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Grinat J, Shriever NP, Christophorou MA. Fantastic proteins and where to find them - histones, in the nucleus and beyond. J Cell Sci 2024; 137:jcs262071. [PMID: 39704565 DOI: 10.1242/jcs.262071] [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] [Indexed: 12/21/2024] Open
Abstract
Animal genomes are packaged into chromatin, a highly dynamic macromolecular structure of DNA and histone proteins organised into nucleosomes. This accommodates packaging of lengthy genomic sequences within the physical confines of the nucleus while also enabling precise regulation of access to genetic information. However, histones existed before chromatin and have lesser-known functions beyond genome regulation. Most notably, histones are potent antimicrobial agents, and the release of chromatin to the extracellular space is a defence mechanism nearly as ancient and widespread as chromatin itself. Histone sequences have changed very little throughout evolution, suggesting the possibility that some of their 'non-canonical' functions are at play in parallel or in concert with their genome regulatory functions. In this Review, we take an evolutionary perspective of histone, nuclear chromatin and extracellular chromatin biology and describe the known extranuclear and extracellular functions of histones. We detail molecular mechanisms of chromatin release and extracellular chromatin sensing, and we discuss their roles in physiology and disease. Finally, we present evidence and give a perspective on the potential of extracellular histones to act as bioactive, cell modulatory factors.
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Yao P, He Q, Wang Y, Sun D, Chen X, Lu L. Genome-wide profiling and functional study of short N-terminal H2B variants in Arabidopsis. J Adv Res 2024:S2090-1232(24)00557-5. [PMID: 39672233 DOI: 10.1016/j.jare.2024.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 10/23/2024] [Accepted: 12/02/2024] [Indexed: 12/15/2024] Open
Abstract
INTRODUCTION Nucleosomes harboring specific histone variants show distinct chromatin localization patterns and regulatory functions, thereby playing crucial roles in epigenetic regulation. Compared to the well-understood variants of H2A and H3, the study about H2B variants is emerging. Deciphering the roles and regulatory mechanisms of H2B variants in plants will provide more knowledges about epigenetic regulations in plant biology. OBJECTIVES Using the model plant Arabidopsis thaliana as the research subject, we systematically analyzed histone H2B variants, four short N-terminal histone H2B variants (snH2Bs) were identified. The genomic distribution characteristics of these snH2Bs, their impact on plant growth, and the potential regulatory mechanisms were studied. METHODS By integrating whole-genome chromatin immunoprecipitation sequencing (ChIP-seq) and fluorescence microscopy localization analysis, the distribution of snH2Bs across the genome was identified. Single, double, and triple knock-out mutants were constructed using CRISPR-Cas9 to further explore the functions of snH2Bs in the growth process of Arabidopsis thaliana, the possible mechanisms were also discussed. RESULTS These snH2B variants are preferentially expressed in reproductive tissues and are detected in the nuclei of pollen grains. Further genome-wide profiling indicates that the snH2Bs distribute at active chromatin regions and are positively correlated with gene expression. By creating knock-out single, double, and triple mutants for these snH2Bs, we demonstrate that H2B.5 influences vegetative to reproductive transition. We also show that H2B.5 is required for proper accumulation of H3 lysine 9 acetylation and H2B mono-ubiquitination. CONCLUSION Overall, our study not only provide insights into the functions and chromatin characteristics of plant snH2Bs, but also supplies examples that illustrate the interplay between histone variants and histone modification. These findings contribute to the understanding of the fundamental principles of epigenetic regulation in eukaryotes and also highlight potential targets for crop improvement.
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Affiliation(s)
- Peng Yao
- Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qin He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ying Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Danyang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiangsong Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; Hubei Hongshan Laboratory, Wuhan 430071, China.
| | - Li Lu
- Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; Hubei Hongshan Laboratory, Wuhan 430071, China.
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Hegazy YA, Dhahri H, El Osmani N, George S, Chandler DP, Fondufe-Mittendorf YN. Histone Variants: The Bricks That Fit Differently. J Biol Chem 2024:108048. [PMID: 39638247 DOI: 10.1016/j.jbc.2024.108048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 10/28/2024] [Accepted: 10/31/2024] [Indexed: 12/07/2024] Open
Abstract
Histone proteins organize nuclear DNA in eukaryotic cells and play crucial roles in regulating chromatin structure and function. Histone variants are produced by distinct histone genes and are produced independently of their canonical counterparts throughout the cell cycle. Even though histone variants may differ by only one or a few amino acids relative to their canonical counterparts, these minor variations can profoundly alter chromatin structure, accessibility, dynamics, and gene expression. Histone variants often interact with dedicated chaperones and remodelers and can have unique post-translational modifications (PTMs) that shape unique gene expression landscapes. Histone variants also play essential roles in DNA replication, damage repair, and histone-protamine transition during spermatogenesis. Importantly, aberrant histone variant expression and DNA mutations in histone variants are linked to various human diseases, including cancer, developmental disorders, and neurodegenerative diseases. In this review, we explore how core histone variants impact nucleosome structure and DNA accessibility, the significance of variant-specific PTMs, how variant-specific chaperones and remodelers contribute to a regulatory network governing chromatin behavior, and discuss current knowledge about the association of histone variants with human diseases.
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Affiliation(s)
- Youssef A Hegazy
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Hejer Dhahri
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA; Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Nour El Osmani
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Smitha George
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Darrell P Chandler
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
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Saddoris SM, Schang LM. The opportunities and challenges of epigenetic approaches to manage herpes simplex infections. Expert Rev Anti Infect Ther 2024; 22:1123-1142. [PMID: 39466139 PMCID: PMC11634640 DOI: 10.1080/14787210.2024.2420329] [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: 05/03/2024] [Revised: 09/24/2024] [Accepted: 10/20/2024] [Indexed: 10/29/2024]
Abstract
INTRODUCTION Despite the existence of antivirals that potently and efficiently inhibit the replication of herpes simplex virus 1 and 2 (HSV-1, -2), their ability to establish and maintain, and reactivate from, latency has precluded the development of curative therapies. Several groups are exploring the opportunities of targeting epigenetic regulation to permanently silence latent HSV genomes or induce their simultaneous reactivation in the presence of antivirals to flush the latent reservoirs, as has been explored for HIV. AREAS COVERED This review covers the basic principles of epigenetic regulation with an emphasis on those mechanisms relevant to the regulation of herpes simplex viruses, as well as the current knowledge on the regulation of lytic infections and the establishment and maintenance of, and reactivation from, latency, with an emphasis on epigenetic regulation. The differences with the epigenetic regulation of viral and cellular gene expression are highlighted as are the effects of known epigenetic regulators on herpes simplex viruses. The major limitations of current models to the development of novel antiviral strategies targeting latency are highlighted. EXPERT OPINION We provide an update on the epigenetic regulation during lytic and latent HSV-1 infection, highlighting the commonalities and differences with cellular gene expression and the potential of epigenetic drugs as antivirals, including the opportunities, challenges, and potential future directions.
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Affiliation(s)
- Sarah M Saddoris
- Department of Microbiology and Immunology and Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University. 235 Hungerford Hill Road, Ithaca, NY, 14850-USA
| | - Luis M Schang
- Department of Microbiology and Immunology and Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University. 235 Hungerford Hill Road, Ithaca, NY, 14850-USA
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Lai PM, Gong X, Chan KM. Roles of Histone H2B, H3 and H4 Variants in Cancer Development and Prognosis. Int J Mol Sci 2024; 25:9699. [PMID: 39273649 PMCID: PMC11395991 DOI: 10.3390/ijms25179699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/29/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024] Open
Abstract
Histone variants are the paralogs of core histones (H2A, H2B, H3 and H4). They are stably expressed throughout the cell cycle in a replication-independent fashion and are capable of replacing canonical counterparts under different fundamental biological processes. Variants have been shown to take part in multiple processes, including DNA damage repair, transcriptional regulation and X chromosome inactivation, with some of them even specializing in lineage-specific roles like spermatogenesis. Several reports have recently identified some unprecedented variants from different histone families and exploited their prognostic value in distinct types of cancer. Among the four classes of canonical histones, the H2A family has the greatest number of variants known to date, followed by H2B, H3 and H4. In our prior review, we focused on summarizing all 19 mammalian histone H2A variants. Here in this review, we aim to complete the full summary of the roles of mammalian histone variants from the remaining histone H2B, H3, and H4 families, along with an overview of their roles in cancer biology and their prognostic value in a clinical context.
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Affiliation(s)
- Po Man Lai
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Xiaoxiang Gong
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
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Yang R, Zhang B, Wang Y, Zhang Y, Zhao Y, Jiang D, Chen L, Tang B, Zhang X. H3K9me3 Levels Affect the Proliferation of Bovine Spermatogonial Stem Cells. Int J Mol Sci 2024; 25:9215. [PMID: 39273164 PMCID: PMC11394725 DOI: 10.3390/ijms25179215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/22/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
Spermatogonial stem cells (SSCs) possess the characteristics of self-renewal and differentiation, as well as the ability to generate functional sperm. Their unique stemness has broad applications in male infertility treatment and species preservation. In rodents, research on SSCs has been widely reported, but progress is slow in large livestock such as cattle and pigs due to long growth cycles, difficult proliferation in vitro, and significant species differences. Previously, we showed that histone 3 (H3) lysine 9 (K9) trimethylation (H3K9me3) is associated with the proliferation of bovine SSCs. Here, we isolated and purified SSCs from calf testicular tissues and investigated the impact of different H3K9me3 levels on the in vitro proliferation of bovine SSCs. The enriched SSCs eventually formed classical stem cell clones in vitro in our feeder-free culture system. These clones expressed glial cell-derived neurotrophic factor family receptor alpha-1 (GFRα1, specific marker for SSCs), NANOG (pluripotency protein), C-KIT (germ cell marker), and strong alkaline phosphatase (AKP) positivity. qRT-PCR analysis further showed that these clones expressed the pluripotency genes NANOG and SOX2, and the SSC-specific marker gene GFRα1. To investigate the dynamic relationship between H3K9me3 levels and SSC proliferation, H3K9me3 levels in bovine SSCs were first downregulated using the methyltransferase inhibitor, chaetocin, or transfection with the siRNA of H3K9 methyltransferase suppressor of variegation 3-9 homologue 1 (SUV39H1). The EDU (5-Ethynyl-2'-deoxyuridine) assay revealed that SSC proliferation was inhibited. Conversely, when H3K9me3 levels in bovine SSCs were upregulated by transfecting lysine demethylase 4D (KDM4D) siRNA, the EDU assay showed a promotion of cell proliferation. In summary, this study established a feeder-free culture system to obtain bovine SSCs and explored its effects on the proliferation of bovine SSCs by regulating H3K9me3 levels, laying the foundation for elucidating the regulatory mechanism underlying histone methylation modification in the proliferation of bovine SSCs.
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Affiliation(s)
- Rui Yang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Boyang Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yueqi Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yan Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yansen Zhao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Daozhen Jiang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Lanxin Chen
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Bo Tang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xueming Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
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Feierman ER, Louzon S, Prescott NA, Biaco T, Gao Q, Qiu Q, Choi K, Palozola KC, Voss AJ, Mehta SD, Quaye CN, Lynch KT, Fuccillo MV, Wu H, David Y, Korb E. Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory. Mol Cell 2024; 84:2822-2837.e11. [PMID: 39025074 PMCID: PMC11316635 DOI: 10.1016/j.molcel.2024.06.025] [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: 12/20/2023] [Revised: 05/02/2024] [Accepted: 06/24/2024] [Indexed: 07/20/2024]
Abstract
Histone proteins affect gene expression through multiple mechanisms, including through exchange with histone variants. Recent findings link histone variants to neurological disorders, yet few are well studied in the brain. Most notably, widely expressed variants of H2B remain elusive. We applied recently developed antibodies, biochemical assays, and sequencing approaches to reveal broad expression of the H2B variant H2BE and defined its role in regulating chromatin structure, neuronal transcription, and mouse behavior. We find that H2BE is enriched at promoters, and a single unique amino acid allows it to dramatically enhance chromatin accessibility. Further, we show that H2BE is critical for synaptic gene expression and long-term memory. Together, these data reveal a mechanism linking histone variants to chromatin accessibility, transcriptional regulation, neuronal function, and memory. This work further identifies a widely expressed H2B variant and uncovers a single histone amino acid with profound effects on genomic structure.
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Affiliation(s)
- Emily R Feierman
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sean Louzon
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicholas A Prescott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Tracy Biaco
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Qingzeng Gao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kyuhyun Choi
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Katherine C Palozola
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Anna J Voss
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shreya D Mehta
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Camille N Quaye
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Katherine T Lynch
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marc V Fuccillo
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Erica Korb
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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8
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Feierman ER, Louzon S, Prescott NA, Biaco T, Gao Q, Qiu Q, Choi K, Palozola KC, Voss AJ, Mehta SD, Quaye CN, Lynch KT, Fuccillo MV, Wu H, David Y, Korb E. Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.575103. [PMID: 38352334 PMCID: PMC10862743 DOI: 10.1101/2024.01.29.575103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Regulation of histone proteins affects gene expression through multiple mechanisms including exchange with histone variants. However, widely expressed variants of H2B remain elusive. Recent findings link histone variants to neurological disorders, yet few are well studied in the brain. We applied new tools including novel antibodies, biochemical assays, and sequencing approaches to reveal broad expression of the H2B variant H2BE, and defined its role in regulating chromatin structure, neuronal transcription, and mouse behavior. We find that H2BE is enriched at promoters and a single unique amino acid allows it to dramatically enhance chromatin accessibility. Lastly, we show that H2BE is critical for synaptic gene expression and long-term memory. Together, these data reveal a novel mechanism linking histone variants to chromatin regulation, neuronal function, and memory. This work further identifies the first widely expressed H2B variant and uncovers a single histone amino acid with profound effects on genomic structure.
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Affiliation(s)
- Emily R. Feierman
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Sean Louzon
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Nicholas A. Prescott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Tracy Biaco
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Qingzeng Gao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Kyuhyun Choi
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine C. Palozola
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Anna J. Voss
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Shreya D. Mehta
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Camille N. Quaye
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine T. Lynch
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Marc V. Fuccillo
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Erica Korb
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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Singh S, Anderson N, Chu D, Roy SW. Nematode histone H2A variant evolution reveals diverse histories of retention and loss and evidence for conserved core-like variant histone genes. PLoS One 2024; 19:e0300190. [PMID: 38814971 PMCID: PMC11139335 DOI: 10.1371/journal.pone.0300190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/22/2024] [Indexed: 06/01/2024] Open
Abstract
Histone variants are paralogs that replace canonical histones in nucleosomes, often imparting novel functions. However, how histone variants arise and evolve is poorly understood. Reconstruction of histone protein evolution is challenging due to large differences in evolutionary rates across gene lineages and sites. Here we used intron position data from 108 nematode genomes in combination with amino acid sequence data to find disparate evolutionary histories of the three H2A variants found in Caenorhabditis elegans: the ancient H2A.ZHTZ-1, the sperm-specific HTAS-1, and HIS-35, which differs from the canonical S-phase H2A by a single glycine-to-alanine C-terminal change. Although the H2A.ZHTZ-1 protein sequence is highly conserved, its gene exhibits recurrent intron gain and loss. This pattern suggests that specific intron sequences or positions may not be important to H2A.Z functionality. For HTAS-1 and HIS-35, we find variant-specific intron positions that are conserved across species. Patterns of intron position conservation indicate that the sperm-specific variant HTAS-1 arose more recently in the ancestor of a subset of Caenorhabditis species, while HIS-35 arose in the ancestor of Caenorhabditis and its sister group, including the genus Diploscapter. HIS-35 exhibits gene retention in some descendent lineages but gene loss in others, suggesting that histone variant use or functionality can be highly flexible. Surprisingly, we find the single amino acid differentiating HIS-35 from core H2A is ancestral and common across canonical Caenorhabditis H2A sequences. Thus, we speculate that the role of HIS-35 lies not in encoding a functionally distinct protein, but instead in enabling H2A expression across the cell cycle or in distinct tissues. This work illustrates how genes encoding such partially-redundant functions may be advantageous yet relatively replaceable over evolutionary timescales, consistent with the patchwork pattern of retention and loss of both genes. Our study shows the utility of intron positions for reconstructing evolutionary histories of gene families, particularly those undergoing idiosyncratic sequence evolution.
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Affiliation(s)
- Swadha Singh
- Quantitative & Systems Biology, University of California, Merced, Merced, California, United States of America
| | - Noelle Anderson
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Diana Chu
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Scott W. Roy
- Quantitative & Systems Biology, University of California, Merced, Merced, California, United States of America
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
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10
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Brown AL, Meiborg AB, Franz-Wachtel M, Macek B, Gordon S, Rog O, Weadick CJ, Werner MS. Characterization of the Pristionchus pacificus "epigenetic toolkit" reveals the evolutionary loss of the histone methyltransferase complex PRC2. Genetics 2024; 227:iyae041. [PMID: 38513719 PMCID: PMC11075575 DOI: 10.1093/genetics/iyae041] [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: 12/04/2023] [Revised: 12/04/2023] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Comparative approaches have revealed both divergent and convergent paths to achieving shared developmental outcomes. Thus, only through assembling multiple case studies can we understand biological principles. Yet, despite appreciating the conservation-or lack thereof-of developmental networks, the conservation of epigenetic mechanisms regulating these networks is poorly understood. The nematode Pristionchus pacificus has emerged as a model system of plasticity and epigenetic regulation as it exhibits a bacterivorous or omnivorous morph depending on its environment. Here, we determined the "epigenetic toolkit" available to P. pacificus as a resource for future functional work on plasticity, and as a comparison with Caenorhabditis elegans to investigate the conservation of epigenetic mechanisms. Broadly, we observed a similar cast of genes with putative epigenetic function between C. elegans and P. pacificus. However, we also found striking differences. Most notably, the histone methyltransferase complex PRC2 appears to be missing in P. pacificus. We described the deletion/pseudogenization of the PRC2 genes mes-2 and mes-6 and concluded that both were lost in the last common ancestor of P. pacificus and a related species P. arcanus. Interestingly, we observed the enzymatic product of PRC2 (H3K27me3) by mass spectrometry and immunofluorescence, suggesting that a currently unknown methyltransferase has been co-opted for heterochromatin silencing. Altogether, we have provided an inventory of epigenetic genes in P. pacificus to compare with C. elegans. This inventory will enable reverse-genetic experiments related to plasticity and has revealed the first loss of PRC2 in a multicellular organism.
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Affiliation(s)
- Audrey L Brown
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
| | - Adriaan B Meiborg
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Faculty of Biosciences, Collaboration for joint PhD degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany
| | | | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, 72074 Tübingen, Germany
| | - Spencer Gordon
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
| | - Ofer Rog
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
| | | | - Michael S Werner
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
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11
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Pepino MMC, Manalili SE, Sekida S, Mezaki T, Okumura T, Kubota S. Gene expression profiles of Japanese precious coral Corallium japonicum during gametogenesis. PeerJ 2024; 12:e17182. [PMID: 38646482 PMCID: PMC11027906 DOI: 10.7717/peerj.17182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/11/2024] [Indexed: 04/23/2024] Open
Abstract
Background Corallium japonicum, a prized resource in Japan, plays a vital role in traditional arts and fishing industries. Because of diminished stock due to overexploitation, ongoing efforts are focused on restoration through transplantation. This study aimed to enhance our understanding of the reproductive biology of these valuable corals and find more efficient methods for sex determination, which may significantly contribute to conservation initiatives. Methods We used 12 three-month aquarium reared C. japonicum colony fragments, conducted histological analysis for maturity and sex verification, and performed transcriptome analysis via de novo assembly and mapping using the C. rubrum transcriptome to explore gene expression differences between female and male C. japonicum. Results Our histological observations enabled sex identification in 33% of incompletely mature samples. However, the sex of the remaining 67% of samples, classified as immature, could not be identified. RNA-seq yielded approximately 21-31 million short reads from 12 samples. De novo assembly yielded 404,439 highly expressed transcripts. Among them, 855 showed significant differential expression, with 786 differentially expressed transcripts between females and males. Heatmap analysis highlighted 283 female-specific and 525 male-specific upregulated transcripts. Transcriptome assembly mapped to C. rubrum yielded 28,092 contigs, leading to the identification of 190 highly differentially expressed genes, with 113 upregulated exclusively in females and 70 upregulated exclusively in males. Blastp analysis provided putative protein annotations for 83 female and 72 male transcripts. Annotation analysis revealed that female biological processes were related to oocyte proliferation and reproduction, whereas those in males were associated with cell adhesion. Discussion Transcriptome analysis revealed sex-specific gene upregulation in incompletely mature C. japonicum and shared transcripts with C. rubrum, providing insight into its gene expression patterns. This study highlights the importance of using both de novo and reference-based assembly methods. Functional enrichment analysis showed that females exhibited enrichment in cell proliferation and reproduction pathways, while males exhibited enrichment in cell adhesion pathways. To the best of our knowledge, this is the first report on the gene expressions of each sex during the spawning season. Our findings offer valuable insights into the physiological ecology of incompletely mature red Japanese precious corals and suggest a method for identifying sex using various genes expressed in female and male individuals. In the future, techniques such as transplantation, artificial fertilization, and larval rearing may involve sex determination methods based on differences in gene expression to help conserve precious coral resources and ecosystems.
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Affiliation(s)
- Ma. Marivic Capitle Pepino
- Kuroshio Science Program, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Kochi, Japan
| | - Sam Edward Manalili
- Kuroshio Science Program, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Kochi, Japan
| | - Satoko Sekida
- Kuroshio Science Unit, Multidisciplinary Science Cluster, Kochi University, Nankoku, Kochi, Japan
| | - Takuma Mezaki
- Kuroshio Biological Research Foundation, Otsuki, Kochi, Japan
| | - Tomoyo Okumura
- Marine Core Research Institute, Kochi University, Nankoku, Kochi, Japan
| | - Satoshi Kubota
- Kuroshio Science Unit, Multidisciplinary Science Cluster, Kochi University, Nankoku, Kochi, Japan
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12
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Jamge B, Lorković ZJ, Axelsson E, Osakabe A, Shukla V, Yelagandula R, Akimcheva S, Kuehn AL, Berger F. Histone variants shape chromatin states in Arabidopsis. eLife 2023; 12:RP87714. [PMID: 37467143 PMCID: PMC10393023 DOI: 10.7554/elife.87714] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
How different intrinsic sequence variations and regulatory modifications of histones combine in nucleosomes remain unclear. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in the Arabidopsis thaliana genome. We showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role of the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of constitutive heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks.
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Affiliation(s)
- Bhagyshree Jamge
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Vienna BioCenterViennaAustria
| | - Zdravko J Lorković
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Akihisa Osakabe
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-kuTokyoJapan
- PRESTO, Japan Science and Technology Agency, HonchoKawaguchiJapan
| | - Vikas Shukla
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Vienna BioCenterViennaAustria
| | - Ramesh Yelagandula
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Institute of Molecular Biotechnology, IMBA, Dr. Bohr-Gasse 3ViennaAustria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Annika Luisa Kuehn
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
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13
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Karam G, Molaro A. Casting histone variants during mammalian reproduction. Chromosoma 2023:10.1007/s00412-023-00803-9. [PMID: 37347315 PMCID: PMC10356639 DOI: 10.1007/s00412-023-00803-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023]
Abstract
During mammalian reproduction, germ cell chromatin packaging is key to prepare parental genomes for fertilization and to initiate embryonic development. While chromatin modifications such as DNA methylation and histone post-translational modifications are well known to carry regulatory information, histone variants have received less attention in this context. Histone variants alter the stability, structure and function of nucleosomes and, as such, contribute to chromatin organization in germ cells. Here, we review histone variants expression dynamics during the production of male and female germ cells, and what is currently known about their parent-of-origin effects during reproduction. Finally, we discuss the apparent conundrum behind these important functions and their recent evolutionary diversification.
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Affiliation(s)
- Germaine Karam
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Antoine Molaro
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France.
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14
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de la Iglesia A, Jodar M, Oliva R, Castillo J. Insights into the sperm chromatin and implications for male infertility from a protein perspective. WIREs Mech Dis 2023; 15:e1588. [PMID: 36181449 DOI: 10.1002/wsbm.1588] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022]
Abstract
Male germ cells undergo an extreme but fascinating process of chromatin remodeling that begins in the testis during the last phase of spermatogenesis and continues through epididymal sperm maturation. Most of the histones are replaced by small proteins named protamines, whose high basicity leads to a tight genomic compaction. This process is epigenetically regulated at many levels, not only by posttranslational modifications, but also by readers, writers, and erasers, in a context of a highly coordinated postmeiotic gene expression program. Protamines are key proteins for acquiring this highly specialized chromatin conformation, needed for sperm functionality. Interestingly, and contrary to what could be inferred from its very specific DNA-packaging function across protamine-containing species, human sperm chromatin contains a wide spectrum of protamine proteoforms, including truncated and posttranslationally modified proteoforms. The generation of protamine knock-out models revealed not only chromatin compaction defects, but also collateral sperm alterations contributing to infertile phenotypes, evidencing the importance of sperm chromatin protamination toward the generation of a new individual. The unique features of sperm chromatin have motivated its study, applying from conventional to the most ground-breaking techniques to disentangle its peculiarities and the cellular mechanisms governing its successful conferment, especially relevant from the protein point of view due to the important epigenetic role of sperm nuclear proteins. Gathering and contextualizing the most striking discoveries will provide a global understanding of the importance and complexity of achieving a proper chromatin compaction and exploring its implications on postfertilization events and beyond. This article is categorized under: Reproductive System Diseases > Genetics/Genomics/Epigenetics Reproductive System Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Alberto de la Iglesia
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain
| | - Meritxell Jodar
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain.,Biochemistry and Molecular Genetics Service, Hospital Clinic, Barcelona, Spain
| | - Rafael Oliva
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain.,Biochemistry and Molecular Genetics Service, Hospital Clinic, Barcelona, Spain
| | - Judit Castillo
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain
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15
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Chang CH, Mejia Natividad I, Malik HS. Expansion and loss of sperm nuclear basic protein genes in Drosophila correspond with genetic conflicts between sex chromosomes. eLife 2023; 12:85249. [PMID: 36763410 PMCID: PMC9917458 DOI: 10.7554/elife.85249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023] Open
Abstract
Many animal species employ sperm nuclear basic proteins (SNBPs) or protamines to package sperm genomes tightly. SNBPs vary across animal lineages and evolve rapidly in mammals. We used a phylogenomic approach to investigate SNBP diversification in Drosophila species. We found that most SNBP genes in Drosophila melanogaster evolve under positive selection except for genes essential for male fertility. Unexpectedly, evolutionarily young SNBP genes are more likely to be critical for fertility than ancient, conserved SNBP genes. For example, CG30056 is dispensable for male fertility despite being one of three SNBP genes universally retained in Drosophila species. We found 19 independent SNBP gene amplification events that occurred preferentially on sex chromosomes. Conversely, the montium group of Drosophila species lost otherwise-conserved SNBP genes, coincident with an X-Y chromosomal fusion. Furthermore, SNBP genes that became linked to sex chromosomes via chromosomal fusions were more likely to degenerate or relocate back to autosomes. We hypothesize that autosomal SNBP genes suppress meiotic drive, whereas sex-chromosomal SNBP expansions lead to meiotic drive. X-Y fusions in the montium group render autosomal SNBPs dispensable by making X-versus-Y meiotic drive obsolete or costly. Thus, genetic conflicts between sex chromosomes may drive SNBP rapid evolution during spermatogenesis in Drosophila species.
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Affiliation(s)
- Ching-Ho Chang
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, United States
| | - Isabel Mejia Natividad
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, United States.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, United States
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, United States.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, United States
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16
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Seal RL, Braschi B, Gray K, Jones TEM, Tweedie S, Haim-Vilmovsky L, Bruford EA. Genenames.org: the HGNC resources in 2023. Nucleic Acids Res 2022; 51:D1003-D1009. [PMID: 36243972 PMCID: PMC9825485 DOI: 10.1093/nar/gkac888] [Citation(s) in RCA: 168] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 01/30/2023] Open
Abstract
The HUGO Gene Nomenclature Committee (HGNC) assigns unique symbols and names to human genes. The HGNC database (www.genenames.org) currently contains over 43 000 approved gene symbols, over 19 200 of which are assigned to protein-coding genes, 14 000 to pseudogenes and nearly 9000 to non-coding RNA genes. The public website, www.genenames.org, displays all approved nomenclature within Symbol Reports that contain data curated by HGNC nomenclature advisors and links to related genomic, clinical, and proteomic information. Here, we describe updates to our resource, including improvements to our search facility and new download features.
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Affiliation(s)
- Ruth L Seal
- To whom correspondence should be addressed. Tel: +44 1223 494444; Fax: +44 1223 494446;
| | - Bryony Braschi
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kristian Gray
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK,Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge CB2 0PT, UK
| | - Tamsin E M Jones
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Susan Tweedie
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Liora Haim-Vilmovsky
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Elspeth A Bruford
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK,Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge CB2 0PT, UK
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17
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Seal RL, Denny P, Bruford EA, Gribkova AK, Landsman D, Marzluff WF, McAndrews M, Panchenko AR, Shaytan AK, Talbert PB. A standardized nomenclature for mammalian histone genes. Epigenetics Chromatin 2022; 15:34. [PMID: 36180920 PMCID: PMC9526256 DOI: 10.1186/s13072-022-00467-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
Histones have a long history of research in a wide range of species, leaving a legacy of complex nomenclature in the literature. Community-led discussions at the EMBO Workshop on Histone Variants in 2011 resulted in agreement amongst experts on a revised systematic protein nomenclature for histones, which is based on a combination of phylogenetic classification and historical symbol usage. Human and mouse histone gene symbols previously followed a genome-centric system that was not applicable across all vertebrate species and did not reflect the systematic histone protein nomenclature. This prompted a collaboration between histone experts, the Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC) and Mouse Genomic Nomenclature Committee (MGNC) to revise human and mouse histone gene nomenclature aiming, where possible, to follow the new protein nomenclature whilst conforming to the guidelines for vertebrate gene naming. The updated nomenclature has also been applied to orthologous histone genes in chimpanzee, rhesus macaque, dog, cat, pig, horse and cattle, and can serve as a framework for naming other vertebrate histone genes in the future.
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Affiliation(s)
- Ruth L Seal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
- Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0PT, UK.
| | - Paul Denny
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Elspeth A Bruford
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0PT, UK
| | - Anna K Gribkova
- Department of Biology, Lomonosov Moscow State University, 119234, Moscow, Russia
| | - David Landsman
- Intramural Research Program, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - William F Marzluff
- Integrated Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Monica McAndrews
- Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Alexey K Shaytan
- Department of Biology, Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA, 98109, USA
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18
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Berger F. Histone variants: The architects of chromatin. Semin Cell Dev Biol 2022; 135:1-2. [PMID: 35779977 DOI: 10.1016/j.semcdb.2022.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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19
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Brown JAR, Cui JH, Ling MYM, Gao EXC, Howe LJ, Teves SS. 43rd International Asilomar Chromatin, Chromosomes, and Epigenetics Conference. Biochem Cell Biol 2022; 100:437-443. [PMID: 35728263 DOI: 10.1139/bcb-2022-0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The 43rd Asilomar Chromatin, Chromosomes, and Epigenetics Conference was held in an entirely online format from December 9-11, 2021. The conference enabled presenters at various career stages to share promising new findings, and presentations covered modern chromatin research across an array of model systems. Topics ranged from the fundamental principles of nuclear organization and transcription regulation to key mechanisms underlying human disease. The meeting featured five keynote speakers from diverse backgrounds and was organized by: Juan Ausió, University of Victoria (British Columbia, Canada), James Davie, University of Manitoba (Manitoba, Canada), Philippe T. Georgel, Marshall University (West Virginia, USA), Michael Goldman, San Francisco State University (California, USA), LeAnn Howe, University of British Columbia (British Columbia, Canada), Jennifer A. Mitchell, University of Toronto (Ontario, Canada), and Sally G. Pasion, San Francisco State University (California, USA).
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Affiliation(s)
- Joshua A R Brown
- The University of British Columbia Faculty of Medicine, 12358, Department of Biochemistry and Molecular Biology, Vancouver, British Columbia, Canada;
| | - Jieying Hazel Cui
- The University of British Columbia Faculty of Medicine, 12358, Department of Biochemistry and Molecular Biology, Vancouver, British Columbia, Canada;
| | - Maggie Y M Ling
- The University of British Columbia Faculty of Medicine, 12358, Department of Biochemistry and Molecular Biology, Vancouver, British Columbia, Canada;
| | - Ellia X C Gao
- The University of British Columbia Faculty of Medicine, 12358, Department of Biochemistry and Molecular Biology, Vancouver, British Columbia, Canada;
| | - LeAnn J Howe
- The University of British Columbia Faculty of Medicine, 12358, Department of Biochemistry and Molecular Biology, Vancouver, British Columbia, Canada;
| | - Sheila S Teves
- The University of British Columbia Faculty of Medicine, 12358, Department of Biochemistry and Molecular Biology, Vancouver, British Columbia, Canada;
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20
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Montjean D, Neyroud AS, Yefimova MG, Benkhalifa M, Cabry R, Ravel C. Impact of Endocrine Disruptors upon Non-Genetic Inheritance. Int J Mol Sci 2022; 23:3350. [PMID: 35328771 PMCID: PMC8950994 DOI: 10.3390/ijms23063350] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 02/06/2023] Open
Abstract
Similar to environmental factors, EDCs (endocrine-disrupting chemicals) can influence gene expression without modifying the DNA sequence. It is commonly accepted that the transgenerational inheritance of parentally acquired traits is conveyed by epigenetic alterations also known as "epimutations". DNA methylation, acetylation, histone modification, RNA-mediated effects and extracellular vesicle effects are the mechanisms that have been described so far to be responsible for these epimutations. They may lead to the transgenerational inheritance of diverse phenotypes in the progeny when they occur in the germ cells of an affected individual. While EDC-induced health effects have dramatically increased over the past decade, limited effects on sperm epigenetics have been described. However, there has been a gain of interest in this issue in recent years. The gametes (sperm and oocyte) represent targets for EDCs and thus a route for environmentally induced changes over several generations. This review aims at providing an overview of the epigenetic mechanisms that might be implicated in this transgenerational inheritance.
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Affiliation(s)
- Debbie Montjean
- Fertilys Fertility Center, 1950 Rue Maurice-Gauvin #103, Laval, QC H7S 1Z5, Canada;
| | - Anne-Sophie Neyroud
- CHU de Rennes, Département de Gynécologie Obstétrique et Reproduction Humaine-CECOS, Hôpital Sud, 16 Boulevard de Bulgarie, 35000 Rennes, France;
| | - Marina G. Yefimova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 194223 St-Petersburg, Russia;
| | - Moncef Benkhalifa
- Fertilys Fertility Center, 1950 Rue Maurice-Gauvin #103, Laval, QC H7S 1Z5, Canada;
- Médecine et Biologie de la Reproduction, CECOS de Picardie, CHU Amiens, 80054 Amiens, France;
- UFR de Médecine, Université de Picardie Jules Verne, 80054 Amiens, France
- Peritox, Centre Universitaire de Recherche en Santé, Université de Picardie Jules Verne, 80054 Amiens, France
| | - Rosalie Cabry
- Médecine et Biologie de la Reproduction, CECOS de Picardie, CHU Amiens, 80054 Amiens, France;
- UFR de Médecine, Université de Picardie Jules Verne, 80054 Amiens, France
- Peritox, Centre Universitaire de Recherche en Santé, Université de Picardie Jules Verne, 80054 Amiens, France
| | - Célia Ravel
- CHU de Rennes, Département de Gynécologie Obstétrique et Reproduction Humaine-CECOS, Hôpital Sud, 16 Boulevard de Bulgarie, 35000 Rennes, France;
- CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR_S 1085, University Rennes, 35000 Rennes, France
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