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Rodriguez-Rodriguez P, Arroyo-Garcia LE, Tsagkogianni C, Li L, Wang W, Végvári Á, Salas-Allende I, Plautz Z, Cedazo-Minguez A, Sinha SC, Troyanskaya O, Flajolet M, Yao V, Roussarie JP. A cell autonomous regulator of neuronal excitability modulates tau in Alzheimer's disease vulnerable neurons. Brain 2024; 147:2384-2399. [PMID: 38462574 PMCID: PMC11224620 DOI: 10.1093/brain/awae051] [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: 10/17/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 03/12/2024] Open
Abstract
Neurons from layer II of the entorhinal cortex (ECII) are the first to accumulate tau protein aggregates and degenerate during prodromal Alzheimer's disease. Gaining insight into the molecular mechanisms underlying this vulnerability will help reveal genes and pathways at play during incipient stages of the disease. Here, we use a data-driven functional genomics approach to model ECII neurons in silico and identify the proto-oncogene DEK as a regulator of tau pathology. We show that epigenetic changes caused by Dek silencing alter activity-induced transcription, with major effects on neuronal excitability. This is accompanied by the gradual accumulation of tau in the somatodendritic compartment of mouse ECII neurons in vivo, reactivity of surrounding microglia, and microglia-mediated neuron loss. These features are all characteristic of early Alzheimer's disease. The existence of a cell-autonomous mechanism linking Alzheimer's disease pathogenic mechanisms in the precise neuron type where the disease starts provides unique evidence that synaptic homeostasis dysregulation is of central importance in the onset of tau pathology in Alzheimer's disease.
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Affiliation(s)
| | | | - Christina Tsagkogianni
- Department of Neurobiology Care Sciences and Society, Karolinska Institutet, 17 164, Solna, Sweden
| | - Lechuan Li
- Department of Computer Science, Rice University, Houston, TX 77004, USA
| | - Wei Wang
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 164, Solna, Sweden
| | - Isabella Salas-Allende
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065, USA
| | - Zakary Plautz
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065, USA
| | - Angel Cedazo-Minguez
- Department of Neurobiology Care Sciences and Society, Karolinska Institutet, 17 164, Solna, Sweden
| | - Subhash C Sinha
- Helen and Robert Appel Alzheimer’s Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olga Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ 08540, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065, USA
| | - Vicky Yao
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 164, Solna, Sweden
| | - Jean-Pierre Roussarie
- Department of Anatomy & Neurobiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
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2
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Karri S, Yang Y, Zhou J, Dickinson Q, Jia J, Huang Y, Wang Z, Gan H, Yu C. Defective transfer of parental histone decreases frequency of homologous recombination by increasing free histone pools in budding yeast. Nucleic Acids Res 2024; 52:5138-5151. [PMID: 38554108 PMCID: PMC11109958 DOI: 10.1093/nar/gkae205] [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: 01/13/2023] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 04/01/2024] Open
Abstract
Recycling of parental histones is an important step in epigenetic inheritance. During DNA replication, DNA polymerase epsilon subunit DPB3/DPB4 and DNA replication helicase subunit MCM2 are involved in the transfer of parental histones to the leading and lagging strands, respectively. Single Dpb3 deletion (dpb3Δ) or Mcm2 mutation (mcm2-3A), which each disrupts one parental histone transfer pathway, leads to the other's predominance. However, the biological impact of the two histone transfer pathways on chromatin structure and DNA repair remains elusive. In this study, we used budding yeast Saccharomyces cerevisiae to determine the genetic and epigenetic outcomes from disruption of parental histone H3-H4 tetramer transfer. We found that a dpb3Δ mcm2-3A double mutant did not exhibit the asymmetric parental histone patterns caused by a single dpb3Δ or mcm2-3A mutation, suggesting that the processes by which parental histones are transferred to the leading and lagging strands are independent. Surprisingly, the frequency of homologous recombination was significantly lower in dpb3Δ, mcm2-3A and dpb3Δ mcm2-3A mutants, likely due to the elevated levels of free histones detected in the mutant cells. Together, these findings indicate that proper transfer of parental histones during DNA replication is essential for maintaining chromatin structure and that lower homologous recombination activity due to parental histone transfer defects is detrimental to cells.
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Affiliation(s)
- Srinivasu Karri
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Yi Yang
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Jiaqi Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Quinn Dickinson
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Jing Jia
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Yuxin Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Haiyun Gan
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chuanhe Yu
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
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3
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Liu Y, Zeng JM, Zhao H, Ao CY, Ao LH, Ban JQ, Li J. Mechanism of KAT2A regulation of H3K36ac in manganese-induced oxidative damage to mitochondria in the nervous system and intervention by curcumin. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116155. [PMID: 38417317 DOI: 10.1016/j.ecoenv.2024.116155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Excessive exposure to manganese in the environment or workplace is strongly linked to neurodegeneration and cognitive impairment, but the precise pathogenic mechanism and preventive measures are still not fully understood. The study aimed to investigate manganese -induced oxidative damage in the nervous system from an epigenetic perspective, focusing on the H3K36ac-dependent antioxidant pathway. Additionally, it sought to examine the potential of curcumin in preventing manganese-induced oxidative damage. Histopathology and transmission electron microscopy revealed that apoptosis and necrosis of neurons and mitochondrial ultrastructure damage were observed in the striatum of manganese-exposed rats. manganese suppressed the expression of mitochondrial antioxidant genes, leading to oxidative damage in the rats' striatum and SH-SY5Y cells. With higher doses of manganese, levels of histone acetyltransferase lysine acetyltransferase 2 A (KAT2A) expression and H3K36ac level decreased. ChIP-qPCR confirmed that H3K36ac enrichment in the promoter regions of antioxidant genes SOD2, PRDX3, and TXN2 was reduced in SH-SY5Y cells after manganese exposure, leading to decreased expression of these genes. Overexpression of KAT2A confirms that it attenuates manganese-induced mitochondrial oxidative damage by regulating H3K36ac levels, which in turn controls the expression of antioxidant genes SOD2, PRDX3, and TXN2 in the manganese-exposed cell model. Furthermore, curcumin might control H3K36ac levels by influencing KAT2A expression, boosting antioxidant genes expression, and reducing manganese-induced mitochondrial oxidative damage. In conclusion, the regulation of mitochondrial oxidative stress by histone acetylation may be an important mechanism of manganese-induced neurotoxicity. This regulation could be achieved by reducing the level of H3K36ac near the promoter region of mitochondrial-associated antioxidant genes via KAT2A. Curcumin mitigates manganese-induced oxidative damage in mitochondria and plays a crucial protective role in manganese-induced oxidative injury in the nervous system.
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Affiliation(s)
- Yan Liu
- School of Public Heath, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang ,Guizhou 561113, China
| | - Jia-Min Zeng
- School of Public Heath, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang ,Guizhou 561113, China
| | - Hua Zhao
- School of Public Heath, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang ,Guizhou 561113, China
| | - Chun-Yan Ao
- School of Public Heath, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang ,Guizhou 561113, China
| | - Li-Hong Ao
- School of Public Heath, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang ,Guizhou 561113, China
| | - Jia-Qi Ban
- School of Public Heath, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang ,Guizhou 561113, China..
| | - Jun Li
- School of Public Heath, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang ,Guizhou 561113, China..
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4
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Yu Y, Zhao F, Yue Y, Zhao Y, Zhou DX. Lysine acetylation of histone acetyltransferase adaptor protein ADA2 is a mechanism of metabolic control of chromatin modification in plants. NATURE PLANTS 2024; 10:439-452. [PMID: 38326652 DOI: 10.1038/s41477-024-01623-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
Histone acetylation is a predominant active chromatin mark deposited by histone acetyltransferases (HATs) that transfer the acetyl group from acetyl coenzyme A (acetyl-CoA) to lysine ε-amino groups in histones. GENERAL CONTROL NON-REPRESSED PROTEIN 5 (GCN5) is one of the best-characterized HATs and functions in association with several adaptor proteins such as ADA2 within multiprotein HAT complexes. ADA2-GCN5 interaction increases GCN5 binding to acetyl-CoA and stimulates its HAT activity. It remains unclear whether the HAT activity of GCN5 (which acetylates not only histones but also cellular proteins) is regulated by acetyl-CoA levels, which vary greatly in cells under different metabolic and nutrition conditions. Here we show that the ADA2 protein itself is acetylated by GCN5 in rice cells. Lysine acetylation exposes ADA2 to a specific E3 ubiquitin ligase and reduces its protein stability. In rice plants, ADA2 protein accumulation reversely parallels its lysine acetylation and acetyl-CoA levels, both of which are dynamically regulated under varying growth conditions. Stress-induced ADA2 accumulation could stimulate GCN5 HAT activity to compensate for the reduced acetyl-CoA levels for histone acetylation. These results indicate that ADA2 lysine acetylation that senses cellular acetyl-CoA variations is a mechanism to regulate HAT activity and histone acetylation homeostasis in plants under changing environments.
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Affiliation(s)
- Yue Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Feng Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yaping Yue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, France.
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5
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Li J, Cao Y, Yang Y, Ma H, Zhao J, Zhang Y, Liu N. Quantitative Acetylomics Reveals Substrates of Lysine Acetyltransferase GCN5 in Adult and Aging Drosophila. J Proteome Res 2023; 22:2909-2924. [PMID: 37545086 DOI: 10.1021/acs.jproteome.3c00247] [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] [Indexed: 08/08/2023]
Abstract
Protein lysine acetylation is a dynamic post-translational modification (PTM) that regulates a wide spectrum of cellular events including aging. General control nonderepressible 5 (GCN5) is a highly conserved lysine acetyltransferase (KAT). However, the acetylation substrates of GCN5 in vivo remain poorly studied, and moreover, how lysine acetylation changes with age and the contribution of KATs to aging remain to be addressed. Here, using Drosophila, we perform label-free quantitative acetylomic analysis, identifying new substrates of GCN5 in the adult and aging process. We further characterize the dynamics of protein acetylation with age, which exhibits a trend of increase. Since the expression of endogenous fly Gcn5 progressively increases during aging, we reason that, by combining the substrate analysis, the increase in acetylation with age is triggered, at least in part, by GCN5. Collectively, our study substantially expands the atlas of GCN5 substrates in vivo, provides a resource of protein acetylation that naturally occurs with age, and demonstrates how individual KAT contributes to the aging acetylome.
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Affiliation(s)
- Jingshu Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ye Cao
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Yang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huanhuan Ma
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Zhao
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- Shanghai Key Laboratory of Aging Studies, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
| | - Nan Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- Shanghai Key Laboratory of Aging Studies, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
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6
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Nguyen AV, Soto JM, Gonzalez SM, Murillo J, Trumble ER, Shan FY, Huang JH. H3G34-Mutant Gliomas-A Review of Molecular Pathogenesis and Therapeutic Options. Biomedicines 2023; 11:2002. [PMID: 37509641 PMCID: PMC10377039 DOI: 10.3390/biomedicines11072002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The 2021 World Health Organization Classification of Tumors of the Central Nervous System reflected advances in understanding of the roles of oncohistones in gliomagenesis with the introduction of the H3.3-G34R/V mutant glioma to the already recognized H3-K27M altered glioma, which represent the diagnoses of pediatric-type diffuse hemispheric glioma and diffuse midline glioma, respectively. Despite advances in research regarding these disease entities, the prognosis remains poor. While many studies and clinical trials focus on H3-K27M-altered-glioma patients, those with H3.3-G34R/V mutant gliomas represent a particularly understudied population. Thus, we sought to review the current knowledge regarding the molecular mechanisms underpinning the gliomagenesis of H3.3-G34R/V mutant gliomas and the diagnosis, treatment, long-term outcomes, and possible future therapeutics.
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Affiliation(s)
- Anthony V Nguyen
- Department of Neurosurgery, Baylor Scott and White Medical Center, Temple, TX 76508, USA
| | - Jose M Soto
- Department of Neurosurgery, Baylor Scott and White Medical Center, Temple, TX 76508, USA
| | - Sarah-Marie Gonzalez
- Department of Neurosurgery, Baylor Scott and White Medical Center, Temple, TX 76508, USA
| | - Jennifer Murillo
- Department of Neurosurgery, Baylor Scott and White Medical Center, Temple, TX 76508, USA
- Department of Neurology, Baylor Scott and White Medical Center, Temple, TX 76508, USA
| | - Eric R Trumble
- Department of Neurosurgery, Baylor Scott and White Medical Center, Temple, TX 76508, USA
| | - Frank Y Shan
- Department of Neurosurgery, Baylor Scott and White Medical Center, Temple, TX 76508, USA
- Department of Pathology, Baylor Scott and White Medical Center, Temple, TX 76508, USA
| | - Jason H Huang
- Department of Neurosurgery, Baylor Scott and White Medical Center, Temple, TX 76508, USA
- Department of Surgery, Texas A&M University College of Medicine, Temple, TX 76508, USA
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7
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Jain K, Marunde MR, Burg JM, Gloor SL, Joseph FM, Poncha KF, Gillespie ZB, Rodriguez KL, Popova IK, Hall NW, Vaidya A, Howard SA, Taylor HF, Mukhsinova L, Onuoha UC, Patteson EF, Cooke SW, Taylor BC, Weinzapfel EN, Cheek MA, Meiners MJ, Fox GC, Namitz KEW, Cowles MW, Krajewski K, Sun ZW, Cosgrove MS, Young NL, Keogh MC, Strahl BD. An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability. eLife 2023; 12:e82596. [PMID: 37204295 PMCID: PMC10229121 DOI: 10.7554/elife.82596] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/18/2023] [Indexed: 05/20/2023] Open
Abstract
In nucleosomes, histone N-terminal tails exist in dynamic equilibrium between free/accessible and collapsed/DNA-bound states. The latter state is expected to impact histone N-termini availability to the epigenetic machinery. Notably, H3 tail acetylation (e.g. K9ac, K14ac, K18ac) is linked to increased H3K4me3 engagement by the BPTF PHD finger, but it is unknown if this mechanism has a broader extension. Here, we show that H3 tail acetylation promotes nucleosomal accessibility to other H3K4 methyl readers, and importantly, extends to H3K4 writers, notably methyltransferase MLL1. This regulation is not observed on peptide substrates yet occurs on the cis H3 tail, as determined with fully-defined heterotypic nucleosomes. In vivo, H3 tail acetylation is directly and dynamically coupled with cis H3K4 methylation levels. Together, these observations reveal an acetylation 'chromatin switch' on the H3 tail that modulates read-write accessibility in nucleosomes and resolves the long-standing question of why H3K4me3 levels are coupled with H3 acetylation.
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Affiliation(s)
- Kanishk Jain
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
| | | | | | | | - Faith M Joseph
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | - Karl F Poncha
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | | | | | | | | | | | | | | | | | | | | | - Spencer W Cooke
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
| | - Bethany C Taylor
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | | | | | | | - Geoffrey C Fox
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
| | | | | | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
| | | | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology, Upstate Medical UniversitySyracuseUnited States
| | - Nicolas L Young
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | | | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
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8
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Karri S, Yang Y, Zhou J, Dickson Q, Wang Z, Gan H, Yu C. Defective transfer of parental histone decreases frequency of homologous recombination in budding yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523501. [PMID: 36711718 PMCID: PMC9882084 DOI: 10.1101/2023.01.10.523501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Recycling of parental histones is an important step in epigenetic inheritance. During DNA replication, DNA polymerase epsilon subunit DPB3/DPB4 and DNA replication helicase subunit MCM2 are involved in the transfer of parental histones to the leading and lagging DNA strands, respectively. Single Dpb3 deletion ( dpb3Δ ) or Mcm2 mutation ( mcm2-3A ), which each disrupt one parental histone transfer pathway, leads to the other's predominance. However, the impact of the two histone transfer pathways on chromatin structure and DNA repair remains elusive. In this study, we used budding yeast Saccharomyces cerevisiae to determine the genetic and epigenetic outcomes from disruption of parental histone H3-H4 tetramer transfer. We found that a dpb3Δ / mcm2-3A double mutant did not exhibit the single dpb3Δ and mcm2-3A mutants' asymmetric parental histone patterns, suggesting that the processes by which parental histones are transferred to the leading and lagging strands are independent. Surprisingly, the frequency of homologous recombination was significantly lower in dpb3Δ, mcm2-3A , and dpb3Δ / mcm2-3A mutants relative to the wild-type strain, likely due to the elevated levels of free histones detected in the mutant cells. Together, these findings indicate that proper transfer of parental histones to the leading and lagging strands during DNA replication is essential for maintaining chromatin structure and that high levels of free histones due to parental histone transfer defects are detrimental to cells.
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9
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Lu X, Xin DE, Du JK, Zou QC, Wu Q, Zhang YS, Deng W, Yue J, Fan XS, Zeng Y, Cheng X, Li X, Hou Z, Mohan M, Zhao TC, Lu X, Chang Z, Xu L, Sun Y, Zu X, Zhang Y, Chinn YE. Loss of LOXL2 Promotes Uterine Hypertrophy and Tumor Progression by Enhancing H3K36ac-Dependent Gene Expression. Cancer Res 2022; 82:4400-4413. [PMID: 36197797 DOI: 10.1158/0008-5472.can-22-0848] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/23/2022] [Accepted: 09/30/2022] [Indexed: 02/05/2023]
Abstract
UNLABELLED Lysyl oxidase-like 2 (LOXL2) is a member of the scavenger receptor cysteine-rich (SRCR) repeat carrying LOX family. Although LOXL2 is suspected to be involved in histone association and chromatin modification, the role of LOXL2 in epigenetic regulation during tumorigenesis and cancer progression remains unclear. Here, we report that nuclear LOXL2 associates with histone H3 and catalyzes H3K36ac deacetylation and deacetylimination. Both the N-terminal SRCR repeats and the C-terminal catalytic domain of LOXL2 carry redundant deacetylase catalytic activity. Overexpression of LOXL2 markedly reduced H3K36 acetylation and blocked H3K36ac-dependent transcription of genes, including c-MYC, CCND1, HIF1A, and CD44. Consequently, LOXL2 overexpression reduced cancer cell proliferation in vitro and inhibited xenograft tumor growth in vivo. In contrast, LOXL2 deficiency resulted in increased H3K36 acetylation and aberrant expression of H3K36ac-dependent genes involved in multiple oncogenic signaling pathways. Female LOXL2-deficient mice spontaneously developed uterine hypertrophy and uterine carcinoma. Moreover, silencing LOXL2 in cancer cells enhanced tumor progression and reduced the efficacy of cisplatin and anti-programmed cell death 1 (PD-1) combination therapy. Clinically, low nuclear LOXL2 expression and high H3K36ac levels corresponded to poor prognosis in uterine endometrial carcinoma patients. These results suggest that nuclear LOXL2 restricts cancer development in the female reproductive system via the regulation of H3K36ac deacetylation. SIGNIFICANCE LOXL2 loss reprograms the epigenetic landscape to promote uterine cancer initiation and progression and repress the efficacy of anti-PD-1 immunotherapy, indicating that LOXL2 is a tumor suppressor.
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Affiliation(s)
- Xufeng Lu
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang; Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
| | - Dazhuan E Xin
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang
- Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
| | - Juanjuan K Du
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang
- Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
| | - Quanli C Zou
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qian Wu
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang; Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
| | - Yanan S Zhang
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang; Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
| | - Wenhai Deng
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang; Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
| | - Jicheng Yue
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
| | - Xing S Fan
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuanyuan Zeng
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
| | - Xiaju Cheng
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
| | - Xue Li
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang; Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
| | - Zhaoyuan Hou
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Man Mohan
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ting C Zhao
- Departments of Surgery and Medicine, Brown University School of Medicine-Rhode Island Hospital, Providence, Rhode Island
| | - Xiaomei Lu
- Cancer Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Zhijie Chang
- State Key Laboratory of Membrane Biology, Tsinghua University School of Medicine, Beijing, China
| | - Liyan Xu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Yu Sun
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiongbing Zu
- Departments of Urology and Obstetrics and Gynecology, Xiangya Hospital, Central South University, Hunan, China
| | - Yu Zhang
- Departments of Urology and Obstetrics and Gynecology, Xiangya Hospital, Central South University, Hunan, China
| | - Y Eugene Chinn
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang
- Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
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10
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Sharda A, Humphrey TC. The role of histone H3K36me3 writers, readers and erasers in maintaining genome stability. DNA Repair (Amst) 2022; 119:103407. [PMID: 36155242 DOI: 10.1016/j.dnarep.2022.103407] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/03/2022]
Abstract
Histone Post-Translational Modifications (PTMs) play fundamental roles in mediating DNA-related processes such as transcription, replication and repair. The histone mark H3K36me3 and its associated methyltransferase SETD2 (Set2 in yeast) are archetypical in this regard, performing critical roles in each of these DNA transactions. Here, we present an overview of H3K36me3 regulation and the roles of its writers, readers and erasers in maintaining genome stability through facilitating DNA double-strand break (DSB) repair, checkpoint signalling and replication stress responses. Further, we consider how loss of SETD2 and H3K36me3, frequently observed in a number of different cancer types, can be specifically targeted in the clinic through exploiting loss of particular genome stability functions.
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Affiliation(s)
- Asmita Sharda
- CRUK and MRC Oxford Institute for Radiation Oncology, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Timothy C Humphrey
- CRUK and MRC Oxford Institute for Radiation Oncology, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
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11
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Etier A, Dumetz F, Chéreau S, Ponts N. Post-Translational Modifications of Histones Are Versatile Regulators of Fungal Development and Secondary Metabolism. Toxins (Basel) 2022; 14:toxins14050317. [PMID: 35622565 PMCID: PMC9145779 DOI: 10.3390/toxins14050317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 02/04/2023] Open
Abstract
Chromatin structure is a major regulator of DNA-associated processes, such as transcription, DNA repair, and replication. Histone post-translational modifications, or PTMs, play a key role on chromatin dynamics. PTMs are involved in a wide range of biological processes in eukaryotes, including fungal species. Their deposition/removal and their underlying functions have been extensively investigated in yeasts but much less in other fungi. Nonetheless, the major role of histone PTMs in regulating primary and secondary metabolisms of filamentous fungi, including human and plant pathogens, has been pinpointed. In this review, an overview of major identified PTMs and their respective functions in fungi is provided, with a focus on filamentous fungi when knowledge is available. To date, most of these studies investigated histone acetylations and methylations, but the development of new methodologies and technologies increasingly allows the wider exploration of other PTMs, such as phosphorylation, ubiquitylation, sumoylation, and acylation. Considering the increasing number of known PTMs and the full range of their possible interactions, investigations of the subsequent Histone Code, i.e., the biological consequence of the combinatorial language of all histone PTMs, from a functional point of view, are exponentially complex. Better knowledge about histone PTMs would make it possible to efficiently fight plant or human contamination, avoid the production of toxic secondary metabolites, or optimize the industrial biosynthesis of certain beneficial compounds.
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12
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Abstract
Although tumourigenesis occurs due to genetic mutations, the role of epigenetic dysregulations in cancer is also well established. Epigenetic dysregulations in cancer may occur as a result of mutations in genes encoding histone/DNA-modifying enzymes and chromatin remodellers or mutations in histone protein itself. It is also true that misregulated gene expression without genetic mutations in these factors could also support tumour initiation and progression. Interestingly, metabolic rewiring has emerged as a hallmark of cancer due to gene mutations in specific metabolic enzymes or dietary/environmental factors. Recent studies report an intricate cross-talk between epigenetic and metabolic reprogramming in cancer. This review discusses the role of epigenetic and metabolic dysregulations and their cross-talk in tumourigenesis with a special focus on gliomagenesis. We also discuss the role of recently developed human embryonic stem cells/induced pluripotent stem cells-derived organoid models of gliomas and how these models are proving instrumental in uncovering human-specific cellular and molecular complexities of gliomagenesis.
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Affiliation(s)
- Bismi Phasaludeen
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Suraiya Anjum Ansari
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
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13
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Geng Q, Li H, Wang D, Sheng RC, Zhu H, Klosterman SJ, Subbarao KV, Chen JY, Chen FM, Zhang DD. The Verticillium dahliae Spt-Ada-Gcn5 Acetyltransferase Complex Subunit Ada1 Is Essential for Conidia and Microsclerotia Production and Contributes to Virulence. Front Microbiol 2022; 13:852571. [PMID: 35283850 PMCID: PMC8905346 DOI: 10.3389/fmicb.2022.852571] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/31/2022] [Indexed: 12/16/2022] Open
Abstract
Verticillium dahliae is a destructive soil-borne pathogen of many economically important dicots. The genetics of pathogenesis in V. dahliae has been extensively studied. Spt-Ada-Gcn5 acetyltransferase complex (SAGA) is an ATP-independent multifunctional chromatin remodeling complex that contributes to diverse transcriptional regulatory functions. As members of the core module in the SAGA complex in Saccharomyces cerevisiae, Ada1, together with Spt7 and Spt20, play an important role in maintaining the integrity of the complex. In this study, we identified homologs of the SAGA complex in V. dahliae and found that deletion of the Ada1 subunit (VdAda1) causes severe defects in the formation of conidia and microsclerotia, and in melanin biosynthesis and virulence. The effect of VdAda1 on histone acetylation in V. dahliae was confirmed by western blot analysis. The deletion of VdAda1 resulted in genome-wide alteration of the V. dahliae transcriptome, including genes encoding transcription factors and secreted proteins, suggesting its prominent role in the regulation of transcription and virulence. Overall, we demonstrated that VdAda1, a member of the SAGA complex, modulates multiple physiological processes by regulating global gene expression that impinge on virulence and survival in V. dahliae.
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Affiliation(s)
- Qi Geng
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Huan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dan Wang
- Team of Crop Verticillium Wilt, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruo-Cheng Sheng
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - He Zhu
- National Cotton Industry Technology System Liaohe Comprehensive Experimental Station, The Cotton Research Center of Liaoning Academy of Agricultural Sciences, Liaoning Provincial Institute of Economic Crops, Liaoyang, China
| | - Steven J Klosterman
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, United States
| | - Krishna V Subbarao
- Department of Plant Pathology, c/o U.S. Agricultural Research Station, University of California, Davis, Salinas, CA, United States
| | - Jie-Yin Chen
- Team of Crop Verticillium Wilt, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feng-Mao Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dan-Dan Zhang
- Team of Crop Verticillium Wilt, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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14
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Cayuela H, Jacob S, Schtickzelle N, Verdonck R, Philippe H, Laporte M, Huet M, Bernatchez L, Legrand D. Transgenerational plasticity of dispersal‐related traits in a ciliate: genotype‐dependency and fitness consequences. OIKOS 2022. [DOI: 10.1111/oik.08846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hugo Cayuela
- Dépt de Biologie, Inst. de Biologie Intégrative et des Systèmes (IBIS), Univ. Laval, Pavillon Charles‐Eugène‐Marchand Québec QC Canada
- Dept of Ecology and Evolution, Univ. of Lausanne Lausanne Switzerland
| | - Staffan Jacob
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
| | - Nicolas Schtickzelle
- Univ. Catholique de Louvain, Earth and Life Inst., Biodiversity Research Centre Louvain‐la‐Neuve Belgium
| | - Rik Verdonck
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
| | - Hervé Philippe
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
- Dépt de Biochimie, Centre Robert‐Cedergren, Univ. de Montréal Montréal QC Canada
| | - Martin Laporte
- Ministère des Forêts, de la Faune et des Parc (MFFP) du Québec Québec QC Canada
| | - Michèle Huet
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
| | - Louis Bernatchez
- Dépt de Biologie, Inst. de Biologie Intégrative et des Systèmes (IBIS), Univ. Laval, Pavillon Charles‐Eugène‐Marchand Québec QC Canada
| | - Delphine Legrand
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
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15
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Hawar A, Xiong S, Yang Z, Sun B. Histone Acetyltransferase SlGCN5 Regulates Shoot Meristem and Flower Development in Solanum lycopersicum. FRONTIERS IN PLANT SCIENCE 2022; 12:805879. [PMID: 35126431 PMCID: PMC8814577 DOI: 10.3389/fpls.2021.805879] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/21/2021] [Indexed: 06/02/2023]
Abstract
The histone acetyltransferase (HAT) general control non-repressed protein 5 (GCN5) plays important roles in plant development via epigenetic regulation of its target genes. However, the role of GCN5 in tomato, especially in the regulation of tomato shoot meristem and flower development, has not been well-understood. In this study, we found that silencing of Solanum lycopersicum GCN5 (SlGCN5, Solyc10g045400.1.1) by virus-induced gene silencing (VIGS) and RNA interference (RNAi) resulted in the loss of shoot apical dominance, reduced shoot apical meristem (SAM) size, and dwarf and bushy plant phenotype. Besides, we occasionally observed extra carpelloid stamens and carpels fused with stamens at the late stages of flower development. Through gene expression analysis, we noticed that SlGCN5 could enhance SlWUS transcript levels in both SAM and floral meristem (FM). Similar to the known function of GCN5 in Arabidopsis, we demonstrated that SIGCN5 may form a HAT unit with S. lycopersicum alteration/deficiency in activation 2a (SlADA2a) and SlADA2b proteins in tomato. Therefore, our results provide insights in the SlGCN5-mediated regulation of SAM maintenance and floral development in tomato.
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16
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Murphy ZC, Murphy K, Myers J, Getman M, Couch T, Schulz VP, Lezon-Geyda K, Palumbo C, Yan H, Mohandas N, Gallagher PG, Steiner LA. Regulation of RNA polymerase II activity is essential for terminal erythroid maturation. Blood 2021; 138:1740-1756. [PMID: 34075391 PMCID: PMC8569412 DOI: 10.1182/blood.2020009903] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/30/2021] [Indexed: 11/20/2022] Open
Abstract
The terminal maturation of human erythroblasts requires significant changes in gene expression in the context of dramatic nuclear condensation. Defects in this process are associated with inherited anemias and myelodysplastic syndromes. The progressively dense appearance of the condensing nucleus in maturing erythroblasts led to the assumption that heterochromatin accumulation underlies this process, but despite extensive study, the precise mechanisms underlying this essential biologic process remain elusive. To delineate the epigenetic changes associated with the terminal maturation of human erythroblasts, we performed mass spectrometry of histone posttranslational modifications combined with chromatin immunoprecipitation coupled with high-throughput sequencing, Assay for Transposase Accessible Chromatin, and RNA sequencing. Our studies revealed that the terminal maturation of human erythroblasts is associated with a dramatic decline in histone marks associated with active transcription elongation, without accumulation of heterochromatin. Chromatin structure and gene expression were instead correlated with dynamic changes in occupancy of elongation competent RNA polymerase II, suggesting that terminal erythroid maturation is controlled largely at the level of transcription. We further demonstrate that RNA polymerase II "pausing" is highly correlated with transcriptional repression, with elongation competent RNA polymerase II becoming a scare resource in late-stage erythroblasts, allocated to erythroid-specific genes. Functional studies confirmed an essential role for maturation stage-specific regulation of RNA polymerase II activity during erythroid maturation and demonstrate a critical role for HEXIM1 in the regulation of gene expression and RNA polymerase II activity in maturing erythroblasts. Taken together, our findings reveal important insights into the mechanisms that regulate terminal erythroid maturation and provide a novel paradigm for understanding normal and perturbed erythropoiesis.
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Affiliation(s)
| | | | - Jacquelyn Myers
- Department of Pediatrics and
- Genomics Resource Center, University of Rochester, Rochester, NY
| | | | | | | | | | - Cal Palumbo
- Genomics Resource Center, University of Rochester, Rochester, NY
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17
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Chen YC, Hsu PY, Chin CH, Hsiao CC, Liou CW, Wang TY, Lin YY, Lee CP, Lin HC, Lin MC, Su MC. H3K23/H3K36 hypoacetylation and HDAC1 up-regulation are associated with adverse consequences in obstructive sleep apnea patients. Sci Rep 2021; 11:20697. [PMID: 34667186 PMCID: PMC8526826 DOI: 10.1038/s41598-021-00052-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 09/20/2021] [Indexed: 12/23/2022] Open
Abstract
The aim of this study is to determine the roles of global histone acetylation (Ac)/methylation (me), their modifying enzymes, and gene-specific histone enrichment in obstructive sleep apnea (OSA). Global histone modifications, and their modifying enzyme expressions were assessed in peripheral blood mononuclear cells from 56 patients with OSA and 16 matched subjects with primary snoring (PS). HIF-1α gene promoter-specific H3K36Ac enrichment was assessed in another cohort (28 OSA, 8 PS). Both global histone H3K23Ac and H3K36Ac expressions were decreased in OSA patients versus PS subjects. H3K23Ac expressions were further decreased in OSA patients with prevalent hypertension. HDAC1 expressions were higher in OSA patients, especially in those with excessive daytime sleepiness, and reduced after more than 6 months of continuous positive airway pressure treatment. H3K79me3 expression was increased in those with high C-reactive protein levels. Decreased KDM6B protein expressions were noted in those with a high hypoxic load, and associated with a higher risk for incident cardiovascular events or hypertension. HIF-1α gene promoter-specific H3K36Ac enrichment was decreased in OSA patients versus PS subjects. In vitro intermittent hypoxia with re-oxygenation stimuli resulted in HDAC1 over-expression and HIF-1α gene promoter-specific H3K36Ac under-expression, while HDAC1 inhibitor, SAHA, reversed oxidative stress through inhibiting NOX1. In conclusions, H3K23/H3K36 hypoacetylation is associated with the development of hypertension and disease severity in sleep-disordered breathing patients, probably through up-regulation of HDAC1, while H3K79 hypermethylation is associated with higher risk of cardiovascular diseases, probably through down-regulation of KDM6B.
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Affiliation(s)
- Yung-Che Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan.,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Po-Yuan Hsu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan.,Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chien-Hung Chin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan.,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chang-Chun Hsiao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan. .,Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taouyan, 33302, Taiwan.
| | - Chia-Wei Liou
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ting-Ya Wang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan
| | - Yong-Yong Lin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan
| | - Chiu-Ping Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan
| | - Hsin-Ching Lin
- Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Meng-Chih Lin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan. .,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan. .,Department of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Mao-Chang Su
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan. .,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan. .,Chang Gung University of Science and Technology, Chia-yi, Taiwan.
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18
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Mendieta JP, Marand AP, Ricci WA, Zhang X, Schmitz RJ. Leveraging histone modifications to improve genome annotations. G3 (BETHESDA, MD.) 2021; 11:jkab263. [PMID: 34568920 PMCID: PMC8473982 DOI: 10.1093/g3journal/jkab263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/15/2021] [Indexed: 12/27/2022]
Abstract
Accurate genome annotations are essential to modern biology; however, they remain challenging to produce. Variation in gene structure and expression across species, as well as within an organism, make correctly annotating genes arduous; an issue exacerbated by pitfalls in current in silico methods. These issues necessitate complementary approaches to add additional confidence and rectify potential misannotations. Integration of epigenomic data into genome annotation is one such approach. In this study, we utilized sets of histone modification data, which are precisely distributed at either gene bodies or promoters to evaluate the annotation of the Zea mays genome. We leveraged these data genome wide, allowing for identification of annotations discordant with empirical data. In total, 13,159 annotation discrepancies were found in Z. mays upon integrating data across three different tissues, which were corroborated using RNA-based approaches. Upon correction, genes were extended by an average of 2128 base pairs, and we identified 2529 novel genes. Application of this method to five additional plant genomes identified a series of misannotations, as well as identified novel genes, including 13,836 in Asparagus officinalis, 2724 in Setaria viridis, 2446 in Sorghum bicolor, 8631 in Glycine max, and 2585 in Phaseolous vulgaris. This study demonstrates that histone modification data can be leveraged to rapidly improve current genome annotations across diverse plant lineages.
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Affiliation(s)
| | | | - William A Ricci
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Xuan Zhang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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19
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Separovich RJ, Wilkins MR. Ready, SET, Go: Post-translational regulation of the histone lysine methylation network in budding yeast. J Biol Chem 2021; 297:100939. [PMID: 34224729 PMCID: PMC8329514 DOI: 10.1016/j.jbc.2021.100939] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 11/21/2022] Open
Abstract
Histone lysine methylation is a key epigenetic modification that regulates eukaryotic transcription. Here, we comprehensively review the function and regulation of the histone methylation network in the budding yeast and model eukaryote, Saccharomyces cerevisiae. First, we outline the lysine methylation sites that are found on histone proteins in yeast (H3K4me1/2/3, H3K36me1/2/3, H3K79me1/2/3, and H4K5/8/12me1) and discuss their biological and cellular roles. Next, we detail the reduced but evolutionarily conserved suite of methyltransferase (Set1p, Set2p, Dot1p, and Set5p) and demethylase (Jhd1p, Jhd2p, Rph1p, and Gis1p) enzymes that are known to control histone lysine methylation in budding yeast cells. Specifically, we illustrate the domain architecture of the methylation enzymes and highlight the structural features that are required for their respective functions and molecular interactions. Finally, we discuss the prevalence of post-translational modifications on yeast histone methylation enzymes and how phosphorylation, acetylation, and ubiquitination in particular are emerging as key regulators of enzyme function. We note that it will be possible to completely connect the histone methylation network to the cell's signaling system, given that all methylation sites and cognate enzymes are known, most phosphosites on the enzymes are known, and the mapping of kinases to phosphosites is tractable owing to the modest set of protein kinases in yeast. Moving forward, we expect that the rich variety of post-translational modifications that decorates the histone methylation machinery will explain many of the unresolved questions surrounding the function and dynamics of this intricate epigenetic network.
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Affiliation(s)
- Ryan J Separovich
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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20
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Vlachonasios K, Poulios S, Mougiou N. The Histone Acetyltransferase GCN5 and the Associated Coactivators ADA2: From Evolution of the SAGA Complex to the Biological Roles in Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:308. [PMID: 33562796 PMCID: PMC7915528 DOI: 10.3390/plants10020308] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 01/08/2023]
Abstract
Transcription of protein-encoding genes starts with forming a pre-initiation complex comprised of RNA polymerase II and several general transcription factors. To activate gene expression, transcription factors must overcome repressive chromatin structure, which is accomplished with multiprotein complexes. One such complex, SAGA, modifies the nucleosomal histones through acetylation and other histone modifications. A prototypical histone acetyltransferase (HAT) known as general control non-repressed protein 5 (GCN5), was defined biochemically as the first transcription-linked HAT with specificity for histone H3 lysine 14. In this review, we analyze the components of the putative plant SAGA complex during plant evolution, and current knowledge on the biological role of the key components of the HAT module, GCN5 and ADA2b in plants, will be summarized.
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Affiliation(s)
- Konstantinos Vlachonasios
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.P.); (N.M.)
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21
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The N-Terminal Tail of Histone H3 Regulates Copper Homeostasis in Saccharomyces cerevisiae. Mol Cell Biol 2021; 41:MCB.00210-20. [PMID: 33257505 DOI: 10.1128/mcb.00210-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/22/2020] [Indexed: 11/20/2022] Open
Abstract
Copper homeostasis is crucial for various cellular processes. The balance between nutritional and toxic copper levels is maintained through the regulation of its uptake, distribution, and detoxification via antagonistic actions of two transcription factors, Ace1 and Mac1. Ace1 responds to toxic copper levels by transcriptionally regulating detoxification genes CUP1 and CRS5 Cup1 metallothionein confers protection against toxic copper levels. CUP1 gene regulation is a multifactorial event requiring Ace1, TATA-binding protein (TBP), chromatin remodeler, acetyltransferase (Spt10), and histones. However, the role of histone H3 residues has not been fully elucidated. To investigate the role of the H3 tail in CUP1 transcriptional regulation, we screened the library of histone mutants in copper stress. We identified mutations in H3 (K23Q, K27R, K36Q, Δ5-16, Δ13-16, Δ13-28, Δ25-28, Δ28-31, and Δ29-32) that reduce CUP1 expression. We detected reduced Ace1 occupancy across the CUP1 promoter in K23Q, K36Q, Δ5-16, Δ13-28, Δ25-28, and Δ28-31 mutations correlating with the reduced CUP1 transcription. The majority of these mutations affect TBP occupancy at the CUP1 promoter, augmenting the CUP1 transcription defect. Additionally, some mutants displayed cytosolic protein aggregation upon copper stress. Altogether, our data establish previously unidentified residues of the H3 N-terminal tail and their modifications in CUP1 regulation.
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Culbertson SJ, Shogren-Knaak MA. Mechanisms of stimulation of SAGA-mediated nucleosome acetylation by a transcriptional activator. Biochem Biophys Rep 2021; 25:100884. [PMID: 33437882 PMCID: PMC7786029 DOI: 10.1016/j.bbrep.2020.100884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 11/06/2020] [Accepted: 12/18/2020] [Indexed: 12/02/2022] Open
Abstract
Eukaryotic gene expression requires the coordination of multiple factors to overcome the repressive nature of chromatin. However, the mechanistic details of this coordination are not well understood. The SAGA family of transcriptional coactivators interacts with DNA-binding activators to establish regions of hyperacetylation. We have previously shown that, contrary to the prevailing model in which activator protein increases SAGA affinity for nucleosome substrate, the Gal4-VP16 activator model system augments the rate of acetylation turnover for the SAGA complex from budding yeast. To better understand how this stimulation occurs, we have identified necessary components using both kinetics assays and binding interactions studies. We find that Gal4-VP16-mediated stimulation requires activator binding to DNA flanking the nucleosome, as it cannot be reproduced in trans by activator protein alone or by exogenous DNA containing the activator binding site in combination with the activator protein. Further, activator-mediated stimulation requires subunits outside of the histone acetylation (HAT) module, with the Tra1 subunit being responsible for the majority of the stimulation. Interestingly, for the HAT module alone, nucleosome acetylation is inhibited by activator proteins due to non-specific binding of the activator to the nucleosomes. This inhibition is not observed for the yeast ADA complex, a small complex comprised mostly of the HAT module, suggesting that subunits outside of the HAT module in both it and SAGA can overcome non-specific activator binding to nucleosomes. However, this activity appears distinct from activator-mediated stimulation, as ADA complex acetylation is not stimulated by Gal4-VP16. Stimulation of nucleosome acetylation by SAGA requires activator in cis Tra1 mediates the majority of activator stimulation The core HAT complex of SAGA is inhibited by activator due to non-specific binding The related ADA complex is neither stimulated nor inhibited by activator
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Affiliation(s)
- Sannie J Culbertson
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, United States
| | - Michael A Shogren-Knaak
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, United States
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Haase S, Nuñez FM, Gauss JC, Thompson S, Brumley E, Lowenstein P, Castro MG. Hemispherical Pediatric High-Grade Glioma: Molecular Basis and Therapeutic Opportunities. Int J Mol Sci 2020; 21:ijms21249654. [PMID: 33348922 PMCID: PMC7766684 DOI: 10.3390/ijms21249654] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
In this review, we discuss the molecular characteristics, development, evolution, and therapeutic perspectives for pediatric high-grade glioma (pHGG) arising in cerebral hemispheres. Recently, the understanding of biology of pHGG experienced a revolution with discoveries arising from genomic and epigenomic high-throughput profiling techniques. These findings led to identification of prevalent molecular alterations in pHGG and revealed a strong connection between epigenetic dysregulation and pHGG development. Although we are only beginning to unravel the molecular biology underlying pHGG, there is a desperate need to develop therapies that would improve the outcome of pHGG patients, as current therapies do not elicit significant improvement in median survival for this patient population. We explore the molecular and cell biology and clinical state-of-the-art of pediatric high-grade gliomas (pHGGs) arising in cerebral hemispheres. We discuss the role of driving mutations, with a special consideration of the role of epigenetic-disrupting mutations. We will also discuss the possibilities of targeting unique molecular vulnerabilities of hemispherical pHGG to design innovative tailored therapies.
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Affiliation(s)
- Santiago Haase
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Fernando M. Nuñez
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jessica C. Gauss
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sarah Thompson
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Emily Brumley
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Pedro Lowenstein
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria G. Castro
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Correspondence:
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Rezinciuc S, Tian Z, Wu S, Hengel S, Pasa-Tolic L, Smallwood HS. Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells. Viruses 2020; 12:v12121409. [PMID: 33302437 PMCID: PMC7762524 DOI: 10.3390/v12121409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 12/25/2022] Open
Abstract
T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) to histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis by MS can detect species missed by bottom-up approaches. We used a novel approach of online two-dimensional liquid chromatography-tandem MS with high-resolution reversed-phase liquid chromatography (RPLC), alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. The first online RPLC separation sorted histone families, then RPLC or weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative identifications were assigned by matching proteoform masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for histone-intact protein PTM mapping (HiPTMap) to identify and quantify proteoforms purified from CD8 T cells after in vivo influenza infection. Activation significantly altered PTMs following influenza infection, histone maps changed as T cells migrated to the site of infection, and T cells responding to secondary infections had significantly more transcription enhancing modifications. Thus, HiPTMap identified and quantified proteoforms and determined changes in CD8 T cell histone PTMs over the course of infection.
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Affiliation(s)
- Svetlana Rezinciuc
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Zhixin Tian
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Si Wu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Shawna Hengel
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Heather S. Smallwood
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
- Children’s Foundation Research Institute, Memphis, TN 38105, USA
- Correspondence: ; Tel.: +1-(901)-448–3068
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Strahl BD, Briggs SD. The SAGA continues: The rise of cis- and trans-histone crosstalk pathways. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194600. [PMID: 32645359 DOI: 10.1016/j.bbagrm.2020.194600] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 06/25/2020] [Indexed: 01/30/2023]
Abstract
Fueled by key technological innovations during the last several decades, chromatin-based research has greatly advanced our mechanistic understanding of how genes are regulated by epigenetic factors and their associated histone-modifying activities. Most notably, the landmark finding that linked histone acetylation by Gcn5 of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex to gene activation ushered in a new area of chromatin research and a realization that histone-modifying activities have integral genome functions. This review will discuss past and recent studies that have shaped our understanding of how the histone-modifying activities of SAGA are regulated by, and modulate the outcomes of, other histone modifications during gene transcription. Because much of our understanding of SAGA was established with budding yeast, we will focus on yeast as a model. We discuss the actions of cis- and trans-histone crosstalk pathways that involve the histone acetyltransferase, deubiquitylase, and reader domains of SAGA. We conclude by considering unanswered questions about SAGA and related complexes.
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Affiliation(s)
- Brian D Strahl
- Department of Biochemistry and Biophysics, 120 Mason Farm Rd, University of North Carolina at Chapel Hill, NC 27599, USA.
| | - Scott D Briggs
- Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, Hansen Life Science Research Building, 201S, University Street, West Lafayette, IN 47907; USA.
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Somuncu S, Somuncu ÖS, Ballıca B, Tabandeh B. Deficiency of epithelial-mesenchymal transition causes child indirect inguinal hernia. J Pediatr Surg 2020; 55:665-671. [PMID: 31288923 DOI: 10.1016/j.jpedsurg.2019.06.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/11/2019] [Accepted: 06/21/2019] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Epithelial-mesenchymal transition (EMT) describes rapid changes in cellular phenotype. During EMT, epithelial cells down-modulate cell-cell adhesion, alter polarity, reorganize cytoskeleton, become isolated, motile, and resistant to anoikis. Epithelial breakdown and epithelial cell migration are the key processes involved in the obliteration of processus vaginalis. The great majority of abnormalities are because of nonobliteration or incomplete fusion of PV. We aimed to analyze the quantitative changes of epithelial genes in adult/child patients and their controls to examine differences of the genesis of these hernias. We also aimed to investigate the potential epigenetic causes of indirect inguinal hernia in adult patients. METHODS Ten adult, ten child indirect inguinal hernia sacs and ten adult, ten child parietal peritonea were used. Hernial sac samples were obtained from indirect inguinal hernia surgeries. Peritonea of adult patients who underwent open cholecystectomy for cholelithiasis via subcostal incision were included in the study as the healthy control groups. Ages of the children were selected to be between 0 and 5 whereas the age of adults was chosen as 35-55, respectively. Total RNA isolation and cDNA synthesis were made from hernia sacs and peritoneum samples. Relative Keratin 1, Keratin 15, Filaggrin2 and STAT3 expressions were analyzed via qPCR. Indirect inguinal hernia sac cells were seeded and grown in vitro. Child diseased cells were employed in immunocytochemistry (ICC) analysis for Cytokeratin 15, Filaggrin2 and Bcl-2. Adult indirect inguinal hernia cells were examined for H3 modifications through ICC. RESULTS In child indirect inguinal hernia, Keratin expressions were found higher than their controls. They were meaningfully lower than the healthy group in adult indirect inguinal hernia. Keratin 15, Keratin 1 and Filaggrin2 expressions were all correlating since they are members of related pathways. STAT3 expressions were opposite to Keratin and Filaggrin expressions suggesting that adult cells might have a switch to the mesenchymal state from the epithelial state. Adult indirect inguinal hernia samples have switched to the mesenchymal state whereas child indirect inguinal hernia samples have shown lack of transition. CONCLUSION Irregular changes of EMT associated genes act in the progression of indirect inguinal hernia. Hence, the information on the epigenetic regulation of EMT in patients with primary inguinal hernia can aid to comprehend the pathogenesis in adults and infers new therapeutic approaches for this disease. TYPE OF STUDY Prognosis study. LEVEL OF EVIDENCE Level 2.
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Affiliation(s)
- Salih Somuncu
- Bezmialem Vakıf University Hospital, Department of Pediatric Surgery, Turkey.
| | - Özge Sezin Somuncu
- Bahçeşehir University, Faculty of Medicine, Department of Basic Sciences, Turkey
| | | | - Babek Tabandeh
- Bahçeşehir University, Faculty of Medicine, Department of General Surgery, Turkey
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27
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Zaghi M, Broccoli V, Sessa A. H3K36 Methylation in Neural Development and Associated Diseases. Front Genet 2020; 10:1291. [PMID: 31998360 PMCID: PMC6962298 DOI: 10.3389/fgene.2019.01291] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022] Open
Abstract
Post-translational methylation of H3 lysine 36 (H3K36) is an important epigenetic marker that majorly contributes to the functionality of the chromatin. This mark is interpreted by the cell in several crucial biological processes including gene transcription and DNA methylation. The homeostasis of H3K36 methylation is finely regulated by different enzyme classes which, when impaired, lead to a plethora of diseases; ranging from multi-organ syndromes to cancer, to pure neurological diseases often associated with brain development. This mini-review summarizes current knowledge on these important epigenetic signals with emphasis on the molecular mechanisms that (i) regulate their abundance, (ii) are influenced by H3K36 methylation, and (iii) the associated diseases.
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Affiliation(s)
- Mattia Zaghi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Vania Broccoli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy.,Concilio Nazionale Delle Ricerche (CNR), Instituto di Neuroscienze, Milan, Italy
| | - Alessandro Sessa
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
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28
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Donczew R, Warfield L, Pacheco D, Erijman A, Hahn S. Two roles for the yeast transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA. eLife 2020; 9:e50109. [PMID: 31913117 PMCID: PMC6977968 DOI: 10.7554/elife.50109] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 01/07/2020] [Indexed: 12/31/2022] Open
Abstract
Deletions within genes coding for subunits of the transcription coactivator SAGA caused strong genome-wide defects in transcription and SAGA-mediated chromatin modifications. In contrast, rapid SAGA depletion produced only modest transcription defects at 13% of protein-coding genes - genes that are generally more sensitive to rapid TFIID depletion. However, transcription of these 'coactivator-redundant' genes is strongly affected by rapid depletion of both factors, showing the overlapping functions of TFIID and SAGA at this gene set. We suggest that this overlapping function is linked to TBP-DNA recruitment. The remaining 87% of expressed genes that we term 'TFIID-dependent' are highly sensitive to rapid TFIID depletion and insensitive to rapid SAGA depletion. Genome-wide mapping of SAGA and TFIID found binding of both factors at many genes independent of gene class. Promoter analysis suggests that the distinction between the gene classes is due to multiple components rather than any single regulatory factor or promoter sequence motif.
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Affiliation(s)
- Rafal Donczew
- Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Linda Warfield
- Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Derek Pacheco
- Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Ariel Erijman
- Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Steven Hahn
- Fred Hutchinson Cancer Research CenterSeattleUnited States
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29
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Zhao M, Tao Y, Peng GH. The Role of Histone Acetyltransferases and Histone Deacetylases in Photoreceptor Differentiation and Degeneration. Int J Med Sci 2020; 17:1307-1314. [PMID: 32624685 PMCID: PMC7330661 DOI: 10.7150/ijms.43140] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/10/2020] [Indexed: 12/18/2022] Open
Abstract
Photoreceptors are critical components of the retina and play a role in the first step of the conversion of light to electrical signals. The differentiation and degeneration of photoreceptors are regulated by specific genes and proteins. With the development of epigenetic approaches, scientists have discovered that histone modifications, such as acetylation, methylation, ubiquitylation, and phosphorylation, may modulate the processes of photoreceptor differentiation and degeneration. Histone acetylation is regulated by two opposing classes of enzymes, namely, histone acetyltransferases (HATs) and histone deacetylases (HDACs), which add and remove acetyl groups to and from target histones, respectively, causing changes in transcriptional activity. Herein, we review the effects of HATs and HDACs on the differentiation and degeneration of photoreceptors and discuss the underlying mechanisms of these effects.
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Affiliation(s)
- Meng Zhao
- Laboratory of Visual Cell Differentiation and Regulation, Basic Medical College, Zhengzhou University, Zhengzhou 450001, China.,Department of Pathophysiology, Basic Medical College, Zhengzhou University, Zhengzhou 450001, China
| | - Ye Tao
- Laboratory of Visual Cell Differentiation and Regulation, Basic Medical College, Zhengzhou University, Zhengzhou 450001, China.,Department of Physiology, Basic Medical College, Zhengzhou University, Zhengzhou 450001, China
| | - Guang-Hua Peng
- Laboratory of Visual Cell Differentiation and Regulation, Basic Medical College, Zhengzhou University, Zhengzhou 450001, China.,Department of Pathophysiology, Basic Medical College, Zhengzhou University, Zhengzhou 450001, China
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30
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Pan YY, Yang JX, Mao W, Wang XX. RNA-binding protein SFPQ cooperates with HDAC1 to suppress CD40 transcription in pulmonary adventitial fibroblasts. Cell Biol Int 2020; 44:166-176. [PMID: 31393052 DOI: 10.1002/cbin.11216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/04/2019] [Indexed: 01/24/2023]
Abstract
Pulmonary artery adventitial fibroblasts, the most abundant cellular constituent of adventitia, are often the first to be activated and reprogrammed to then influence the tone and structure of the vessel wall in pulmonary arterial hypertension (PAH). Our previous study found that interruption of CD40 ligand (CD40L)-CD40 signaling improves the efficacy of transplanted endothelial progenitor cells in monocrotaline induced-PAH. However, whether CD40L-CD40 signaling is involved in the activation of adventitial fibroblasts in PAH and whether Drosophila behavior human splicing (DBHS) protein family members have any roles during adventitial fibroblasts activation are completely unclear. Here, we show that soluble CD40L (sCD40L) stimulation progressively increases pro-inflammatory activity, proliferation, and migration of pulmonary adventitial fibroblasts. Besides, sCD40L stimulation decreases splicing factor proline- and glutamine-rich protein (SFPQ) protein (one member of DBHS protein family) expression, while SFPQ overexpression suppresses sCD40L stimulation-induced proliferation and migration of pulmonary adventitial fibroblasts by repressing CD40 transcription. Moreover, ChIP assays found that sCD40L stimulation promotes histone H3 tri-methylation at lysine 4 (H3K4me3), H3K36me3, and H3K27 acetylation (H3K27ac) modifications on CD40 promoter region in pulmonary adventitial fibroblasts, while SFPQ overexpression decreases H3K36me3 modification and increases H3K36ac on CD40 promoter region by interacting with histone deacetylase-1 (HDAC1) to inhibit CD40 transcription. This in-depth study shows that CD40L-CD40 signaling promotes activation of pulmonary adventitial fibroblasts by increasing proliferation, migration, and pro-inflammatory activity of adventitial fibroblasts, and SFPQ could inhibit CD40 transcription though switching H3K36me3 to H3K36ac modifications on its promoter by interacting with HDAC1. This study, first, uncovers the roles of SFPQ on CD40L-CD40 signaling-mediated activation of pulmonary adventitial fibroblasts.
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Affiliation(s)
- Yan-Yun Pan
- Department of Cardiology, the First Affiliated Hospital of Zhejiang Chinese Medical University, No. 54 Youdian Road, Hangzhou, Zhejiang, 310006, PR China
| | - Jin-Xiu Yang
- Department of Cardiology, the First Affiliated Hospital of Zhejiang Chinese Medical University, No. 54 Youdian Road, Hangzhou, Zhejiang, 310006, PR China
| | - Wei Mao
- Department of Cardiology, the First Affiliated Hospital of Zhejiang Chinese Medical University, No. 54 Youdian Road, Hangzhou, Zhejiang, 310006, PR China
| | - Xing-Xiang Wang
- Department of Cardiology, the First Affiliated Hospital, School of Medicine, Zhejiang University, No. 79 Qingchun Road, Hangzhou, Zhejiang, 310006, PR China
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31
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Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD. The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome. Nucleic Acids Res 2019; 46:4978-4990. [PMID: 29850894 PMCID: PMC6007315 DOI: 10.1093/nar/gky206] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/16/2018] [Indexed: 01/21/2023] Open
Abstract
Chromatin remodelers are ATP-dependent motors that reorganize DNA packaging by disrupting canonical histone–DNA contacts within the nucleosome. Here, we show that the Chd1 chromatin remodeler stimulates DNA unwrapping from the edge of the nucleosome in a nucleotide-dependent and DNA sequence-sensitive fashion. Nucleosome binding, monitored by stopped flow, was complex and sensitive to nucleotide, with AMP–PNP promoting faster binding than ADP·BeF3–. Nucleosome unwrapping by Chd1, examined by bulk FRET, occurred in the presence and absence of nucleotide and did not require the Chd1 DNA-binding domain. In AMP–PNP conditions, Chd1 unwrapped one side of the Widom 601 DNA more easily than the other, consistent with previous observations of 601 asymmetry and indicating that Chd1 amplifies intrinsic sequence properties of nucleosomal DNA. Using small angle X-ray scattering (SAXS) with contrast variation, we found distinct DNA conformations depending on the nucleotide analog bound to Chd1: with AMP–PNP, DNA primarily unwrapped in-plane with the nucleosomal disk, whereas with ADP·BeF3–, a significant fraction showed distinctive out-of-plane unwrapping as well. Taken together, our findings show tight coupling between entry/exit DNA of the nucleosome and the Chd1 ATPase motor, suggesting that dynamic nucleosome unwrapping is coupled to nucleosome binding and remodeling by Chd1.
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Affiliation(s)
- Joshua M Tokuda
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Ren Ren
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Robert F Levendosky
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Rebecca J Tay
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Ming Yan
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
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Wang WW, Angulo-Ibanez M, Lyu J, Kurra Y, Tong Z, Wu B, Zhang L, Sharma V, Zhou J, Lin H, Gao YQ, Li W, Chua KF, Liu WR. A Click Chemistry Approach Reveals the Chromatin-Dependent Histone H3K36 Deacylase Nature of SIRT7. J Am Chem Soc 2019; 141:2462-2473. [PMID: 30653310 PMCID: PMC6812484 DOI: 10.1021/jacs.8b12083] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Using an engineered pyrrolysyl-tRNA synthetase mutant together with tRNACUAPyl, we have genetically encoded Nε-(7-azidoheptanoyl)-l-lysine (AzHeK) by amber codon in Escherichia coli for recombinant expression of a number of AzHeK-containing histone H3 proteins. We assembled in vitro acyl-nucleosomes from these recombinant acyl-H3 histones. All these acyl-nucleosomes contained an azide functionality that allowed quick click labeling with a strained alkyne dye for in-gel fluorescence analysis. Using these acyl-nucleosomes as substrates and click labeling as a detection method, we systematically investigated chromatin deacylation activities of SIRT7, a class III NAD+-dependent histone deacylase with roles in aging and cancer biology. Besides confirming the previously reported histone H3K18 deacylation activity, our results revealed that SIRT7 has an astonishingly high activity to catalyze deacylation of H3K36 and is also catalytically active to deacylate H3K37. We further demonstrated that this H3K36 deacylation activity is nucleosome dependent and can be significantly enhanced when appending the acyl-nucleosome substrate with a short double-stranded DNA that mimics the bridging DNA between nucleosomes in native chromatin. By overexpressing SIRT7 in human cells, we verified that SIRT7 natively removes acetylation from histone H3K36. Moreover, SIRT7-deficient cells exhibited H3K36 hyperacetylation in whole cell extracts, at rDNA sequences in nucleoli, and at select SIRT7 target loci, demonstrating the physiologic importance of SIRT7 in determining endogenous H3K36 acetylation levels. H3K36 acetylation has been detected at active gene promoters, but little is understood about its regulation and functions. Our findings establish H3K36 as a physiologic substrate of SIRT7 and implicate this modification in potential SIRT7 pathways in heterochromatin silencing and genomic stability.
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Affiliation(s)
- Wesley Wei Wang
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Maria Angulo-Ibanez
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jie Lyu
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Yadagiri Kurra
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Zhen Tong
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Bo Wu
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Ling Zhang
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Vangmayee Sharma
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Jennifer Zhou
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Yi Qin Gao
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wei Li
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Katrin F. Chua
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Geriatric Research, Education, and Clinical Center, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Wenshe Ray Liu
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
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33
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Juárez-Reyes A, Castaño I. Chromatin architecture and virulence-related gene expression in eukaryotic microbial pathogens. Curr Genet 2018; 65:435-443. [PMID: 30443783 DOI: 10.1007/s00294-018-0903-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/30/2018] [Accepted: 11/10/2018] [Indexed: 12/19/2022]
Abstract
A fundamental question in biology is to understand how appropriate transcriptional regulation and dense packaging of the genetic material within the eukaryotic nucleus are achieved. The exquisite gene expression control and other metabolic processes of DNA require a highly complex, multilayered, three-dimensional architecture of the chromatin and its specific compartmentalization within the nucleus. Some of these architectural and sub-nuclear positioning mechanisms have been extensively co-opted by eukaryotic pathogens to keep fine expression control and expansion of virulence-related gene families in Plasmodium falciparum, Trypanosoma brucei and Candida glabrata. For example non-linear interactions between distant cis-acting regions and the formation of chromatin loops are required for appropriate regulation of the expression of virulence-related multi-gene families encoding cell surface proteins. These gene families are located near the chromosome ends and tethered to the nuclear periphery. Consequently, only one or very few genes of the family are expressed at a time. These genes are involved in antigenic variation in parasites and the generation of subpopulations of cells with diverse antigenic proteins at the surface in some pathogenic fungi, making them highly efficient pathogens.
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Affiliation(s)
- Alejandro Juárez-Reyes
- División de Biología Molecular, IPICYT, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, 78216, San Luis Potosí, SLP, Mexico
| | - Irene Castaño
- División de Biología Molecular, IPICYT, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, 78216, San Luis Potosí, SLP, Mexico.
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34
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Radhakrishnan S, Literman R, Neuwald JL, Valenzuela N. Thermal Response of Epigenetic Genes Informs Turtle Sex Determination with and without Sex Chromosomes. Sex Dev 2018; 12:308-319. [PMID: 30278451 DOI: 10.1159/000492188] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2018] [Indexed: 12/20/2022] Open
Abstract
Vertebrate sexual fate can be established by environmental cues (e.g., temperature-dependent sex determination, TSD) or by genetic content (genotypic sex determination, GSD). While methylation is implicated in TSD, the influence of broader epigenetic processes in sexual development remains obscure. Here, we investigated for the first time the embryonic gonadal expression of the genome-wide epigenetic machinery in turtles, including genes and noncoding RNAs (ncRNAs) involved in DNA/histone acetylation, methylation, ubiquitination, phosphorylation, and RNAi. This machinery was active and differentially thermosensitive in TSD versus GSD (ZZ/ZW) turtles. Methylation and histone acetylation genes responded the strongest. The results suggest these working hypotheses: (i) TSD might be mediated by epigenetically controlled hormonal pathways (via acetylation, methylation, and ncRNAs), or by (ii) hormonally controlled epigenetic processes, and (iii) key epigenetic events prior to the canonical thermosensitive period may explain differences between TSD and GSD. Novel epigenetic candidate regulators other than methylation were identified, including previously unknown ncRNAs that could potentially mediate gonadogenesis. These findings illuminate the molecular ecology of reptilian sex determination and permitted hypothesis building to help guide future functional studies on the epigenetic transduction of external cues in TSD versus GSD systems.
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35
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Mittal C, Culbertson SJ, Shogren-Knaak MA. Distinct requirements of linker DNA and transcriptional activators in promoting SAGA-mediated nucleosome acetylation. J Biol Chem 2018; 293:13736-13749. [PMID: 30054274 DOI: 10.1074/jbc.ra118.004487] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/20/2018] [Indexed: 01/08/2023] Open
Abstract
The Spt-Ada-Gcn5 acetyltransferase (SAGA) family of transcriptional coactivators are prototypical nucleosome acetyltransferase complexes that regulate multiple steps in gene transcription. The size and complexity of both the SAGA enzyme and the chromatin substrate provide numerous opportunities for regulating the acetylation process. To better probe this regulation, here we developed a bead-based nucleosome acetylation assay to characterize the binding interactions and kinetics of acetylation with different nucleosomal substrates and the full SAGA complex purified from budding yeast (Saccharomyces cerevisiae). We found that SAGA-mediated nucleosome acetylation is stimulated up to 9-fold by DNA flanking the nucleosome, both by facilitating the binding of SAGA and by accelerating acetylation turnover. This stimulation required that flanking DNA is present on both sides of the nucleosome and that one side is >15 bp long. The Gal4-VP16 transcriptional activator fusion protein could also augment nucleosome acetylation up to 5-fold. However, contrary to our expectations, this stimulation did not appear to occur by stabilizing the binding of SAGA toward nucleosomes containing an activator-binding site. Instead, increased acetylation turnover by SAGA stimulated nucleosome acetylation. These results suggest that the Gal4-VP16 transcriptional activator directly stimulates acetylation via a dual interaction with both flanking DNA and SAGA. Altogether, these findings uncover several critical mechanisms of SAGA regulation by chromatin substrates.
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Affiliation(s)
- Chitvan Mittal
- From the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Sannie J Culbertson
- From the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Michael A Shogren-Knaak
- From the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011
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36
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Kim H, Jo H, Seo HD, Park HS, Lee D. Chd1p recognizes H3K36Ac to maintain nucleosome positioning near the transcription start site. Biochem Biophys Res Commun 2018; 503:1200-1206. [PMID: 30005873 DOI: 10.1016/j.bbrc.2018.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 01/01/2023]
Abstract
In Saccharomyces cerevisiae, the ATP-dependent chromatin remodeler, Chd1p, globally affects nucleosome positioning at coding regions, where nucleosomes are specifically and directionally aligned with respect to the transcription start site (TSS). Various auxiliary domains of remodelers play critical roles by performing specialized functions that are unique to the type of remodeler. Here, we report that yeast Chd1p directly binds to acetylated histone H3K36 (H3K36Ac) via its chromodomain, and that H3K36Ac stimulates the nucleosome sliding activity of Chd1p in vitro. Furthermore, we use genome-wide analysis to demonstrate that H3K36Ac promotes the remodeling activity of Chd1p to maintain chromatin stability at the 5' ends of genes in vivo. Our work linking Chd1p with H3K36Ac provides novel insights into how the nucleosome remodeling activity of Chd1p is controlled near the TSS.
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Affiliation(s)
- Hyunhee Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea
| | - Hyelim Jo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea
| | - Hogyu David Seo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea
| | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea.
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37
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Sindikubwabo F, Ding S, Hussain T, Ortet P, Barakat M, Baumgarten S, Cannella D, Palencia A, Bougdour A, Belmudes L, Couté Y, Tardieux I, Botté CY, Scherf A, Hakimi MA. Modifications at K31 on the lateral surface of histone H4 contribute to genome structure and expression in apicomplexan parasites. eLife 2017; 6:29391. [PMID: 29101771 PMCID: PMC5685513 DOI: 10.7554/elife.29391] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/02/2017] [Indexed: 12/22/2022] Open
Abstract
An unusual genome architecture characterizes the two related human parasitic pathogens Plasmodium falciparum and Toxoplasma gondii. A major fraction of the bulk parasite genome is packaged as transcriptionally permissive euchromatin with few loci embedded in silenced heterochromatin. Primary chromatin shapers include histone modifications at the nucleosome lateral surface close to the DNA but their mode of action remains unclear. We now identify versatile modifications at Lys31 within the globular domain of histone H4 that crucially determine genome organization and expression in Apicomplexa parasites. H4K31 acetylation at the promoter correlates with, and perhaps directly regulates, gene expression in both parasites. By contrast, monomethylated H4K31 is enriched in the core body of T. gondii active genes but inversely correlates with transcription, whereas it is unexpectedly enriched at transcriptionally inactive pericentromeric heterochromatin in P. falciparum, a region devoid of the characteristic H3K9me3 histone mark and its downstream effector HP1.
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Affiliation(s)
- Fabien Sindikubwabo
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Shuai Ding
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, CNRS, ERL 9195, INSERM, Unit U1201, Paris, France
| | - Tahir Hussain
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Philippe Ortet
- Aix-Marseille Univ, CEA, CNRS, UMR 7265, BIAM-LEMIRE, St-Paul-lez-Durance, France
| | - Mohamed Barakat
- Aix-Marseille Univ, CEA, CNRS, UMR 7265, BIAM-LEMIRE, St-Paul-lez-Durance, France
| | - Sebastian Baumgarten
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, CNRS, ERL 9195, INSERM, Unit U1201, Paris, France
| | - Dominique Cannella
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Alexandre Bougdour
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Lucid Belmudes
- Université Grenoble Alpes, CEA, INSERM, Grenoble, France
| | - Yohann Couté
- Université Grenoble Alpes, CEA, INSERM, Grenoble, France
| | - Isabelle Tardieux
- Institute for Advanced Biosciences (IAB), Team Membrane and Cell Dynamics of Host Parasite Interactions, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Cyrille Y Botté
- Institute for Advanced Biosciences (IAB), Team ApicoLipid, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Artur Scherf
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, CNRS, ERL 9195, INSERM, Unit U1201, Paris, France
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
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38
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Histone 3 lysine 36 to methionine mutations stably interact with and sequester SDG8 in Arabidopsis thaliana. SCIENCE CHINA-LIFE SCIENCES 2017; 61:225-234. [PMID: 28975546 DOI: 10.1007/s11427-017-9162-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/05/2017] [Indexed: 10/18/2022]
Abstract
Post-transcriptional modifications of histones play important roles in various biological processes. Here, we report that Arabidopsis plants overexpressing histone H3 lysine to methionine mutations at histone H3.1K36 (H3.1K36M) and H3.3K36 (H3.3K36M) have serious developmental defects with early-flowering and change in the modifications of endogenous histone H3, including acetylation at lysine 9 (H3K9ac), trimethylation at lysine 27 (H3K27me3), di- and tri-methylation at lysine 36 (H3K36me2 and H3K36me3). In addition, H3K36M mutation alters its subcellular localization and interacts with H3K36 methyltransferase SDG8. Our results support a model in which H3K36M stably interacts with SDG8, and inhibits the activity of SDG8 by sequestering SDG8, resulting in a dominant negative effect to affect the proper expression levels of a variety of genes and plant development.
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39
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Ichikawa Y, Connelly CF, Appleboim A, Miller TC, Jacobi H, Abshiru NA, Chou HJ, Chen Y, Sharma U, Zheng Y, Thomas PM, Chen HV, Bajaj V, Müller CW, Kelleher NL, Friedman N, Bolon DN, Rando OJ, Kaufman PD. A synthetic biology approach to probing nucleosome symmetry. eLife 2017; 6:28836. [PMID: 28895528 PMCID: PMC5626479 DOI: 10.7554/elife.28836] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/12/2017] [Indexed: 11/13/2022] Open
Abstract
The repeating subunit of chromatin, the nucleosome, includes two copies of each of the four core histones, and several recent studies have reported that asymmetrically-modified nucleosomes occur at regulatory elements in vivo. To probe the mechanisms by which histone modifications are read out, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, which we extensively validated genetically and biochemically. Comparing the effects of asymmetric histone tail point mutants with those of symmetric double mutants revealed that a single methylated H3K36 per nucleosome was sufficient to silence cryptic transcription in vivo. We also demonstrate the utility of this system for analysis of histone modification crosstalk, using mass spectrometry to separately identify modifications on each H3 molecule within asymmetric nucleosomes. The ability to generate asymmetric nucleosomes in vivo and in vitro provides a powerful and generalizable tool to probe the mechanisms by which H3 tails are read out by effector proteins in the cell.
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Affiliation(s)
- Yuichi Ichikawa
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Caitlin F Connelly
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Alon Appleboim
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.,The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Thomas Cr Miller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hadas Jacobi
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.,The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nebiyu A Abshiru
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, United States
| | - Hsin-Jung Chou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Yuanyuan Chen
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Upasna Sharma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Yupeng Zheng
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, United States
| | - Paul M Thomas
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, United States
| | - Hsuiyi V Chen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Vineeta Bajaj
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, United States
| | - Nir Friedman
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.,The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Na Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Paul D Kaufman
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
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40
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Yadav RK, Jablonowski CM, Fernandez AG, Lowe BR, Henry RA, Finkelstein D, Barnum KJ, Pidoux AL, Kuo YM, Huang J, O’Connell MJ, Andrews AJ, Onar-Thomas A, Allshire RC, Partridge JF. Histone H3G34R mutation causes replication stress, homologous recombination defects and genomic instability in S. pombe. eLife 2017; 6:e27406. [PMID: 28718400 PMCID: PMC5515577 DOI: 10.7554/elife.27406] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 06/20/2017] [Indexed: 12/12/2022] Open
Abstract
Recurrent somatic mutations of H3F3A in aggressive pediatric high-grade gliomas generate K27M or G34R/V mutant histone H3.3. H3.3-G34R/V mutants are common in tumors with mutations in p53 and ATRX, an H3.3-specific chromatin remodeler. To gain insight into the role of H3-G34R, we generated fission yeast that express only the mutant histone H3. H3-G34R specifically reduces H3K36 tri-methylation and H3K36 acetylation, and mutants show partial transcriptional overlap with set2 deletions. H3-G34R mutants exhibit genomic instability and increased replication stress, including slowed replication fork restart, although DNA replication checkpoints are functional. H3-G34R mutants are defective for DNA damage repair by homologous recombination (HR), and have altered HR protein dynamics in both damaged and untreated cells. These data suggest H3-G34R slows resolution of HR-mediated repair and that unresolved replication intermediates impair chromosome segregation. This analysis of H3-G34R mutant fission yeast provides mechanistic insight into how G34R mutation may promote genomic instability in glioma.
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Affiliation(s)
- Rajesh K Yadav
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, United States
| | - Carolyn M Jablonowski
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, United States
| | - Alfonso G Fernandez
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, United States
| | - Brandon R Lowe
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, United States
| | - Ryan A Henry
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, United States
| | - David Finkelstein
- Department of Bioinformatics, St. Jude Children’s Research Hospital, Memphis, United States
| | - Kevin J Barnum
- Department of Oncological Sciences and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Alison L Pidoux
- Wellcome Trust School for Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Yin-Ming Kuo
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, United States
| | - Jie Huang
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, United States
| | - Matthew J O’Connell
- Department of Oncological Sciences and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Andrew J Andrews
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, United States
| | - Arzu Onar-Thomas
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, United States
| | - Robin C Allshire
- Wellcome Trust School for Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Janet F Partridge
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, United States
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41
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Shliaha PV, Baird MA, Nielsen MM, Gorshkov V, Bowman AP, Kaszycki JL, Jensen ON, Shvartsburg AA. Characterization of Complete Histone Tail Proteoforms Using Differential Ion Mobility Spectrometry. Anal Chem 2017; 89:5461-5466. [PMID: 28406606 PMCID: PMC5436587 DOI: 10.1021/acs.analchem.7b00379] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Histone proteins are subject to dynamic post-translational modifications (PTMs) that cooperatively modulate the chromatin structure and function. Nearly all functional PTMs are found on the N-terminal histone domains (tails) of ∼50 residues protruding from the nucleosome core. Using high-definition differential ion mobility spectrometry (FAIMS) with electron transfer dissociation, we demonstrate rapid baseline gas-phase separation and identification of tails involving monomethylation, trimethylation, acetylation, or phosphorylation in biologically relevant positions. These are by far the largest variant peptides resolved by any method, some with PTM contributing just 0.25% to the mass. This opens the door to similar separations for intact proteins and in top-down proteomics.
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Affiliation(s)
- Pavel V Shliaha
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Matthew A Baird
- Department of Chemistry, Wichita State University , 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Mogens M Nielsen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Andrew P Bowman
- Department of Chemistry, Wichita State University , 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Julia L Kaszycki
- Department of Chemistry, Wichita State University , 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University , 1845 Fairmount, Wichita, Kansas 67260, United States
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42
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Theofel I, Bartkuhn M, Boettger T, Gärtner SMK, Kreher J, Brehm A, Rathke C. tBRD-1 and tBRD-2 regulate expression of genes necessary for spermatid differentiation. Biol Open 2017; 6:439-448. [PMID: 28235844 PMCID: PMC5399552 DOI: 10.1242/bio.022467] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Male germ cell differentiation proceeds to a large extent in the absence of active gene transcription. In Drosophila, hundreds of genes whose proteins are required during post-meiotic spermatid differentiation (spermiogenesis) are transcribed in primary spermatocytes. Transcription of these genes depends on the sequential action of the testis meiotic arrest complex (tMAC), Mediator complex, and testis-specific TFIID (tTFIID) complex. How the action of these protein complexes is coordinated and which other factors are involved in the regulation of transcription in spermatocytes is not well understood. Here, we show that the bromodomain proteins tBRD-1 and tBRD-2 regulate gene expression in primary spermatocytes and share a subset of target genes. The function of tBRD-1 was essential for the sub-cellular localization of endogenous tBRD-2 but dispensable for its protein stability. Our comparison of different microarray data sets showed that in primary spermatocytes, the expression of a defined number of genes depends on the function of the bromodomain proteins tBRD-1 and tBRD-2, the tMAC component Aly, the Mediator component Med22, and the tTAF Sa.
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Affiliation(s)
- Ina Theofel
- Philipps-Universität Marburg, Department of Biology, Marburg 35043, Germany
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig-Universität, Giessen 35392, Germany
| | - Thomas Boettger
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | | | - Judith Kreher
- Philipps-Universität Marburg, Institute of Molecular Biology and Tumor Research, Marburg 35037, Germany
| | - Alexander Brehm
- Philipps-Universität Marburg, Institute of Molecular Biology and Tumor Research, Marburg 35037, Germany
| | - Christina Rathke
- Philipps-Universität Marburg, Department of Biology, Marburg 35043, Germany
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43
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Epigenetic regulation of skeletal muscle metabolism. Clin Sci (Lond) 2017; 130:1051-63. [PMID: 27215678 DOI: 10.1042/cs20160115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/15/2016] [Indexed: 01/04/2023]
Abstract
Normal skeletal muscle metabolism is essential for whole body metabolic homoeostasis and disruptions in muscle metabolism are associated with a number of chronic diseases. Transcriptional control of metabolic enzyme expression is a major regulatory mechanism for muscle metabolic processes. Substantial evidence is emerging that highlights the importance of epigenetic mechanisms in this process. This review will examine the importance of epigenetics in the regulation of muscle metabolism, with a particular emphasis on DNA methylation and histone acetylation as epigenetic control points. The emerging cross-talk between metabolism and epigenetics in the context of health and disease will also be examined. The concept of inheritance of skeletal muscle metabolic phenotypes will be discussed, in addition to emerging epigenetic therapies that could be used to alter muscle metabolism in chronic disease states.
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The NF-κB-dependent and -independent transcriptome and chromatin landscapes of human coronavirus 229E-infected cells. PLoS Pathog 2017; 13:e1006286. [PMID: 28355270 PMCID: PMC5386326 DOI: 10.1371/journal.ppat.1006286] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/10/2017] [Accepted: 03/09/2017] [Indexed: 12/20/2022] Open
Abstract
Coronavirus replication takes place in the host cell cytoplasm and triggers inflammatory gene expression by poorly characterized mechanisms. To obtain more insight into the signals and molecular events that coordinate global host responses in the nucleus of coronavirus-infected cells, first, transcriptome dynamics was studied in human coronavirus 229E (HCoV-229E)-infected A549 and HuH7 cells, respectively, revealing a core signature of upregulated genes in these cells. Compared to treatment with the prototypical inflammatory cytokine interleukin(IL)-1, HCoV-229E replication was found to attenuate the inducible activity of the transcription factor (TF) NF-κB and to restrict the nuclear concentration of NF-κB subunits by (i) an unusual mechanism involving partial degradation of IKKβ, NEMO and IκBα and (ii) upregulation of TNFAIP3 (A20), although constitutive IKK activity and basal TNFAIP3 expression levels were shown to be required for efficient virus replication. Second, we characterized actively transcribed genomic regions and enhancers in HCoV-229E-infected cells and systematically correlated the genome-wide gene expression changes with the recruitment of Ser5-phosphorylated RNA polymerase II and prototypical histone modifications (H3K9ac, H3K36ac, H4K5ac, H3K27ac, H3K4me1). The data revealed that, in HCoV-infected (but not IL-1-treated) cells, an extensive set of genes was activated without inducible p65 NF-κB being recruited. Furthermore, both HCoV-229E replication and IL-1 were shown to upregulate a small set of genes encoding immunomodulatory factors that bind p65 at promoters and require IKKβ activity and p65 for expression. Also, HCoV-229E and IL-1 activated a common set of 440 p65-bound enhancers that differed from another 992 HCoV-229E-specific enhancer regions by distinct TF-binding motif combinations. Taken together, the study shows that cytoplasmic RNA viruses fine-tune NF-κB signaling at multiple levels and profoundly reprogram the host cellular chromatin landscape, thereby orchestrating the timely coordinated expression of genes involved in multiple signaling, immunoregulatory and metabolic processes. Coronaviruses are major human and animal pathogens. They belong to a family of plus-strand RNA viruses that have extremely large genomes and encode a variety of proteins involved in virus-host interactions. The four common coronaviruses (HCoV-229E, NL63, OC43, HKU1) cause mainly upper respiratory tract infections, while zoonotic coronaviruses (SARS-CoV and MERS-CoV) cause severe lung disease, including acute respiratory distress syndrome (ARDS). The molecular basis for this fundamentally different pathology is incompletely understood. Our study provides a genome-wide investigation of epigenetic changes occurring in response to HCoV-229E. We identify at high resolution a large number of regulatory regions in the genome of infected cells that coordinate de novo gene transcription. Many of these genes have immunomodulatory functions and, most likely, contribute to limiting viral replication, while other factors may promote viral replication. The study provides an intriguing example of a virus that completes its entire life cycle in the cytoplasm while sending multiple signals to the nuclear chromatin compartment to adjust the host cell repertoire of transcribed genes. The approach taken in this study is expected to provide a suitable framework for future studies aimed at dissecting and comparing host responses to representative coronaviruses with different pathogenic potential in humans.
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H3F3 mutation status of giant cell tumors of the bone, chondroblastomas and their mimics: a combined high resolution melting and pyrosequencing approach. Mod Pathol 2017; 30:393-406. [PMID: 28059095 DOI: 10.1038/modpathol.2016.212] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 12/25/2022]
Abstract
Behjati et al recently described recurrent mutations of H3F3 genes in giant cell tumors of the bone and chondroblastomas. Both these entities belong to the spectrum of giant cell-rich bone lesions, often presenting a diagnostic challenge for the pathologist. Our aim was to investigate the value of searching for H3F3 mutations in the diagnosis of giant cell tumors of the bone and giant cell-rich chondroblastomas. Two hundred eighty-one bone lesion samples, including 170 giant cell tumors of the bone, 26 chondroblastomas and 85 other giant cell-rich and/or epiphyseal tumors, were analyzed. Mutation status was determined using first high resolution melting screening and then mutation profiling pyrosequencing. Mutational status was compared with clinical data and, for giant cell tumors of the bone, with p63 immunostaining status. As histone methylation changes have been reported in association with H3F3 mutations, the methylation status of lysine 37 was investigated. H3F3A and H3F3B were found in 85% of giant cell tumors of the bone and 88% of chondroblastomas. In addition to the major G35W mutation, we found two rare H3F3A mutations: one G35R and one G35V. Among the other tumors studied, we only found H3F3A gene mutations in two cases of 'dedifferentiated chondrosarcoma mimicking giant cell tumor of the bone'. A H3F3B mutation was also observed in one case of dedifferentiated chondroblastoma. P63 expression in giant cell tumors of the bone seems to be associated with H3F3 gene mutations (P=0.004). H3F3 mutations did not correlate with clinical data, outcome or methylation changes in Lysin 37. In conclusion, H3F3 mutations are sensitive and specific markers of giant cell tumors of the bone and chondroblastomas. High resolution melting and pyrosequencing procedures are high-performance tools in this context. Determination of H3F3 mutation will allow reclassification of some entities belonging to the spectrum of giant cell-rich lesions.
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Kaszycki JL, Shvartsburg AA. A Priori Intrinsic PTM Size Parameters for Predicting the Ion Mobilities of Modified Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:294-302. [PMID: 27975328 DOI: 10.1007/s13361-016-1553-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/28/2016] [Accepted: 11/04/2016] [Indexed: 06/06/2023]
Abstract
The rising profile of ion mobility spectrometry (IMS) in proteomics has driven the efforts to predict peptide cross-sections. In the simplest approach, these are derived by adding the contributions of all amino acid residues and post-translational modifications (PTMs) defined by their intrinsic size parameters (ISPs). We show that the ISPs for PTMs can be calculated from properties of constituent atoms, and introduce the "impact scores" that govern the shift of cross-sections from the central mass-dependent trend for unmodified peptides. The ISPs and scores tabulated for 100 more common PTMs enable predicting the domains for modified peptides in the IMS/MS space that would guide subproteome investigations. Graphical Abstract ᅟ.
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Affiliation(s)
- Julia L Kaszycki
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS, 67260, USA
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Navarro E, Funtikova AN, Fíto M, Schröder H. Prenatal nutrition and the risk of adult obesity: Long-term effects of nutrition on epigenetic mechanisms regulating gene expression. J Nutr Biochem 2017; 39:1-14. [DOI: 10.1016/j.jnutbio.2016.03.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 03/23/2016] [Accepted: 03/27/2016] [Indexed: 12/19/2022]
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Choose Your Own Adventure: The Role of Histone Modifications in Yeast Cell Fate. J Mol Biol 2016; 429:1946-1957. [PMID: 27769718 DOI: 10.1016/j.jmb.2016.10.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/07/2016] [Accepted: 10/07/2016] [Indexed: 12/16/2022]
Abstract
When yeast cells are challenged by a fluctuating environment, signaling networks activate differentiation programs that promote their individual or collective survival. These programs include the initiation of meiotic sporulation, the formation of filamentous growth structures, and the activation of programmed cell death pathways. The establishment and maintenance of these distinct cell fates are driven by massive gene expression programs that promote the necessary changes in morphology and physiology. While these genomic reprogramming events depend on a specialized network of transcription factors, a diverse set of chromatin regulators, including histone-modifying enzymes, chromatin remodelers, and histone variants, also play essential roles. Here, we review the broad functions of histone modifications in initiating cell fate transitions, with particular focus on their contribution to the control of expression of key genes required for the differentiation programs and chromatin reorganization that accompanies these cell fates.
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49
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50
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Mahrez W, Arellano MST, Moreno-Romero J, Nakamura M, Shu H, Nanni P, Köhler C, Gruissem W, Hennig L. H3K36ac Is an Evolutionary Conserved Plant Histone Modification That Marks Active Genes. PLANT PHYSIOLOGY 2016; 170:1566-77. [PMID: 26764380 PMCID: PMC4775133 DOI: 10.1104/pp.15.01744] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/13/2016] [Indexed: 05/07/2023]
Abstract
In eukaryotic cells, histones are subject to a large number of posttranslational modifications whose sequential or combinatorial action affects chromatin structure and genome function. We identified acetylation at Lys-36 in histone H3 (H3K36ac) as a new chromatin modification in plants. The H3K36ac modification is evolutionary conserved in seed plants, including the gymnosperm Norway spruce (Picea abies) and the angiosperms rice (Oryza sativa), tobacco (Nicotiana tabacum), and Arabidopsis (Arabidopsis thaliana). In Arabidopsis, H3K36ac is highly enriched in euchromatin but not in heterochromatin. Genome-wide chromatin immunoprecipitation sequencing experiments revealed that H3K36ac peaks at the 5' end of genes, mainly on the two nucleosomes immediately distal to the transcription start site, independently of gene length. H3K36ac overlaps with H3K4me3 and the H2A.Z histone variant. The histone acetyl transferase GCN5 and the histone deacetylase HDA19 are required for H3K36ac homeostasis. H3K36ac and H3K36me3 show negative crosstalk, which is mediated by GCN5 and the histone methyl transferase SDG8. Although H3K36ac is associated with gene activity, we did not find a linear relationship between H3K36ac and transcript levels, suggesting that H3K36ac is a binary indicator of transcription.
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Affiliation(s)
- Walid Mahrez
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (W.M., M.S.T.A., J.M.-R., M.N., C.K., L.H.);Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092 Zurich, Switzerland (W.M., H.S., W.G.); and Functional Genomics Center Zurich, University of Zurich/ETH Zurich, CH-8057 Zurich, Switzerland (P.N.)
| | - Minerva Susana Trejo Arellano
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (W.M., M.S.T.A., J.M.-R., M.N., C.K., L.H.);Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092 Zurich, Switzerland (W.M., H.S., W.G.); and Functional Genomics Center Zurich, University of Zurich/ETH Zurich, CH-8057 Zurich, Switzerland (P.N.)
| | - Jordi Moreno-Romero
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (W.M., M.S.T.A., J.M.-R., M.N., C.K., L.H.);Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092 Zurich, Switzerland (W.M., H.S., W.G.); and Functional Genomics Center Zurich, University of Zurich/ETH Zurich, CH-8057 Zurich, Switzerland (P.N.)
| | - Miyuki Nakamura
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (W.M., M.S.T.A., J.M.-R., M.N., C.K., L.H.);Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092 Zurich, Switzerland (W.M., H.S., W.G.); and Functional Genomics Center Zurich, University of Zurich/ETH Zurich, CH-8057 Zurich, Switzerland (P.N.)
| | - Huan Shu
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (W.M., M.S.T.A., J.M.-R., M.N., C.K., L.H.);Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092 Zurich, Switzerland (W.M., H.S., W.G.); and Functional Genomics Center Zurich, University of Zurich/ETH Zurich, CH-8057 Zurich, Switzerland (P.N.)
| | - Paolo Nanni
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (W.M., M.S.T.A., J.M.-R., M.N., C.K., L.H.);Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092 Zurich, Switzerland (W.M., H.S., W.G.); and Functional Genomics Center Zurich, University of Zurich/ETH Zurich, CH-8057 Zurich, Switzerland (P.N.)
| | - Claudia Köhler
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (W.M., M.S.T.A., J.M.-R., M.N., C.K., L.H.);Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092 Zurich, Switzerland (W.M., H.S., W.G.); and Functional Genomics Center Zurich, University of Zurich/ETH Zurich, CH-8057 Zurich, Switzerland (P.N.)
| | - Wilhelm Gruissem
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (W.M., M.S.T.A., J.M.-R., M.N., C.K., L.H.);Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092 Zurich, Switzerland (W.M., H.S., W.G.); and Functional Genomics Center Zurich, University of Zurich/ETH Zurich, CH-8057 Zurich, Switzerland (P.N.)
| | - Lars Hennig
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (W.M., M.S.T.A., J.M.-R., M.N., C.K., L.H.);Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092 Zurich, Switzerland (W.M., H.S., W.G.); and Functional Genomics Center Zurich, University of Zurich/ETH Zurich, CH-8057 Zurich, Switzerland (P.N.)
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