, Tian W, Su H, Jiang Y, Holness SE, Stasiowski E, Tsimring LS, Pillus L, Hasty J, Hao N. Age-dependent aggregation of ribosomal RNA-binding proteins links deterioration in chromatin stability with challenges to proteostasis. eLife 2022; 11:e75978. [PMID: 36194205 PMCID: PMC9578700 DOI: 10.7554/elife.75978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatin instability and protein homeostasis (proteostasis) stress are two well-established hallmarks of aging, which have been considered largely independent of each other. Using microfluidics and single-cell imaging approaches, we observed that, during the replicative aging of Saccharomyces cerevisiae, a challenge to proteostasis occurs specifically in the fraction of cells with decreased stability within the ribosomal DNA (rDNA). A screen of 170 yeast RNA-binding proteins identified ribosomal RNA (rRNA)-binding proteins as the most enriched group that aggregate upon a decrease in rDNA stability induced by inhibition of a conserved lysine deacetylase Sir2. Further, loss of rDNA stability induces age-dependent aggregation of rRNA-binding proteins through aberrant overproduction of rRNAs. These aggregates contribute to age-induced proteostasis decline and limit cellular lifespan. Our findings reveal a mechanism underlying the interconnection between chromatin instability and proteostasis stress and highlight the importance of cell-to-cell variability in aging processes.
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Affiliation(s)
- Julie Paxman
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Zhen Zhou
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Richard O'Laughlin
- Department of Bioengineering, University of California, San DiegoLa JollaUnited States
| | - Yuting Liu
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Yang Li
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Wanying Tian
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Hetian Su
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Yanfei Jiang
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Shayna E Holness
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
| | - Elizabeth Stasiowski
- Department of Bioengineering, University of California, San DiegoLa JollaUnited States
| | - Lev S Tsimring
- Synthetic Biology Institute, University of California, San DiegoLa JollaUnited States
| | - Lorraine Pillus
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
- UCSD Moores Cancer Center, University of California San, DiegoLa JollaUnited States
| | - Jeff Hasty
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
- Department of Bioengineering, University of California, San DiegoLa JollaUnited States
- Synthetic Biology Institute, University of California, San DiegoLa JollaUnited States
| | - Nan Hao
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
- Department of Bioengineering, University of California, San DiegoLa JollaUnited States
- Synthetic Biology Institute, University of California, San DiegoLa JollaUnited States
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20
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Abdulla AZ, Vaillant C, Jost D. Painters in chromatin: a unified quantitative framework to systematically characterize epigenome regulation and memory. Nucleic Acids Res 2022; 50:9083-9104. [PMID: 36018799 PMCID: PMC9458448 DOI: 10.1093/nar/gkac702] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/03/2022] [Indexed: 12/24/2022] Open
Abstract
In eukaryotes, many stable and heritable phenotypes arise from the same DNA sequence, owing to epigenetic regulatory mechanisms relying on the molecular cooperativity of 'reader-writer' enzymes. In this work, we focus on the fundamental, generic mechanisms behind the epigenome memory encoded by post-translational modifications of histone tails. Based on experimental knowledge, we introduce a unified modeling framework, the painter model, describing the mechanistic interplay between sequence-specific recruitment of chromatin regulators, chromatin-state-specific reader-writer processes and long-range spreading mechanisms. A systematic analysis of the model building blocks highlights the crucial impact of tridimensional chromatin organization and state-specific recruitment of enzymes on the stability of epigenomic domains and on gene expression. In particular, we show that enhanced 3D compaction of the genome and enzyme limitation facilitate the formation of ultra-stable, confined chromatin domains. The model also captures how chromatin state dynamics impact the intrinsic transcriptional properties of the region, slower kinetics leading to noisier expression. We finally apply our framework to analyze experimental data, from the propagation of γH2AX around DNA breaks in human cells to the maintenance of heterochromatin in fission yeast, illustrating how the painter model can be used to extract quantitative information on epigenomic molecular processes.
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Affiliation(s)
- Amith Z Abdulla
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d’Italie, 69007 Lyon, France,École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d’Italie, 69007 Lyon, France
| | - Cédric Vaillant
- Correspondence may also be addressed to Cédric Vaillant. Tel: +33 4 72 72 81 54; Fax: +33 4 72 72 80 00;
| | - Daniel Jost
- To whom correspondence should be addressed. Tel: +33 4 72 72 86 30; Fax: +33 4 72 72 80 00;
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21
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Sump B, Brickner DG, D'Urso A, Kim SH, Brickner JH. Mitotically heritable, RNA polymerase II-independent H3K4 dimethylation stimulates INO1 transcriptional memory. eLife 2022; 11:e77646. [PMID: 35579426 PMCID: PMC9129879 DOI: 10.7554/elife.77646] [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: 02/06/2022] [Accepted: 05/15/2022] [Indexed: 11/13/2022] Open
Abstract
For some inducible genes, the rate and molecular mechanism of transcriptional activation depend on the prior experiences of the cell. This phenomenon, called epigenetic transcriptional memory, accelerates reactivation, and requires both changes in chromatin structure and recruitment of poised RNA polymerase II (RNAPII) to the promoter. Memory of inositol starvation in budding yeast involves a positive feedback loop between transcription factor-dependent interaction with the nuclear pore complex and histone H3 lysine 4 dimethylation (H3K4me2). While H3K4me2 is essential for recruitment of RNAPII and faster reactivation, RNAPII is not required for H3K4me2. Unlike RNAPII-dependent H3K4me2 associated with transcription, RNAPII-independent H3K4me2 requires Nup100, SET3C, the Leo1 subunit of the Paf1 complex and, upon degradation of an essential transcription factor, is inherited through multiple cell cycles. The writer of this mark (COMPASS) physically interacts with the potential reader (SET3C), suggesting a molecular mechanism for the spreading and re-incorporation of H3K4me2 following DNA replication.
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Affiliation(s)
- Bethany Sump
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Donna G Brickner
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Agustina D'Urso
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Seo Hyun Kim
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
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22
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Substrates of the MAPK Slt2: Shaping Yeast Cell Integrity. J Fungi (Basel) 2022; 8:jof8040368. [PMID: 35448599 PMCID: PMC9031059 DOI: 10.3390/jof8040368] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/04/2023] Open
Abstract
The cell wall integrity (CWI) MAPK pathway of budding yeast Saccharomyces cerevisiae is specialized in responding to cell wall damage, but ongoing research shows that it participates in many other stressful conditions, suggesting that it has functional diversity. The output of this pathway is mainly driven by the activity of the MAPK Slt2, which regulates important processes for yeast physiology such as fine-tuning of signaling through the CWI and other pathways, transcriptional activation in response to cell wall damage, cell cycle, or determination of the fate of some organelles. To this end, Slt2 precisely phosphorylates protein substrates, modulating their activity, stability, protein interaction, and subcellular localization. Here, after recapitulating the methods that have been employed in the discovery of proteins phosphorylated by Slt2, we review the bona fide substrates of this MAPK and the growing set of candidates still to be confirmed. In the context of the complexity of MAPK signaling regulation, we discuss how Slt2 determines yeast cell integrity through phosphorylation of these substrates. Increasing data from large-scale analyses and the available methodological approaches pave the road to early identification of new Slt2 substrates and functions.
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23
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Odoh CK, Guo X, Arnone JT, Wang X, Zhao ZK. The role of NAD and NAD precursors on longevity and lifespan modulation in the budding yeast, Saccharomyces cerevisiae. Biogerontology 2022; 23:169-199. [PMID: 35260986 PMCID: PMC8904166 DOI: 10.1007/s10522-022-09958-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/16/2022] [Indexed: 11/26/2022]
Abstract
Molecular causes of aging and longevity interventions have witnessed an upsurge in the last decade. The resurgent interests in the application of small molecules as potential geroprotectors and/or pharmacogenomics point to nicotinamide adenine dinucleotide (NAD) and its precursors, nicotinamide riboside, nicotinamide mononucleotide, nicotinamide, and nicotinic acid as potentially intriguing molecules. Upon supplementation, these compounds have shown to ameliorate aging related conditions and possibly prevent death in model organisms. Besides being a molecule essential in all living cells, our understanding of the mechanism of NAD metabolism and its regulation remain incomplete owing to its omnipresent nature. Here we discuss recent advances and techniques in the study of chronological lifespan (CLS) and replicative lifespan (RLS) in the model unicellular organism Saccharomyces cerevisiae. We then follow with the mechanism and biology of NAD precursors and their roles in aging and longevity. Finally, we review potential biotechnological applications through engineering of microbial lifespan, and laid perspective on the promising candidature of alternative redox compounds for extending lifespan.
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Affiliation(s)
- Chuks Kenneth Odoh
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiaojia Guo
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China
| | - James T Arnone
- Department of Biology, William Paterson University, Wayne, NJ, 07470, USA
| | - Xueying Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China
| | - Zongbao K Zhao
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China.
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China.
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24
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Brothers M, Rine J. Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae. eLife 2022; 11:75653. [PMID: 35073254 PMCID: PMC8830885 DOI: 10.7554/elife.75653] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
The formation of heterochromatin at HML, HMR, and telomeres in Saccharomyces cerevisiae involves two main steps: Recruitment of Sir proteins to silencers and their spread throughout the silenced domain. We developed a method to study these two processes at single base-pair resolution. Using a fusion protein between the heterochromatin protein Sir3 and the non-site-specific bacterial adenine methyltransferase M.EcoGII, we mapped sites of Sir3-chromatin interactions genome-wide using long-read Nanopore sequencing to detect adenines methylated by the fusion protein and by ChIP-seq to map the distribution of Sir3-M.EcoGII. A silencing-deficient mutant of Sir3 lacking its Bromo-Adjacent Homology (BAH) domain, sir3-bah∆, was still recruited to HML, HMR, and telomeres. However, in the absence of the BAH domain, it was unable to spread away from those recruitment sites. Overexpression of Sir3 did not lead to further spreading at HML, HMR, and most telomeres. A few exceptional telomeres, like 6R, exhibited a small amount of Sir3 spreading, suggesting that boundaries at telomeres responded variably to Sir3 overexpression. Finally, by using a temperature-sensitive allele of SIR3 fused to M.ECOGII, we tracked the positions first methylated after induction and found that repression of genes at HML and HMR began before Sir3 occupied the entire locus.
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Affiliation(s)
- Molly Brothers
- Department of Molecular and Cell Biology, University of California, Berkeley
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley
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25
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Rosas Bringas FR, Stinus S, de Zoeten P, Cohn M, Chang M. Rif2 protects Rap1-depleted telomeres from MRX-mediated degradation in Saccharomyces cerevisiae. eLife 2022; 11:74090. [PMID: 35044907 PMCID: PMC8791636 DOI: 10.7554/elife.74090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/17/2022] [Indexed: 12/01/2022] Open
Abstract
Rap1 is the main protein that binds double-stranded telomeric DNA in Saccharomyces cerevisiae. Examination of the telomere functions of Rap1 is complicated by the fact that it also acts as a transcriptional regulator of hundreds of genes and is encoded by an essential gene. In this study, we disrupt Rap1 telomere association by expressing a mutant telomerase RNA subunit (tlc1-tm) that introduces mutant telomeric repeats. tlc1-tm cells grow similar to wild-type cells, although depletion of Rap1 at telomeres causes defects in telomere length regulation and telomere capping. Rif2 is a protein normally recruited to telomeres by Rap1, but we show that Rif2 can still associate with Rap1-depleted tlc1-tm telomeres, and that this association is required to inhibit telomere degradation by the MRX complex. Rif2 and the Ku complex work in parallel to prevent tlc1-tm telomere degradation; tlc1-tm cells lacking Rif2 and the Ku complex are inviable. The partially redundant mechanisms may explain the rapid evolution of telomere components in budding yeast species.
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Affiliation(s)
| | - Sonia Stinus
- European Research Institute for the Biology of Ageing, University Medical Center Groningen
| | - Pien de Zoeten
- European Research Institute for the Biology of Ageing, University Medical Center Groningen
| | | | - Michael Chang
- European Research Institute for the Biology of Ageing, University Medical Center Groningen
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26
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Yeom S, Oh J, Lee JS. Spreading-dependent or independent Sir2-mediated gene silencing in budding yeast. Genes Genomics 2022; 44:359-367. [PMID: 35034281 DOI: 10.1007/s13258-021-01203-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/02/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND In the budding yeast Saccharomyces cerevisiae, a silent chromatin structure is formed at three distinct loci, including telomeres, rDNA, and mating-type loci, which silence the expression of genes within their structures. Sir2 is the only common factor, regulating the three silent chromatin regions. S. cerevisiae has 32 telomeres, but studies on gene silencing in budding yeast have been performed using some reporter genes, artificially inserted in the telomeric regions. Therefore, insights into the global landscape of Sir-dependent silencing of genes within the silent chromatin regions are required. OBJECTIVE This study aimed to obtain global insights into Sir2-dependent gene silencing on all silent chromatin regions in budding yeast. METHODS RNA-sequencing was performed to identify genes that are silenced by Sir2. By comparing with the chromatin immunoprecipitation-sequencing (ChIP-seq) of Sir2 in the wild-type strain, we confirmed Sir2-regulated genes. RESULTS Using Sir2 ChIP-seq data, we identified that the Sir2 binding domain length caused by Sir2 spreading from the chromosomal end is different in each telomere in budding yeast. Expression of most subtelomeric genes increased in the ∆sir2 strain. Some Sir2-regulated subtelomeric genes were positioned within the telomeric Sir2-binding domain, while the others were outside the Sir2-binding domain. In addition, Sir2 was bound to the mating-type loci and rDNA region, and gene expression increased in the ∆sir2 strain. CONCLUSION We concluded that S. cerevisiae has two modes of Sir2-mediated gene silencing: one is dependent on chromatin binding and spreading of Sir2, and the other is independent of spreading of Sir2.
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Affiliation(s)
- Soojin Yeom
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea
| | - Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea.
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27
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Bordelet H, Costa R, Brocas C, Dépagne J, Veaute X, Busso D, Batté A, Guérois R, Marcand S, Dubrana K. Sir3 heterochromatin protein promotes non-homologous end joining by direct inhibition of Sae2. EMBO J 2022; 41:e108813. [PMID: 34817085 PMCID: PMC8724767 DOI: 10.15252/embj.2021108813] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 01/07/2023] Open
Abstract
Heterochromatin is a conserved feature of eukaryotic chromosomes, with central roles in gene expression regulation and maintenance of genome stability. How heterochromatin proteins regulate DNA repair remains poorly described. In the yeast Saccharomyces cerevisiae, the silent information regulator (SIR) complex assembles heterochromatin-like chromatin at sub-telomeric chromosomal regions. SIR-mediated repressive chromatin limits DNA double-strand break (DSB) resection, thus protecting damaged chromosome ends during homologous recombination (HR). As resection initiation represents the crossroads between repair by non-homologous end joining (NHEJ) or HR, we asked whether SIR-mediated heterochromatin regulates NHEJ. We show that SIRs promote NHEJ through two pathways, one depending on repressive chromatin assembly, and the other relying on Sir3 in a manner that is independent of its heterochromatin-promoting function. Via physical interaction with the Sae2 protein, Sir3 impairs Sae2-dependent functions of the MRX (Mre11-Rad50-Xrs2) complex, thereby limiting Mre11-mediated resection, delaying MRX removal from DSB ends, and promoting NHEJ.
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Affiliation(s)
- Hélène Bordelet
- Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
- Régulation spatiale des génomes, Institut Pasteur, CNRS UMR3525ParisFrance
| | - Rafaël Costa
- Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
| | - Clémentine Brocas
- Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
| | - Jordane Dépagne
- CIGEx platform. Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
| | - Xavier Veaute
- CIGEx platform. Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
| | - Didier Busso
- CIGEx platform. Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
| | - Amandine Batté
- Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
- Center for Integrative GenomicsBâtiment GénopodeUniversity of LausanneLausanneSwitzerland
| | - Raphaël Guérois
- Institute for Integrative Biology of the Cell (I2BC)CEA, CNRS, Université Paris‐Sud, Université Paris‐SaclayGif‐sur‐YvetteFrance
| | - Stéphane Marcand
- Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
| | - Karine Dubrana
- Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
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28
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Measuring the buffering capacity of gene silencing in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2021; 118:2111841118. [PMID: 34857629 PMCID: PMC8670432 DOI: 10.1073/pnas.2111841118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2021] [Indexed: 11/18/2022] Open
Abstract
Gene silencing, once established, is stably maintained for several generations. Despite the high fidelity of the inheritance of the silent state, individual components of silenced chromatin are in constant flux. Models suggest that silent loci can tolerate fluctuations in Sir proteins and histone acetylation levels, but the level of tolerance is unknown. To understand the quantitative relationships between H4K16 acetylation, Sir proteins, and silencing, we developed assays to quantitatively alter a H4K16 acetylation mimic allele and Sir protein levels and measure the effects of these changes on silencing. Our data suggest that a two- to threefold change in levels of histone marks and specific Sir proteins affects the stability of the silent state of a large chromatin domain. Gene silencing in budding yeast is mediated by Sir protein binding to unacetylated nucleosomes to form a chromatin structure that inhibits transcription. Transcriptional silencing is characterized by the high-fidelity transmission of the silent state. Despite its relative stability, the constituent parts of the silent state are in constant flux, giving rise to a model that silent loci can tolerate such fluctuations without functional consequences. However, the level of tolerance is unknown, and we developed methods to measure the threshold of histone acetylation that causes the silent chromatin state to switch to the active state as well as to measure the levels of the enzymes and structural proteins necessary for silencing. We show that loss of silencing required 50 to 75% acetyl-mimic histones, though the precise levels were influenced by silencer strength and upstream activating sequence (UAS) enhancer/promoter strength. Measurements of repressor protein levels necessary for silencing showed that reducing SIR4 gene dosage two- to threefold significantly weakened silencing, though reducing the gene copy numbers for Sir2 or Sir3 to the same extent did not significantly affect silencing suggesting that Sir4 was a limiting component in gene silencing. Calculations suggest that a mere twofold reduction in the ability of acetyltransferases to acetylate nucleosomes across a large array of nucleosomes may be sufficient to generate a transcriptionally silent domain.
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29
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Cell division in the shoot apical meristem is a trigger for miR156 decline and vegetative phase transition in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2115667118. [PMID: 34750273 DOI: 10.1073/pnas.2115667118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
What determines the rate at which a multicellular organism matures is a fundamental question in biology. In plants, the decline of miR156 with age serves as an intrinsic, evolutionarily conserved timer for the juvenile-to-adult phase transition. However, the way in which age regulates miR156 abundance is poorly understood. Here, we show that the rate of decline in miR156 is correlated with developmental age rather than chronological age. Mechanistically, we found that cell division in the apical meristem is a trigger for miR156 decline. The transcriptional activity of MIR156 genes is gradually attenuated by the deposition of the repressive histone mark H3K27me3 along with cell division. Our findings thus provide a plausible explanation of why the maturation program of a multicellular organism is unidirectional and irreversible under normal growth conditions and suggest that cell quiescence is the fountain of youth in plants.
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30
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Loïodice I, Garnier M, Nikolov I, Taddei A. An Inducible System for Silencing Establishment Reveals a Stepwise Mechanism in Which Anchoring at the Nuclear Periphery Precedes Heterochromatin Formation. Cells 2021; 10:cells10112810. [PMID: 34831033 PMCID: PMC8616196 DOI: 10.3390/cells10112810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 12/02/2022] Open
Abstract
In eukaryotic cells, silent chromatin is mainly found at the nuclear periphery forming subnuclear compartments that favor silencing establishment. Here, we set up an inducible system to monitor silencing establishment at an ectopic locus in relation with its subnuclear localization in budding yeast. We previously showed that introducing LacI bound lacO arrays in proximity to gene flanked by HML silencers favors the recruitment of the yeast silencing complex SIR at this locus, leading to its silencing and anchoring at the nuclear periphery. Using an inducible version of this system, we show that silencing establishment is a stepwise process occurring over several cell cycles, with the progressive recruitment of the SIR complex. In contrast, we observed a rapid, SIR-independent perinuclear anchoring, induced by the high amount of LacI binding at the lacO array leading to nucleosome eviction at this array and to the phosphorylation of H2A in the neighboring nucleosomes by Mec1 kinase. While the initial phosphorylation of H2A (H2A-P) and perinuclear anchoring are independent of the SIR complex, its latter recruitment stabilizes H2A-P and reinforces the perinuclear anchoring. Finally, we showed that Sir3 spreading stabilizes nucleosomes and limits the access of specific DNA-binding protein to DNA.
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Affiliation(s)
- Isabelle Loïodice
- Nuclear Dynamics Unit, CNRS, Institut Curie, PSL University, Sorbonne Université, 75005 Paris, France; (I.L.); (M.G.); (I.N.)
| | - Mickael Garnier
- Nuclear Dynamics Unit, CNRS, Institut Curie, PSL University, Sorbonne Université, 75005 Paris, France; (I.L.); (M.G.); (I.N.)
| | - Ivaylo Nikolov
- Nuclear Dynamics Unit, CNRS, Institut Curie, PSL University, Sorbonne Université, 75005 Paris, France; (I.L.); (M.G.); (I.N.)
| | - Angela Taddei
- Nuclear Dynamics Unit, CNRS, Institut Curie, PSL University, Sorbonne Université, 75005 Paris, France; (I.L.); (M.G.); (I.N.)
- Cogitamus Laboratory, F-75005 Paris, France
- Correspondence:
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31
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Corda Y, Maestroni L, Luciano P, Najem MY, Géli V. Genome stability is guarded by yeast Rtt105 through multiple mechanisms. Genetics 2021; 217:6126811. [PMID: 33724421 DOI: 10.1093/genetics/iyaa035] [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: 06/11/2020] [Accepted: 02/03/2021] [Indexed: 12/15/2022] Open
Abstract
Ty1 mobile DNA element is the most abundant and mutagenic retrotransposon present in the genome of the budding yeast Saccharomyces cerevisiae. Protein regulator of Ty1 transposition 105 (Rtt105) associates with large subunit of RPA and facilitates its loading onto a single-stranded DNA at replication forks. Here, we dissect the role of RTT105 in the maintenance of genome stability under normal conditions and upon various replication stresses through multiple genetic analyses. RTT105 is essential for viability in cells experiencing replication problems and in cells lacking functional S-phase checkpoints and DNA repair pathways involving homologous recombination. Our genetic analyses also indicate that RTT105 is crucial when cohesion is affected and is required for the establishment of normal heterochromatic structures. Moreover, RTT105 plays a role in telomere maintenance as its function is important for the telomere elongation phenotype resulting from the Est1 tethering to telomeres. Genetic analyses indicate that rtt105Δ affects the growth of several rfa1 mutants but does not aggravate their telomere length defects. Analysis of the phenotypes of rtt105Δ cells expressing NLS-Rfa1 fusion protein reveals that RTT105 safeguards genome stability through its role in RPA nuclear import but also by directly affecting RPA function in genome stability maintenance during replication.
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Affiliation(s)
- Yves Corda
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Laetitia Maestroni
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Pierre Luciano
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Maria Y Najem
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Vincent Géli
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
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32
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Vallabhaneni AR, Kabashi M, Haymowicz M, Bhatt K, Wayman V, Ahmed S, Conrad-Webb H. HSF1 induces RNA polymerase II synthesis of ribosomal RNA in S. cerevisiae during nitrogen deprivation. Curr Genet 2021; 67:937-951. [PMID: 34363098 PMCID: PMC8594204 DOI: 10.1007/s00294-021-01197-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 11/29/2022]
Abstract
The resource intensive process of accurate ribosome synthesis is essential for cell viability in all organisms. Ribosome synthesis regulation centers on RNA polymerase I (pol I) transcription of a 35S rRNA precursor that is processed into the mature 18S, 5.8S and 25S rRNAs. During nutrient deprivation or stress, pol I synthesis of rRNA is dramatically reduced. Conversely, chronic stress such as mitochondrial dysfunction induces RNA polymerase II (pol II) to transcribe functional rRNA using an evolutionarily conserved cryptic pol II rDNA promoter suggesting a universal phenomenon. However, this polymerase switches and its role in regulation of rRNA synthesis remain unclear. In this paper, we demonstrate that extended nitrogen deprivation induces the polymerase switch via components of the environmental stress response. We further show that the switch is repressed by Sch9 and activated by the stress kinase Rim15. Like stress-induced genes, the switch requires not only pol II transcription machinery, including the mediator, but also requires the HDAC, Rpd3 and stress transcription factor Hsf1. The current work shows that the constitutive allele, Hsf1PO4* displays elevated levels of induction in non-stress conditions while binding to a conserved site in the pol II rDNA promoter upstream of the pol I promoter. Whether the polymerase switch serves to provide rRNA when pol I transcription is inhibited or fine-tunes pol I initiation via RNA interactions is yet to be determined. Identifying the underlying mechanism for this evolutionary conserved phenomenon will help understand the mechanism of pol II rRNA synthesis and its role in stress adaptation.
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Affiliation(s)
- Arjuna Rao Vallabhaneni
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA
| | - Merita Kabashi
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA
| | - Matt Haymowicz
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA
| | - Kushal Bhatt
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA.,Department of Bioinformatics, University of Texas Southwestern, 5323 Harry Hines Blvd., Dallas, Texas, 75390, USA
| | - Violet Wayman
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA
| | - Shazia Ahmed
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA
| | - Heather Conrad-Webb
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA.
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33
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Li B, Zhao Y. Regulation of Antigenic Variation by Trypanosoma brucei Telomere Proteins Depends on Their Unique DNA Binding Activities. Pathogens 2021; 10:pathogens10080967. [PMID: 34451431 PMCID: PMC8402208 DOI: 10.3390/pathogens10080967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 01/17/2023] Open
Abstract
Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, Variant Surface Glycoprotein (VSG), to evade the host immune response. Such antigenic variation is a key pathogenesis mechanism that enables T. brucei to establish long-term infections. VSG is expressed exclusively from subtelomere loci in a strictly monoallelic manner, and DNA recombination is an important VSG switching pathway. The integrity of telomere and subtelomere structure, maintained by multiple telomere proteins, is essential for T. brucei viability and for regulating the monoallelic VSG expression and VSG switching. Here we will focus on T. brucei TRF and RAP1, two telomere proteins with unique nucleic acid binding activities, and summarize their functions in telomere integrity and stability, VSG switching, and monoallelic VSG expression. Targeting the unique features of TbTRF and TbRAP1′s nucleic acid binding activities to perturb the integrity of telomere structure and disrupt VSG monoallelic expression may serve as potential therapeutic strategy against T. brucei.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
- Center for RNA Science and Therapeutics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Correspondence: (B.L.); (Y.Z.)
| | - Yanxiang Zhao
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen, China
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
- Correspondence: (B.L.); (Y.Z.)
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Pobiega S, Alibert O, Marcand S. A new assay capturing chromosome fusions shows a protection trade-off at telomeres and NHEJ vulnerability to low-density ionizing radiation. Nucleic Acids Res 2021; 49:6817-6831. [PMID: 34125900 PMCID: PMC8266670 DOI: 10.1093/nar/gkab502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/31/2021] [Accepted: 05/27/2021] [Indexed: 11/14/2022] Open
Abstract
Chromosome fusions threaten genome integrity and promote cancer by engaging catastrophic mutational processes, namely chromosome breakage-fusion-bridge cycles and chromothripsis. Chromosome fusions are frequent in cells incurring telomere dysfunctions or those exposed to DNA breakage. Their occurrence and therefore their contribution to genome instability in unchallenged cells is unknown. To address this issue, we constructed a genetic assay able to capture and quantify rare chromosome fusions in budding yeast. This chromosome fusion capture (CFC) assay relies on the controlled inactivation of one centromere to rescue unstable dicentric chromosome fusions. It is sensitive enough to quantify the basal rate of end-to-end chromosome fusions occurring in wild-type cells. These fusions depend on canonical nonhomologous end joining (NHEJ). Our results show that chromosome end protection results from a trade-off at telomeres between positive effectors (Rif2, Sir4, telomerase) and a negative effector partially antagonizing them (Rif1). The CFC assay also captures NHEJ-dependent chromosome fusions induced by ionizing radiation. It provides evidence for chromosomal rearrangements stemming from a single photon-matter interaction.
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Affiliation(s)
- Sabrina Pobiega
- Université de Paris and Université Paris-Saclay, Inserm, CEA IBFJ/iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, 92265 Fontenay-au-Roses, France
| | | | - Stéphane Marcand
- To whom correspondence should be addressed. Tel: +33 1 46 54 82 33;
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Innate immunity to prions: anti-prion systems turn a tsunami of prions into a slow drip. Curr Genet 2021; 67:833-847. [PMID: 34319422 DOI: 10.1007/s00294-021-01203-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/17/2022]
Abstract
The yeast prions (infectious proteins) [URE3] and [PSI+] are essentially non-functional (or even toxic) amyloid forms of Ure2p and Sup35p, whose normal function is in nitrogen catabolite repression and translation termination, respectively. Yeast has an array of systems working in normal cells that largely block infection with prions, block most prion formation, cure most nascent prions and mitigate the toxic effects of those prions that escape the first three types of systems. Here we review recent progress in defining these anti-prion systems, how they work and how they are regulated. Polymorphisms of the prion domains partially block infection with prions. Ribosome-associated chaperones ensure proper folding of nascent proteins, thus reducing [PSI+] prion formation and curing many [PSI+] variants that do form. Btn2p is a sequestering protein which gathers [URE3] amyloid filaments to one place in the cells so that the prion is often lost by progeny cells. Proteasome impairment produces massive overexpression of Btn2p and paralog Cur1p, resulting in [URE3] curing. Inversely, increased proteasome activity, by derepression of proteasome component gene transcription or by 60S ribosomal subunit gene mutation, prevents prion curing by Btn2p or Cur1p. The nonsense-mediated decay proteins (Upf1,2,3) cure many nascent [PSI+] variants by associating with Sup35p directly. Normal levels of the disaggregating chaperone Hsp104 can also cure many [PSI+] prion variants. By keeping the cellular levels of certain inositol polyphosphates / pyrophosphates low, Siw14p cures certain [PSI+] variants. It is hoped that exploration of the yeast innate immunity to prions will lead to discovery of similar systems in humans.
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Feng MW, Adams PD. A new mechanistic insight into fate decisions during yeast cell aging process. Mech Ageing Dev 2021; 198:111542. [PMID: 34273382 DOI: 10.1016/j.mad.2021.111542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Despite massive technological advances in mammalian models in recent years, studies in yeast still have the power to inform on the basic mechanisms of aging. Illustrating this, in Nan Hao's recent article published in the journal Science, he and his lab use microfluidics and fluorescent imaging technology to analyze the dynamics and interactions of aging mechanisms within yeast cells. They focused in on the Sir2 gene and the heme activator protein and, through the manipulation of these two molecular aging pathways, were able to determine that yeast cells can undergo one of three modes of aging, with one of them having a significantly longer lifespan than the others. These findings provide unexpected insights into mechanisms of aging, apparently as regulated fate-decision process, and open up avenues for future research.
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Affiliation(s)
- Morgan W Feng
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, United States
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, United States.
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37
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Host Chromatin Regulators Required for Aggregatibacter actinomycetemcomitans Cytolethal Distending Toxin Activity in Saccharomyces cerevisiae Model. Infect Immun 2021; 89:e0003621. [PMID: 33941581 DOI: 10.1128/iai.00036-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytolethal distending toxin (CDT) is a bacterial genotoxin that causes host cell cycle arrest and death. We previously employed a Saccharomyces cerevisiae model with inducible expression of the CDT catalytic subunit from Aggregatibacter actinomycetemcomitans, AaCdtB, and showed that a wide variety of host factors play a role in facilitating the activity of CdtB. Our observation that a yeast H2B mutant defective in chromatin condensation was partially resistant to CdtB implies that chromatin structure may affect CDT function. In this study, we identified host chromatin regulatory genes required for CdtB cytotoxicity. We found that the deletion of HTZ1 or certain subunits of SWR, INO80, and SIR complexes increased cellular resistance to CdtB. We hypothesized that CdtB may interact with Htz1 or the chromatin, but immunoprecipitation experiments failed to detect physical interaction between CdtB and Htz1 or the chromatin. However, we observed reduced nuclear localization of CdtB in several mutants, suggesting that impaired nuclear translocation may, at least partly, explain the mechanisms of CdtB resistance. In addition, mutations in chromatin regulatory genes induce changes in the global gene expression profile, and these may indirectly affect CdtB toxicity. Our results suggest that decreased expression of endoplasmic reticulum (ER)-Golgi transport-related genes that may be involved in CdtB transport and/or increased expression of DNA repair genes may contribute to CdtB resistance. These results suggest that the functions of chromatin regulators may contribute to the activity of CDT in host cells.
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38
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Moradi‐Fard S, Mojumdar A, Chan M, Harkness TA, Cobb JA. Smc5/6 in the rDNA modulates lifespan independently of Fob1. Aging Cell 2021; 20:e13373. [PMID: 33979898 PMCID: PMC8208791 DOI: 10.1111/acel.13373] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/18/2021] [Accepted: 04/08/2021] [Indexed: 12/28/2022] Open
Abstract
The ribosomal DNA (rDNA) in Saccharomycescerevisiae is in one tandem repeat array on Chromosome XII. Two regions within each repetitive element, called intergenic spacer 1 (IGS1) and IGS2, are important for organizing the rDNA within the nucleolus. The Smc5/6 complex localizes to IGS1 and IGS2. We show that Smc5/6 has a function in the rDNA beyond its role in homologous recombination (HR) at the replication fork barrier (RFB) located in IGS1. Fob1 is required for optimal binding of Smc5/6 at IGS1 whereas the canonical silencing factor Sir2 is required for its optimal binding at IGS2, independently of Fob1. Through interdependent interactions, Smc5/6 stabilizes Sir2 and Cohibin at both IGS and its recovery at IGS2 is important for nucleolar compaction and transcriptional silencing, which in turn supports rDNA stability and lifespan.
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Affiliation(s)
- Sarah Moradi‐Fard
- Departments of Biochemistry & Molecular Biology and Oncology Robson DNA Science Centre Arnie Charbonneau Cancer Institute Cumming School of Medicine University of Calgary Calgary AB Canada
| | - Aditya Mojumdar
- Departments of Biochemistry & Molecular Biology and Oncology Robson DNA Science Centre Arnie Charbonneau Cancer Institute Cumming School of Medicine University of Calgary Calgary AB Canada
| | - Megan Chan
- Departments of Biochemistry & Molecular Biology and Oncology Robson DNA Science Centre Arnie Charbonneau Cancer Institute Cumming School of Medicine University of Calgary Calgary AB Canada
| | - Troy A.A. Harkness
- Department of Biochemistry, Microbiology and Immunology University of Saskatchewan Saskatoon SK Canada
| | - Jennifer A. Cobb
- Departments of Biochemistry & Molecular Biology and Oncology Robson DNA Science Centre Arnie Charbonneau Cancer Institute Cumming School of Medicine University of Calgary Calgary AB Canada
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39
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Pérez-Ortín JE, Mena A, Barba-Aliaga M, Singh A, Chávez S, García-Martínez J. Cell volume homeostatically controls the rDNA repeat copy number and rRNA synthesis rate in yeast. PLoS Genet 2021; 17:e1009520. [PMID: 33826644 PMCID: PMC8055003 DOI: 10.1371/journal.pgen.1009520] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/19/2021] [Accepted: 03/25/2021] [Indexed: 01/20/2023] Open
Abstract
The adjustment of transcription and translation rates to the changing needs of cells is of utmost importance for their fitness and survival. We have previously shown that the global transcription rate for RNA polymerase II in budding yeast Saccharomyces cerevisiae is regulated in relation to cell volume. Total mRNA concentration is constant with cell volume since global RNApol II-dependent nascent transcription rate (nTR) also keeps constant but mRNA stability increases with cell size. In this paper, we focus on the case of rRNA and RNA polymerase I. Contrarily to that found for RNA pol II, we detected that RNA polymerase I nTR increases proportionally to genome copies and cell size in polyploid cells. In haploid mutant cells with larger cell sizes, the rDNA repeat copy number rises. By combining mathematical modeling and experimental work with the large-size cln3 strain, we observed that the increasing repeat copy number is based on a feedback mechanism in which Sir2 histone deacetylase homeostatically controls the amplification of rDNA repeats in a volume-dependent manner. This amplification is paralleled with an increase in rRNA nTR, which indicates a control of the RNA pol I synthesis rate by cell volume. Synthesis rates of biological macromolecules should be strictly regulated and adjusted to the changing conditions of cells. The change in volume is one of the commonest variables along individual cell life and also when comparing different cell types. We previously found that cells with asymmetric division, such as budding yeasts, use a compensatory change in the global RNA polymerase II synthesis rate and mRNA decay rate to maintain mRNA homeostasis. In the present study, we address the same issue for the RNA polymerase that makes rRNAs, which are essential components of ribosomes and the most abundant RNAs in the cell. We found that the copy number of the gene encoding 35S rRNA, transcribed by RNA polymerase I, changes proportionally to the cell volume in budding yeast via a feedback mechanism based on the Sir2 histone deacetylase, which guarantees that yeast cells have the appropriate RNA polymerase I synthesis rate required for rRNA homeostasis.
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Affiliation(s)
- José E. Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Spain
- * E-mail: (JEP-O); (JG-M)
| | - Adriana Mena
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Spain
| | - Marina Barba-Aliaga
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Spain
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, United States of America
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla. Campus Hospital Universitario Virgen del Rocío, Seville, Spain
| | - José García-Martínez
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Spain
- * E-mail: (JEP-O); (JG-M)
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40
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Edskes HK, Stroobant EE, DeWilde MP, Bezsonov EE, Wickner RB. Proteasome Control of [URE3] Prion Propagation by Degradation of Anti-Prion Proteins Cur1 and Btn2 in Saccharomyces cerevisiae. Genetics 2021; 218:6179111. [PMID: 33742650 DOI: 10.1093/genetics/iyab037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/27/2021] [Indexed: 01/16/2023] Open
Abstract
[URE3] is a prion of the nitrogen catabolism controller, Ure2p, and [PSI+] is a prion of the translation termination factor Sup35p in S. cerevisiae. Btn2p cures [URE3] by sequestration of Ure2p amyloid filaments. Cur1p, paralogous to Btn2p, also cures [URE3], but by a different (unknown) mechanism. We find that an array of mutations impairing proteasome assembly or MG132 inhibition of proteasome activity result in loss of [URE3]. In proportion to their prion-curing effects, each mutation affecting proteasomes elevates the cellular concentration of the anti-prion proteins Btn2 and Cur1. Of >4,600 proteins detected by SILAC, Btn2p was easily the most overexpressed in a pre9Δ (α3 core subunit) strain. Indeed, deletion of BTN2 and CUR1 prevents the prion-curing effects of proteasome impairment. Surprisingly, the 15 most unstable yeast proteins are not increased in pre9Δ cells suggesting altered proteasome specificity rather than simple inactivation. Hsp42, a chaperone that cooperates with Btn2 and Cur1 in curing [URE3], is also necessary for the curing produced by proteasome defects, although Hsp42p levels are not substantially altered by a proteasome defect. We find that pre9Δ and proteasome chaperone mutants that most efficiently lose [URE3], do not destabilize [PSI+] or alter cellular levels of Sup35p. A tof2 mutation or deletion likewise destabilizes [URE3], and elevates Btn2p, suggesting that Tof2p deficiency inactivates proteasomes. We suggest that when proteasomes are saturated with denatured/misfolded proteins, their reduced degradation of Btn2p and Cur1p automatically upregulates these aggregate-handling systems to assist in the clean-up.
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Affiliation(s)
- Herman K Edskes
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
| | - Emily E Stroobant
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
| | - Morgan P DeWilde
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
| | - Evgeny E Bezsonov
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
| | - Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
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41
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Farris D, Saxton DS, Rine J. A novel allele of SIR2 reveals a heritable intermediate state of gene silencing. Genetics 2021; 218:6169529. [PMID: 33713126 DOI: 10.1093/genetics/iyab041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/08/2021] [Indexed: 12/22/2022] Open
Abstract
Genetic information acquires additional meaning through epigenetic regulation, the process by which genetically identical cells can exhibit heritable differences in gene expression and phenotype. Inheritance of epigenetic information is a critical step in maintaining cellular identity and organismal health. In Saccharomyces cerevisiae, one form of epigenetic regulation is the transcriptional silencing of two mating-type loci, HML and HMR, by the SIR-protein complex. To focus on the epigenetic dimension of this gene regulation, we conducted a forward mutagenesis screen to identify mutants exhibiting an epigenetic or metastable silencing defect. We utilized fluorescent reporters at HML and HMR, and screened yeast colonies for epigenetic silencing defects. We uncovered numerous independent sir1 alleles, a gene known to be required for stable epigenetic inheritance. More interestingly, we recovered a missense mutation within SIR2, which encodes a highly conserved histone deacetylase. In contrast to sir1Δ, which exhibits states that are either fully silenced or fully expressed, this sir2 allele exhibited heritable states that were either fully silenced or expressed at an intermediate level. The heritable nature of this unique silencing defect was influenced by, but not completely dependent on, changes in rDNA copy number. Therefore, this study revealed a heritable state of intermediate silencing and linked this state to a central silencing factor, Sir2.
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Affiliation(s)
- Delaney Farris
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Daniel S Saxton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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42
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Cardoso da Silva R, Vader G. Getting there: understanding the chromosomal recruitment of the AAA+ ATPase Pch2/TRIP13 during meiosis. Curr Genet 2021; 67:553-565. [PMID: 33712914 PMCID: PMC8254700 DOI: 10.1007/s00294-021-01166-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/21/2022]
Abstract
The generally conserved AAA+ ATPase Pch2/TRIP13 is involved in diverse aspects of meiosis, such as prophase checkpoint function, DNA break regulation, and meiotic recombination. The controlled recruitment of Pch2 to meiotic chromosomes allows it to use its ATPase activity to influence HORMA protein-dependent signaling. Because of the connection between Pch2 chromosomal recruitment and its functional roles in meiosis, it is important to reveal the molecular details that govern Pch2 localization. Here, we review the current understanding of the different factors that control the recruitment of Pch2 to meiotic chromosomes, with a focus on research performed in budding yeast. During meiosis in this organism, Pch2 is enriched within the nucleolus, where it likely associates with the specialized chromatin of the ribosomal (r)DNA. Pch2 is also found on non-rDNA euchromatin, where its recruitment is contingent on Zip1, a component of the synaptonemal complex (SC) that assembles between homologous chromosomes. We discuss recent findings connecting the recruitment of Pch2 with its association with the Origin Recognition Complex (ORC) and reliance on RNA Polymerase II-dependent transcription. In total, we provide a comprehensive overview of the pathways that control the chromosomal association of an important meiotic regulator.
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Affiliation(s)
- Richard Cardoso da Silva
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany. .,Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
| | - Gerben Vader
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany. .,Department of Clinical Genetics, Section of Oncogenetics, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands.
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43
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Shaban K, Sauty SM, Yankulov K. Variation, Variegation and Heritable Gene Repression in S. cerevisiae. Front Genet 2021; 12:630506. [PMID: 33747046 PMCID: PMC7970126 DOI: 10.3389/fgene.2021.630506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/08/2021] [Indexed: 11/13/2022] Open
Abstract
Phenotypic heterogeneity provides growth advantages for a population upon changes of the environment. In S. cerevisiae, such heterogeneity has been observed as "on/off" states in the expression of individual genes in individual cells. These variations can persist for a limited or extended number of mitotic divisions. Such traits are known to be mediated by heritable chromatin structures, by the mitotic transmission of transcription factors involved in gene regulatory circuits or by the cytoplasmic partition of prions or other unstructured proteins. The significance of such epigenetic diversity is obvious, however, we have limited insight into the mechanisms that generate it. In this review, we summarize the current knowledge of epigenetically maintained heterogeneity of gene expression and point out similarities and converging points between different mechanisms. We discuss how the sharing of limiting repression or activation factors can contribute to cell-to-cell variations in gene expression and to the coordination between short- and long- term epigenetic strategies. Finally, we discuss the implications of such variations and strategies in adaptation and aging.
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Affiliation(s)
- Kholoud Shaban
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Safia Mahabub Sauty
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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44
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Ruault M, Scolari VF, Lazar-Stefanita L, Hocher A, Loïodice I, Koszul R, Taddei A. Sir3 mediates long-range chromosome interactions in budding yeast. Genome Res 2021; 31:411-425. [PMID: 33579753 PMCID: PMC7919453 DOI: 10.1101/gr.267872.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/30/2020] [Indexed: 11/24/2022]
Abstract
Physical contacts between distant loci contribute to regulate genome function. However, the molecular mechanisms responsible for settling and maintaining such interactions remain poorly understood. Here, we investigate the well-conserved interactions between heterochromatin loci. In budding yeast, the 32 telomeres cluster in 3–5 foci in exponentially growing cells. This clustering is functionally linked to the formation of heterochromatin in subtelomeric regions through the recruitment of the silencing SIR complex composed of Sir2/3/4. Combining microscopy and Hi-C on strains expressing different alleles of SIR3, we show that the binding of Sir3 directly promotes long-range contacts between distant regions, including the rDNA, telomeres, and internal Sir3-bound sites. Furthermore, we unveil a new property of Sir3 in promoting rDNA compaction. Finally, using a synthetic approach, we demonstrate that Sir3 can bond loci belonging to different chromosomes together, when targeted to these loci, independently of its interaction with its known partners (Rap1, Sir4), Sir2 activity, or chromosome context. Altogether, these data suggest that Sir3 acts as a molecular bridge that stabilizes long-range interactions.
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Affiliation(s)
- Myriam Ruault
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - Vittore F Scolari
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France.,Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756, F-75015 Paris, France
| | - Luciana Lazar-Stefanita
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756, F-75015 Paris, France.,Sorbonne Université, collège Doctoral, F-75005 Paris, France
| | - Antoine Hocher
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - Isabelle Loïodice
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756, F-75015 Paris, France.,Cogitamus Laboratory, F-75005 Paris, France
| | - Angela Taddei
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France.,Cogitamus Laboratory, F-75005 Paris, France
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45
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Bhagwat NR, Owens SN, Ito M, Boinapalli JV, Poa P, Ditzel A, Kopparapu S, Mahalawat M, Davies OR, Collins SR, Johnson JR, Krogan NJ, Hunter N. SUMO is a pervasive regulator of meiosis. eLife 2021; 10:57720. [PMID: 33502312 PMCID: PMC7924959 DOI: 10.7554/elife.57720] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Protein modification by SUMO helps orchestrate the elaborate events of meiosis to faithfully produce haploid gametes. To date, only a handful of meiotic SUMO targets have been identified. Here, we delineate a multidimensional SUMO-modified meiotic proteome in budding yeast, identifying 2747 conjugation sites in 775 targets, and defining their relative levels and dynamics. Modified sites cluster in disordered regions and only a minority match consensus motifs. Target identities and modification dynamics imply that SUMOylation regulates all levels of chromosome organization and each step of meiotic prophase I. Execution-point analysis confirms these inferences, revealing functions for SUMO in S-phase, the initiation of recombination, chromosome synapsis and crossing over. K15-linked SUMO chains become prominent as chromosomes synapse and recombine, consistent with roles in these processes. SUMO also modifies ubiquitin, forming hybrid oligomers with potential to modulate ubiquitin signaling. We conclude that SUMO plays diverse and unanticipated roles in regulating meiotic chromosome metabolism. Most mammalian, yeast and other eukaryote cells have two sets of chromosomes, one from each parent, which contain all the cell’s DNA. Sex cells – like the sperm and egg – however, have half the number of chromosomes and are formed by a specialized type of cell division known as meiosis. At the start of meiosis, each cell replicates its chromosomes so that it has twice the amount of DNA. The cell then undergoes two rounds of division to form sex cells which each contain only one set of chromosomes. Before the cell divides, the two duplicated sets of chromosomes pair up and swap sections of their DNA. This exchange allows each new sex cell to have a unique combination of DNA, resulting in offspring that are genetically distinct from their parents. This complex series of events is tightly regulated, in part, by a protein called the 'small ubiquitin-like modifier' (or SUMO for short), which attaches itself to other proteins and modifies their behavior. This process, known as SUMOylation, can affect a protein’s stability, where it is located in the cell and how it interacts with other proteins. However, despite SUMO being known as a key regulator of meiosis, only a handful of its protein targets have been identified. To gain a better understanding of what SUMO does during meiosis, Bhagwat et al. set out to find which proteins are targeted by SUMO in budding yeast and to map the specific sites of modification. The experiments identified 2,747 different sites on 775 different proteins, suggesting that SUMO regulates all aspects of meiosis. Consistently, inactivating SUMOylation at different times revealed SUMO plays a role at every stage of meiosis, including the replication of DNA and the exchanges between chromosomes. In depth analysis of the targeted proteins also revealed that SUMOylation targets different groups of proteins at different stages of meiosis and interacts with other protein modifications, including the ubiquitin system which tags proteins for destruction. The data gathered by Bhagwat et al. provide a starting point for future research into precisely how SUMO proteins control meiosis in yeast and other organisms. In humans, errors in meiosis are the leading cause of pregnancy loss and congenital diseases. Most of the proteins identified as SUMO targets in budding yeast are also present in humans. So, this research could provide a platform for medical advances in the future. The next step is to study mammalian models, such as mice, to confirm that the regulation of meiosis by SUMO is the same in mammals as in yeast.
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Affiliation(s)
- Nikhil R Bhagwat
- Howard Hughes Medical Institute, University of California Davis, Davis, United States.,Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Shannon N Owens
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Masaru Ito
- Howard Hughes Medical Institute, University of California Davis, Davis, United States.,Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Jay V Boinapalli
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Philip Poa
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Alexander Ditzel
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Srujan Kopparapu
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Meghan Mahalawat
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Owen Richard Davies
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Sean R Collins
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Jeffrey R Johnson
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, United States
| | - Nevan J Krogan
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, United States
| | - Neil Hunter
- Howard Hughes Medical Institute, University of California Davis, Davis, United States.,Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States.,Department of Molecular & Cellular Biology, University of California Davis, Davis, United States
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46
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Zhang S, Yu X, Zhang Y, Xue X, Yu Q, Zha Z, Gogol M, Workman JL, Li S. Metabolic regulation of telomere silencing by SESAME complex-catalyzed H3T11 phosphorylation. Nat Commun 2021; 12:594. [PMID: 33500413 PMCID: PMC7838282 DOI: 10.1038/s41467-020-20711-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023] Open
Abstract
Telomeres are organized into a heterochromatin structure and maintenance of silent heterochromatin is required for chromosome stability. How telomere heterochromatin is dynamically regulated in response to stimuli remains unknown. Pyruvate kinase Pyk1 forms a complex named SESAME (Serine-responsive SAM-containing Metabolic Enzyme complex) to regulate gene expression by phosphorylating histone H3T11 (H3pT11). Here, we identify a function of SESAME in regulating telomere heterochromatin structure. SESAME phosphorylates H3T11 at telomeres, which maintains SIR (silent information regulator) complex occupancy at telomeres and protects Sir2 from degradation by autophagy. Moreover, SESAME-catalyzed H3pT11 directly represses autophagy-related gene expression to further prevent autophagy-mediated Sir2 degradation. By promoting H3pT11, serine increases Sir2 protein levels and enhances telomere silencing. Loss of H3pT11 leads to reduced Sir2 and compromised telomere silencing during chronological aging. Together, our study provides insights into dynamic regulation of silent heterochromatin by histone modifications and autophagy in response to cell metabolism and aging.
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Affiliation(s)
- Shihao Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Yuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xiangyan Xue
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Zitong Zha
- Human Aging Research Institute (HARI), School of Life Science, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Madelaine Gogol
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
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47
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Sprenger M, Brunke S, Hube B, Kasper L. A TRP1-marker-based system for gene complementation, overexpression, reporter gene expression and gene modification in Candida glabrata. FEMS Yeast Res 2020; 20:6027539. [PMID: 33289831 PMCID: PMC7787354 DOI: 10.1093/femsyr/foaa066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/04/2020] [Indexed: 01/14/2023] Open
Abstract
Although less prevalent than its relative Candida albicans, the yeast Candida glabrata is a successful pathogen of humans, which causes life-threatening candidiasis. It is thus vital to understand the pathogenicity mechanisms and contributing genes in C. glabrata. However, gene complementation as a tool for restoring the function of a previously deleted gene is not standardized in C. glabrata, and it is less frequently used than in C. albicans. In this study, we established a gene complementation strategy using genomic integration at the TRP1 locus. We prove that our approach can not only be used for integration of complementation cassettes, but also for overexpression of markers like fluorescent proteins and the antigen ovalbumin, or of potential pathogenicity-related factors like the biotin transporter gene VHT1. With urea amidolyase Dur1,2 as an example, we demonstrate the application of the gene complementation approach for the expression of sequence-modified genes. With this approach, we found that a lysine-to-arginine mutation in the biotinylation motif of Dur1,2 impairs urea-dependent growth of C. glabrata and C. albicans. Taken together, the TRP1-based gene complementation approach is a valuable tool for investigating novel gene functions and for elucidating their role in the pathobiology of C. glabrata.
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Affiliation(s)
- Marcel Sprenger
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Sascha Brunke
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Bernhard Hube
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany.,Institute of Microbiology, Friedrich Schiller University, Neugasse 25, 07743 Jena, Germany
| | - Lydia Kasper
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
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48
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Gnügge R, Symington LS. Efficient DNA double-strand break formation at single or multiple defined sites in the Saccharomyces cerevisiae genome. Nucleic Acids Res 2020; 48:e115. [PMID: 33053188 PMCID: PMC7672422 DOI: 10.1093/nar/gkaa833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 08/18/2020] [Accepted: 09/28/2020] [Indexed: 01/08/2023] Open
Abstract
DNA double-strand breaks (DSBs) are common genome lesions that threaten genome stability and cell survival. Cells use sophisticated repair machineries to detect and heal DSBs. To study DSB repair pathways and associated factors, inducible site-specific endonucleases have proven to be fundamental tools. In Saccharomyces cerevisiae, galactose-inducible rare-cutting endonucleases are commonly used to create a single DSB at a unique cleavage site. Galactose induction requires cell cultivation in suboptimal growth media, which is tedious especially when working with slow growing DSB repair mutants. Moreover, endonucleases that simultaneously create DSBs in multiple defined and unique loci of the yeast genome are not available, hindering studies of DSB repair in different genomic regions and chromatin contexts. Here, we present new tools to overcome these limitations. We employ a heterologous media-independent induction system to express the yeast HO endonuclease or bacterial restriction enzymes for single or multiple DSB formation, respectively. The systems facilitate tightly controlled and efficient DSB formation at defined genomic sites and will be valuable tools to study DSB repair at a local and genome-wide scale.
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Affiliation(s)
- Robert Gnügge
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.,Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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49
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Sauty SM, Shaban K, Yankulov K. Gene repression in S. cerevisiae-looking beyond Sir-dependent gene silencing. Curr Genet 2020; 67:3-17. [PMID: 33037902 DOI: 10.1007/s00294-020-01114-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/24/2020] [Indexed: 01/09/2023]
Abstract
Gene silencing by the SIR (Silent Information Region) family of proteins in S. cerevisiae has been extensively studied and has served as a founding paradigm for our general understanding of gene repression and its links to histone deacetylation and chromatin structure. In recent years, our understanding of other mechanisms of gene repression in S.cerevisiae was significantly advanced. In this review, we focus on such Sir-independent mechanisms of gene repression executed by various Histone Deacetylases (HDACs) and Histone Methyl Transferases (HMTs). We focus on the genes regulated by these enzymes and their known mechanisms of action. We describe the cooperation and redundancy between HDACs and HMTs, and their involvement in gene repression by non-coding RNAs or by their non-histone substrates. We also propose models of epigenetic transmission of the chromatin structures produced by these enzymes and discuss these in the context of gene repression phenomena in other organisms. These include the recycling of the epigenetic marks imposed by HMTs or the recycling of the complexes harboring HDACs.
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Affiliation(s)
- Safia Mahabub Sauty
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Kholoud Shaban
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada.
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50
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Li Y, Jiang Y, Paxman J, O'Laughlin R, Klepin S, Zhu Y, Pillus L, Tsimring LS, Hasty J, Hao N. A programmable fate decision landscape underlies single-cell aging in yeast. Science 2020; 369:325-329. [PMID: 32675375 DOI: 10.1126/science.aax9552] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 01/24/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022]
Abstract
Chromatin instability and mitochondrial decline are conserved processes that contribute to cellular aging. Although both processes have been explored individually in the context of their distinct signaling pathways, the mechanism that determines which process dominates during aging of individual cells is unknown. We show that interactions between the chromatin silencing and mitochondrial pathways lead to an epigenetic landscape of yeast replicative aging with multiple equilibrium states that represent different types of terminal states of aging. The structure of the landscape drives single-cell differentiation toward one of these states during aging, whereby the fate is determined quite early and is insensitive to intracellular noise. Guided by a quantitative model of the aging landscape, we genetically engineered a long-lived equilibrium state characterized by an extended life span.
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Affiliation(s)
- Yang Li
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Yanfei Jiang
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Julie Paxman
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Richard O'Laughlin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Stephen Klepin
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Yuelian Zhu
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.,BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA. .,BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
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