51
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De Intinis C, Bodini M, Maffione D, De Mot L, Coccia M, Medini D, Siena E. Systematic characterization of human response to H1N1 influenza vaccination through the construction and integration of personalized transcriptome response profiles. Sci Rep 2021; 11:20821. [PMID: 34675324 PMCID: PMC8531369 DOI: 10.1038/s41598-021-99870-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/24/2021] [Indexed: 11/09/2022] Open
Abstract
Gene expression data is commonly used in vaccine studies to characterize differences between treatment groups or sampling time points. Group-wise comparisons of the transcriptional perturbations induced by vaccination have been applied extensively for investigating the mechanisms of action of vaccines. Such approaches, however, may not be sensitive enough for detecting changes occurring within a minority of the population under investigation or in single individuals. In this study, we developed a data analysis framework to characterize individual subject response profiles in the context of repeated measure experiments, which are typical of vaccine mode of action studies. Following the definition of the methodology, this was applied to the analysis of human transcriptome responses induced by vaccination with a subunit influenza vaccine. Results highlighted a substantial heterogeneity in how different subjects respond to vaccination. Moreover, the extent of transcriptional modulation experienced by each individual subject was found to be associated with the magnitude of vaccine-specific functional antibody response, pointing to a mechanistic link between genes involved in protein production and innate antiviral response. Overall, we propose that the improved characterization of the intersubject heterogeneity, enabled by our approach, can help driving the improvement and optimization of current and next-generation vaccines.
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Affiliation(s)
- Carlo De Intinis
- University of Turin, 10124, Turin, Italy.,GSK, 53100, Siena, Italy
| | | | | | - Laurane De Mot
- GSK, 1330, Rixensart, Belgium.,Clarivate Analytics, 2600, Berchem, Belgium
| | | | - Duccio Medini
- GSK, 53100, Siena, Italy.,Toscana Life Sciences, 53100, Siena, Italy
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52
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Zhang J, Chang Y, Xia H, Xu L, Wei X. HIST1H2BN induced cell proliferation and EMT phenotype in prostate cancer via NF-κB signal pathway. Genes Genomics 2021; 43:1361-1369. [PMID: 34537918 DOI: 10.1007/s13258-021-01164-2] [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: 06/10/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND The potential role of HIST1H2BN in prostate cancer remains unclear. OBJECTIVE To evaluate the carcinogenic role of HIST1H2BN in prostate cancer. METHODS The expression of HIST1H2BN in prostate cancer was analyzed using TCGA database and clinical samples. The roles and mechanisms of HIST1H2BN were investigated in DU145 and PC3 cells. RESULTS HIST1H2BN was significantly upregulated in prostate cancer. HIST1H2BN knockdown inhibited cell proliferation, migration and EMT phenotype in prostate cancer cells. Downregulating HIST1H2BN diminished the expression and binding activity of NF-κB p65, then influenced the expression of MMP2 and MMP9. CONCLUSION : This is the first study to elaborate a HIST1H2BN-NF-κB-EMT regulatory axis in oncogenesis, indicating that HIST1H2BN might be potential therapeutic target for prostate cancer.
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Affiliation(s)
- Juan Zhang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China
| | - Yuhan Chang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China
| | - Haiyan Xia
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China.
| | - Luwei Xu
- Department of Urinary surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China.
| | - Xiaowei Wei
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China.
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53
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Abstract
The current model of replication-dependent (RD) histone biosynthesis posits that RD histone gene expression is coupled to DNA replication, occurring only in S phase of the cell cycle once DNA synthesis has begun. However, several key factors in the RD histone biosynthesis pathway are up-regulated by E2F or phosphorylated by CDK2, suggesting these processes may instead begin much earlier, at the point of cell-cycle commitment. In this study, we use both fixed- and live-cell imaging of human cells to address this question, revealing a hybrid model in which RD histone biosynthesis is first initiated in G1, followed by a strong increase in histone production in S phase of the cell cycle. This suggests a mechanism by which cells that have committed to the cell cycle build up an initial small pool of RD histones to be available for the start of DNA replication, before producing most of the necessary histones required in S phase. Thus, a clear distinction exists at completion of mitosis between cells that are born with the intention of proceeding through the cell cycle and replicating their DNA and cells that have chosen to exit the cell cycle and have no immediate need for histone synthesis.
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54
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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55
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García-Giménez JL, Garcés C, Romá-Mateo C, Pallardó FV. Oxidative stress-mediated alterations in histone post-translational modifications. Free Radic Biol Med 2021; 170:6-18. [PMID: 33689846 DOI: 10.1016/j.freeradbiomed.2021.02.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/15/2022]
Abstract
Epigenetic regulation of gene expression provides a finely tuned response capacity for cells when undergoing environmental changes. However, in the context of human physiology or disease, any cellular imbalance that modulates homeostasis has the potential to trigger molecular changes that result either in physiological adaptation to a new situation or pathological conditions. These effects are partly due to alterations in the functionality of epigenetic regulators, which cause long-term and often heritable changes in cell lineages. As such, free radicals resulting from unbalanced/extended oxidative stress have been proved to act as modulators of epigenetic agents, resulting in alterations of the epigenetic landscape. In the present review we will focus on the particular effect that oxidative stress and free radicals produce in histone post-translational modifications that contribute to altering the histone code and, consequently, gene expression. The pathological consequences of the changes in this epigenetic layer of regulation of gene expression are thoroughly evidenced by data gathered in many physiological adaptive processes and in human diseases that range from age-related neurodegenerative pathologies to cancer, and that include respiratory syndromes, infertility, and systemic inflammatory conditions like sepsis.
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Affiliation(s)
- José-Luis García-Giménez
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain; Associated Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Concepción Garcés
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain
| | - Carlos Romá-Mateo
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain; Associated Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Federico V Pallardó
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain; Associated Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
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56
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Anuntakarun S, Larbcharoensub N, Payungporn S, Reamtong O. Identification of genes associated with Kikuchi-Fujimoto disease using RNA and exome sequencing. Mol Cell Probes 2021; 57:101728. [PMID: 33819568 DOI: 10.1016/j.mcp.2021.101728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/16/2021] [Accepted: 03/29/2021] [Indexed: 12/15/2022]
Abstract
Kikuchi-Fujimoto disease (KFD) is an extremely rare disease, and although it is reported to have a worldwide distribution, young Asian women are most likely to be affected. Although this disease is generally benign and self-limiting, distinguishing it from other diseases that cause lymphadenopathy (e.g., leukemia, lymphoma, and infectious diseases) is challenging. A lymph node biopsy is a definitive diagnostic technique for KFD and only requires skillful pathologists. There are no specific symptoms or laboratory tests for KFD, and more than 50% of KFD patients have suffered from being misdiagnosed with lymphoma, which leads to improper treatment. In this study, lymph node tissue samples from KFD patients were used to reveal their exomes and transcriptomes using a high-throughput nucleotide sequencer. Fourteen single nucleotide polymorphisms (SNPs) were identified as candidate KFD markers and were compared with a healthy lymph node exome dataset. The mutation of these genes caused disruptive impact in the proteins. Several SNPs associated with KFD involve genes related to human cancers, olfaction, and osteoblast differentiation. According to the transcriptome data, there were 238 up-regulated and 1,519 down-regulated genes. RANBP2-like and ribosomal protein L13 were the most up-regulated and down-regulated genes in KFD patients, respectively. The altered gene expression involved in the human immune system, chromatin remodeling, and gene transcription. A comparison of KFD and healthy datasets of exomes and transcriptomes may allow further insights into the KFD phenotype. The results may also facilitate future KFD diagnosis and treatment.
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Affiliation(s)
- Songtham Anuntakarun
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Noppadol Larbcharoensub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand; Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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57
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Amatori S, Tavolaro S, Gambardella S, Fanelli M. The dark side of histones: genomic organization and role of oncohistones in cancer. Clin Epigenetics 2021; 13:71. [PMID: 33827674 PMCID: PMC8025322 DOI: 10.1186/s13148-021-01057-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
Background The oncogenic role of histone mutations is one of the most relevant discovery in cancer epigenetics. Recurrent mutations targeting histone genes have been described in pediatric brain tumors, chondroblastoma, giant cell tumor of bone and other tumor types. The demonstration that mutant histones can be oncogenic and drive the tumorigenesis in pediatric tumors, led to the coining of the term “oncohistones.” The first identified histone mutations were localized at or near residues normally targeted by post-translational modifications (PTMs) in the histone N-terminal tails and suggested a possible interference with histone PTMs regulation and reading. Main body In this review, we describe the peculiar organization of the multiple genes that encode histone proteins, and the latter advances in both the identification and the biological role of histone mutations in cancer. Recent works show that recurrent somatic mutations target both N-terminal tails and globular histone fold domain in diverse tumor types. Oncohistones are often dominant-negative and occur at higher frequencies in tumors affecting children and adolescents. Notably, in many cases the mutations target selectively only some of the genes coding the same histone protein and are frequently associated with specific tumor types or, as documented for histone variant H3.3 in pediatric glioma, with peculiar tumors arising from specific anatomic locations. Conclusion The overview of the most recent advances suggests that the oncogenic potential of histone mutations can be exerted, together with the alteration of histone PTMs, through the destabilization of nucleosome and DNA–nucleosome interactions, as well as through the disruption of higher-order chromatin structure. However, further studies are necessary to fully elucidate the mechanism of action of oncohistones, as well as to evaluate their possible application to cancer classification, prognosis and to the identification of new therapies.
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Affiliation(s)
- Stefano Amatori
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.
| | - Simona Tavolaro
- Fredis Associazione, Via Edoardo Jenner 30, 00151, Rome, Italy
| | - Stefano Gambardella
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.,IRCCS Neuromed, Via Atinense 18, 86077, Pozzilli, IS, Italy
| | - Mirco Fanelli
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.
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58
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Flaus A, Downs JA, Owen-Hughes T. Histone isoforms and the oncohistone code. Curr Opin Genet Dev 2021; 67:61-66. [PMID: 33285512 DOI: 10.1016/j.gde.2020.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/07/2020] [Indexed: 12/18/2022]
Abstract
Recent studies have highlighted the potential for missense mutations in histones to act as oncogenic drivers, leading to the term 'oncohistones'. While histone proteins are highly conserved, they are encoded by multigene families. There is heterogeneity among these genes at the level of the underlying sequence, the amino acid composition of the encoded histone isoform, and the expression levels. One question that arises, therefore, is whether all histone-encoding genes function equally as oncohistones. In this review, we consider this question and explore what this means in terms of the mechanisms by which oncohistones can exert their effects in chromatin.
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Affiliation(s)
- Andrew Flaus
- Centre for Chromosome Biology, Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Jessica A Downs
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
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59
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Kemp JP, Yang XC, Dominski Z, Marzluff WF, Duronio RJ. Superresolution light microscopy of the Drosophila histone locus body reveals a core-shell organization associated with expression of replication-dependent histone genes. Mol Biol Cell 2021; 32:942-955. [PMID: 33788585 PMCID: PMC8108526 DOI: 10.1091/mbc.e20-10-0645] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The histone locus body (HLB) is an evolutionarily conserved nuclear body that regulates the transcription and processing of replication-dependent (RD) histone mRNAs, which are the only eukaryotic mRNAs lacking a poly-A tail. Many nuclear bodies contain distinct domains, but how internal organization is related to nuclear body function is not fully understood. Here, we demonstrate using structured illumination microscopy that Drosophila HLBs have a “core–shell” organization in which the internal core contains transcriptionally active RD histone genes. The N-terminus of Mxc, which contains a domain required for Mxc oligomerization, HLB assembly, and RD histone gene expression, is enriched in the HLB core. In contrast, the C-terminus of Mxc is enriched in the HLB outer shell as is FLASH, a component of the active U7 snRNP that cotranscriptionally cleaves RD histone pre-mRNA. Consistent with these results, we show biochemically that FLASH binds directly to the Mxc C-terminal region. In the rapid S-M nuclear cycles of syncytial blastoderm Drosophila embryos, the HLB disassembles at mitosis and reassembles the core–shell arrangement as histone gene transcription is activated immediately after mitosis. Thus, the core–shell organization is coupled to zygotic histone gene transcription, revealing a link between HLB internal organization and RD histone gene expression.
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Affiliation(s)
- James P Kemp
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Zbigniew Dominski
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - William F Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Robert J Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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60
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Abstract
Eukaryotic nucleosomes organize chromatin by wrapping 147 bp of DNA around a histone core particle comprising two molecules each of histone H2A, H2B, H3 and H4. The DNA entering and exiting the particle may be bound by the linker histone H1. Whereas deposition of bulk histones is confined to S-phase, paralogs of the common histones, known as histone variants, are available to carry out functions throughout the cell cycle and accumulate in post-mitotic cells. Histone variants confer different structural properties on nucleosomes by wrapping more or less DNA or by altering nucleosome stability. They carry out specialized functions in DNA repair, chromosome segregation and regulation of transcription initiation, or perform tissue-specific roles. In this Cell Science at a Glance article and the accompanying poster, we briefly examine new insights into histone origins and discuss variants from each of the histone families, focusing on how structural differences may alter their functions. Summary: Histone variants change the structural properties of nucleosomes by wrapping more or less DNA, altering nucleosome stability or carrying out specialized functions.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
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61
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Imada T, Shimi T, Kaiho A, Saeki Y, Kimura H. RNA polymerase II condensate formation and association with Cajal and histone locus bodies in living human cells. Genes Cells 2021; 26:298-312. [PMID: 33608942 PMCID: PMC8252594 DOI: 10.1111/gtc.12840] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/24/2022]
Abstract
In eukaryotic nuclei, a number of phase‐separated nuclear bodies (NBs) are present. RNA polymerase II (Pol II) is the main player in transcription and forms large condensates in addition to localizing at numerous transcription foci. Cajal bodies (CBs) and histone locus bodies (HLBs) are NBs that are involved in transcriptional and post‐transcriptional regulation of small nuclear RNA and histone genes. By live‐cell imaging using human HCT116 cells, we here show that Pol II condensates (PCs) nucleated near CBs and HLBs, and the number of PCs increased during S phase concomitantly with the activation period of histone genes. Ternary PC–CB–HLB associates were formed via three pathways: nucleation of PCs and HLBs near CBs, interaction between preformed PC–HLBs with CBs and nucleation of PCs near preformed CB–HLBs. Coilin knockout increased the co‐localization rate between PCs and HLBs, whereas the number, nucleation timing and phosphorylation status of PCs remained unchanged. Depletion of PCs did not affect CBs and HLBs. Treatment with 1,6‐hexanediol revealed that PCs were more liquid‐like than CBs and HLBs. Thus, PCs are dynamic structures often nucleated following the activation of gene clusters associated with other NBs.
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Affiliation(s)
- Takashi Imada
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Takeshi Shimi
- World Research Hub InitiativeInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
- Cell Biology CenterInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
| | - Ai Kaiho
- Protein Metabolism ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
- Institute for Advanced Life SciencesHoshi UniversityTokyoJapan
| | - Yasushi Saeki
- Protein Metabolism ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Hiroshi Kimura
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
- World Research Hub InitiativeInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
- Cell Biology CenterInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
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62
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Dual RNA 3'-end processing of H2A.X messenger RNA maintains DNA damage repair throughout the cell cycle. Nat Commun 2021; 12:359. [PMID: 33441544 PMCID: PMC7807067 DOI: 10.1038/s41467-020-20520-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 12/04/2020] [Indexed: 12/11/2022] Open
Abstract
Phosphorylated H2A.X is a critical chromatin marker of DNA damage repair (DDR) in higher eukaryotes. However, H2A.X gene expression remains relatively uncharacterised. Replication-dependent (RD) histone genes generate poly(A)- mRNA encoding new histones to package DNA during replication. In contrast, replication-independent (RI) histone genes synthesise poly(A)+ mRNA throughout the cell cycle, translated into histone variants that confer specific epigenetic patterns on chromatin. Remarkably H2AFX, encoding H2A.X, is a hybrid histone gene, generating both poly(A)+ and poly(A)- mRNA isoforms. Here we report that the selective removal of either mRNA isoform reveals different effects in different cell types. In some cells, RD H2A.X poly(A)- mRNA generates sufficient histone for deposition onto DDR associated chromatin. In contrast, cells making predominantly poly(A)+ mRNA require this isoform for de novo H2A.X synthesis, required for efficient DDR. This highlights the importance of differential H2A.X mRNA 3’-end processing in the maintenance of effective DDR. H2A.X histone variant gene encodes poly(A)+ and poly(A)- mRNA isoforms which are differentially expressed depending on cell lines. Here the authors show that upon DNA damage, cells expressing more poly(A)+ isoform require this isoform for de novo H2A.X synthesis while cells with more poly(A)- isoform have sufficient H2A.X present in chromatin.
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63
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Saul D, Kosinsky RL. Epigenetics of Aging and Aging-Associated Diseases. Int J Mol Sci 2021; 22:ijms22010401. [PMID: 33401659 PMCID: PMC7794926 DOI: 10.3390/ijms22010401] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/19/2020] [Accepted: 12/26/2020] [Indexed: 12/17/2022] Open
Abstract
Aging represents the multifactorial decline in physiological function of every living organism. Over the past decades, several hallmarks of aging have been defined, including epigenetic deregulation. Indeed, multiple epigenetic events were found altered across different species during aging. Epigenetic changes directly contributing to aging and aging-related diseases include the accumulation of histone variants, changes in chromatin accessibility, loss of histones and heterochromatin, aberrant histone modifications, and deregulated expression/activity of miRNAs. As a consequence, cellular processes are affected, which results in the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, and neurodegenerative disorders. In this review, we focus on epigenetic mechanisms underlying aging-related processes in various species and describe how these deregulations contribute to human diseases.
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Affiliation(s)
- Dominik Saul
- Kogod Center on Aging and Division of Endocrinology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA;
- Department of Trauma, Orthopedics and Reconstructive Surgery, Georg-August-University of Goettingen, 37075 Goettingen, Germany
| | - Robyn Laura Kosinsky
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
- Correspondence: ; Tel.: +1-507-293-2386
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64
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Histone Variant H3.3 Mutations in Defining the Chromatin Function in Mammals. Cells 2020; 9:cells9122716. [PMID: 33353064 PMCID: PMC7766983 DOI: 10.3390/cells9122716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 12/26/2022] Open
Abstract
The systematic mutation of histone 3 (H3) genes in model organisms has proven to be a valuable tool to distinguish the functional role of histone residues. No system exists in mammalian cells to directly manipulate canonical histone H3 due to a large number of clustered and multi-loci histone genes. Over the years, oncogenic histone mutations in a subset of H3 have been identified in humans, and have advanced our understanding of the function of histone residues in health and disease. The oncogenic mutations are often found in one allele of the histone variant H3.3 genes, but they prompt severe changes in the epigenetic landscape of cells, and contribute to cancer development. Therefore, mutation approaches using H3.3 genes could be relevant to the determination of the functional role of histone residues in mammalian development without the replacement of canonical H3 genes. In this review, we describe the key findings from the H3 mutation studies in model organisms wherein the genetic replacement of canonical H3 is possible. We then turn our attention to H3.3 mutations in human cancers, and discuss H3.3 substitutions in the N-terminus, which were generated in order to explore the specific residue or associated post-translational modification.
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65
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Uggenti C, Lepelley A, Depp M, Badrock AP, Rodero MP, El-Daher MT, Rice GI, Dhir S, Wheeler AP, Dhir A, Albawardi W, Frémond ML, Seabra L, Doig J, Blair N, Martin-Niclos MJ, Della Mina E, Rubio-Roldán A, García-Pérez JL, Sproul D, Rehwinkel J, Hertzog J, Boland-Auge A, Olaso R, Deleuze JF, Baruteau J, Brochard K, Buckley J, Cavallera V, Cereda C, De Waele LMH, Dobbie A, Doummar D, Elmslie F, Koch-Hogrebe M, Kumar R, Lamb K, Livingston JH, Majumdar A, Lorenço CM, Orcesi S, Peudenier S, Rostasy K, Salmon CA, Scott C, Tonduti D, Touati G, Valente M, van der Linden H, Van Esch H, Vermelle M, Webb K, Jackson AP, Reijns MAM, Gilbert N, Crow YJ. cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing. Nat Genet 2020; 52:1364-1372. [PMID: 33230297 DOI: 10.1038/s41588-020-00737-3] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/09/2020] [Indexed: 12/25/2022]
Abstract
Inappropriate stimulation or defective negative regulation of the type I interferon response can lead to autoinflammation. In genetically uncharacterized cases of the type I interferonopathy Aicardi-Goutières syndrome, we identified biallelic mutations in LSM11 and RNU7-1, which encode components of the replication-dependent histone pre-mRNA-processing complex. Mutations were associated with the misprocessing of canonical histone transcripts and a disturbance of linker histone stoichiometry. Additionally, we observed an altered distribution of nuclear cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS) and enhanced interferon signaling mediated by the cGAS-stimulator of interferon genes (STING) pathway in patient-derived fibroblasts. Finally, we established that chromatin without linker histone stimulates cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) production in vitro more efficiently. We conclude that nuclear histones, as key constituents of chromatin, are essential in suppressing the immunogenicity of self-DNA.
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Affiliation(s)
- Carolina Uggenti
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Alice Lepelley
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Marine Depp
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Andrew P Badrock
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Mathieu P Rodero
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Marie-Thérèse El-Daher
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Gillian I Rice
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Somdutta Dhir
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Ann P Wheeler
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Ashish Dhir
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Waad Albawardi
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Marie-Louise Frémond
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Luis Seabra
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Jennifer Doig
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Natalie Blair
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Maria José Martin-Niclos
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Erika Della Mina
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Alejandro Rubio-Roldán
- Centre for Genomics and Oncological Research (GENyO), Pfizer-University of Granada-Andalusian Regional Government, Parque Tecnico de la Ciencia de Salud, Granada, Spain
| | - Jose L García-Pérez
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
- Centre for Genomics and Oncological Research (GENyO), Pfizer-University of Granada-Andalusian Regional Government, Parque Tecnico de la Ciencia de Salud, Granada, Spain
| | - Duncan Sproul
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jonny Hertzog
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Anne Boland-Auge
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine, Évry, France
| | - Robert Olaso
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine, Évry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine, Évry, France
| | - Julien Baruteau
- University College London Great Ormond Street Institute of Child Health, London, UK
| | - Karine Brochard
- Service de Médecine Interne Néphrologie Pédiatrique, Hôpital des Enfants, Toulouse, France
| | - Jonathan Buckley
- Department of Paediatric Nephrology, University of Cape Town, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Vanessa Cavallera
- Child Neurology and Psychiatry Unit, Istituto di Ricovero e Cura a Carattere Scientifico, Mondino Foundation, Pavia, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, Istituto di Ricovero e Cura a Carattere Scientifico, Mondino Foundation, Pavia, Italy
| | | | - Angus Dobbie
- Yorkshire Clinical Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Diane Doummar
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Département de Neuropédiatrie, Centre de Référence de Neurogénétique et Mouvements Anormaux de l'Enfant, Hôpital Armand Trousseau, Paris, France
| | - Frances Elmslie
- South West Thames Regional Genetics Service, St George's, University of London, London, UK
| | - Margarete Koch-Hogrebe
- Department of Paediatric Neurology, Children's Hospital Datteln, Witten/Herdecke University, Datteln, Germany
| | - Ram Kumar
- Department of Paediatric Neurology, Alder Hey Children's National Health Service Foundation Trust, Liverpool, UK
| | - Kate Lamb
- Department of Paediatrics, Gloucestershire Royal Hospital, Gloucester, UK
| | - John H Livingston
- Department of Paediatric Neurology, Leeds Teaching Hospitals National Health Service Trust, Leeds, UK
| | - Anirban Majumdar
- Department of Paediatric Neurology, Bristol Children's Hospital, Bristol, UK
| | - Charles Marques Lorenço
- Faculdade de Medicina - Centro Universitário Estácio de Ribeirão Preto, Ribeirão Preto, Brazil
| | - Simona Orcesi
- Child Neurology and Psychiatry Unit, Istituto di Ricovero e Cura a Carattere Scientifico, Mondino Foundation, Pavia, Italy
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Sylviane Peudenier
- Centre de Référence des Déficiences Intellectuelles de Causes Rares et Polyhandicap, Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Kevin Rostasy
- Department of Paediatric Neurology, Children's Hospital Datteln, Witten/Herdecke University, Datteln, Germany
| | - Caroline A Salmon
- Department of Paediatrics, Royal Surrey County Hospital, Guildford, UK
| | - Christiaan Scott
- University of Cape Town, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Davide Tonduti
- Center for diagnosis and treatment of Leukodystrophies, Pediatric Neurology Unit, V. Buzzi Children's Hospital, Milano, Italy
| | - Guy Touati
- Reference Center for Inborn Errors of Metabolism-Department of Pediatrics, Hôpital des Enfants-Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Marialuisa Valente
- Genomic and Post-Genomic Center, Istituto di Ricovero e Cura a Carattere Scientifico, Mondino Foundation, Pavia, Italy
| | - Hélio van der Linden
- Department of Paediatric Neurology, Neurological Institute of Goiânia, Goiânia, Brazil
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Marie Vermelle
- Department of Paediatrics, Centre Hospitalier de Dunkerque, Dunkerque, France
| | - Kate Webb
- University of Cape Town, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Andrew P Jackson
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Martin A M Reijns
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Yanick J Crow
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK.
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France.
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66
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Papadogianni G, Ravens I, Dittrich-Breiholz O, Bernhardt G, Georgiev H. Impact of Aging on the Phenotype of Invariant Natural Killer T Cells in Mouse Thymus. Front Immunol 2020; 11:575764. [PMID: 33193368 PMCID: PMC7662090 DOI: 10.3389/fimmu.2020.575764] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/12/2020] [Indexed: 11/16/2022] Open
Abstract
Invariant natural killer T (iNKT) cells represent a subclass of T cells possessing a restricted repertoire of T cell receptors enabling them to recognize lipid derived ligands. iNKT cells are continuously generated in thymus and differentiate into three main subpopulations: iNKT1, iNKT2, and iNKT17 cells. We investigated the transcriptomes of these subsets comparing cells isolated from young adult (6–10 weeks old) and aged BALB/c mice (25–30 weeks of age) in order to identify genes subject to an age-related regulation of expression. These time points were selected to take into consideration the consequences of thymic involution that radically alter the existing micro-milieu. Significant differences were detected in the expression of histone genes affecting all iNKT subsets. Also the proliferative capacity of iNKT cells decreased substantially upon aging. Several genes were identified as possible candidates causing significant age-dependent changes in iNKT cell generation and/or function such as genes coding for granzyme A, ZO-1, EZH2, SOX4, IGF1 receptor, FLT4, and CD25. Moreover, we provide evidence that IL2 differentially affects homeostasis of iNKT subsets with iNKT17 cells engaging a unique mechanism to respond to IL2 by initiating a slow rate of proliferation.
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Affiliation(s)
| | - Inga Ravens
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | | | - Günter Bernhardt
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Hristo Georgiev
- Institute of Immunology, Hannover Medical School, Hannover, Germany
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67
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Peng LX, Wang MD, Xie P, Yang JP, Sun R, Zheng LS, Mei Y, Meng DF, Peng XS, Lang YH, Qiang YY, Li CZ, Xu L, Liu ZJ, Guo LL, Xie DH, Shu DT, Lin ST, Luo FF, Huang BJ, Qian CN. LACTB promotes metastasis of nasopharyngeal carcinoma via activation of ERBB3/EGFR-ERK signaling resulting in unfavorable patient survival. Cancer Lett 2020; 498:165-177. [PMID: 33152401 DOI: 10.1016/j.canlet.2020.10.051] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/25/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Nasopharyngeal carcinoma (NPC) originates in the nasopharyngeal epithelium and has the highest metastatic rate among head and neck cancers. Distant metastasis is the main reason for treatment failure with the underlying mechanisms remaining unclear. By comparing the expression profiling of NPCs versus non-cancerous nasopharyngeal tissues, we found LACTB was highly expressed in the tumor tissues. We found that elevated expression of the LACTB protein in primary NPCs correlated with poorer patient survival. LACTB is known to be a serine protease and a ubiquitous mitochondrial protein localized in the intermembrane space. Its role in tumor biology remains controversial. We found that the different methylation pattern of LACTB promoter led to its differential expression in NPC cells. Overexpressing LACTB in NPC cells promoted their motility in vitro and metastasis in vivo. While knocking down LACTB reduced the metastasis capability of NPC cells. However, LACTB did not influence cellular proliferation. We further found the role of LACTB in promoting NPC metastasis depended on the activation of ERBB3/EGFR-ERK signaling, which in turn, affected the stability and the following acetylation of histone H3. These findings may shed light on unveiling the mechanisms of NPC metastasis.
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Affiliation(s)
- Li-Xia Peng
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Ming-Dian Wang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Ping Xie
- Department of Radiation Oncology, Xiang an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jun-Ping Yang
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Rui Sun
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Li-Sheng Zheng
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yan Mei
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Dong-Fang Meng
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Xing-Si Peng
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Yan-Hong Lang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yuan-Yuan Qiang
- Ningxia Key Laboratory for Cerebrocranical Disease, Ningxia Medical University, Yinchuan, 750001, Ningxia, China
| | - Chang-Zhi Li
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Liang Xu
- Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China
| | - Zhi-Jie Liu
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Ling-Ling Guo
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - De-Huan Xie
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Di-Tian Shu
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Si-Ting Lin
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Fei-Fei Luo
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Bi-Jun Huang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Chao-Nan Qian
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
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Tafessu A, Banaszynski LA. Establishment and function of chromatin modification at enhancers. Open Biol 2020; 10:200255. [PMID: 33050790 PMCID: PMC7653351 DOI: 10.1098/rsob.200255] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
How a single genome can give rise to distinct cell types remains a fundamental question in biology. Mammals are able to specify and maintain hundreds of cell fates by selectively activating unique subsets of their genome. This is achieved, in part, by enhancers-genetic elements that can increase transcription of both nearby and distal genes. Enhancers can be identified by their unique chromatin signature, including transcription factor binding and the enrichment of specific histone post-translational modifications, histone variants, and chromatin-associated cofactors. How each of these chromatin features contributes to enhancer function remains an area of intense study. In this review, we provide an overview of enhancer-associated chromatin states, and the proteins and enzymes involved in their establishment. We discuss recent insights into the effects of the enhancer chromatin state on ongoing transcription versus their role in the establishment of new transcription programmes, such as those that occur developmentally. Finally, we highlight the role of enhancer chromatin in new conceptual advances in gene regulation such as condensate formation.
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Affiliation(s)
| | - Laura A. Banaszynski
- UT Southwestern Medical Center, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, Hamon Center for Regenerative Science and Medicine, Dallas, TX 75390-8511, USA
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69
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Van Rechem C, Ji F, Mishra S, Chakraborty D, Murphy SE, Dillingham ME, Sadreyev RI, Whetstine JR. The lysine demethylase KDM4A controls the cell-cycle expression of replicative canonical histone genes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194624. [PMID: 32798738 DOI: 10.1016/j.bbagrm.2020.194624] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/22/2020] [Accepted: 08/10/2020] [Indexed: 12/27/2022]
Abstract
Chromatin modulation provides a key checkpoint for controlling cell cycle regulated gene networks. The replicative canonical histone genes are one such gene family under tight regulation during cell division. These genes are most highly expressed during S phase when histones are needed to chromatinize the new DNA template. While this fact has been known for a while, limited knowledge exists about the specific chromatin regulators controlling their temporal expression during cell cycle. Since histones and their associated mutations are emerging as major players in diseases such as cancer, identifying the chromatin factors modulating their expression is critical. The histone lysine tri-demethylase KDM4A is regulated over cell cycle and plays a direct role in DNA replication timing, site-specific rereplication, and DNA amplifications during S phase. Here, we establish an unappreciated role for the catalytically active KDM4A in directly regulating canonical replicative histone gene networks during cell cycle. Of interest, we further demonstrate that KDM4A interacts with proteins controlling histone expression and RNA processing (i.e., hnRNPUL1 and FUS/TLS). Together, this study provides a new function for KDM4A in modulating canonical histone gene expression.
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Affiliation(s)
- Capucine Van Rechem
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Fei Ji
- Massachusetts General Hospital, Department of Molecular Biology, Simches Research Center, Boston, MA 02114, United States of America
| | - Sweta Mishra
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Damayanti Chakraborty
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Sedona E Murphy
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Megan E Dillingham
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Ruslan I Sadreyev
- Massachusetts General Hospital, Department of Molecular Biology, Simches Research Center, Boston, MA 02114, United States of America; Massachusetts General Hospital, Department of Pathology and Harvard Medical School, Simches Research Center, Boston, MA 02114, United States of America.
| | - Johnathan R Whetstine
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America; Fox Chase Cancer Center, 333 Cottman Avenue West 260, Philadelphia, PA 19111, United States of America.
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70
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Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary. Proc Natl Acad Sci U S A 2020; 117:20015-20026. [PMID: 32759216 PMCID: PMC7443898 DOI: 10.1073/pnas.2005570117] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This paper improves knowledge of the somatic and germ cells of the developing mouse ovary that assemble into ovarian follicles, by determining cellular gene expression, and tracing lineage relationships. The study covers the last week of fetal development through the first five days of postnatal development. During this time, many critically important processes take place, including sex determination, follicle assembly, and the initial events of meiosis. We report expression differences between pregranulosa cells of wave 1 follicles that function at puberty and wave 2 follicles that sustain fertility. These studies illuminate ovarian somatic cells and provide a resource to study the development, physiology, and evolutionary conservation of mammalian ovarian follicle formation. We sequenced more than 52,500 single cells from embryonic day 11.5 (E11.5) postembryonic day 5 (P5) gonads and performed lineage tracing to analyze primordial follicles and wave 1 medullar follicles during mouse fetal and perinatal oogenesis. Germ cells clustered into six meiotic substages, as well as dying/nurse cells. Wnt-expressing bipotential precursors already present at E11.5 are followed at each developmental stage by two groups of ovarian pregranulosa (PG) cells. One PG group, bipotential pregranulosa (BPG) cells, derives directly from bipotential precursors, expresses Foxl2 early, and associates with cysts throughout the ovary by E12.5. A second PG group, epithelial pregranulosa (EPG) cells, arises in the ovarian surface epithelium, ingresses cortically by E12.5 or earlier, expresses Lgr5, but delays robust Foxl2 expression until after birth. By E19.5, EPG cells predominate in the cortex and differentiate into granulosa cells of quiescent primordial follicles. In contrast, medullar BPG cells differentiate along a distinct pathway to become wave 1 granulosa cells. Reflecting their separate somatic cellular lineages, second wave follicles were ablated by diptheria toxin treatment of Lgr5-DTR-EGFP mice at E16.5 while first wave follicles developed normally and supported fertility. These studies provide insights into ovarian somatic cells and a resource to study the development, physiology, and evolutionary conservation of mammalian ovarian follicles.
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Scott WA, Campos EI. Interactions With Histone H3 & Tools to Study Them. Front Cell Dev Biol 2020; 8:701. [PMID: 32850821 PMCID: PMC7411163 DOI: 10.3389/fcell.2020.00701] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/10/2020] [Indexed: 01/12/2023] Open
Abstract
Histones are an integral part of chromatin and thereby influence its structure, dynamics, and functions. The effects of histone variants, posttranslational modifications, and binding proteins is therefore of great interest. From the moment that they are deposited on chromatin, nucleosomal histones undergo dynamic changes in function of the cell cycle, and as DNA is transcribed and replicated. In the process, histones are not only modified and bound by various proteins, but also shuffled, evicted, or replaced. Technologies and tools to study such dynamic events continue to evolve and better our understanding of chromatin and of histone proteins proper. Here, we provide an overview of H3.1 and H3.3 histone dynamics throughout the cell cycle, while highlighting some of the tools used to study their protein–protein interactions. We specifically discuss how histones are chaperoned, modified, and bound by various proteins at different stages of the cell cycle. Established and select emerging technologies that furthered (or have a high potential of furthering) our understanding of the dynamic histone–protein interactions are emphasized. This includes experimental tools to investigate spatiotemporal changes on chromatin, the role of histone chaperones, histone posttranslational modifications, and histone-binding effector proteins.
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Affiliation(s)
- William A Scott
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eric I Campos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Bucholc K, Skrajna A, Adamska K, Yang XC, Krajewski K, Poznański J, Dadlez M, Domiński Z, Zhukov I. Structural Analysis of the SANT/Myb Domain of FLASH and YARP Proteins and Their Complex with the C-Terminal Fragment of NPAT by NMR Spectroscopy and Computer Simulations. Int J Mol Sci 2020; 21:ijms21155268. [PMID: 32722282 PMCID: PMC7432317 DOI: 10.3390/ijms21155268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 11/16/2022] Open
Abstract
FLICE-associated huge protein (FLASH), Yin Yang 1-Associated Protein-Related Protein (YARP) and Nuclear Protein, Ataxia-Telangiectasia Locus (NPAT) localize to discrete nuclear structures called histone locus bodies (HLBs) where they control various steps in histone gene expression. Near the C-terminus, FLASH and YARP contain a highly homologous domain that interacts with the C-terminal region of NPAT. Structural aspects of the FLASH-NPAT and YARP-NPAT complexes and their role in histone gene expression remain largely unknown. In this study, we used multidimensional NMR spectroscopy and in silico modeling to analyze the C-terminal domain in FLASH and YARP in an unbound form and in a complex with the last 31 amino acids of NPAT. Our results demonstrate that FLASH and YARP domains share the same fold of a triple α -helical bundle that resembles the DNA binding domain of Myb transcriptional factors and the SANT domain found in chromatin-modifying and remodeling complexes. The NPAT peptide contains a single α -helix that makes multiple contacts with α -helices I and III of the FLASH and YARP domains. Surprisingly, in spite of sharing a significant amino acid similarity, each domain likely binds NPAT using a unique network of interactions, yielding two distinct complexes. In silico modeling suggests that both complexes are structurally compatible with DNA binding, raising the possibility that they may function in identifying specific sequences within histone gene clusters, hence initiating the assembly of HLBs and regulating histone gene expression during cell cycle progression.
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Affiliation(s)
- Katarzyna Bucholc
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Aleksandra Skrajna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Kinga Adamska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Zbigniew Domiński
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Correspondence: (Z.D.); (I.Z.); Tel.: +48-22-592-2038 (I.Z.)
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
- NanoBioMedical Centre, Adam Mickiewicz University, ul. Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland
- Correspondence: (Z.D.); (I.Z.); Tel.: +48-22-592-2038 (I.Z.)
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73
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Hur W, Kemp JP, Tarzia M, Deneke VE, Marzluff WF, Duronio RJ, Di Talia S. CDK-Regulated Phase Separation Seeded by Histone Genes Ensures Precise Growth and Function of Histone Locus Bodies. Dev Cell 2020; 54:379-394.e6. [PMID: 32579968 DOI: 10.1016/j.devcel.2020.06.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 02/17/2020] [Accepted: 05/30/2020] [Indexed: 10/24/2022]
Abstract
Many membraneless organelles form through liquid-liquid phase separation, but how their size is controlled and whether size is linked to function remain poorly understood. The histone locus body (HLB) is an evolutionarily conserved nuclear body that regulates the transcription and processing of histone mRNAs. Here, we show that Drosophila HLBs form through phase separation. During embryogenesis, the size of HLBs is controlled in a precise and dynamic manner that is dependent on the cell cycle and zygotic histone gene activation. Control of HLB growth is achieved by a mechanism integrating nascent mRNAs at the histone locus, which facilitates phase separation, and the nuclear concentration of the scaffold protein multi-sex combs (Mxc), which is controlled by the activity of cyclin-dependent kinases. Reduced Cdk2 activity results in smaller HLBs and the appearance of nascent, misprocessed histone mRNAs. Thus, our experiments identify a mechanism linking nuclear body growth and size with gene expression.
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Affiliation(s)
- Woonyung Hur
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - James P Kemp
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marco Tarzia
- LPTMC, CNRS-UMR 7600, Sorbonne Université, 4 Pl. Jussieu, 75005 Paris, France
| | - Victoria E Deneke
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - William F Marzluff
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert J Duronio
- Department of Biology, Department of Genetics, Integrative Program for Biological and Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA.
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74
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Fortin J, Tian R, Zarrabi I, Hill G, Williams E, Sanchez-Duffhues G, Thorikay M, Ramachandran P, Siddaway R, Wong JF, Wu A, Apuzzo LN, Haight J, You-Ten A, Snow BE, Wakeham A, Goldhamer DJ, Schramek D, Bullock AN, Dijke PT, Hawkins C, Mak TW. Mutant ACVR1 Arrests Glial Cell Differentiation to Drive Tumorigenesis in Pediatric Gliomas. Cancer Cell 2020; 37:308-323.e12. [PMID: 32142668 PMCID: PMC7105820 DOI: 10.1016/j.ccell.2020.02.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 12/02/2019] [Accepted: 02/04/2020] [Indexed: 12/30/2022]
Abstract
Diffuse intrinsic pontine gliomas (DIPGs) are aggressive pediatric brain tumors for which there is currently no effective treatment. Some of these tumors combine gain-of-function mutations in ACVR1, PIK3CA, and histone H3-encoding genes. The oncogenic mechanisms of action of ACVR1 mutations are currently unknown. Using mouse models, we demonstrate that Acvr1G328V arrests the differentiation of oligodendroglial lineage cells, and cooperates with Hist1h3bK27M and Pik3caH1047R to generate high-grade diffuse gliomas. Mechanistically, Acvr1G328V upregulates transcription factors which control differentiation and DIPG cell fitness. Furthermore, we characterize E6201 as a dual inhibitor of ACVR1 and MEK1/2, and demonstrate its efficacy toward tumor cells in vivo. Collectively, our results describe an oncogenic mechanism of action for ACVR1 mutations, and suggest therapeutic strategies for DIPGs.
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MESH Headings
- Activin Receptors, Type I/antagonists & inhibitors
- Activin Receptors, Type I/chemistry
- Activin Receptors, Type I/genetics
- Activin Receptors, Type I/metabolism
- Animals
- Basic Helix-Loop-Helix Transcription Factors/genetics
- Basic Helix-Loop-Helix Transcription Factors/metabolism
- Bone Morphogenetic Proteins/genetics
- Bone Morphogenetic Proteins/metabolism
- Brain Neoplasms/drug therapy
- Brain Neoplasms/genetics
- Brain Neoplasms/pathology
- Cell Differentiation/genetics
- Cell Line, Tumor
- Class I Phosphatidylinositol 3-Kinases/genetics
- Class I Phosphatidylinositol 3-Kinases/metabolism
- Female
- Glioma/drug therapy
- Glioma/genetics
- Glioma/pathology
- Histones/genetics
- Histones/metabolism
- Humans
- Lactones/pharmacology
- Male
- Mice, Transgenic
- Mutation
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/pathology
- Neuroglia/metabolism
- Neuroglia/pathology
- Oligodendroglia/pathology
- Receptor, Platelet-Derived Growth Factor alpha/genetics
- Receptor, Platelet-Derived Growth Factor alpha/metabolism
- SOXC Transcription Factors/genetics
- SOXC Transcription Factors/metabolism
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Affiliation(s)
- Jerome Fortin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
| | - Ruxiao Tian
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Ida Zarrabi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Graham Hill
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Eleanor Williams
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Gonzalo Sanchez-Duffhues
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, P.O. Box 9600 RC, Leiden, the Netherlands
| | - Midory Thorikay
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, P.O. Box 9600 RC, Leiden, the Netherlands
| | | | - Robert Siddaway
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G1X8, Canada
| | - Jong Fu Wong
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Annette Wu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Lorraine N Apuzzo
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA
| | - Jillian Haight
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Annick You-Ten
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Bryan E Snow
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Andrew Wakeham
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - David J Goldhamer
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA
| | - Daniel Schramek
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alex N Bullock
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Peter Ten Dijke
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, P.O. Box 9600 RC, Leiden, the Netherlands
| | - Cynthia Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G1X8, Canada; Division of Pathology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Tak W Mak
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
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75
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Histone H2A isoforms: Potential implications in epigenome plasticity and diseases in eukaryotes. J Biosci 2020. [DOI: 10.1007/s12038-019-9985-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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76
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Abstract
In eukaryotes, DNA is highly compacted within the nucleus into a structure known as chromatin. Modulation of chromatin structure allows for precise regulation of gene expression, and thereby controls cell fate decisions. Specific chromatin organization is established and preserved by numerous factors to generate desired cellular outcomes. In embryonic stem (ES) cells, chromatin is precisely regulated to preserve their two defining characteristics: self-renewal and pluripotent state. This action is accomplished by a litany of nucleosome remodelers, histone variants, epigenetic marks, and other chromatin regulatory factors. These highly dynamic regulatory factors come together to precisely define a chromatin state that is conducive to ES cell maintenance and development, where dysregulation threatens the survival and fitness of the developing organism.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States.
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77
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Monteonofrio L, Valente D, Rinaldo C, Soddu S. Extrachromosomal Histone H2B Contributes to the Formation of the Abscission Site for Cell Division. Cells 2019; 8:cells8111391. [PMID: 31694230 PMCID: PMC6912571 DOI: 10.3390/cells8111391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/25/2019] [Accepted: 10/31/2019] [Indexed: 12/13/2022] Open
Abstract
Histones are constitutive components of nucleosomes and key regulators of chromatin structure. We previously observed that an extrachromosomal histone H2B (ecH2B) localizes at the intercellular bridge (ICB) connecting the two daughter cells during cytokinesis independently of DNA and RNA. Here, we show that ecH2B binds and colocalizes with CHMP4B, a key component of the ESCRT-III machinery responsible for abscission, the final step of cell division. Abscission requires the formation of an abscission site at the ICB where the ESCRT-III complex organizes into narrowing cortical helices that drive the physical separation of sibling cells. ecH2B depletion does not prevent membrane cleavage rather results in abscission delay and accumulation of abnormally long and thin ICBs. In the absence of ecH2B, CHMP4B and other components of the fission machinery, such as IST1 and Spastin, are recruited to the ICB and localize at the midbody. However, in the late stage of abscission, these fission factors fail to re-localize at the periphery of the midbody and the abscission site fails to form. These results show that extrachromosomal activity of histone H2B is required in the formation of the abscission site and the proper localization of the fission machinery.
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Affiliation(s)
- Laura Monteonofrio
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (D.V.); (C.R.)
- Correspondence: (L.M.); (S.S.); Tel.: +1-(443)-410-9571 (L.M.); +39-065266-2492 (S.S.)
| | - Davide Valente
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (D.V.); (C.R.)
| | - Cinzia Rinaldo
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (D.V.); (C.R.)
- Institutes of Molecular Biology and Pathology (IBPM), National Research Council (CNR), c/o Sapienza University, 00185 Rome, Italy
| | - Silvia Soddu
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (D.V.); (C.R.)
- Correspondence: (L.M.); (S.S.); Tel.: +1-(443)-410-9571 (L.M.); +39-065266-2492 (S.S.)
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78
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Garciaz S, N'guyen Dasi L, Finetti P, Chevalier C, Vernerey J, Poplineau M, Platet N, Audebert S, Pophillat M, Camoin L, Bertucci F, Calmels B, Récher C, Birnbaum D, Chabannon C, Vey N, Duprez E. Epigenetic down-regulation of the HIST1 locus predicts better prognosis in acute myeloid leukemia with NPM1 mutation. Clin Epigenetics 2019; 11:141. [PMID: 31606046 PMCID: PMC6790061 DOI: 10.1186/s13148-019-0738-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/05/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The epigenetic machinery is frequently altered in acute myeloid leukemia. Focusing on cytogenetically normal (CN) AML, we previously described an abnormal H3K27me3 enrichment covering 70 kb on the HIST1 cluster (6.p22) in CN-AML patient blasts. Here, we further investigate the molecular, functional, and prognosis significance of this epigenetic alteration named H3K27me3 HIST1 in NPM1-mutated (NPM1mut) CN-AML. RESULTS We found that three quarter of the NPM1mut CN-AML patients were H3K27me3 HIST1high. H3K27me3 HIST1high group of patients was associated with a favorable outcome independently of known molecular risk factors. In gene expression profiling, the H3K27me3 HIST1high mark was associated with lower expression of the histone genes HIST1H1D, HIST1H2BG, HIST1H2AE, and HIST1H3F and an upregulation of genes involved in myelomonocytic differentiation. Mass spectrometry analyses confirmed that the linker histone protein H1d, but not the other histone H1 subtypes, was downregulated in the H3K27me3 HIST1high group of patients. H1d knockdown primed ATRA-mediated differentiation of OCI-AML3 and U937 AML cell lines, as assessed on CD11b/CD11c markers, morphological and gene expression analyses. CONCLUSIONS Our data suggest that NPM1mut AML prognosis depends on the epigenetic silencing of the HIST1 cluster and that, among the H3K27me3 silenced histone genes, HIST1H1D plays a role in AML blast differentiation.
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Affiliation(s)
- Sylvain Garciaz
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France
| | - Lia N'guyen Dasi
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France
| | - Pascal Finetti
- Predictive Oncology Laboratory, CRCM, Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France
| | - Christine Chevalier
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France.,Institut Pasteur, G5 Chromatin and Infection, Paris, France
| | - Julien Vernerey
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France
| | - Mathilde Poplineau
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France
| | - Nadine Platet
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France
| | - Stéphane Audebert
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Matthieu Pophillat
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Luc Camoin
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - François Bertucci
- Predictive Oncology Laboratory, CRCM, Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France
| | - Boris Calmels
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France.,Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Centre d'Investigations Cliniques en Biothérapies, Marseille, France
| | - Christian Récher
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France Université Toulouse III Paul Sabatier, Cancer Research Center of Toulouse, UMR1037-INSERM, ERL5294 CNRS, Toulouse, France
| | - Daniel Birnbaum
- Predictive Oncology Laboratory, CRCM, Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France
| | - Christian Chabannon
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France.,Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Centre d'Investigations Cliniques en Biothérapies, Marseille, France
| | - Norbert Vey
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Estelle Duprez
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France.
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79
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Choi S, Pfleger J, Jeon YH, Yang Z, He M, Shin H, Sayed D, Astrof S, Abdellatif M. Oxoglutarate dehydrogenase and acetyl-CoA acyltransferase 2 selectively associate with H2A.Z-occupied promoters and are required for histone modifications. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:194436. [PMID: 31682939 PMCID: PMC7187930 DOI: 10.1016/j.bbagrm.2019.194436] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/17/2019] [Accepted: 09/27/2019] [Indexed: 12/26/2022]
Abstract
Histone H2A.Z plays an essential role in regulating transcriptional rates and memory. Interestingly, H2A.Z-bound nucleosomes are located in both transcriptionally active and inactive promotors, with no clear understanding of the mechanisms via which it differentially regulates transcription. We hypothesized that its functions are mediated through recruitment of regulatory proteins to promoters. Using rapid chromatin immunoprecipitation-mass spectrometry, we uncovered the association of H2A.Z-bound chromatin with the metabolic enzymes, oxoglutarate dehydrogenase (OGDH) and acetyl-CoA acyltransferase 2 (ACAA2). Recombinant green florescence fusion proteins, combined with mutations of predicted nuclear localization signals, confirmed their nuclear localization and chromatin binding. Conclusively, chromatin immunoprecipitation-deep sequencing, confirmed the predominant association of OGDH and ACAA2 with H2A.Z-occupied transcription start sites and enhancers, the former of which we confirmed is conserved in both mouse and human tissue. Furthermore, H2A.Z-deficient human HAP1 cells exhibited reduced chromatin-bound metabolic enzymes, accompanied with reduced posttranslational histone modifications, including acetylation and succinylation. Specifically, knockdown of OGDH diminished H4 succinylation. Thus, the data reveal that select metabolic enzymes are assembled at active, H2A.Z-occupied, promoters, for potential site-directed production of metabolic intermediates that are required for histone modifications.
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Affiliation(s)
- Sujung Choi
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Jessica Pfleger
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Yong Heui Jeon
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Zhi Yang
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Minzhen He
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Hyewon Shin
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Danish Sayed
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Sophie Astrof
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Maha Abdellatif
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America.
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80
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Lü S, Liu Y, Cui J, Yang B, Li G, Guo Y, Kuang H, Wang Q. Mechanism of Caulophyllum robustum Maxim against rheumatoid arthritis using LncRNA-mRNA chip analysis. Gene 2019; 722:144105. [PMID: 31521702 DOI: 10.1016/j.gene.2019.144105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Caulophyllum robustum Maxim (CRM) is a medicinal compound of the Northeast and is commonly used in China for the treatment of rheumatic pain and rheumatoid arthritis (RA). A preliminary study found that CRM has good anti-inflammatory, analgesic and immunosuppressive effects. However, the specific links and targets for its function remain unclear. Our study aimed to provide a mechanism for the action of Caulophyllum robustum Maxim extraction (CRME) against RA and to establish a method for studying disease treatment using Chinese medicine. METHODS The 3-(4, 5-dimethyl-2-thiazolyl)-2, 5-diphenyl-2-H-tetrazolium bromide (MTT) method was used to detect the toxicity of CRME in L929 cells, and the concentration ranges of the blank, model, and CRME drug groups were determined. Differentially expressed long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) were identified between the three groups. Gene Ontology (GO) and pathway enrichment analyses were performed to analyze the biological functions and pathways of the differentially expressed genes. Expression of Hist1h2bj, Hist1h2ba, Zfp36, Ccl3, Cxcl2 and Egr1 in the blank, model and drug groups was detected by quantitative real-time PCR (qRT-PCR), and the role of CRME on the above factors was determined to ensure consistency with the chip data. RESULTS A total of 329 significantly upregulated genes and 141 downregulated genes were identified between the blank and model groups. A total of 218 significantly upregulated genes and 191 downregulated genes were identified between the CRME drug group and model group. CRME has a significant role in multiple pathways involved in the occurrence and development of RA. Additionally, Hist1h2bj, Hist1h2ba, Zfp36, Ccl3, Cxcl2, and Egr1 were observed in modules of the lncRNA-mRNA weighted co-expression network, consistent with the chip data. CONCLUSIONS CRME has regulatory effects on inflammatory factors, the histone family, chemokines and their ligands that are related to RA-related cytokines, the RA pathway, the TNF signaling pathway, the Toll receptor-like signaling pathway, the chemokine signaling pathways and other pathways are related to the course of RA.
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Affiliation(s)
- Shaowa Lü
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin 150040, China
| | - Yutian Liu
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin 150040, China
| | - Jie Cui
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin 150040, China
| | - Bingyou Yang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin 150040, China
| | - Guoyu Li
- Pharmaceutical College, Harbin University of Commerce, Harbin 150086, China
| | - Yuyan Guo
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin 150040, China
| | - Haixue Kuang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin 150040, China.
| | - Qiuhong Wang
- Pharmaceutical College, Guangdong Pharmaceutical University, Guangzhou 510224, China.
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81
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Rai LS, Singha R, Sanchez H, Chakraborty T, Chand B, Bachellier-Bassi S, Chowdhury S, d’Enfert C, Andes DR, Sanyal K. The Candida albicans biofilm gene circuit modulated at the chromatin level by a recent molecular histone innovation. PLoS Biol 2019; 17:e3000422. [PMID: 31398188 PMCID: PMC6703697 DOI: 10.1371/journal.pbio.3000422] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/21/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023] Open
Abstract
Histone H3 and its variants regulate gene expression but the latter are absent in most ascomycetous fungi. Here, we report the identification of a variant histone H3, which we have designated H3VCTG because of its exclusive presence in the CTG clade of ascomycetes, including Candida albicans, a human pathogen. C. albicans grows both as single yeast cells and hyphal filaments in the planktonic mode of growth. It also forms a three-dimensional biofilm structure in the host as well as on human catheter materials under suitable conditions. H3VCTG null (hht1/hht1) cells of C. albicans are viable but produce more robust biofilms than wild-type cells in both in vitro and in vivo conditions. Indeed, a comparative transcriptome analysis of planktonic and biofilm cells reveals that the biofilm circuitry is significantly altered in H3VCTG null cells. H3VCTG binds more efficiently to the promoters of many biofilm-related genes in the planktonic cells than during biofilm growth, whereas the binding of the core canonical histone H3 on the corresponding promoters largely remains unchanged. Furthermore, biofilm defects associated with master regulators, namely, biofilm and cell wall regulator 1 (Bcr1), transposon enhancement control 1 (Tec1), and non-dityrosine 80 (Ndt80), are significantly rescued in cells lacking H3VCTG. The occupancy of the transcription factor Bcr1 at its cognate promoter binding sites was found to be enhanced in the absence of H3VCTG in the planktonic form of growth resulting in enhanced transcription of biofilm-specific genes. Further, we demonstrate that co-occurrence of valine and serine at the 31st and 32nd positions in H3VCTG, respectively, is essential for its function. Taken together, we show that even in a unicellular organism, differential gene expression patterns are modulated by the relative occupancy of the specific histone H3 type at the chromatin level. A variant histone H3 specific to the CTG clade of ascomycete fungi modulates the expression of the majority of the biofilm genes in the human pathogen Candida albicans by binding differentially to biofilm-relevant gene promoters.
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Affiliation(s)
- Laxmi Shanker Rai
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, USC2019 INRA, Paris, France
| | - Rima Singha
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Hiram Sanchez
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Tanmoy Chakraborty
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Bipin Chand
- Genotypic Technology Private Limited, Bangalore, India
| | | | - Shantanu Chowdhury
- GNR Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Christophe d’Enfert
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, USC2019 INRA, Paris, France
| | - David R. Andes
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- * E-mail:
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82
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Gruber JJ, Geller B, Lipchik AM, Chen J, Salahudeen AA, Ram AN, Ford JM, Kuo CJ, Snyder MP. HAT1 Coordinates Histone Production and Acetylation via H4 Promoter Binding. Mol Cell 2019; 75:711-724.e5. [PMID: 31278053 DOI: 10.1016/j.molcel.2019.05.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 03/08/2019] [Accepted: 05/28/2019] [Indexed: 12/18/2022]
Abstract
The energetic costs of duplicating chromatin are large and therefore likely depend on nutrient sensing checkpoints and metabolic inputs. By studying chromatin modifiers regulated by epithelial growth factor, we identified histone acetyltransferase 1 (HAT1) as an induced gene that enhances proliferation through coordinating histone production, acetylation, and glucose metabolism. In addition to its canonical role as a cytoplasmic histone H4 acetyltransferase, we isolated a HAT1-containing complex bound specifically at promoters of H4 genes. HAT1-dependent transcription of H4 genes required an acetate-sensitive promoter element. HAT1 expression was critical for S-phase progression and maintenance of H3 lysine 9 acetylation at proliferation-associated genes, including histone genes. Therefore, these data describe a feedforward circuit whereby HAT1 captures acetyl groups on nascent histones and drives H4 production by chromatin binding to support chromatin replication and acetylation. These findings have important implications for human disease, since high HAT1 levels associate with poor outcomes across multiple cancer types.
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Affiliation(s)
- Joshua J Gruber
- Department of Medicine, Oncology Division, Stanford School of Medicine, Stanford University, Palo Alto, CA 94304, USA; Department of Genetics, Stanford School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Benjamin Geller
- Department of Genetics, Stanford School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Andrew M Lipchik
- Department of Genetics, Stanford School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Justin Chen
- Department of Genetics, Stanford School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Ameen A Salahudeen
- Department of Medicine, Hematology Division, Stanford School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Ashwin N Ram
- Department of Genetics, Stanford School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - James M Ford
- Department of Medicine, Oncology Division, Stanford School of Medicine, Stanford University, Palo Alto, CA 94304, USA; Department of Genetics, Stanford School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Calvin J Kuo
- Department of Medicine, Hematology Division, Stanford School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
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83
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Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W, Horikoshi N, Sun J, Shi L, Kusakabe M, Harata M, Ohkawa Y, Tashiro S, Kimura H, Ikura T, Kurumizaka H. Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome. Nucleic Acids Res 2019; 46:10007-10018. [PMID: 30053102 PMCID: PMC6212774 DOI: 10.1093/nar/gky661] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/11/2018] [Indexed: 01/09/2023] Open
Abstract
Mutations of the Glu76 residue of canonical histone H2B are frequently found in cancer cells. However, it is quite mysterious how a single amino acid substitution in one of the multiple H2B genes affects cell fate. Here we found that the H2B E76K mutation, in which Glu76 is replaced by Lys (E76K), distorted the interface between H2B and H4 in the nucleosome, as revealed by the crystal structure and induced nucleosome instability in vivo and in vitro. Exogenous production of the H2B E76K mutant robustly enhanced the colony formation ability of the expressing cells, indicating that the H2B E76K mutant has the potential to promote oncogenic transformation in the presence of wild-type H2B. We found that other cancer-associated mutations of histones, H3.1 E97K and H2A.Z.1 R80C, also induced nucleosome instability. Interestingly, like the H2B E76K mutant, the H3.1 E97K mutant was minimally incorporated into chromatin in cells, but it enhanced the colony formation ability. In contrast, the H2A.Z.1 R80C mutant was incorporated into chromatin in cells, and had minor effects on the colony formation ability of the cells. These characteristics of histones with cancer-associated mutations may provide important information toward understanding how the mutations promote cancer progression.
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Affiliation(s)
- Yasuhiro Arimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Masae Ikura
- Laboratory of Chromatin Regulatory Network, Department of Genome Biology, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Risa Fujita
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Mamiko Noda
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Wataru Kobayashi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Naoki Horikoshi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Jiying Sun
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Lin Shi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Masayuki Kusakabe
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, 468-1 Aoba, Aramaki, Aoba-ku, Sendai 980-0845, Japan
| | - Masahiko Harata
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, 468-1 Aoba, Aramaki, Aoba-ku, Sendai 980-0845, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoshi Tashiro
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Tsuyoshi Ikura
- Laboratory of Chromatin Regulatory Network, Department of Genome Biology, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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84
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Singh R, Bassett E, Chakravarti A, Parthun MR. Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function. Nucleic Acids Res 2019; 46:8665-8678. [PMID: 30165676 PMCID: PMC6158624 DOI: 10.1093/nar/gky768] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/24/2018] [Indexed: 12/11/2022] Open
Abstract
Replication-dependent histones are expressed in a cell cycle regulated manner and supply the histones necessary to support DNA replication. In mammals, the replication-dependent histones are encoded by a family of genes that are located in several clusters. In humans, these include 16 genes for histone H2A, 22 genes for histone H2B, 14 genes for histone H3, 14 genes for histone H4 and 6 genes for histone H1. While the proteins encoded by these genes are highly similar, they are not identical. For many years, these genes were thought to encode functionally equivalent histone proteins. However, several lines of evidence have emerged that suggest that the replication-dependent histone genes can have specific functions and may constitute a novel layer of chromatin regulation. This Survey and Summary reviews the literature on replication-dependent histone isoforms and discusses potential mechanisms by which the small variations in primary sequence between the isoforms can alter chromatin function. In addition, we summarize the wealth of data implicating altered regulation of histone isoform expression in cancer.
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Affiliation(s)
- Rajbir Singh
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Emily Bassett
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Mark R Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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85
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Non-neutral evolution of H3.3-encoding genes occurs without alterations in protein sequence. Sci Rep 2019; 9:8472. [PMID: 31186448 PMCID: PMC6560044 DOI: 10.1038/s41598-019-44800-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/14/2019] [Indexed: 11/08/2022] Open
Abstract
Histone H3.3 is a developmentally essential variant encoded by two independent genes in human (H3F3A and H3F3B). While this two-gene arrangement is evolutionarily conserved, its origins and function remain unknown. Phylogenetics, synteny and gene structure analyses of H3.3 genes from 32 metazoan genomes indicate independent evolutionary paths for H3F3A and H3F3B. While H3F3B bears similarities with H3.3 genes in distant organisms and with canonical H3 genes, H3F3A is sarcopterygian-specific and evolves under strong purifying selection. Additionally, H3F3B codon-usage preferences resemble those of broadly expressed genes and 'cell differentiation-induced' genes, while codon-usage of H3F3A resembles that of 'cell proliferation-induced' genes. We infer that H3F3B is more similar to the ancestral H3.3 gene and likely evolutionarily adapted for a broad expression pattern in diverse cellular programs, while H3F3A adapted for a subset of gene expression programs. Thus, the arrangement of two independent H3.3 genes facilitates fine-tuning of H3.3 expression across cellular programs.
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86
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Yeast epigenetics: the inheritance of histone modification states. Biosci Rep 2019; 39:BSR20182006. [PMID: 30877183 PMCID: PMC6504666 DOI: 10.1042/bsr20182006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 01/12/2023] Open
Abstract
Saccharomyces cerevisiae (budding yeast) and Schizosaccharomyces pombe (fission yeast) are two of the most recognised and well-studied model systems for epigenetic regulation and the inheritance of chromatin states. Their silent loci serve as a proxy for heterochromatic chromatin in higher eukaryotes, and as such both species have provided a wealth of information on the mechanisms behind the establishment and maintenance of epigenetic states, not only in yeast, but in higher eukaryotes. This review focuses specifically on the role of histone modifications in governing telomeric silencing in S. cerevisiae and centromeric silencing in S. pombe as examples of genetic loci that exemplify epigenetic inheritance. We discuss the recent advancements that for the first time provide a mechanistic understanding of how heterochromatin, dictated by histone modifications specifically, is preserved during S-phase. We also discuss the current state of our understanding of yeast nucleosome dynamics during DNA replication, an essential component in delineating the contribution of histone modifications to epigenetic inheritance.
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87
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Kaya-Okur HS, Wu SJ, Codomo CA, Pledger ES, Bryson TD, Henikoff JG, Ahmad K, Henikoff S. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun 2019; 10:1930. [PMID: 31036827 PMCID: PMC6488672 DOI: 10.1038/s41467-019-09982-5] [Citation(s) in RCA: 973] [Impact Index Per Article: 194.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/05/2019] [Indexed: 01/11/2023] Open
Abstract
Many chromatin features play critical roles in regulating gene expression. A complete understanding of gene regulation will require the mapping of specific chromatin features in small samples of cells at high resolution. Here we describe Cleavage Under Targets and Tagmentation (CUT&Tag), an enzyme-tethering strategy that provides efficient high-resolution sequencing libraries for profiling diverse chromatin components. In CUT&Tag, a chromatin protein is bound in situ by a specific antibody, which then tethers a protein A-Tn5 transposase fusion protein. Activation of the transposase efficiently generates fragment libraries with high resolution and exceptionally low background. All steps from live cells to sequencing-ready libraries can be performed in a single tube on the benchtop or a microwell in a high-throughput pipeline, and the entire procedure can be performed in one day. We demonstrate the utility of CUT&Tag by profiling histone modifications, RNA Polymerase II and transcription factors on low cell numbers and single cells.
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Affiliation(s)
- Hatice S. Kaya-Okur
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100N. FairviewAve, Seattle, WA 98109 USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Steven J. Wu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100N. FairviewAve, Seattle, WA 98109 USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA 98195 USA
| | - Christine A. Codomo
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100N. FairviewAve, Seattle, WA 98109 USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Erica S. Pledger
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100N. FairviewAve, Seattle, WA 98109 USA
| | - Terri D. Bryson
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100N. FairviewAve, Seattle, WA 98109 USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Jorja G. Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100N. FairviewAve, Seattle, WA 98109 USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100N. FairviewAve, Seattle, WA 98109 USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100N. FairviewAve, Seattle, WA 98109 USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
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88
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Acetylation & Co: an expanding repertoire of histone acylations regulates chromatin and transcription. Essays Biochem 2019; 63:97-107. [PMID: 30940741 PMCID: PMC6484784 DOI: 10.1042/ebc20180061] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022]
Abstract
Packaging the long and fragile genomes of eukaryotic species into nucleosomes is all well and good, but how do cells gain access to the DNA again after it has been bundled away? The solution, in every species from yeast to man, is to post-translationally modify histones, altering their chemical properties to either relax the chromatin, label it for remodelling or make it more compact still. Histones are subject to a myriad of modifications: acetylation, methylation, phosphorylation, ubiquitination etc. This review focuses on histone acylations, a diverse group of modifications which occur on the ε-amino group of Lysine residues and includes the well-characterised Lysine acetylation. Over the last 50 years, histone acetylation has been extensively characterised, with the discovery of histone acetyltransferases (HATs) and histone deacetylases (HDACs), and global mapping experiments, revealing an association of hyperacetylated histones with accessible, transcriptionally active chromatin. More recently, there has been an explosion in the number of unique short chain ‘acylations’ identified by MS, including: propionylation, butyrylation, crotonylation, succinylation, malonylation and 2-hydroxyisobutyrylation. These novel modifications add a range of chemical environments to histones, and similar to acetylation, appear to accumulate at transcriptional start sites and correlate with gene activity.
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89
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Vetrivel S, Tiso N, Kügler A, Irmler M, Horsch M, Beckers J, Hladik D, Giesert F, Gailus-Durner V, Fuchs H, Sabrautzki S, Hrabě de Angelis M, Graw J. Mutation in the mouse histone gene Hist2h3c1 leads to degeneration of the lens vesicle and severe microphthalmia. Exp Eye Res 2019; 188:107632. [PMID: 30991053 PMCID: PMC6876282 DOI: 10.1016/j.exer.2019.03.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/20/2019] [Accepted: 03/30/2019] [Indexed: 12/21/2022]
Abstract
During an ENU (N-ethyl-N-nitrosourea) mutagenesis screen, we observed a dominant small-eye mutant mouse with viable homozygotes. A corresponding mutant line was established and referred to as Aey69 (abnormality of the eye #69). Comprehensive phenotyping of the homozygous Aey69 mutants in the German Mouse Clinic revealed only a subset of statistically significant alterations between wild types and homozygous mutants. The mutation causes microphthalmia without a lens but with retinal hyperproliferation. Linkage was demonstrated to mouse chromosome 3 between the markers D3Mit188 and D3Mit11. Sequencing revealed a 358 A-> C mutation (Ile120Leu) in the Hist2h3c1 gene and a 71 T-> C (Val24Ala) mutation in the Gja8 gene. Detailed analysis of eye development in the homozygous mutant mice documented a perturbed lens development starting from the lens vesicle stage including decreasing expression of crystallins as well as of lens-specific transcription factors like PITX3 and FOXE3. In contrast, we observed an early expression of retinal progenitor cells characterized by several markers including BRN3 (retinal ganglion cells) and OTX2 (cone photoreceptors). The changes in the retina at the early embryonic stages of E11.5-E15.5 happen in parallel with apoptotic processes in the lens at the respective stages. The excessive retinal hyperproliferation is characterized by an increased level of Ki67. The hyperproliferation, however, does not disrupt the differentiation and appearance of the principal retinal cell types at postnatal stages, even if the overgrowing retina covers finally the entire bulbus of the eye. Morpholino-mediated knock-down of the hist2h3ca1 gene in zebrafish leads to a specific perturbation of lens development. When injected into zebrafish zygotes, only the mutant mouse mRNA leads to severe malformations, ranging from cyclopia to severe microphthalmia. The wild-type Hist2h3c1 mRNA can rescue the morpholino-induced defects corroborating its specific function in lens development. Based upon these data, it is concluded that the ocular function of the Hist2h3c1 gene (encoding a canonical H3.2 variant) is conserved throughout evolution. Moreover, the data highlight also the importance of Hist2h3c1 in the coordinated formation of lens and retina during eye development. A dominant small-eye mutant mouse is caused by a mutation in the histone gene Hist2H3c1. Morpholino-mediated knock-down of hist2h3ca1 in the zebrafish validated this finding. The mutation leads to degeneration of the lens vesicle and retina hyperproliferation.
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Affiliation(s)
- Sharmilee Vetrivel
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany
| | - Natascia Tiso
- Department of Biology, University of Padova, I-35131 Padova, Italy.
| | - Andrea Kügler
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany
| | - Martin Irmler
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Marion Horsch
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Johannes Beckers
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, D-85354 Freising, Germany; German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
| | - Daniela Hladik
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany
| | - Florian Giesert
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany
| | - Valerie Gailus-Durner
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Helmut Fuchs
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Sibylle Sabrautzki
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany; Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit Comparative Medicine, D-85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, D-85354 Freising, Germany; German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
| | - Jochen Graw
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany.
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90
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Histone stress: an unexplored source of chromosomal instability in cancer? Curr Genet 2019; 65:1081-1088. [DOI: 10.1007/s00294-019-00967-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 02/27/2019] [Accepted: 04/03/2019] [Indexed: 01/24/2023]
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91
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Meas R, Wyrick JJ, Smerdon MJ. Nucleosomes Regulate Base Excision Repair in Chromatin. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2019; 780:29-36. [PMID: 31388331 PMCID: PMC6684245 DOI: 10.1016/j.mrrev.2017.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chromatin is a significant barrier to many DNA damage response (DDR) factors, such as DNA repair enzymes, that process DNA lesions to reduce mutations and prevent cell death; yet, paradoxically, chromatin also has a critical role in many signaling pathways that regulate the DDR. The primary level of DNA packaging in chromatin is the nucleosome core particle (NCP), consisting of DNA wrapped around an octamer of the core histones H2A, H2B, H3 and H4. Here, we review recent studies characterizing how the packaging of DNA into nucleosomes modulates the activity of the base excision repair (BER) pathway and dictates BER subpathway choice. We also review new evidence indicating that the histone amino-terminal tails coordinately regulate multiple DDR pathways during the repair of alkylation damage in the budding yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Rithy Meas
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520
| | - Michael J. Smerdon
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520
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92
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Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC, Odom DT. Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis. Nat Commun 2019; 10:1251. [PMID: 30890697 PMCID: PMC6424977 DOI: 10.1038/s41467-019-09182-1] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/15/2019] [Indexed: 12/21/2022] Open
Abstract
Male gametes are generated through a specialised differentiation pathway involving a series of developmental transitions that are poorly characterised at the molecular level. Here, we use droplet-based single-cell RNA-Sequencing to profile spermatogenesis in adult animals and at multiple stages during juvenile development. By exploiting the first wave of spermatogenesis, we both precisely stage germ cell development and enrich for rare somatic cell-types and spermatogonia. To capture the full complexity of spermatogenesis including cells that have low transcriptional activity, we apply a statistical tool that identifies previously uncharacterised populations of leptotene and zygotene spermatocytes. Focusing on post-meiotic events, we characterise the temporal dynamics of X chromosome re-activation and profile the associated chromatin state using CUT&RUN. This identifies a set of genes strongly repressed by H3K9me3 in spermatocytes, which then undergo extensive chromatin remodelling post-meiosis, thus acquiring an active chromatin state and spermatid-specific expression.
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Affiliation(s)
- Christina Ernst
- European Molecular Biology Laboratory, European Bioinformatics Institute, (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Nils Eling
- European Molecular Biology Laboratory, European Bioinformatics Institute, (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Celia P Martinez-Jimenez
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics, 69120, Heidelberg, Germany.
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93
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Chen R, She Y, Fu Q, Chen X, Shi H, Lei S, Zhou S, Ou J, Liu Y. Differentially expressed coding and noncoding RNAs in CoCl2-induced cytotoxicity of C2C12 cells. Epigenomics 2019; 11:423-438. [PMID: 30785338 DOI: 10.2217/epi-2018-0087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aim: We aimed to explore potential regulators of coding and noncoding RNAs (ncRNAs) in Co(II) ion-induced myo cytotoxicity. Materials & methods: We confirmed the toxic effects of Co(II) on mouse skeletal C2C12 myotubes by CoCl2, and performed the expression profiles of circular RNAs (circRNAs), long noncoding RNAs (lncRNAs) and mRNAs using microarray analysis. We constructed co-expression, competing endogenous RNA and cis/trans regulation networks for ncRNAs, and filtered 71 candidate circRNAs with coding potential. Results: We identify 605 differentially expressed circRNAs, 4409 long noncoding RNAs and 3965 mRNAs. We also provided several ncRNAs regulation networks and presumed functions of circRNAs with coding potential. Conclusion: Our findings may reveal novel regulatory mechanisms underlying the noxious effects of CoCl2 in skeletal muscle.
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Affiliation(s)
- Rui Chen
- Guangdong Traditional Medical & Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, 466 Xin Gang Zhong Road, Guangzhou 510317, PR China
| | - Yanling She
- Guangdong Traditional Medical & Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, 466 Xin Gang Zhong Road, Guangzhou 510317, PR China
| | - Qiang Fu
- Department of Prosthodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, 56 Ling Yuan Xi Road, Guangzhou 510055, PR China
| | - Xiaodan Chen
- Department of Prosthodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, 56 Ling Yuan Xi Road, Guangzhou 510055, PR China
| | - Huacai Shi
- Guangdong Traditional Medical & Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, 466 Xin Gang Zhong Road, Guangzhou 510317, PR China
| | - Si Lei
- Guangdong Traditional Medical & Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, 466 Xin Gang Zhong Road, Guangzhou 510317, PR China
| | - Shanyao Zhou
- Guangdong Traditional Medical & Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, 466 Xin Gang Zhong Road, Guangzhou 510317, PR China
| | - Jun Ou
- Guangzhou FitGene Biotechnology CO., LTD, Building D, 3 Ju Quan Road, Guangzhou 510663, PR China
| | - Yulin Liu
- Guangzhou FitGene Biotechnology CO., LTD, Building D, 3 Ju Quan Road, Guangzhou 510663, PR China
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94
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Probing the Function of Metazoan Histones with a Systematic Library of H3 and H4 Mutants. Dev Cell 2018; 48:406-419.e5. [PMID: 30595536 DOI: 10.1016/j.devcel.2018.11.047] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/15/2018] [Accepted: 11/28/2018] [Indexed: 11/21/2022]
Abstract
Replication-dependent histone genes often reside in tandemly arrayed gene clusters, hindering systematic loss-of-function analyses. Here, we used CRISPR/Cas9 and the attP/attB double-integration system to alter numbers and sequences of histone genes in their original genomic context in Drosophila melanogaster. As few as 8 copies of the histone gene unit supported embryo development and adult viability, whereas flies with 20 copies were indistinguishable from wild-types. By hierarchical assembly, 40 alanine-substitution mutations (covering all known modified residues in histones H3 and H4) were introduced and characterized. Mutations at multiple residues compromised viability, fertility, and DNA-damage responses. In particular, H4K16 was necessary for expression of male X-linked genes, male viability, and maintenance of ovarian germline stem cells, whereas H3K27 was essential for late embryogenesis. Simplified mosaic analysis showed that H3R26 is required for H3K27 trimethylation. We have developed a powerful strategy and valuable reagents to systematically probe histone functions in D. melanogaster.
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95
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Sanson KR, Hanna RE, Hegde M, Donovan KF, Strand C, Sullender ME, Vaimberg EW, Goodale A, Root DE, Piccioni F, Doench JG. Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities. Nat Commun 2018; 9:5416. [PMID: 30575746 PMCID: PMC6303322 DOI: 10.1038/s41467-018-07901-8] [Citation(s) in RCA: 443] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/05/2018] [Indexed: 12/26/2022] Open
Abstract
The creation of genome-wide libraries for CRISPR knockout (CRISPRko), interference (CRISPRi), and activation (CRISPRa) has enabled the systematic interrogation of gene function. Here, we show that our recently-described CRISPRko library (Brunello) is more effective than previously published libraries at distinguishing essential and non-essential genes, providing approximately the same perturbation-level performance improvement over GeCKO libraries as GeCKO provided over RNAi. Additionally, we present genome-wide libraries for CRISPRi (Dolcetto) and CRISPRa (Calabrese), and show in negative selection screens that Dolcetto, with fewer sgRNAs per gene, outperforms existing CRISPRi libraries and achieves comparable performance to CRISPRko in detecting essential genes. We also perform positive selection CRISPRa screens and demonstrate that Calabrese outperforms the SAM approach at identifying vemurafenib resistance genes. We further compare CRISPRa to genome-scale libraries of open reading frames (ORFs). Together, these libraries represent a suite of genome-wide tools to efficiently interrogate gene function with multiple modalities.
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Affiliation(s)
- Kendall R Sanson
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Ruth E Hanna
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Mudra Hegde
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Katherine F Donovan
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Christine Strand
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Meagan E Sullender
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Emma W Vaimberg
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Amy Goodale
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - David E Root
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Federica Piccioni
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.
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96
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Pettinati I, Grzechnik P, Ribeiro de Almeida C, Brem J, McDonough MA, Dhir S, Proudfoot NJ, Schofield CJ. Biosynthesis of histone messenger RNA employs a specific 3' end endonuclease. eLife 2018; 7:39865. [PMID: 30507380 PMCID: PMC6303110 DOI: 10.7554/elife.39865] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022] Open
Abstract
Replication-dependent (RD) core histone mRNA produced during S-phase is the only known metazoan protein-coding mRNA presenting a 3' stem-loop instead of the otherwise universal polyA tail. A metallo β-lactamase (MBL) fold enzyme, cleavage and polyadenylation specificity factor 73 (CPSF73), is proposed to be the sole endonuclease responsible for 3' end processing of both mRNA classes. We report cellular, genetic, biochemical, substrate selectivity, and crystallographic studies providing evidence that an additional endoribonuclease, MBL domain containing protein 1 (MBLAC1), is selective for 3' processing of RD histone pre-mRNA during the S-phase of the cell cycle. Depletion of MBLAC1 in cells significantly affects cell cycle progression thus identifying MBLAC1 as a new type of S-phase-specific cancer target.
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Affiliation(s)
- Ilaria Pettinati
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Pawel Grzechnik
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | | | - Jurgen Brem
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | | | - Somdutta Dhir
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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97
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Mizuno S, Hanamura I, Ota A, Karnan S, Kanasugi J, Nakamura A, Takasugi S, Uchino K, Horio T, Goto M, Murakami S, Gotou M, Yamamoto H, Watarai M, Shikami M, Hosokawa Y, Miwa H, Taniwaki M, Ueda R, Nitta M, Takami A. Establishment and characterization of a novel vincristine-resistant diffuse large B-cell lymphoma cell line containing the 8q24 homogeneously staining region. FEBS Open Bio 2018; 8:1977-1991. [PMID: 30524948 PMCID: PMC6275272 DOI: 10.1002/2211-5463.12538] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 11/27/2022] Open
Abstract
Chromosome band 8q24 is the most frequently amplified locus in various types of cancers. MYC has been identified as the primary oncogene at the 8q24 locus, whereas a long noncoding gene, PVT1, which lies adjacent to MYC, has recently emerged as another potential oncogenic regulator at this position. In this study, we established and characterized a novel cell line, AMU‐ML2, from a patient with diffuse large B‐cell lymphoma (DLBCL), displaying homogeneously staining regions at the 8q24 locus. Fluorescence in situ hybridization clearly detected an elevation in MYC copy numbers corresponding to the homogenously staining region. In addition, a comparative genomic hybridization analysis using high‐resolution arrays revealed that the 8q24 amplicon size was 1.4 Mb, containing the entire MYC and PVT1 regions. We also demonstrated a loss of heterozygosity for TP53 at 17p13 in conjunction with a TP53 frameshift mutation. Notably, AMU‐ML2 cells exhibited resistance to vincristine, and cell proliferation was markedly inhibited by MYC‐shRNA‐mediated knockdown. Furthermore, genes involved in cyclin D, mTOR, and Ras signaling were downregulated following MYC knockdown, suggesting that MYC expression was closely associated with tumor cell growth. In conclusion, AMU‐ML2 cells are uniquely characterized by homogenously staining regions at the 8q24 locus, thus providing useful insights into the pathogenesis of DLBCL with 8q24 abnormalities.
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Affiliation(s)
- Shohei Mizuno
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Ichiro Hanamura
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Akinobu Ota
- Department of Biochemistry Aichi Medical University Japan
| | | | - Jo Kanasugi
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Ayano Nakamura
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Souichi Takasugi
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Kaori Uchino
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Tomohiro Horio
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Mineaki Goto
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Satsuki Murakami
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Mayuko Gotou
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Hidesuke Yamamoto
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Masaya Watarai
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Masato Shikami
- Department of Hematology Daiyukai General Hospital Aichi Japan
| | | | | | - Masafumi Taniwaki
- Department of Hematology and Oncology Graduate School of Medical Science Kyoto Prefectural University of Medicine Japan
| | - Ryuzo Ueda
- Department of Tumor Immunology Aichi Medical University School of Medicine Japan
| | - Masakazu Nitta
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Akiyoshi Takami
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
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98
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Meaux SA, Holmquist CE, Marzluff WF. Role of oligouridylation in normal metabolism and regulated degradation of mammalian histone mRNAs. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0170. [PMID: 30397106 DOI: 10.1098/rstb.2018.0170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2018] [Indexed: 01/18/2023] Open
Abstract
Metazoan replication-dependent histone mRNAs are the only known cellular mRNAs that are not polyadenylated. Histone mRNAs are present in large amounts only in S-phase cells, and their levels are coordinately regulated with the rate of DNA replication. In mammals, the stemloop at the 3' end of histone mRNA is bound to stemloop binding protein, a protein required for both synthesis and degradation of histone mRNA, and an exonuclease, 3'hExo (ERI1). Histone mRNAs are rapidly degraded when DNA synthesis is inhibited in S-phase cells and at the end of S-phase. Upf1 is also required for rapid degradation of histone mRNA as is the S-phase checkpoint. We report that Smg1 is required for histone mRNA degradation when DNA replication is inhibited, suggesting it is the PI-like kinase that activates Upf1 for histone mRNA degradation. We also show that some mutant Upf1 proteins are recruited to histone mRNAs when DNA replication is inhibited and act as dominant negative factors in histone mRNA degradation. We report that the pathway of rapid histone mRNA degradation when DNA replication is inhibited in S-phase cells that are activating the S-phase checkpoint is similar to the pathway of rapid degradation of histone mRNA at the end of S-phase.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Stacie A Meaux
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - William F Marzluff
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA .,Integrated Program for Biological and Genome Science, University of North Carolina, Chapel Hill, NC 27599, USA
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99
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Holmquist CE, Marzluff WF. Determining degradation intermediates and the pathway of 3' to 5' degradation of histone mRNA using high-throughput sequencing. Methods 2018; 155:104-115. [PMID: 30408609 DOI: 10.1016/j.ymeth.2018.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/30/2018] [Accepted: 11/01/2018] [Indexed: 11/24/2022] Open
Abstract
The half-life of an mRNA is an important parameter contributing to the steady-state level of the mRNA. Rapid changes in mRNA levels can result from decreasing the half-life of an mRNA. Establishing the detailed pathway of mRNA degradation for a particular class of mRNAs requires the ability to isolate mRNA degradation intermediates. High-throughput sequencing provides a method for detecting these intermediates. Here we describe a method for determining the intermediates in 3' to 5' degradation. Characterizing these intermediates requires not only determining the precise 3' end of the molecule to a single nucleotide resolution, but also the ability to detect and characterize any untemplated nucleotides present on the intermediates. We achieve this by ligating a known sequence to all the 3' termini in the cell, and then sequence the 3' termini and the ligated linker to identify any alterations to the genomic reference sequence. We have applied this method to characterize the intermediates in histone mRNA metabolism, allowing us to deduce the pathway of 3' to 5' degradation. This method can potentially be applied to any RNA, and we discuss possible strategies for extending the method to include simultaneous determination of the 3' and 5' end of the same RNA molecule.
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Affiliation(s)
- Christopher E Holmquist
- Department of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, NC 27599, United States
| | - William F Marzluff
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, United States.
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100
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Mendiratta S, Gatto A, Almouzni G. Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle. J Cell Biol 2018; 218:39-54. [PMID: 30257851 PMCID: PMC6314538 DOI: 10.1083/jcb.201807179] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mendiratta et al. review the interplay between the different regulatory layers that affect the transcription and dynamics of distinct histone H3 variants along the cell cycle. As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulation, we highlight situations where perturbations in histone balance may lead to cellular dysfunction and pathologies.
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Affiliation(s)
- Shweta Mendiratta
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Alberto Gatto
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Genevieve Almouzni
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France .,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
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