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García‐Gomis D, López J, Calderón A, Andrés M, Ponte I, Roque A. Proteasome-dependent degradation of histone H1 subtypes is mediated by its C-terminal domain. Protein Sci 2024; 33:e4970. [PMID: 38591484 PMCID: PMC11002908 DOI: 10.1002/pro.4970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/29/2024] [Accepted: 03/10/2024] [Indexed: 04/10/2024]
Abstract
Histone H1 is involved in chromatin compaction and dynamics. In human cells, the H1 complement is formed by different amounts of somatic H1 subtypes, H1.0-H1.5 and H1X. The amount of each variant depends on the cell type, the cell cycle phase, and the time of development and can be altered in disease. However, the mechanisms regulating H1 protein levels have not been described. We have analyzed the contribution of the proteasome to the degradation of H1 subtypes in human cells using two different inhibitors: MG132 and bortezomib. H1 subtypes accumulate upon treatment with both drugs, indicating that the proteasome is involved in the regulation of H1 protein levels. Proteasome inhibition caused a global increase in cytoplasmatic H1, with slight changes in the composition of H1 bound to chromatin and chromatin accessibility and no alterations in the nucleosome repeat length. The analysis of the proteasome degradation pathway showed that H1 degradation is ubiquitin-independent. The whole protein and its C-terminal domain can be degraded directly by the 20S proteasome in vitro. Partial depletion of PA28γ revealed that this regulatory subunit contributes to H1 degradation within the cell. Our study shows that histone H1 protein levels are under tight regulation to prevent its accumulation in the nucleus. We revealed a new regulatory mechanism for histone H1 degradation, where the C-terminal disordered domain is responsible for its targeting and degradation by the 20S proteasome, a process enhanced by the regulatory subunit PA28γ.
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Affiliation(s)
- D. García‐Gomis
- Biochemistry and Molecular Biology Department, Biosciences FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - J. López
- Biochemistry and Molecular Biology Department, Biosciences FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - A. Calderón
- Biochemistry and Molecular Biology Department, Biosciences FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - M. Andrés
- Biochemistry and Molecular Biology Department, Biosciences FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - I. Ponte
- Biochemistry and Molecular Biology Department, Biosciences FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - A. Roque
- Biochemistry and Molecular Biology Department, Biosciences FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
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2
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Rogers AM, Neri NR, Chigweshe L, Holmes SG. Histone variant H2A.Z and linker histone H1 influence chromosome condensation in Saccharomyces cerevisiae. Genetics 2024; 226:iyae022. [PMID: 38366024 PMCID: PMC10990423 DOI: 10.1093/genetics/iyae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 10/15/2023] [Accepted: 01/17/2024] [Indexed: 02/18/2024] Open
Abstract
Chromosome condensation is essential for the fidelity of chromosome segregation during mitosis and meiosis. Condensation is associated both with local changes in nucleosome structure and larger-scale alterations in chromosome topology mediated by the condensin complex. We examined the influence of linker histone H1 and variant histone H2A.Z on chromosome condensation in budding yeast cells. Linker histone H1 has been implicated in local and global compaction of chromatin in multiple eukaryotes, but we observe normal condensation of the rDNA locus in yeast strains lacking H1. However, deletion of the yeast HTZ1 gene, coding for variant histone H2A.Z, causes a significant defect in rDNA condensation. Loss of H2A.Z does not change condensin association with the rDNA locus or significantly affect condensin mRNA levels. Prior studies reported that several phenotypes caused by loss of H2A.Z are suppressed by eliminating Swr1, a key component of the SWR complex that deposits H2A.Z in chromatin. We observe that an htz1Δ swr1Δ strain has near-normal rDNA condensation. Unexpectedly, we find that elimination of the linker histone H1 can also suppress the rDNA condensation defect of htz1Δ strains. Our experiments demonstrate that histone H2A.Z promotes chromosome condensation, in part by counteracting activities of histone H1 and the SWR complex.
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Affiliation(s)
- Anna M Rogers
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Nola R Neri
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Lorencia Chigweshe
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Scott G Holmes
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
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3
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Salinas-Pena M, Rebollo E, Jordan A. Imaging analysis of six human histone H1 variants reveals universal enrichment of H1.2, H1.3, and H1.5 at the nuclear periphery and nucleolar H1X presence. eLife 2024; 12:RP91306. [PMID: 38530350 DOI: 10.7554/elife.91306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
Histone H1 participates in chromatin condensation and regulates nuclear processes. Human somatic cells may contain up to seven histone H1 variants, although their functional heterogeneity is not fully understood. Here, we have profiled the differential nuclear distribution of the somatic H1 repertoire in human cells through imaging techniques including super-resolution microscopy. H1 variants exhibit characteristic distribution patterns in both interphase and mitosis. H1.2, H1.3, and H1.5 are universally enriched at the nuclear periphery in all cell lines analyzed and co-localize with compacted DNA. H1.0 shows a less pronounced peripheral localization, with apparent variability among different cell lines. On the other hand, H1.4 and H1X are distributed throughout the nucleus, being H1X universally enriched in high-GC regions and abundant in the nucleoli. Interestingly, H1.4 and H1.0 show a more peripheral distribution in cell lines lacking H1.3 and H1.5. The differential distribution patterns of H1 suggest specific functionalities in organizing lamina-associated domains or nucleolar activity, which is further supported by a distinct response of H1X or phosphorylated H1.4 to the inhibition of ribosomal DNA transcription. Moreover, H1 variants depletion affects chromatin structure in a variant-specific manner. Concretely, H1.2 knock-down, either alone or combined, triggers a global chromatin decompaction. Overall, imaging has allowed us to distinguish H1 variants distribution beyond the segregation in two groups denoted by previous ChIP-Seq determinations. Our results support H1 variants heterogeneity and suggest that variant-specific functionality can be shared between different cell types.
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Affiliation(s)
| | - Elena Rebollo
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Albert Jordan
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
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4
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Rajeev R, Mishra RK, Khosla S. DNMT3L interacts with Piwi and modulates the expression of piRNAs in transgenic Drosophila. Epigenomics 2024; 16:375-388. [PMID: 38440884 DOI: 10.2217/epi-2023-0405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Abstract
Aim: To explore the role of Piwi protein and piRNAs in DNMT3L-mediated epigenetic inheritance. Materials & methods: Transgenic Drosophila were used to examine the effect of ectopically expressed DNMT3L on the profile of piRNAs by sequencing of small RNAs. Results & conclusion: Our previous work showed accumulation and inheritance of epimutations across multiple generations in transgenic DNMT3L Drosophila. Here, we show interaction of DNMT3L with Piwi and a significant alteration in the piRNA profile across multiple generations in transgenic Drosophila. In the light of its interaction with histone H1, we propose that in addition to its role of modulating core histone modifications, DNMT3L allows for inheritance of epigenetic information through its collaboration with Piwi, piRNAs and histone H1.
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Affiliation(s)
- Ramisetti Rajeev
- Centre for DNA Fingerprinting & Diagnostics, Hyderabad, 500 039, India
- Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Rakesh K Mishra
- CSIR-Centre for Cellular & Molecular Biology, Hyderabad, 500 007, India
| | - Sanjeev Khosla
- Centre for DNA Fingerprinting & Diagnostics, Hyderabad, 500 039, India
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
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5
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Archacki R. Finding a good balance: two distinct chromatin factors fine-tune stress response in Arabidopsis seedlings. New Phytol 2024; 241:7-9. [PMID: 37919230 DOI: 10.1111/nph.19357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Affiliation(s)
- Rafal Archacki
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106, Warsaw, Poland
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Abstract
The eukaryotic nucleus displays a variety of membraneless compartments with distinct biomolecular composition and specific cellular activities. Emerging evidence indicates that protein-based liquid-liquid phase separation (LLPS) plays an essential role in the formation and dynamic regulation of heterochromatin compartmentalization. This feature is especially conspicuous at the pericentric heterochromatin domains. In this review, we will describe our understanding of heterochromatin organization and LLPS. In addition, we will highlight the increasing importance of multivalent weak homo- and heteromolecular interactions in LLPS-mediated heterochromatin compartmentalization in the complex environment inside living cells.
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Affiliation(s)
- Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Weihua Qin
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Hector Romero
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany,CONTACT M. Cristina Cardoso Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287Darmstadt, Germany
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Siqueira E, Kim BH, Reser L, Chow R, Delaney K, Esteller M, Ross MM, Shabanowitz J, Hunt DF, Guil S, Ausió J. Analysis of the interplay between MeCP2 and histone H1 during in vitro differentiation of human ReNCell neural progenitor cells. Epigenetics 2023; 18:2276425. [PMID: 37976174 PMCID: PMC10769555 DOI: 10.1080/15592294.2023.2276425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023] Open
Abstract
An immortalized neural cell line derived from the human ventral mesencephalon, called ReNCell, and its MeCP2 knock out were used. With it, we characterized the chromatin compositional transitions undergone during differentiation, with special emphasis on linker histones. While the WT cells displayed the development of dendrites and axons the KO cells did not, despite undergoing differentiation as monitored by NeuN. ReNCell expressed minimal amounts of histone H1.0 and their linker histone complement consisted mainly of histone H1.2, H1.4 and H1.5. The overall level of histone H1 exhibited a trend to increase during the differentiation of MeCP2 KO cells. The phosphorylation levels of histone H1 proteins decreased dramatically during ReNCell's cell differentiation independently of the presence of MeCP2. Immunofluorescence analysis showed that MeCP2 exhibits an extensive co-localization with linker histones. Interestingly, the average size of the nucleus decreased during differentiation but in the MeCP2 KO cells, the smaller size of the nuclei at the start of differentiation increased by almost 40% after differentiation by 8 days (8 DIV). In summary, our data provide a compelling perspective on the dynamic changes of H1 histones during neural differentiation, coupled with the intricate interplay between H1 variants and MeCP2.Abbreviations: ACN, acetonitrile; A230, absorbance at 230 nm; bFGF, basic fibroblast growth factor; CM, chicken erythrocyte histone marker; CNS, central nervous system; CRISPR, clustered regulated interspaced short palindromic repeatsDAPI, 4,'6-diaminidino-2-phenylindole; DIV, days in vitro (days after differentiation is induced); DMEM, Dulbecco's modified Eagle medium; EGF, epidermal growth factor; ESC, embryonic stem cell; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GFAP, glial fibrillary acidic proteinHPLC, high-performance liquid chromatography; IF, immunofluorescence; iPSCs, induced pluripotent stem cells; MAP2, microtubule-associated protein 2; MBD, methyl-binding domain; MeCP2, methyl-CpG binding protein 2; MS, mass spectrometry; NCP, nucleosome core particle; NeuN, neuron nuclear antigen; NPC, neural progenitor cellPAGE, polyacrylamide gel electrophoresis; PBS, phosphate buffered saline; PFA, paraformaldehyde; PTM, posttranslational modification; RP-HPLC, reversed phase HPLC; ReNCells, ReNCells VM; RPLP0, ribosomal protein lateral stalk subunit P0; RT-qPCR, reverse transcription quantitative polymerase-chain reaction; RTT, Rett Syndrome; SDS, sodium dodecyl sulphate; TAD, topologically associating domain; Triple KO, triple knockout.
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Affiliation(s)
- Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- National Council for Scientific and Technological Development (CNPq), Brasilia, Federal District, Brazil
| | - Bo-Hyun Kim
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Larry Reser
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Robert Chow
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Kerry Delaney
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Mark M. Ross
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
- Department of Pathology, University of Virginia, Charlottesville, Virginia, USA
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- GermansTrias i Pujol Health Science Research Institute, Badalona, Barcelona, Catalonia, Spain
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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Wan J, Zhang J, Zan X, Zhu J, Chen H, Li X, Zhou Z, Gao X, Chen R, Huang Z, Xu Z, Li L. Overexpression of Rice Histone H1 Gene Reduces Tolerance to Cold and Heat Stress. Plants (Basel) 2023; 12:2408. [PMID: 37446969 DOI: 10.3390/plants12132408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023]
Abstract
Temperature stresses, including low- and high-temperature stresses, are the main abiotic stresses affecting rice yield. Due to global climate change, the impact of temperature pressure on rice yield is gradually increasing, which is also a major concern for researchers. In this study, an H1 histone in Oryza sativa (OsHis1.1, LOC_Os04g18090) was cloned, and its role in rice's response to temperature stresses was functionally characterized. The GUS staining analysis of OsHis1.1 promoter-GUS transgenic rice showed that OsHis1.1 was widely expressed in various rice tissues. Transient expression demonstrated that OsHis1.1 was localized in the nucleus. The overexpression of OsHis1.1 reduces the tolerance to temperature stress in rice by inhibiting the expression of genes that are responsive to heat and cold stress. Under stress conditions, the POD activity and chlorophyll and proline contents of OsHis1.1-overexpression rice lines were significantly lower than those of the wild type, while the malondialdehyde content was higher than that of the wild type. Compared with Nip, OsHis1.1-overexpression rice suffered more serious oxidative stress and cell damage under temperature stress. Furthermore, OsHis1.1-overexpression rice showed changes in agronomic traits.
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Affiliation(s)
- Jiale Wan
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jia Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaofei Zan
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiali Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Hao Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaohong Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhanmei Zhou
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoling Gao
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Rongjun Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Zhengjian Huang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Zhengjun Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Lihua Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
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9
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Belousova EA, Lavrik OI. The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response. Genes (Basel) 2022; 14. [PMID: 36672853 DOI: 10.3390/genes14010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
The functioning of the eukaryotic cell genome is mediated by sophisticated protein-nucleic-acid complexes, whose minimal structural unit is the nucleosome. After the damage to genomic DNA, repair proteins need to gain access directly to the lesion; therefore, the initiation of the DNA damage response inevitably leads to local chromatin reorganisation. This review focuses on the possible involvement of PARP1, as well as proteins acting nucleosome compaction, linker histone H1 and non-histone chromatin protein HMGB1. The polymer of ADP-ribose is considered the main regulator during the development of the DNA damage response and in the course of assembly of the correct repair complex.
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10
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Severo V, Souza R, Vitorino F, Cunha J, Ávila A, Arrizabalaga G, Nardelli S. Previously Unidentified Histone H1-Like Protein Is Involved in Cell Division and Ribosome Biosynthesis in Toxoplasma gondii. mSphere 2022; 7:e0040322. [PMID: 36468865 DOI: 10.1128/msphere.00403-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chromatin dynamics can regulate all DNA-dependent processes. Access to DNA within chromatin is orchestrated mainly by histones and their posttranslational modifications (PTMs). Like other eukaryotes, the apicomplexan parasite Toxoplasma gondii encodes four canonical histones and five histone variants. In contrast, the linker histone (H1) has never been identified in apicomplexan parasites. In other eukaryotes, histone H1 compacts the chromatin by linking the nucleosome and increasing the DNA compaction. H1 is a multifunctional protein and can be involved in different steps of DNA metabolism or associated with protein complexes related to distinct biological processes. We have identified a novel protein in T. gondii ("TgH1-like") that, although lacking the globular domain of mammalian H1, is remarkably like the H1-like proteins of bacteria and trypanosomatids. Our results demonstrate that TgH1-like is a nuclear protein associated with chromatin and other histones. Curiously, TgH1-like is also in the nucleolus and associated with ribosomal proteins, indicating a versatile function in this parasite. Although knockout of the tgh1-like gene does not affect the cell cycle, it causes endopolygeny and asynchronous division. Interestingly, mutation of posttranslationally modified amino acids results in defects in cell division like those in the Δtgh1-like mutant, showing that these sites are important for protein function. Furthermore, in the bradyzoite stage, this protein is expressed only in dividing parasites, reinforcing its importance in cell division. Indeed, the absence of TgH1-like decreases compaction of peripheral chromatin, confirming its role in the chromatin modulation in T. gondii. IMPORTANCE Histone H1, or linker histone, is an important protein that binds to the nucleosome, aiding chromatin compaction. Here, we characterize for the first time a linker histone in T. gondii, named TgH1-like. It is a small and basic protein that corresponds only to the C-terminal portion of the human H1 but is similar to histone H1 from trypanosomatids and bacteria. TgH1-like is located in the nucleus, interacts with nucleosome histones, and acts in chromatin structure and cell division. Our findings show for the first time the presence of a histone H1 protein in an apicomplexan parasite and will provide new insights into cell division and chromatin dynamics in T. gondii and related parasites.
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Fernández-Justel JM, Santa-María C, Martín-Vírgala S, Ramesh S, Ferrera-Lagoa A, Salinas-Pena M, Isoler-Alcaraz J, Maslon MM, Jordan A, Cáceres JF, Gómez M. Histone H1 regulates non-coding RNA turnover on chromatin in a m6A-dependent manner. Cell Rep 2022; 40:111329. [PMID: 36103831 PMCID: PMC7613722 DOI: 10.1016/j.celrep.2022.111329] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/04/2022] [Accepted: 08/17/2022] [Indexed: 12/24/2022] Open
Abstract
Linker histones are highly abundant chromatin-associated proteins with well-established structural roles in chromatin and as general transcriptional repressors. In addition, it has been long proposed that histone H1 exerts context-specific effects on gene expression. Here, we identify a function of histone H1 in chromatin structure and transcription using a range of genomic approaches. In the absence of histone H1, there is an increase in the transcription of non-coding RNAs, together with reduced levels of m6A modification leading to their accumulation on chromatin and causing replication-transcription conflicts. This strongly suggests that histone H1 prevents non-coding RNA transcription and regulates non-coding transcript turnover on chromatin. Accordingly, altering the m6A RNA methylation pathway rescues the replicative phenotype of H1 loss. This work unveils unexpected regulatory roles of histone H1 on non-coding RNA turnover and m6A deposition, highlighting the intimate relationship between chromatin conformation, RNA metabolism, and DNA replication to maintain genome performance.
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Affiliation(s)
- José Miguel Fernández-Justel
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Cristina Santa-María
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Sara Martín-Vírgala
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Shreya Ramesh
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Alberto Ferrera-Lagoa
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Mónica Salinas-Pena
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Carrer de Baldiri Reixac, 15, 08028 Barcelona, Spain
| | - Javier Isoler-Alcaraz
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Magdalena M Maslon
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe South Road, Edinburgh EH4 2XU, UK
| | - Albert Jordan
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Carrer de Baldiri Reixac, 15, 08028 Barcelona, Spain
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe South Road, Edinburgh EH4 2XU, UK
| | - María Gómez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain.
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12
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Arimura Y, Shih RM, Froom R, Funabiki H. Structural features of nucleosomes in interphase and metaphase chromosomes. Mol Cell 2021; 81:4377-4397.e12. [PMID: 34478647 PMCID: PMC8571072 DOI: 10.1016/j.molcel.2021.08.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/17/2022]
Abstract
Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo-EM structures of protein complexes from interphase or metaphase chromosomes. The reconstructed interphase and metaphase nucleosome structures are on average indistinguishable from canonical nucleosome structures, despite DNA sequence heterogeneity, cell-cycle-specific posttranslational modifications, and interacting proteins. Nucleosome structures determined by a decoy-classifying method and structure variability analyses reveal the nucleosome structural variations in linker DNA, histone tails, and nucleosome core particle configurations, suggesting that the opening of linker DNA, which is correlated with H2A C-terminal tail positioning, is suppressed in chromosomes. High-resolution (3.4-3.5 Å) nucleosome structures indicate DNA-sequence-independent stabilization of superhelical locations ±0-1 and ±3.5-4.5. The linker histone H1.8 preferentially binds to metaphase chromatin, from which chromatosome cryo-EM structures with H1.8 at the on-dyad position are reconstituted. This study presents the structural characteristics of nucleosomes in chromosomes.
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Affiliation(s)
- Yasuhiro Arimura
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Rochelle M Shih
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Ruby Froom
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
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13
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Hagihara H, Shoji H, Otabi H, Toyoda A, Katoh K, Namihira M, Miyakawa T. Protein lactylation induced by neural excitation. Cell Rep 2021; 37:109820. [PMID: 34644564 DOI: 10.1016/j.celrep.2021.109820] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/20/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
Lactate has diverse roles in the brain at the molecular and behavioral levels under physiological and pathophysiological conditions. This study investigates whether lysine lactylation (Kla), a lactate-derived post-translational modification in macrophages, occurs in brain cells and if it does, whether Kla is induced by the stimuli that accompany changes in lactate levels. Here, we show that Kla in brain cells is regulated by neural excitation and social stress, with parallel changes in lactate levels. These stimuli increase Kla, which is associated with the expression of the neuronal activity marker c-Fos, as well as with decreased social behavior and increased anxiety-like behavior in the stress model. In addition, we identify 63 candidate lysine-lactylated proteins and find that stress preferentially increases histone H1 Kla. This study may open an avenue for the exploration of a role of neuronal activity-induced lactate mediated by protein lactylation in the brain.
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Affiliation(s)
- Hideo Hagihara
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Hirotaka Shoji
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Hikari Otabi
- College of Agriculture, Ibaraki University, Ami, Ibaraki 300-0393, Japan; United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8538, Japan
| | - Atsushi Toyoda
- College of Agriculture, Ibaraki University, Ami, Ibaraki 300-0393, Japan; United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8538, Japan; Ibaraki University Cooperation between Agriculture and Medical Science (IUCAM), Ami, Ibaraki 300-0393, Japan
| | - Kaoru Katoh
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan; Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Masakazu Namihira
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan.
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14
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Abstract
Histone H1s or the linker histones are a family of dynamic chromatin compacting proteins that are essential for higher-order chromatin organization. These highly positively charged proteins were previously thought to function solely as repressors of transcription. However, over the last decade, there is a growing interest in understanding this multi-protein family, finding that not all variants act as repressors. Indeed, the H1 family members appear to have distinct affinities for chromatin and may potentially affect distinct functions. This would suggest a more nuanced contribution of H1 to chromatin organization. The advent of new technologies to probe H1 dynamics in vivo, combined with powerful computational biology, and in vitro imaging tools have greatly enhanced our knowledge of the mechanisms by which H1 interacts with chromatin. This family of proteins can be metaphorically compared to the Golden Snitch from the Harry Potter series, buzzing on and off several regions of the chromatin, in combat with competing transcription factors and chromatin remodellers, thereby critical to the epigenetic endgame on short and long temporal scales in the life of the nucleus. Here, we summarize recent efforts spanning structural, computational, genomic and genetic experiments which examine the linker histone as an unseen architect of chromatin fibre in normal and diseased cells and explore unanswered fundamental questions in the field.
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Affiliation(s)
- Ankita Saha
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yamini Dalal
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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15
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Cui C, Chakraborty K, Tang XA, Zhou G, Schoenfelt KQ, Becker KM, Hoffman A, Chang YF, Blank A, Reardon CA, Kenny HA, Vaisar T, Lengyel E, Greene G, Becker L. Neutrophil elastase selectively kills cancer cells and attenuates tumorigenesis. Cell 2021; 184:3163-3177.e21. [PMID: 33964209 PMCID: PMC10712736 DOI: 10.1016/j.cell.2021.04.016] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/30/2021] [Accepted: 04/09/2021] [Indexed: 12/15/2022]
Abstract
Cancer cell genetic variability and similarity to host cells have stymied development of broad anti-cancer therapeutics. Our innate immune system evolved to clear genetically diverse pathogens and limit host toxicity; however, whether/how innate immunity can produce similar effects in cancer is unknown. Here, we show that human, but not murine, neutrophils release catalytically active neutrophil elastase (ELANE) to kill many cancer cell types while sparing non-cancer cells. ELANE proteolytically liberates the CD95 death domain, which interacts with histone H1 isoforms to selectively eradicate cancer cells. ELANE attenuates primary tumor growth and produces a CD8+T cell-mediated abscopal effect to attack distant metastases. Porcine pancreatic elastase (ELANE homolog) resists tumor-derived protease inhibitors and exhibits markedly improved therapeutic efficacy. Altogether, our studies suggest that ELANE kills genetically diverse cancer cells with minimal toxicity to non-cancer cells, raising the possibility of developing it as a broad anti-cancer therapy.
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Affiliation(s)
- Chang Cui
- Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Kasturi Chakraborty
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Xu Anna Tang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Guolin Zhou
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Kelly Q Schoenfelt
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Kristen M Becker
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Alexandria Hoffman
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA; Committee on Molecular Metabolism and Nutrition, The University of Chicago, Chicago, IL 60637, USA
| | - Ya-Fang Chang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Ariane Blank
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Catherine A Reardon
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Hilary A Kenny
- Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Obstetrics and Gynecology, Section of Gynecological Oncology, The University of Chicago, Chicago, IL 60637, USA
| | - Tomas Vaisar
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Ernst Lengyel
- Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Obstetrics and Gynecology, Section of Gynecological Oncology, The University of Chicago, Chicago, IL 60637, USA; University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637, USA
| | - Geoffrey Greene
- Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA; University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637, USA
| | - Lev Becker
- Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA; Committee on Molecular Metabolism and Nutrition, The University of Chicago, Chicago, IL 60637, USA; University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637, USA.
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16
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Biggar KK, Charih F, Liu H, Ruiz-Blanco YB, Stalker L, Chopra A, Connolly J, Adhikary H, Frensemier K, Hoekstra M, Galka M, Fang Q, Wynder C, Stanford WL, Green JR, Li SS. Proteome-wide Prediction of Lysine Methylation Leads to Identification of H2BK43 Methylation and Outlines the Potential Methyllysine Proteome. Cell Rep 2020; 32:107896. [PMID: 32668242 DOI: 10.1016/j.celrep.2020.107896] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/29/2020] [Accepted: 06/22/2020] [Indexed: 12/15/2022] Open
Abstract
Protein Lys methylation plays a critical role in numerous cellular processes, but it is challenging to identify Lys methylation in a systematic manner. Here we present an approach combining in silico prediction with targeted mass spectrometry (MS) to identify Lys methylation (Kme) sites at the proteome level. We develop MethylSight, a program that predicts Kme events solely on the physicochemical properties of residues surrounding the putative methylation sites, which then requires validation by targeted MS. Using this approach, we identify 70 new histone Kme marks with a 90% validation rate. H2BK43me2, which undergoes dynamic changes during stem cell differentiation, is found to be a substrate of KDM5b. Furthermore, MethylSight predicts that Lys methylation is a prevalent post-translational modification in the human proteome. Our work provides a useful resource for guiding systematic exploration of the role of Lys methylation in human health and disease.
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17
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Malik R, Fazal S. Insights into the Dynamic Fluctuations of the Protein HPV16 E1 and Identification of Motifs by Using Elastic Network Modeling. Protein Pept Lett 2021; 28:1061-1070. [PMID: 33858307 DOI: 10.2174/0929866528666210415114858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 02/14/2021] [Accepted: 02/18/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cancers of cervix, head and neck regions have been found to be associated with Human Papilloma Virus (HPV) infection. E1 protein makes an important papillomavirus replication factor. Among the ORFs of papillomaviruses, the most conserved sequence is that of the E1 ORF. It is the viral helicase with being a member of class of ATPases associated with diverse cellular activities (AAA+) helicases. The interactions of E1 with human DNA and proteins occurs in the presence of short linear peptide motifs on E1 identical to those on human proteins. METHODS Different Motifs were identified on HPV16 E1 by using ELMs. Elastic network models were generated by using 3D structures of E1. Their dynamic fluctuations were analyzed on the basis of B factors, correlation analysis and deformation energies. RESULTS 3 motifs were identified on E1 which can interact with Cdk and Cyclin domains of human proteins. 11 motifs identified on E1 have their CDs of Pkinase on human proteins. LIG_MYND_2 has been identified as involved in stabilizing interaction of E1 with Hsp40 and Hsp70. These motifs and amino acids comprising these motifs play a major role in maintaining interactions with human proteins, ultimately causing infections leading to cancers. CONCLUSION Our study identified various motifs on E1 which interact with specific counter domains found in human proteins, already reported having the interactions with E1. We also validated the involvement of these specific motifs containing regions of E1 by modeling elastic networks of E1. These motif involving interactions could be used as drug targets.
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Affiliation(s)
- Rabbiah Malik
- Capital University of Science and Technology, Islamabad. Pakistan
| | - Sahar Fazal
- Capital University of Science and Technology, Islamabad. Pakistan
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18
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Kowalski A, Knaga S. A variety-specific arrangement of histone H1 subtype (H1.b and H1.z) polymorphic variants in differently plumaged quails. Br Poult Sci 2021; 62:166-171. [PMID: 33325274 DOI: 10.1080/00071668.2020.1842854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
1. This study was undertaken to evaluate genetic diversity among three varieties of Japanese quail (British Range, English White and Tuxedo) differing in plumage colour. The level of genetic variation was rated through the histone H1 polymorphic loci (H1.b and H1.z) containing quantitatively similar (P > 0.05) isoforms (H1.b1, H1.b2 and H1.z1, H1.z2) that form both homozygous (b1, b2 and z1, z2) and heterozygous (b1b2 and z1z2) phenotypes.2. The complete set of histone H1 phenotypes were characteristic of the British Range and Tuxedo varieties. Phenotypes b2 and z2 were not detected in the English White variety. A lack of the former phenotypes resulted in excess of heterozygotes at loci H1.b (F = -0.563) and H1.z (F = -0.562), pointing to the presence of outbreeding.3. The English White variety deviated from Hardy-Weinberg proportions (H1.b - Χ2 = 7.61, P < 0.05 and H1.z - Χ2 = 5.84, P < 0.05), in contrast to the British Range variety (H1.b - Χ2 = 0.86, P > 0.05 and H1.z - Χ2 = 0.86, P > 0.05) and Tuxedo (H1.b - Χ2 = 1.6, P > 0.05 and H1.z - Χ2 = 1.6, P > 0.05). The estimated values of the FST index for loci H1.b (0.073) and H1.z (0.099) indicate a moderate genetic diversity of the quail population.4. The distinct array and distribution of histone H1 phenotypes among quail varieties suggested that histone H1 allelic variants might have an individual impact on characteristic pigmentation of poultry.
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Affiliation(s)
- A Kowalski
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University in Kielce, Kielce, Poland
| | - S Knaga
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
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19
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Andrés M, García-Gomis D, Ponte I, Suau P, Roque A. Histone H1 Post-Translational Modifications: Update and Future Perspectives. Int J Mol Sci 2020; 21:E5941. [PMID: 32824860 DOI: 10.3390/ijms21165941] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 12/12/2022] Open
Abstract
Histone H1 is the most variable histone and its role at the epigenetic level is less characterized than that of core histones. In vertebrates, H1 is a multigene family, which can encode up to 11 subtypes. The H1 subtype composition is different among cell types during the cell cycle and differentiation. Mass spectrometry-based proteomics has added a new layer of complexity with the identification of a large number of post-translational modifications (PTMs) in H1. In this review, we summarize histone H1 PTMs from lower eukaryotes to humans, with a particular focus on mammalian PTMs. Special emphasis is made on PTMs, whose molecular function has been described. Post-translational modifications in H1 have been associated with the regulation of chromatin structure during the cell cycle as well as transcriptional activation, DNA damage response, and cellular differentiation. Additionally, PTMs in histone H1 that have been linked to diseases such as cancer, autoimmune disorders, and viral infection are examined. Future perspectives and challenges in the profiling of histone H1 PTMs are also discussed.
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20
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Gibson BA, Doolittle LK, Schneider MWG, Jensen LE, Gamarra N, Henry L, Gerlich DW, Redding S, Rosen MK. Organization of Chromatin by Intrinsic and Regulated Phase Separation. Cell 2019; 179:470-484.e21. [PMID: 31543265 DOI: 10.1016/j.cell.2019.08.037] [Citation(s) in RCA: 545] [Impact Index Per Article: 109.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/12/2019] [Accepted: 08/21/2019] [Indexed: 02/07/2023]
Abstract
Eukaryotic chromatin is highly condensed but dynamically accessible to regulation and organized into subdomains. We demonstrate that reconstituted chromatin undergoes histone tail-driven liquid-liquid phase separation (LLPS) in physiologic salt and when microinjected into cell nuclei, producing dense and dynamic droplets. Linker histone H1 and internucleosome linker lengths shared across eukaryotes promote phase separation of chromatin, tune droplet properties, and coordinate to form condensates of consistent density in manners that parallel chromatin behavior in cells. Histone acetylation by p300 antagonizes chromatin phase separation, dissolving droplets in vitro and decreasing droplet formation in nuclei. In the presence of multi-bromodomain proteins, such as BRD4, highly acetylated chromatin forms a new phase-separated state with droplets of distinct physical properties, which can be immiscible with unmodified chromatin droplets, mimicking nuclear chromatin subdomains. Our data suggest a framework, based on intrinsic phase separation of the chromatin polymer, for understanding the organization and regulation of eukaryotic genomes.
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Affiliation(s)
- Bryan A Gibson
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lynda K Doolittle
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maximillian W G Schneider
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Liv E Jensen
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nathan Gamarra
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lisa Henry
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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21
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D'Ippolito RA, Minamino N, Rivera-Casas C, Cheema MS, Bai DL, Kasinsky HE, Shabanowitz J, Eirin-Lopez JM, Ueda T, Hunt DF, Ausió J. Protamines from liverwort are produced by post-translational cleavage and C-terminal di-aminopropanelation of several male germ-specific H1 histones. J Biol Chem 2019; 294:16364-16373. [PMID: 31527083 DOI: 10.1074/jbc.ra119.010316] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/26/2019] [Indexed: 11/06/2022] Open
Abstract
Protamines are small, highly-specialized, arginine-rich, and intrinsically-disordered chromosomal proteins that replace histones during spermiogenesis in many organisms. Previous evidence supports the notion that, in the animal kingdom, these proteins have evolved from a primitive replication-independent histone H1 involved in terminal cell differentiation. Nevertheless, a direct connection between the two families of chromatin proteins is missing. Here, we primarily used electron transfer dissociation MS-based analyses, revealing that the protamines in the sperm of the liverwort Marchantia polymorpha result from post-translational cleavage of three precursor H1 histones. Moreover, we show that the mature protamines are further post-translationally modified by di-aminopropanelation, and previous studies have reported that they condense spermatid chromatin through a process consisting of liquid-phase assembly likely involving spinodal decomposition. Taken together, our results reveal that the interesting evolutionary ancestry of protamines begins with histone H1 in both the animal and plant kingdoms.
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Affiliation(s)
| | - Naoki Minamino
- Division of Cellular Dynamics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Ciro Rivera-Casas
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International University, North Miami, Florida 33181
| | - Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | - Dina L Bai
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904
| | - Harold E Kasinsky
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904
| | - Jose M Eirin-Lopez
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International University, North Miami, Florida 33181
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Department of Basic Biology, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904.,Department of Pathology, University of Virginia, Charlottesville, Virginia 22903
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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22
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Senigagliesi B, Penzo C, Severino LU, Maraspini R, Petrosino S, Morales-Navarrete H, Pobega E, Ambrosetti E, Parisse P, Pegoraro S, Manfioletti G, Casalis L, Sgarra R. The High Mobility Group A1 (HMGA1) Chromatin Architectural Factor Modulates Nuclear Stiffness in Breast Cancer Cells. Int J Mol Sci 2019; 20:E2733. [PMID: 31167352 DOI: 10.3390/ijms20112733] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/28/2022] Open
Abstract
Plasticity is an essential condition for cancer cells to invade surrounding tissues. The nucleus is the most rigid cellular organelle and it undergoes substantial deformations to get through environmental constrictions. Nuclear stiffness mostly depends on the nuclear lamina and chromatin, which in turn might be affected by nuclear architectural proteins. Among these is the HMGA1 (High Mobility Group A1) protein, a factor that plays a causal role in neoplastic transformation and that is able to disentangle heterochromatic domains by H1 displacement. Here we made use of atomic force microscopy to analyze the stiffness of breast cancer cellular models in which we modulated HMGA1 expression to investigate its role in regulating nuclear plasticity. Since histone H1 is the main modulator of chromatin structure and HMGA1 is a well-established histone H1 competitor, we correlated HMGA1 expression and cellular stiffness with histone H1 expression level, post-translational modifications, and nuclear distribution. Our results showed that HMGA1 expression level correlates with nuclear stiffness, is associated to histone H1 phosphorylation status, and alters both histone H1 chromatin distribution and expression. These data suggest that HMGA1 might promote chromatin relaxation through a histone H1-mediated mechanism strongly impacting on the invasiveness of cancer cells.
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23
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He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife 2019; 8:42530. [PMID: 31135340 PMCID: PMC6594752 DOI: 10.7554/elife.42530] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/26/2019] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell - vegetative cell (VC) - of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.
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Affiliation(s)
- Shengbo He
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Martin Vickers
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Jingyi Zhang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
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24
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Pereira MA, Alexandre-Pires G, Câmara M, Santos M, Martins C, Rodrigues A, Adriana J, Passero LFD, Pereira da Fonseca I, Santos-Gomes G. Canine neutrophils cooperate with macrophages in the early stages of Leishmania infantum in vitro infection. Parasite Immunol 2019; 41:e12617. [PMID: 30735568 DOI: 10.1111/pim.12617] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/31/2019] [Indexed: 11/28/2022]
Abstract
Leishmania infantum is the aetiological agent of human visceral leishmaniasis and canine leishmaniasis, both systemic and potentially fatal diseases. Polymorphonuclear neutrophils (PMN) are the first cells to phagocyte this parasite at the inoculation site, but macrophages (MØ) are the definitive host cells, ensuring parasite replication. The interaction between dog MØ, PMN and L infantum promastigotes was in vitro investigated. It was observed that promastigotes establish contact with blood monocyte-derived MØ mainly by the tip of the flagellum. These cells, that efficiently bind and internalize parasites, underwent major morphological changes, produced nitric oxide (NO) and released histone H1 in order to inactivate the parasite. Transfer of intracellular parasites from PMN to MØ was confirmed by flow cytometry, using L infantum expressing a green fluorescent protein. The interaction of MØ with L infantum-infected PMN lead to NO production and release of extracellular traps, which may contribute to parasite containment and inactivation. This study highlights for the first time the diversity of cellular and molecular events triggered by the interaction between canine PMN and MØ, which can promote a reduction of parasite burden in the early phase of L infantum infection.
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Affiliation(s)
- Maria A Pereira
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisboa, Portugal.,Instituto Politécnico de Portalegre (IPP), Portalegre, Portugal
| | - Graça Alexandre-Pires
- Centro Interdisciplinar de Investigação em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária (FMV), Universidade de Lisboa (UL), Lisboa, Portugal
| | - Margarida Câmara
- Câmara Municipal de Évora, Serviço Veterinário Municipal, Évora, Portugal
| | - Marcos Santos
- Centro Interdisciplinar de Investigação em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária (FMV), Universidade de Lisboa (UL), Lisboa, Portugal
| | - Catarina Martins
- CEDOC-Chronic Diseases Research Center, Immunology, NOVA Medical School, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Armanda Rodrigues
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisboa, Portugal
| | - Jéssica Adriana
- Laboratory of Pathology of Infectious Diseases (LIM50), Department of Pathology, Medical School of São Paulo University, São Paulo, Brazil
| | - Luiz Felipe D Passero
- São Paulo State University (UNESP), Institute of Biosciences, São Paulo, Brazil.,São Paulo State University (UNESP), Institute for Advanced Studies of Ocean, São Paulo, Brazil
| | - Isabel Pereira da Fonseca
- Centro Interdisciplinar de Investigação em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária (FMV), Universidade de Lisboa (UL), Lisboa, Portugal
| | - Gabriela Santos-Gomes
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisboa, Portugal
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25
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Ivic N, Potocnjak M, Solis-Mezarino V, Herzog F, Bilokapic S, Halic M. Fuzzy Interactions Form and Shape the Histone Transport Complex. Mol Cell 2019; 73:1191-1203.e6. [PMID: 30824373 PMCID: PMC6436938 DOI: 10.1016/j.molcel.2019.01.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/01/2018] [Accepted: 01/22/2019] [Indexed: 01/27/2023]
Abstract
Protein transport into the nucleus is mediated by transport receptors. Import of highly charged proteins, such as histone H1 and ribosomal proteins, requires a dimer of two transport receptors. In this study, we determined the cryo-EM structure of the Imp7:Impβ:H1.0 complex, showing that the two importins form a cradle that accommodates the linker histone. The H1.0 globular domain is bound to Impβ, whereas the acidic loops of Impβ and Imp7 chaperone the positively charged C-terminal tail. Although it remains disordered, the H1 tail serves as a zipper that closes and stabilizes the structure through transient non-specific interactions with importins. Moreover, we found that the GGxxF and FxFG motifs in the Imp7 C-terminal tail are essential for Imp7:Impβ dimerization and H1 import, resembling importin interaction with nucleoporins, which, in turn, promote complex disassembly. The architecture of many other complexes might be similarly defined by rapidly exchanging electrostatic interactions mediated by disordered regions. Importin 7 and Importin β form a cradle to chaperone and transport histone H1 Transient and non-specific electrostatic interactions form and shape the complex The H1 tail serves as a zipper that closes and stabilizes Imp7:Impβ:H1 FxFG motifs in nucleoporins facilitate RanGTP-dependent disassembly of the complex
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Affiliation(s)
- Nives Ivic
- Gene Center Munich and Department of Biochemistry, Ludwig Maximilian University of Munich, 81377 Munich, Germany; Department of Physical Chemistry, Rudjer Boskovic Institute, 10000 Zagreb, Croatia
| | - Mia Potocnjak
- Gene Center Munich and Department of Biochemistry, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Victor Solis-Mezarino
- Gene Center Munich and Department of Biochemistry, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Franz Herzog
- Gene Center Munich and Department of Biochemistry, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Silvija Bilokapic
- Gene Center Munich and Department of Biochemistry, Ludwig Maximilian University of Munich, 81377 Munich, Germany; Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Mario Halic
- Gene Center Munich and Department of Biochemistry, Ludwig Maximilian University of Munich, 81377 Munich, Germany; Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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26
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Kleene R, Loers G, Jakovcevski I, Mishra B, Schachner M. Histone H1 improves regeneration after mouse spinal cord injury and changes shape and gene expression of cultured astrocytes. Restor Neurol Neurosci 2019; 37:291-313. [PMID: 31227672 DOI: 10.3233/rnn-190903] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND We have shown that histone H1 is a binding partner for polysialic acid (PSA) and that it improves functional recovery, axon regrowth/sprouting, and target reinnervation after mouse femoral nerve injury. OBJECTIVE Here, we analyzed whether histone H1 affects functional recovery, axon regrowth/sprouting, and target reinnervation after spinal cord injury of adult mice. Furthermore, we tested in vitro histone H1's effect on astrocytic gene expression, cell shape and migration as well as on cell survival of cultured motoneurons. METHODS We applied histone H1 to compressed spinal cord and determined functional recovery and number of fibrillary acidic protein (GFAP)- and neuron-glial antigen 2 (NG2)- positive glial cells, which contribute to glial scarring. Histone H1's effect on migration of astrocytes, astrocytic gene expression and motoneuronal survival was determined using scratch-wounded astroglial monolayer cultures, astrocyte cultures for microarray analysis, and motoneuron cell culture under oxidative stress conditions, respectively. RESULTS Histone H1 application improves locomotor functions and enhances monoaminergic and cholinergic reinnervation of the spinal cord. Expression levels of GFAP and NG2 around the lesion site were decreased in histone H1-treated mice relative to vehicle-treated mice six weeks after injury. Histone H1 reduced astrocytic migration, changed the shape of GFAP- and NG2-positive glial cells and altered gene expression. Gene ontology enrichment analysis indicated that in particular genes coding for proteins involved in proliferation, differentiation, migration and apoptosis are dysregulated. The up- and down-regulation of distinct genes was confirmed by qPCR and Western blot analysis. Moreover, histone H1 reduced hydrogen peroxide-induced cell death of cultured motoneurons. CONCLUSIONS The combined observations indicate that histone H1 locally applied to the lesion site, improves regeneration after spinal cord injury. Some of these beneficial functions of histone H1 in vivo and in vitro can be attributed to its interaction with PSA-carrying neural cell adhesion molecule.
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Affiliation(s)
- Ralf Kleene
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriele Loers
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Igor Jakovcevski
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Bibhudatta Mishra
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Melitta Schachner
- Department of Cell Biology and Neuroscience, Keck Center for Collaborative Neuroscience, Rutgers University, Piscataway, NJ, USA
- Center for Neuroscience, Shantou University Medical College, Shantou, Guangdong, China
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27
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Garcia-Saez I, Menoni H, Boopathi R, Shukla MS, Soueidan L, Noirclerc-Savoye M, Le Roy A, Skoufias DA, Bednar J, Hamiche A, Angelov D, Petosa C, Dimitrov S. Structure of an H1-Bound 6-Nucleosome Array Reveals an Untwisted Two-Start Chromatin Fiber Conformation. Mol Cell 2018; 72:902-915.e7. [PMID: 30392928 DOI: 10.1016/j.molcel.2018.09.027] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 07/27/2018] [Accepted: 09/20/2018] [Indexed: 12/13/2022]
Abstract
Chromatin adopts a diversity of regular and irregular fiber structures in vitro and in vivo. However, how an array of nucleosomes folds into and switches between different fiber conformations is poorly understood. We report the 9.7 Å resolution crystal structure of a 6-nucleosome array bound to linker histone H1 determined under ionic conditions that favor incomplete chromatin condensation. The structure reveals a flat two-start helix with uniform nucleosomal stacking interfaces and a nucleosome packing density that is only half that of a twisted 30-nm fiber. Hydroxyl radical footprinting indicates that H1 binds the array in an on-dyad configuration resembling that observed for mononucleosomes. Biophysical, cryo-EM, and crosslinking data validate the crystal structure and reveal that a minor change in ionic environment shifts the conformational landscape to a more compact, twisted form. These findings provide insights into the structural plasticity of chromatin and suggest a possible assembly pathway for a 30-nm fiber.
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Affiliation(s)
- Isabel Garcia-Saez
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Hervé Menoni
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, 46 Allée d'Italie, 69007 Lyon, France
| | - Ramachandran Boopathi
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, 46 Allée d'Italie, 69007 Lyon, France
| | - Manu S Shukla
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, 46 Allée d'Italie, 69007 Lyon, France
| | - Lama Soueidan
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, 46 Allée d'Italie, 69007 Lyon, France
| | | | - Aline Le Roy
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Dimitrios A Skoufias
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Jan Bednar
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; Laboratory of the Biology and Pathology of the Eye, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00 Prague 2, Czech Republic.
| | - Ali Hamiche
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS, INSERM, 67404 Illkirch Cedex, France.
| | - Dimitar Angelov
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, 46 Allée d'Italie, 69007 Lyon, France.
| | - Carlo Petosa
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.
| | - Stefan Dimitrov
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; "Roumen Tsanev" Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
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28
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Mishra LN, Hayes JJ. A nucleosome-free region locally abrogates histone H1-dependent restriction of linker DNA accessibility in chromatin. J Biol Chem 2018; 293:19191-19200. [PMID: 30373774 DOI: 10.1074/jbc.ra118.005721] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/16/2018] [Indexed: 12/20/2022] Open
Abstract
Eukaryotic genomes are packaged into linker-oligonucleosome assemblies, providing compaction of genomic DNA and contributing to gene regulation and genome integrity. To define minimal requirements for initial steps in the transition of compact, closed chromatin to a transcriptionally active, open state, we developed a model in vitro system containing a single, unique, "target" nucleosome in the center of a 25-nucleosome array and evaluated the accessibility of the linker DNA adjacent to this target nucleosome. We found that condensation of H1-lacking chromatin results in ∼60-fold reduction in linker DNA accessibility and that mimics of acetylation within all four core histone tail domains of the target nucleosome synergize to increase accessibility ∼3-fold. Notably, stoichiometric binding of histone H1 caused >2 orders of magnitude reduction in accessibility that was marginally diminished by histone acetylation mimics. Remarkably, a nucleosome-free region (NFR) in place of the target nucleosome completely abrogated H1-dependent restriction of linker accessibility in the immediate vicinity of the NFR. Our results suggest that linker DNA is as inaccessible as DNA within the nucleosome core in fully condensed, H1-containing chromatin. They further imply that an unrecognized function of NFRs in gene promoter regions is to locally abrogate the severe restriction of linker DNA accessibility imposed by H1s.
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Affiliation(s)
- Laxmi Narayan Mishra
- From the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642
| | - Jeffrey J Hayes
- From the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642
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29
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Turner AL, Watson M, Wilkins OG, Cato L, Travers A, Thomas JO, Stott K. Highly disordered histone H1-DNA model complexes and their condensates. Proc Natl Acad Sci U S A 2018; 115:11964-9. [PMID: 30301810 DOI: 10.1073/pnas.1805943115] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Disordered proteins play an essential role in a wide variety of biological processes, and are often posttranslationally modified. One such protein is histone H1; its highly disordered C-terminal tail (CH1) condenses internucleosomal linker DNA in chromatin in a way that is still poorly understood. Moreover, CH1 is phosphorylated in a cell cycle-dependent manner that correlates with changes in the chromatin condensation level. Here we present a model system that recapitulates key aspects of the in vivo process, and also allows a detailed structural and biophysical analysis of the stages before and after condensation. CH1 remains disordered in the DNA-bound state, despite its nanomolar affinity. Phase-separated droplets (coacervates) form, containing higher-order assemblies of CH1/DNA complexes. Phosphorylation at three serine residues, spaced along the length of the tail, has little effect on the local properties of the condensate. However, it dramatically alters higher-order structure in the coacervate and reduces partitioning to the coacervate phase. These observations show that disordered proteins can bind tightly to DNA without a disorder-to-order transition. Importantly, they also provide mechanistic insights into how higher-order structures can be exquisitely sensitive to perturbation by posttranslational modifications, thus broadening the repertoire of mechanisms that might regulate chromatin and other macromolecular assemblies.
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30
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Clouaire T, Rocher V, Lashgari A, Arnould C, Aguirrebengoa M, Biernacka A, Skrzypczak M, Aymard F, Fongang B, Dojer N, Iacovoni JS, Rowicka M, Ginalski K, Côté J, Legube G. Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures. Mol Cell 2018; 72:250-262.e6. [PMID: 30270107 PMCID: PMC6202423 DOI: 10.1016/j.molcel.2018.08.020] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/13/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022]
Abstract
Double-strand breaks (DSBs) are extremely detrimental DNA lesions that can lead to cancer-driving mutations and translocations. Non-homologous end joining (NHEJ) and homologous recombination (HR) represent the two main repair pathways operating in the context of chromatin to ensure genome stability. Despite extensive efforts, our knowledge of DSB-induced chromatin still remains fragmented. Here, we describe the distribution of 20 chromatin features at multiple DSBs spread throughout the human genome using ChIP-seq. We provide the most comprehensive picture of the chromatin landscape set up at DSBs and identify NHEJ- and HR-specific chromatin events. This study revealed the existence of a DSB-induced monoubiquitination-to-acetylation switch on histone H2B lysine 120, likely mediated by the SAGA complex, as well as higher-order signaling at HR-repaired DSBs whereby histone H1 is evicted while ubiquitin and 53BP1 accumulate over the entire γH2AX domains. DSB-chromatin landscape and HR/NHEJ chromatin signatures uncovered by ChIP-seq H2BK120 undergoes a switch from ubiquitination to acetylation at a local scale H1 is removed and ubiquitin accumulates on entire γH2AX domains, mainly at HR DSB 53BP1 spreads over megabase-sized domains, mostly in G1 at HR-prone DSBs
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Affiliation(s)
- Thomas Clouaire
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France.
| | - Vincent Rocher
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Anahita Lashgari
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada
| | - Coline Arnould
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Marion Aguirrebengoa
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Anna Biernacka
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury Warsaw 93, 02-089, Poland
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury Warsaw 93, 02-089, Poland
| | - François Aymard
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Bernard Fongang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0615, USA
| | - Norbert Dojer
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0615, USA; Institute of Informatics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Jason S Iacovoni
- Bioinformatic Plateau I2MC, INSERM and University of Toulouse, Toulouse 31062, France
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0615, USA
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury Warsaw 93, 02-089, Poland
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France.
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31
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Yang L, Li X, Wu Z, Feng C, Zhang T, Dai S, Dong Q. Inhibition of Methylglyoxal-Induced Histone H1 N ε-Carboxymethyllysine Formation by (+)-Catechin. J Agric Food Chem 2018; 66:5812-5820. [PMID: 29758984 DOI: 10.1021/acs.jafc.8b00826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Reactive dicarbonyl species (RCS) such as methylglyoxal (MGO) and glyoxal (GO) are common intermediates in protein damage, leading to the formation of advanced glycation end products (AGEs) through nonenzymatic glycation. (+)-Catechin, a natural plant extract from tea, has been evaluated for its ability in trapping GO and MGO. However, (+)-catechin is also reported to have both antioxidant ability and pro-oxidant properties. Until now, whether (+)-catechin can inhibit the formation of nonenzymatic glycation and the mechanism of the inhibition in nucleoprotein nonenzymatic glycation is still unclear. In the present study, histone H1 and MGO were used to establish an in vitro (100 mM phosphate buffer solution (PBS), pH 7.4, 37 °C) protein glycation model to study the trapping ability of (+)-catechin. Our data show that MGO caused dose-dependent protein damage, and the content of MGO-induced Schiff base formation was inhibited by (+)-catechin when the molecular ratio of catechin:MGO was 1:6. The formation of Nε-carboxymethyllysine (CML) was reduced significantly when the ratio of (+)-catechin and MGO was 1:1, which was similar to the inhibition effect of aminoguanidine (AG). The formation of CML under in vitro conditions can be inhibited by low concentration (12.5-100 μM) of (+)-catechin but not with high concentration (200-800 μM) of (+)-catechin. The reason is that the high concentration of (+)-catechin did not inhibit CML formations due to H2O2 produced by (+)-catechin. In the presence of catalase, catechin can inhibit MGO-induced CML formation. In conclusion, the trapping ability of (+)-catechin may be more effective at the early stage of nonenzymatic glycation. However, a high concentration (200-800 μM) of (+)-catechin may not inhibit the formation of CML because it induced the increase of H2O2 formation.
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Affiliation(s)
- Lijun Yang
- College of Veterinary Medicine , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Xinping Li
- College of Veterinary Medicine , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Zhaozhen Wu
- College of Veterinary Medicine , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Cuixia Feng
- College of Veterinary Medicine , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Tianyu Zhang
- College of Veterinary Medicine , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Shaohua Dai
- College of Veterinary Medicine , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Qiang Dong
- College of Veterinary Medicine , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
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32
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Iwamoto M, Mori C, Osakada H, Koujin T, Hiraoka Y, Haraguchi T. Nuclear localization signal targeting to macronucleus and micronucleus in binucleated ciliate Tetrahymena thermophila. Genes Cells 2018; 23:568-579. [PMID: 29882620 DOI: 10.1111/gtc.12602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/27/2018] [Accepted: 05/08/2018] [Indexed: 01/25/2023]
Abstract
Ciliated protozoa possess two morphologically and functionally distinct nuclei: a macronucleus (MAC) and a micronucleus (MIC). The MAC is transcriptionally active and functions in all cellular events. The MIC is transcriptionally inactive during cell growth, but functions in meiotic events to produce progeny nuclei. Thus, these two nuclei must be distinguished by the nuclear proteins required for their distinct functions during cellular events such as cell proliferation and meiosis. To understand the mechanism of the nuclear transport specific to either MAC or MIC, we identified specific nuclear localization signals (NLSs) in two MAC- and MIC-specific nuclear proteins, macronuclear histone H1 and micronuclear linker histone-like protein (Mlh1), respectively. By expressing GFP-fused fragments of these proteins in Tetrahymena thermophila cells, two distinct regions in macronuclear histone H1 protein were assigned as independent MAC-specific NLSs and two distinct regions in Mlh1 protein were assigned as independent MIC-specific NLSs. These NLSs contain several essential lysine residues responsible for the MAC- and MIC-specific nuclear transport, but neither contains any consensus sequence with known monopartite or bipartite NLSs in other model organisms. Our findings contribute to understanding how specific nuclear targeting is achieved to perform distinct nuclear functions in binucleated ciliates.
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Affiliation(s)
- Masaaki Iwamoto
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Chie Mori
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Takako Koujin
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
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33
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Bednar J, Garcia-Saez I, Boopathi R, Cutter AR, Papai G, Reymer A, Syed SH, Lone IN, Tonchev O, Crucifix C, Menoni H, Papin C, Skoufias DA, Kurumizaka H, Lavery R, Hamiche A, Hayes JJ, Schultz P, Angelov D, Petosa C, Dimitrov S. Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1. Mol Cell 2017; 66:384-397.e8. [PMID: 28475873 DOI: 10.1016/j.molcel.2017.04.012] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 03/08/2017] [Accepted: 04/17/2017] [Indexed: 10/19/2022]
Abstract
Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp nucleosome bearing symmetric 25 bp linker DNA arms in complex with vertebrate linker histone H1. We determined electron cryo-microscopy (cryo-EM) and crystal structures of unbound and H1-bound nucleosomes and validated these structures by site-directed protein cross-linking and hydroxyl radical footprinting experiments. Histone H1 shifts the conformational landscape of the nucleosome by drawing the two linkers together and reducing their flexibility. The H1 C-terminal domain (CTD) localizes primarily to a single linker, while the H1 globular domain contacts the nucleosome dyad and both linkers, associating more closely with the CTD-distal linker. These findings reveal that H1 imparts a strong degree of asymmetry to the nucleosome, which is likely to influence the assembly and architecture of higher-order structures.
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Affiliation(s)
- Jan Bednar
- Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Isabel Garcia-Saez
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Ramachandran Boopathi
- Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; Université de Lyon, Institut NeuroMyoGène (INMG) CNRS/UCBL UMR5310 & Laboratoire de Biologie et de Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Amber R Cutter
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA
| | - Gabor Papai
- Department of Integrated Structural Biology, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/CNRS/INSERM, 67404 Illkirch Cedex, France
| | - Anna Reymer
- MMSB, University of Lyon I/CNRS UMR 5086, Institut de Biologie et Chimie des Protéines, 69367 Lyon, France
| | - Sajad H Syed
- Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; Université de Lyon, Institut NeuroMyoGène (INMG) CNRS/UCBL UMR5310 & Laboratoire de Biologie et de Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Imtiaz Nisar Lone
- Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; Université de Lyon, Institut NeuroMyoGène (INMG) CNRS/UCBL UMR5310 & Laboratoire de Biologie et de Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Ognyan Tonchev
- Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; Université de Lyon, Institut NeuroMyoGène (INMG) CNRS/UCBL UMR5310 & Laboratoire de Biologie et de Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Corinne Crucifix
- Department of Integrated Structural Biology, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/CNRS/INSERM, 67404 Illkirch Cedex, France
| | - Hervé Menoni
- Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; Université de Lyon, Institut NeuroMyoGène (INMG) CNRS/UCBL UMR5310 & Laboratoire de Biologie et de Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Christophe Papin
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/CNRS/INSERM, 67404 Illkirch Cedex, France
| | - Dimitrios A Skoufias
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Richard Lavery
- MMSB, University of Lyon I/CNRS UMR 5086, Institut de Biologie et Chimie des Protéines, 69367 Lyon, France
| | - Ali Hamiche
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/CNRS/INSERM, 67404 Illkirch Cedex, France.
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA.
| | - Patrick Schultz
- Department of Integrated Structural Biology, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/CNRS/INSERM, 67404 Illkirch Cedex, France.
| | - Dimitar Angelov
- Université de Lyon, Institut NeuroMyoGène (INMG) CNRS/UCBL UMR5310 & Laboratoire de Biologie et de Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL, Ecole Normale Supérieure de Lyon, 69007 Lyon, France.
| | - Carlo Petosa
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France.
| | - Stefan Dimitrov
- Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France.
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Krishnan S, Smits AH, Vermeulen M, Reinberg D. Phospho-H1 Decorates the Inter-chromatid Axis and Is Evicted along with Shugoshin by SET during Mitosis. Mol Cell 2017; 67:579-593.e6. [PMID: 28781233 PMCID: PMC5562512 DOI: 10.1016/j.molcel.2017.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 04/26/2017] [Accepted: 07/06/2017] [Indexed: 12/22/2022]
Abstract
Precise control of sister chromatid separation during mitosis is pivotal to maintaining genomic integrity. Yet, the regulatory mechanisms involved are not well understood. Remarkably, we discovered that linker histone H1 phosphorylated at S/T18 decorated the inter-chromatid axial DNA on mitotic chromosomes. Sister chromatid resolution during mitosis required the eviction of such H1S/T18ph by the chaperone SET, with this process being independent of and most likely downstream of arm-cohesin dissociation. SET also directed the disassembly of Shugoshins in a polo-like kinase 1-augmented manner, aiding centromere resolution. SET ablation compromised mitotic fidelity as evidenced by unresolved sister chromatids with marked accumulation of H1S/T18ph and centromeric Shugoshin. Thus, chaperone-assisted eviction of linker histones and Shugoshins is a fundamental step in mammalian mitotic progression. Our findings also elucidate the functional implications of the decades-old observation of mitotic linker histone phosphorylation, serving as a paradigm to explore the role of linker histones in bio-signaling processes.
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Affiliation(s)
- Swathi Krishnan
- Howard Hughes Medical Institute, New York University Langone School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA
| | - Arne H Smits
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Danny Reinberg
- Howard Hughes Medical Institute, New York University Langone School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.
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Luhrs KA, Pink D, Schulte W, Zijlstra A, Lewis JD, Parseghian MH. In vivo histone H1 migration from necrotic to viable tissue. Oncotarget 2017; 8:16275-16292. [PMID: 28187445 PMCID: PMC5369962 DOI: 10.18632/oncotarget.15181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 01/25/2017] [Indexed: 11/29/2022] Open
Abstract
Necrosis is induced by ischemic conditions within the core of many solid tumors. Using fluorescent fusion proteins, we provide in vivo evidence of histone trafficking among cancer cells in implanted tumors. In particular, the most abundant H1 isoform (H1.2) was found to be transported from necrotic tumor cells into surrounding viable cells where histones are selectively taken up by energy-dependent endocytosis. We propose that intercellular histone trafficking could function as a target for drug delivery. This concept was validated using an anti-histone antibody that was co-internalized with histones from dead cells into viable ones surrounding the necrotic regions of a tumor, where some of the most chemoresistant cells reside. These findings demonstrate that cellular translocation of conjugated drugs using anti-histone antibodies is a promising strategy for targeted drug delivery to chemoresistant tumors.
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Affiliation(s)
- Keith A. Luhrs
- Allergan Inc., Irvine, CA, USA
- Peregrine Pharmaceuticals Inc., Tustin, CA, USA
| | - Desmond Pink
- Innovascreen Inc., Halifax, NS, Canada
- University of Alberta, Edmonton, AB, Canada
| | | | - Andries Zijlstra
- Innovascreen Inc., Halifax, NS, Canada
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - John D. Lewis
- Innovascreen Inc., Halifax, NS, Canada
- University of Alberta, Edmonton, AB, Canada
| | - Missag H. Parseghian
- Rubicon Biotechnology, Lake Forest, CA, USA
- Peregrine Pharmaceuticals Inc., Tustin, CA, USA
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36
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Abstract
H1 is involved in chromatin higher-order structure and gene regulation. H1 has a tripartite structure. The central domain is stably folded in solution, while the N- and C-terminal domains are intrinsically disordered. The terminal domains are encoded by DNA of low sequence complexity, and are thus prone to short insertions/deletions (indels). We have examined the evolution of the H1.1-H1.5 gene family from 27 mammalian species. Multiple sequence alignment has revealed a strong preferential conservation of the number and position of basic residues among paralogs, suggesting that overall H1 basicity is under a strong purifying selection. The presence of a conserved pattern of indels, ancestral to the splitting of mammalian orders, in the N- and C-terminal domains of the paralogs, suggests that slippage may have favored the rapid divergence of the subtypes and that purifying selection has maintained this pattern because it is associated with function. Evolutionary analyses have found evidences of positive selection events in H1.1, both before and after the radiation of mammalian orders. Positive selection ancestral to mammalian radiation involved changes at specific sites that may have contributed to the low relative affinity of H1.1 for chromatin. More recent episodes of positive selection were detected at codon positions encoding amino acids of the C-terminal domain of H1.1, which may modulate the folding of the CTD. The detection of putative recombination points in H1.1-H1.5 subtypes suggests that this process may has been involved in the acquisition of the tripartite H1 structure.
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Affiliation(s)
- Inma Ponte
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Devani Romero
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Daniel Yero
- Instituto de Biotecnología y de Biomedicina (IBB) y Departamento de Genética y Microbiología, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Pedro Suau
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
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Abstract
The centromere is a specialized chromosomal structure that dictates kinetochore assembly and, thus, is essential for accurate chromosome segregation. Centromere identity is determined epigenetically by the presence of a centromere-specific histone H3 variant, CENP-A, that replaces canonical H3 in centromeric chromatin. Here, we discuss recent work by Roulland et al. that identifies structural elements of the nucleosome as essential determinants of centromere function. In particular, CENP-A nucleosomes have flexible DNA ends due to the short αN helix of CENP-A. The higher flexibility of the DNA ends of centromeric nucleosomes impairs binding of linker histones H1, while it facilitates binding of other essential centromeric proteins, such as CENP-C, and is required for mitotic fidelity. This work extends previous observations indicating that the differential structural properties of CENP-A nucleosomes are on the basis of its contribution to centromere identity and function. Here, we discuss the implications of this work and the questions arising from it.
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Affiliation(s)
- Olga Moreno-Moreno
- Institute of Molecular Biology of Barcelona, CSIC, Barcelona, Spain.,Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Mònica Torras-Llort
- Institute of Molecular Biology of Barcelona, CSIC, Barcelona, Spain.,Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, CSIC, Barcelona, Spain.,Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Barcelona, Spain
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38
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Hsieh PH, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proc Natl Acad Sci U S A 2016; 113:15132-7. [PMID: 27956643 DOI: 10.1073/pnas.1619074114] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations.
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Nacht AS, Beato M, Vicent GP. Steroid hormone receptors silence genes by a chromatin-targeted mechanism similar to those used for gene activation. Transcription 2016; 8:15-20. [PMID: 27700223 DOI: 10.1080/21541264.2016.1242456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
How genes are repressed by steroid hormones remains a matter of debate, and several indirect mechanisms have been proposed. We found that the ligand-activated progesterone receptor recruits to the promoter of downregulated genes a repressor complex composed of HP1γ, the lysine demethylase LSD1, histone deacetylases, coREST, the RNA SRA, and the ATPase BRG1. BRG1 is needed for chromatin remodeling and facilitates the deposition of linker histone variant H1.2, which compacts chromatin and hinders RNA polymerase loading and transcription. Thus, steroid hormone receptors can repress genes in ways reminiscent of those used for gene induction, namely by directly targeting factors that remodel chromatin. But while PR-dependent gene induction in T47D cells is mainly achieved by potentiating enhancer activity, repression acts at the level of gene promoters.
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Affiliation(s)
- A Silvina Nacht
- a Centre de Regulació Genòmica (CRG) , The Barcelona Institute for Science and Technology (BIST) , Barcelona , Spain.,b Gene Regulation , Stem Cells and Cancer Program, Universitat Pompeu Fabra (UPF) , Barcelona , Spain
| | - Miguel Beato
- a Centre de Regulació Genòmica (CRG) , The Barcelona Institute for Science and Technology (BIST) , Barcelona , Spain.,b Gene Regulation , Stem Cells and Cancer Program, Universitat Pompeu Fabra (UPF) , Barcelona , Spain
| | - Guillermo P Vicent
- a Centre de Regulació Genòmica (CRG) , The Barcelona Institute for Science and Technology (BIST) , Barcelona , Spain.,b Gene Regulation , Stem Cells and Cancer Program, Universitat Pompeu Fabra (UPF) , Barcelona , Spain
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Liu H, Liang C, Kollipara RK, Matsui M, Ke X, Jeong BC, Wang Z, Yoo KS, Yadav GP, Kinch LN, Grishin NV, Nam Y, Corey DR, Kittler R, Liu Q. HP1BP3, a Chromatin Retention Factor for Co-transcriptional MicroRNA Processing. Mol Cell 2016; 63:420-32. [PMID: 27425409 DOI: 10.1016/j.molcel.2016.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/26/2016] [Accepted: 06/09/2016] [Indexed: 02/08/2023]
Abstract
Recent studies suggest that the microprocessor (Drosha-DGCR8) complex can be recruited to chromatin to catalyze co-transcriptional processing of primary microRNAs (pri-miRNAs) in mammalian cells. However, the molecular mechanism of co-transcriptional miRNA processing is poorly understood. Here we find that HP1BP3, a histone H1-like chromatin protein, specifically associates with the microprocessor and promotes global miRNA biogenesis in human cells. Chromatin immunoprecipitation (ChIP) studies reveal genome-wide co-localization of HP1BP3 and Drosha and HP1BP3-dependent Drosha binding to actively transcribed miRNA loci. Moreover, HP1BP3 specifically binds endogenous pri-miRNAs and facilitates the Drosha/pri-miRNA association in vivo. Knockdown of HP1BP3 compromises pri-miRNA processing by causing premature release of pri-miRNAs from the chromatin. Taken together, these studies suggest that HP1BP3 promotes co-transcriptional miRNA processing via chromatin retention of nascent pri-miRNA transcripts. This work significantly expands the functional repertoire of the H1 family of proteins and suggests the existence of chromatin retention factors for widespread co-transcriptional miRNA processing.
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Affiliation(s)
- Haoming Liu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chunyang Liang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rahul K Kollipara
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Masayuki Matsui
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiong Ke
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Byung-Cheon Jeong
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhiqiang Wang
- International Institute for Integrated Sleep Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Kyoung Shin Yoo
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gaya P Yadav
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa N Kinch
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nicholas V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yunsun Nam
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David R Corey
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ralf Kittler
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qinghua Liu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; International Institute for Integrated Sleep Medicine, University of Tsukuba, Tsukuba 305-8575, Japan; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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41
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Seymour M, Ji L, Santos AM, Kamei M, Sasaki T, Basenko EY, Schmitz RJ, Zhang X, Lewis ZA. Histone H1 Limits DNA Methylation in Neurospora crassa. G3 (Bethesda) 2016; 6:1879-89. [PMID: 27172195 DOI: 10.1534/g3.116.028324] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Histone H1 variants, known as linker histones, are essential chromatin components in higher eukaryotes, yet compared to the core histones relatively little is known about their in vivo functions. The filamentous fungus Neurospora crassa encodes a single H1 protein that is not essential for viability. To investigate the role of N. crassa H1, we constructed a functional FLAG-tagged H1 fusion protein and performed genomic and molecular analyses. Cell fractionation experiments showed that H1-3XFLAG is a chromatin binding protein. Chromatin-immunoprecipitation combined with sequencing (ChIP-seq) revealed that H1-3XFLAG is globally enriched throughout the genome with a subtle preference for promoters of expressed genes. In mammals, the stoichiometry of H1 impacts nucleosome repeat length. To determine if H1 impacts nucleosome occupancy or nucleosome positioning in N. crassa, we performed micrococcal nuclease digestion in the wild-type and the ΔhH1 strain followed by sequencing (MNase-seq). Deletion of hH1 did not significantly impact nucleosome positioning or nucleosome occupancy. Analysis of DNA methylation by whole-genome bisulfite sequencing (MethylC-seq) revealed a modest but global increase in DNA methylation in the ΔhH1 mutant. Together, these data suggest that H1 acts as a nonspecific chromatin binding protein that can limit accessibility of the DNA methylation machinery in N. crassa.
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Abstract
For the past 50 years, understanding the function of histone H1 heterogeneity has been mired in confusion and contradiction. Part of the reason for this is the lack of a working model that tries to explain the large body of data that has been collected about the H1 subtypes so far. In this review, a global model is described largely based on published data from the author and other researchers over the past 20 years. The intrinsic disorder built into H1 protein structure is discussed to help the reader understand that these histones are multi-conformational and adaptable to interactions with different targets. We discuss the role of each structural section of H1 (as we currently understand it), but we focus on the H1's C-terminal domain and its effect on each subtype's affinity, mobility and compaction of chromatin. We review the multiple ways these characteristics have been measured from circular dichroism to FRAP analysis, which has added to the sometimes contradictory assumptions made about each subtype. Based on a tabulation of these measurements, we then organize the H1 variants according to their ability to condense chromatin and produce nucleosome repeat lengths amenable to that compaction. This subtype variation generates a continuum of different chromatin states allowing for fine regulatory control and some overlap in the event one or two subtypes are lost to mutation. We also review the myriad of disparate observations made about each subtype, both somatic and germline specific ones, that lend support to the proposed model. Finally, to demonstrate its adaptability as new data further refines our understanding of H1 subtypes, we show how the model can be applied to experimental observations of telomeric heterochromatin in aging cells.
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Strickfaden H, McDonald D, Kruhlak MJ, Haince JF, Th'ng JPH, Rouleau M, Ishibashi T, Corry GN, Ausio J, Underhill DA, Poirier GG, Hendzel MJ. Poly(ADP-ribosyl)ation-dependent Transient Chromatin Decondensation and Histone Displacement following Laser Microirradiation. J Biol Chem 2015; 291:1789-1802. [PMID: 26559976 DOI: 10.1074/jbc.m115.694992] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 12/29/2022] Open
Abstract
Chromatin undergoes a rapid ATP-dependent, ATM and H2AX-independent decondensation when DNA damage is introduced by laser microirradiation. Although the detailed mechanism of this decondensation remains to be determined, the kinetics of decondensation are similar to the kinetics of poly(ADP-ribosyl)ation. We used laser microirradiation to introduce DNA strand breaks into living cells expressing a photoactivatable GFP-tagged histone H2B. We find that poly(ADP-ribosyl)ation mediated primarily by poly(ADP-ribose) polymerase 1 (PARP1) is responsible for the rapid decondensation of chromatin at sites of DNA damage. This decondensation of chromatin correlates temporally with the displacement of histones, which is sensitive to PARP inhibition and is transient in nature. Contrary to the predictions of the histone shuttle hypothesis, we did not find that histone H1 accumulated on poly(ADP-ribose) (PAR) in vivo. Rather, histone H1, and to a lessor extent, histones H2A and H2B were rapidly depleted from the sites of PAR accumulation. However, histone H1 returns to chromatin and the chromatin recondenses. Thus, the PARP-dependent relaxation of chromatin closely correlates with histone displacement.
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Affiliation(s)
- Hilmar Strickfaden
- From the Department of Oncology, Faculty of Dentistry and Medicine, University of Alberta Alberta T6G 1Z2, Canada
| | - Darin McDonald
- From the Department of Oncology, Faculty of Dentistry and Medicine, University of Alberta Alberta T6G 1Z2, Canada
| | - Michael J Kruhlak
- the Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Jean-Francois Haince
- the Oncology Axis, Laval University Hospital Research Center, CHUQ, Faculty of Medicine, Laval University, Quebec G1V 4G2, Canada
| | - John P H Th'ng
- the Northern Ontario School of Medicine, Thunder Bay, Ontario P7B 5E1, Canada
| | - Michele Rouleau
- the Oncology Axis, Laval University Hospital Research Center, CHUQ, Faculty of Medicine, Laval University, Quebec G1V 4G2, Canada
| | - Toytaka Ishibashi
- the Department of Biochemistry and Microbiology, University of Victoria, Victoria, B.C. V8W 3P6, Canada,; the Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, HKSAR, and
| | - Gareth N Corry
- From the Department of Oncology, Faculty of Dentistry and Medicine, University of Alberta Alberta T6G 1Z2, Canada
| | - Juan Ausio
- the Department of Biochemistry and Microbiology, University of Victoria, Victoria, B.C. V8W 3P6, Canada
| | - D Alan Underhill
- From the Department of Oncology, Faculty of Dentistry and Medicine, University of Alberta Alberta T6G 1Z2, Canada
| | - Guy G Poirier
- From the Department of Oncology, Faculty of Dentistry and Medicine, University of Alberta Alberta T6G 1Z2, Canada
| | - Michael J Hendzel
- From the Department of Oncology, Faculty of Dentistry and Medicine, University of Alberta Alberta T6G 1Z2, Canada,.
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Solovyev VI, Ilinsky Y, Kosterin OE. Genetic integrity of four species of Leptidea (Pieridae, Lepidoptera) as sampled in sympatry in West Siberia. Comp Cytogenet 2015; 9:299-324. [PMID: 26312129 PMCID: PMC4547032 DOI: 10.3897/compcytogen.v9i3.4636] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/27/2015] [Indexed: 06/04/2023]
Abstract
In southern West Siberia, as many as four Leptidea Billberg, 1820 species are present sympatrically: Leptideaamurensis (Ménétriés, 1859), Leptideamorsei (Ménétriés, 1859), Leptideasinapis (Linnaeus, 1758) and Leptideajuvernica Williams, 1946. The two latter were recently recognised as nearly sibling species on morphological and molecular characters. Specimens intermediate as to their subtle diagnostic characters occurring in West Siberia and elsewhere were interpreted as resulted from limited introgression. This supposition was tested via populational morphological and molecular analysis of spring brood specimens of all the four species taken from a limited (4.5 × 0.2 km) area in the suburbs of Novosibirsk. The samples were analysed with respect to the genitalic morphology, external characters, three nuclear (CAD, H1 gene and ITS2) and one mitochondrial (COI) molecular markers, infection of the intracellular maternally inherited bacterial symbiont Wolbachia Hertig, 1836 and its wsp gene coding for a hypervariable surface protein. Interspecific variation of the nuclear CAD and ITS2 sequences and the mitochondrial COI gene in Leptideasinapis and Leptideajuvernica turned out concordant. The absence of molecular evidence of introgression suggests genetic integrity of these two species and allows their reliable identification by molecular characters. The genitalic (lengths of the saccus and valva) and external characters (wing pattern) of males overlap in Leptideasinapis and Leptideajuvernica, as identified by molecular markers and thus are not so helpful in actual species identification. Only the ductus bursae length showed no overlap and can be used for identification of females. The histone H1 gene appeared five times less variable over the four studied species than COI, and found to be identical in species Leptideasinapis and Leptideajuvernica. Wolbachia infection was found in all studied species. We identified three wsp variants of Wolbachia: 1) wsp-10 allele in Leptideaamurensis, Leptideasinapis, Leptideajuvernica; 2) a very similar wsp-687 allele in Leptideasinapis; and 3) wsp-688, highly divergent to the previous ones, in Leptideamorsei.
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Affiliation(s)
- Vladimir I. Solovyev
- Institute of Cytology & Genetics of Siberian Branch of Russian Academy of Sciences, Acad. Lavrentyev ave. 10, Novosibirsk, 630090, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia
| | - Yury Ilinsky
- Institute of Cytology & Genetics of Siberian Branch of Russian Academy of Sciences, Acad. Lavrentyev ave. 10, Novosibirsk, 630090, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia
- Institute of Chemistry and Biology, Immanuil Kant Baltic Federal University, Alexander Nevsky str. 14, 236038 Kaliningrad, Russia
| | - Oleg E. Kosterin
- Institute of Cytology & Genetics of Siberian Branch of Russian Academy of Sciences, Acad. Lavrentyev ave. 10, Novosibirsk, 630090, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia
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Turkina MV, Olofsson A, Magnusson KE, Arnqvist A, Vikström E. Helicobacter pylori vesicles carrying CagA localize in the vicinity of cell-cell contacts and induce histone H1 binding to ATP in epithelial cells. FEMS Microbiol Lett 2015; 362:fnv076. [PMID: 25956174 DOI: 10.1093/femsle/fnv076] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2015] [Indexed: 12/14/2022] Open
Abstract
Helicobacter pylori produces outer membrane vesicles (OMV), delivering bacterial substances including the oncogenic cytotoxin-associated CagA protein to their surroundings. We investigated the effects of H. pylori OMV carrying CagA (OMV-CagA) on cell junctions and ATP-binding proteome of epithelial monolayers, using proteomics, mass spectrometry and imaging. OMV-CagA localized in close vicinity of ZO-1 tight junction protein and induced histone H1 binding to ATP. We suggest the expression of novel events in the interactions between H. pylori OMV and epithelia, which may have an influence on host gene transcription and lead to different outcomes of an infection and development of cancer.
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Affiliation(s)
- Maria V Turkina
- Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, SE-58185 Linköping, Sweden
| | - Annelie Olofsson
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Karl-Eric Magnusson
- Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, SE-58185 Linköping, Sweden
| | - Anna Arnqvist
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Elena Vikström
- Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, SE-58185 Linköping, Sweden
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Siriaco G, Deuring R, Mawla GD, Tamkun JW. A novel approach for studying histone H1 function in vivo. Genetics 2015; 200:29-33. [PMID: 25805849 DOI: 10.1534/genetics.114.170514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 03/17/2015] [Indexed: 11/18/2022] Open
Abstract
In this report, we investigate the mechanisms that regulate Drosophila histone H1 expression and its association with chromatin in vivo. We show that histone H1 is subject to negative autoregulation and exploit this result to examine the effects of mutations of the main phosphorylation site of histone H1.
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Agallou M, Athanasiou E, Koutsoni O, Dotsika E, Karagouni E. Experimental Validation of Multi-Epitope Peptides Including Promising MHC Class I- and II-Restricted Epitopes of Four Known Leishmania infantum Proteins. Front Immunol 2014; 5:268. [PMID: 24959167 PMCID: PMC4051127 DOI: 10.3389/fimmu.2014.00268] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/25/2014] [Indexed: 12/25/2022] Open
Abstract
Leishmaniasis is a significant worldwide health problem for which no vaccine exists. Activation of CD4(+) and CD8(+) T cells is crucial for the generation of protective immunity against parasite. Recent trend in vaccine design has been shifted to epitope-based vaccines that are more specific, safe, and easy to produce. In the present study, four known antigenic Leishmania infantum proteins, cysteine peptidase A (CPA), histone H1, KMP-11, and Leishmania eukaryotic initiation factor (LeIF) were analyzed for the prediction of binding epitopes to H2(d) MHC class I and II molecules, using online available algorithms. Based on in silico analysis, eight peptides including highly scored MHC class I- and II-restricted epitopes were synthesized. Peptide immunogenicity was validated in MHC compatible BALB/c mice immunized with each synthetic peptide emulsified in complete Freund's adjuvant/incomplete Freund's adjuvant. CPA_p2, CPA_p3, H1_p1, and LeIF_p6 induced strong spleen cell proliferation upon in vitro peptide re-stimulation. In addition, the majority of the peptides, except of LeIF_p1 and KMP-11_p1, induced IFN-γ secretion, while KMP-11_p1 indicated a suppressive effect on IL-10 production. CPA_p2, CPA_p3, LeIF_p3, and LeIF_p6 induced IFN-γ-producing CD4(+) T cells indicating a TH1-type response. In addition, CPA_p2, CPA_p3, and H1_p1 induced also the induction of CD8(+) T cells. The induction of peptide-specific IgG in immunized mice designated also the existence of B cell epitopes in peptide sequences. Combining immunoinformatic tools and experimental validation, we demonstrated that CPA_p2, CPA_p3, H1_p1, H1_p3, CPA_p2, LeIF_p3, and LeIF_p6 are likely to include potential epitopes for the induction of protective cytotoxic and/or TH1-type immune responses supporting the feasibility of peptide-based vaccine development for leishmaniasis.
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Affiliation(s)
- Maria Agallou
- Laboratory of Cellular Immunology, Department of Microbiology, Hellenic Pasteur Institute , Athens , Greece
| | - Evita Athanasiou
- Laboratory of Cellular Immunology, Department of Microbiology, Hellenic Pasteur Institute , Athens , Greece
| | - Olga Koutsoni
- Laboratory of Cellular Immunology, Department of Microbiology, Hellenic Pasteur Institute , Athens , Greece
| | - Eleni Dotsika
- Laboratory of Cellular Immunology, Department of Microbiology, Hellenic Pasteur Institute , Athens , Greece
| | - Evdokia Karagouni
- Laboratory of Cellular Immunology, Department of Microbiology, Hellenic Pasteur Institute , Athens , Greece
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Abstract
Histones package DNA in all eukaryotes and play key roles in regulating gene expression. Approximately 150 base pairs of DNA wraps around an octamer of core histones to form the nucleosome, the basic unit of chromatin. Linker histones compact chromatin further by binding to and neutralizing the charge of the DNA between nucleosomes. It is well established that chromatin packing is regulated by a complex pattern of posttranslational modifications (PTMs) to core histones, but linker histone function is less well understood. In this review, we describe the current understanding of the many roles that linker histones play in cellular processes, including gene regulation, cell division, and development, while putting the linker histone in the context of other nuclear proteins. Although intriguing roles for plant linker histones are beginning to emerge, much of our current understanding comes from work in animal systems. Many unanswered questions remain and additional work is required to fully elucidate the complex processes mediated by linker histones in plants.
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Affiliation(s)
| | - Scott D. Michaels
- To whom correspondence should be addressed. E-mail , fax 812-855-6082, tel. 812-856-0302
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Totsingan F, Bell AJ. Interaction of HMG proteins and H1 with hybrid PNA-DNA junctions. Protein Sci 2013; 22:1552-62. [PMID: 23963921 DOI: 10.1002/pro.2342] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 08/15/2013] [Accepted: 08/15/2013] [Indexed: 12/21/2022]
Abstract
The objective of this study was to evaluate the effects of inserting peptide nucleic acid (PNA) sequences into the protein-binding surface of an immobilized four-way junction (4WJ). Here we compare the classic immobile DNA junction, J1, with two PNA containing hybrid junctions (4WJ-PNA1 and 4WJ-PNA3 ). The protein interactions of each 4WJ were evaluated using recombinant high mobility group proteins from rat (HMGB1b and HMGB1b/R26A) and human histone H1. In vitro studies show that both HMG and H1 proteins display high binding affinity toward 4WJ's. A 4WJ can access different conformations depending on ionic environment, most simply interpreted by a two-state equilibrium between: (i) an open-x state favored by absence of Mg(2+), low salt, and protein binding, and (ii) a compact stacked-x state favored by Mg(2+). 4WJ-PNA3, like J1, shifts readily from an open to stacked conformation in the presence of Mg(+2), while 4WJ-PNA1 does not. Circular dichroism spectra indicate that HMGB1b recognizes each of the hybrid junctions. H1, however, displays a strong preference for J1 relative to the hybrids. More extensive binding analysis revealed that HMGB1b binds J1 and 4WJ-PNA3 with nearly identical affinity (K(D)s) and 4WJ-PNA1 with two-fold lower affinity. Thus both the sequence/location of the PNA sequence and the protein determine the structural and protein recognition properties of 4WJs.
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Wójcik K, Zarębski M, Cossarizza A, Dobrucki JW. Daunomycin, an antitumor DNA intercalator, influences histone-DNA interactions. Cancer Biol Ther 2013; 14:823-32. [PMID: 23792590 DOI: 10.4161/cbt.25328] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Although daunomycin and adriamycin are considered effective antitumor drugs and have been used in the clinic for over 40 years, their mechanism of action is still a matter of debate. We investigated the influence of daunomycin on interaction between linker or core histones and DNA in live HeLa cells in vitro, using image and flow cytometry. Exposure to daunomycin at clinically relevant concentrations (25-250 nM) caused dissociation of wild-type H1.1 as well as 4 H1 point mutants from DNA, followed by their accumulation in nucleoli and aggregation of chromatin. A detectable dissociation of H2B core histones occurred only at much higher concentrations of the drug (500 nM). Replication of DNA and synthesis of RNA were not halted by daunomycin (up to 2500 nM); however the characteristic subnuclear distribution of sites of transcription and replication was lost. Dissociation of the H1.1 linker histones and subsequent loss of higher order chromatin structures may constitute an important component of the mechanism of cytotoxicity of daunomycin.
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Affiliation(s)
- Krzysztof Wójcik
- Division of Cell Biophysics; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Kraków, Poland
| | - Mirosław Zarębski
- Division of Cell Biophysics; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Kraków, Poland
| | - Andrea Cossarizza
- University of Modena and Reggio Emilia; School of Medicine; Department of Biomedical Sciences; Modena, Italy
| | - Jurek W Dobrucki
- Division of Cell Biophysics; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Kraków, Poland
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