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Durano D, Di Felice F, Caldarelli F, Lukacs A, D'Alfonso A, Saliola M, Sciubba F, Miccheli A, Zambelli F, Pavesi G, Bianchi ME, Camilloni G. Histone acetylation landscape in S. cerevisiae nhp6ab mutants reflects altered glucose metabolism. Biochim Biophys Acta Gen Subj 2019; 1864:129454. [PMID: 31676292 DOI: 10.1016/j.bbagen.2019.129454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/11/2019] [Accepted: 09/18/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND The execution of many genetic programs, influenced by environmental conditions, is epigenetically controlled. Thus, small molecules of the intermediate metabolism being precursors of most of nutrition-deriving epigenetic modifications, sense the cell surrounding environment. METHODS Here we describe histone H4K16 acetylation distribution in S. cerevisiae nhp6ab mutant, using ChIP-seq analysis; its transcription profile by RNA-seq and its metabolic features by studying the metabolome. We then intersected these three -omic approaches to unveil common crosspoints (if any). RESULTS In the nhp6ab mutant, the glucose metabolism is switched to pathways leading to Acetyl-CoA synthesis. These enhanced pathways could lead to histone hyperacetylation altering RNA transcription, particularly of those metabolic genes that maintain high Acetyl-CoA availability. CONCLUSIONS Thus, the absence of chromatin regulators like Nhp6 A and B, interferes with a regulative circular mechanism where histone modification, transcription and metabolism influence each other and contribute to clarify the more general phenomenon in which gene regulation feeds metabolic alterations on epigenetic basis. GENERAL SIGNIFICANCE This study allowed us to identify, in these two factors, a common element of regulation in metabolism and chromatin acetylation state that could represent a powerful tool to find out relationships existing between metabolism and gene expression in more complex systems.
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Affiliation(s)
- Diletta Durano
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
| | - Francesca Di Felice
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
| | - Federica Caldarelli
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
| | - Andrea Lukacs
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
| | - Anna D'Alfonso
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
| | - Michele Saliola
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
| | - Fabio Sciubba
- Dipartimento di Chimica, Sapienza Università di Roma, Rome, Italy
| | - Alfredo Miccheli
- Dipartimento di Chimica, Sapienza Università di Roma, Rome, Italy
| | | | - Giulio Pavesi
- Dipartimento di Bioscienze, Università di Milano, Milan, Italy
| | - Marco E Bianchi
- Chromatin Dynamics Unit, IRCCS San Raffaele Scientific Institute and San Raffaele University, Milan, Italy
| | - Giorgio Camilloni
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy; Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy; Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Italy.
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Mei Q, Huang J, Chen W, Tang J, Xu C, Yu Q, Cheng Y, Ma L, Yu X, Li S. Regulation of DNA replication-coupled histone gene expression. Oncotarget 2017; 8:95005-95022. [PMID: 29212286 PMCID: PMC5706932 DOI: 10.18632/oncotarget.21887] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/20/2017] [Indexed: 12/21/2022] Open
Abstract
The expression of core histone genes is cell cycle regulated. Large amounts of histones are required to restore duplicated chromatin during S phase when DNA replication occurs. Over-expression and excess accumulation of histones outside S phase are toxic to cells and therefore cells need to restrict histone expression to S phase. Misregulation of histone gene expression leads to defects in cell cycle progression, genome stability, DNA damage response and transcriptional regulation. Here, we discussed the factors involved in histone gene regulation as well as the underlying mechanism. Understanding the histone regulation mechanism will shed lights on elucidating the side effects of certain cancer chemotherapeutic drugs and developing potential biomarkers for tumor cells.
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Affiliation(s)
- Qianyun Mei
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Junhua Huang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Wanping Chen
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.,Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jie Tang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Chen Xu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qi Yu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Ying Cheng
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Lixin Ma
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.,Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Xilan Yu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.,Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.,Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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