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Pascal C, Zonszain J, Hameiri O, Gargi-Levi C, Lev-Maor G, Tammer L, Levy T, Tarabeih A, Roy VR, Ben-Salmon S, Elbaz L, Eid M, Hakim T, Abu Rabe'a S, Shalev N, Jordan A, Meshorer E, Ast G. Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation. Mol Cell 2023; 83:3801-3817.e8. [PMID: 37922872 DOI: 10.1016/j.molcel.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/17/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023]
Abstract
Histones shape chromatin structure and the epigenetic landscape. H1, the most diverse histone in the human genome, has 11 variants. Due to the high structural similarity between the H1s, their unique functions in transferring information from the chromatin to mRNA-processing machineries have remained elusive. Here, we generated human cell lines lacking up to five H1 subtypes, allowing us to characterize the genomic binding profiles of six H1 variants. Most H1s bind to specific sites, and binding depends on multiple factors, including GC content. The highly expressed H1.2 has a high affinity for exons, whereas H1.3 binds intronic sequences. H1s are major splicing regulators, especially of exon skipping and intron retention events, through their effects on the elongation of RNA polymerase II (RNAPII). Thus, H1 variants determine splicing fate by modulating RNAPII elongation.
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Affiliation(s)
- Corina Pascal
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jonathan Zonszain
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ofir Hameiri
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chen Gargi-Levi
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Galit Lev-Maor
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Luna Tammer
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Levy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anan Tarabeih
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Vanessa Rachel Roy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Stav Ben-Salmon
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Liraz Elbaz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mireille Eid
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Hakim
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Salima Abu Rabe'a
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nana Shalev
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Albert Jordan
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Carrer de Baldiri Reixac, 15, 08028 Barcelona, Spain
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Jerusalem 91904, Israel; Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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2
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Zhang L, Cervantes MD, Pan S, Lindsley J, Dabney A, Kapler GM. Transcriptome analysis of the binucleate ciliate Tetrahymena thermophila with asynchronous nuclear cell cycles. Mol Biol Cell 2023; 34:rs1. [PMID: 36475712 PMCID: PMC9930529 DOI: 10.1091/mbc.e22-08-0326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tetrahymena thermophila harbors two functionally and physically distinct nuclei within a shared cytoplasm. During vegetative growth, the "cell cycles" of the diploid micronucleus and polyploid macronucleus are offset. Micronuclear S phase initiates just before cytokinesis and is completed in daughter cells before onset of macronuclear DNA replication. Mitotic micronuclear division occurs mid-cell cycle, while macronuclear amitosis is coupled to cell division. Here we report the first RNA-seq cell cycle analysis of a binucleated ciliated protozoan. RNA was isolated across 1.5 vegetative cell cycles, starting with a macronuclear G1 population synchronized by centrifugal elutriation. Using MetaCycle, 3244 of the 26,000+ predicted genes were shown to be cell cycle regulated. Proteins present in both nuclei exhibit a single mRNA peak that always precedes their macronuclear function. Nucleus-limited genes, including nucleoporins and importins, are expressed before their respective nucleus-specific role. Cyclin D and A/B gene family members exhibit different expression patterns that suggest nucleus-restricted roles. Periodically expressed genes cluster into seven cyclic patterns. Four clusters have known PANTHER gene ontology terms associated with G1/S and G2/M phase. We propose that these clusters encode known and novel factors that coordinate micro- and macronuclear-specific events such as mitosis, amitosis, DNA replication, and cell division.
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Affiliation(s)
- L. Zhang
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,Department of Statistics, Texas A&M University, College Station, TX 77843
| | - M. D. Cervantes
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840
| | - S. Pan
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,Department of Statistics, Texas A&M University, College Station, TX 77843
| | - J. Lindsley
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840
| | - A. Dabney
- Department of Statistics, Texas A&M University, College Station, TX 77843,*Address correspondence to: Geoffrey Kapler (); A. Dabney ()
| | - G. M. Kapler
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,*Address correspondence to: Geoffrey Kapler (); A. Dabney ()
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3
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Previously Unidentified Histone H1-Like Protein Is Involved in Cell Division and Ribosome Biosynthesis in Toxoplasma gondii. mSphere 2022; 7:e0040322. [PMID: 36468865 PMCID: PMC9769792 DOI: 10.1128/msphere.00403-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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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Sokolova V, Sarkar S, Tan D. Histone variants and chromatin structure, update of advances. Comput Struct Biotechnol J 2022; 21:299-311. [PMID: 36582440 PMCID: PMC9764139 DOI: 10.1016/j.csbj.2022.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Histone proteins are highly conserved among all eukaryotes. They have two important functions in the cell: to package the genomic DNA and to regulate gene accessibility. Fundamental to these functions is the ability of histone proteins to interact with DNA and to form the nucleoprotein complex called chromatin. One of the mechanisms the cells use to regulate chromatin and gene expression is through replacing canonical histones with their variants at specific loci to achieve functional consequence. Recent cryo-electron microscope (cryo-EM) studies of chromatin containing histone variants reveal new details that shed light on how variant-specific features influence the structures and functions of chromatin. In this article, we review the current state of knowledge on histone variants biochemistry and discuss the implication of these new structural information on histone variant biology and their functions in transcription.
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Feng H, Zhou BR, Schwieters CD, Bai Y. Structural Mechanism of TAF-Iβ Chaperone Function on Linker Histone H1.10. J Mol Biol 2022; 434:167755. [PMID: 35870650 PMCID: PMC9489631 DOI: 10.1016/j.jmb.2022.167755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/21/2022]
Abstract
Linker histone H1, facilitated by its chaperones, plays an essential role in regulating gene expression by maintaining chromatin's higher-order structure and epigenetic state. However, we know little about the structural mechanism of how the chaperones recognize linker histones and conduct their function. Here, we used biophysical and biochemical methods to investigate the recognition of human linker histone isoform H1.10 by the TAF-Iβ chaperone. Both H1.10 and TAF-Iβ proteins consist of folded cores and disordered tails. We found that H1.10 formed a complex with TAF-Iβ in a 2:2 stoichiometry. Using distance restraints obtained from methyl-TROSY NMR and spin labels, we built a structural model for the core region of the complex. In the model, the TAF-Iβ core interacts with the globular domain of H1.10 mainly through electrostatic interactions. We confirmed the interactions by measuring the effects of mutations on the binding affinity. A comparison of our structural model with the chromatosome structure shows that TAF-Iβ blocks the DNA binding sites of H1.10. Our study provides insights into the structural mechanism whereby TAF-Iβ functions as a chaperone by preventing H1.10 from interacting with DNA directly.
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Affiliation(s)
- Haniqao Feng
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles D Schwieters
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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6
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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] [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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7
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Wu X, Xu J, Meng X, Fang X, Xia M, Zhang J, Cao S, Fan T. Linker histone variant HIS1-3 and WRKY1 oppositely regulate salt stress tolerance in Arabidopsis. PLANT PHYSIOLOGY 2022; 189:1833-1847. [PMID: 35474141 PMCID: PMC9237719 DOI: 10.1093/plphys/kiac174] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/03/2021] [Indexed: 06/12/2023]
Abstract
The salt overly sensitive (SOS) pathway plays an important role in plant salt stress; however, the transcriptional regulation of the genes in this pathway is unclear. In this study, we found that Linker histone variant HIS1-3 and WRKY1 oppositely regulate the salt stress response in Arabidopsis (Arabidopsis thaliana) through the transcriptional regulation of SOS genes. The expression of HIS1-3 was inhibited by salt stress, and the disruption of HIS1-3 resulted in enhanced salt tolerance. Conversely, the expression of WRKY1 was induced by salt stress, and the loss of WRKY1 function led to increased salt sensitivity. The expression of SOS1, SOS2, and SOS3 was repressed and induced by HIS1-3 and WRKY1, respectively, and HIS1-3 regulated the expression of SOS1 and SOS3 by occupying the WRKY1 binding sites on their promoters. Moreover, WRKY1 and HIS1-3 acted upstream of the SOS pathway. Together, our results indicate that HIS1-3 and WRKY1 oppositely modulate salt tolerance in Arabidopsis through transcriptional regulation of SOS genes.
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Affiliation(s)
| | | | | | - Xue Fang
- School of Horticulture, Anhui Agricultural University, Hefei 230009, China
| | - Minghui Xia
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jing Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Shuqing Cao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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8
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Liao R, Chen X, Cao Q, Wang Y, Miao Z, Lei X, Jiang Q, Chen J, Wu X, Li X, Li J, Dong C. HIST1H1B Promotes Basal-Like Breast Cancer Progression by Modulating CSF2 Expression. Front Oncol 2021; 11:780094. [PMID: 34746019 PMCID: PMC8570124 DOI: 10.3389/fonc.2021.780094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/05/2021] [Indexed: 01/09/2023] Open
Abstract
Background Basal-like breast cancer (BLBC) is associated with a poor clinical outcome; however, the mechanism of BLBC aggressiveness is still unclear. It has been shown that a linker histone functions as either a positive or negative regulator of gene expression in tumors. Here, we aimed to investigate the possible involvement and mechanism of HIST1H1B in BLBC progression. Experimental design We analyzed multiple gene expression datasets to determine the relevance of HIST1H1B expression with BLBC. We employed quantitative real-time PCR, transwell assay, colony formation assay, and mammosphere assay to dissect the molecular events associated with the expression of HIST1H1B in human breast cancer. We studied the association of HIST1H1B with CSF2 by ChIP assay. Using tumorigenesis assays, we determine the effect of HIST1H1B expression on tumorigenicity of BLBC cells. Results Here, we show that the linker histone HIST1H1B is dramatically elevated in BLBC due to HIST1H1B copy number amplification and promoter hypomethylation. HIST1H1B upregulates colony-stimulating factor 2 (CSF2) expression by binding the CSF2 promoter. HIST1H1B expression promotes, whereas knockdown of HIST1H1B expression suppresses tumorigenicity. In breast cancer patients, HIST1H1B expression is positively correlated with large tumor size, high grade, metastasis and poor survival. Conclusion HIST1H1B contributes to basal-like breast cancer progression by modulating CSF2 expression, indicating a potential prognostic marker and therapeutic target for this disease.
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Affiliation(s)
- Ruocen Liao
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Xingyu Chen
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianhua Cao
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifan Wang
- Cancer Institute of Integrative Medicine, Zhejiang Academy of Traditional Chinese Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Zhaorui Miao
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Xingyu Lei
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianjin Jiang
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Chen
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuebiao Wu
- Department of Pathophysiology, Gannan Medical University, Gannan, China
| | - Xiaoli Li
- R&D Department of Hangzhou, Abcam Plc, Hangzhou, China
| | - Jun Li
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chenfang Dong
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
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9
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Kimura A, Arakawa N, Kagawa H, Kimura Y, Hirano H. Phosphorylation of Ser1452 on BRG1 inhibits the function of the SWI/SNF complex in chromatin activation. J Proteomics 2021; 247:104319. [PMID: 34237461 DOI: 10.1016/j.jprot.2021.104319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/16/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022]
Abstract
BRG1, one of core subunits of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancers. Previously, we reported significant downregulation of the phosphorylation level of BRG1 on Ser1452 (<10%) in cell lines derived from ovarian clear cell carcinoma with frequent recurrence and acquired drug resistance. In this study, we tried to elucidate the roles of BRG1 phosphorylation, using cell lines expressing wild-type, phosphorylation-mimic (brg1-S1452D), or non-phosphorylatable (brg1-S1452A) BRG1. Quantitative proteomic analyses revealed upregulation of proteins and phosphoproteins related to linker histone H1s, histone methylation, and protein ubiquitylation in brg1-S1452D cells, which may coordinately promote the chromatin inactivation and ubiquitin-dependent degradation of target proteins. Consistent with these results, brg1-S1452D cells exhibited an increase in condensed chromatin and polyubiquitylated proteins. In brg1-S1452D cells, we also detected downregulation of various cancer-related proteins (e.g., EGFR and MET) as well as decreased migration, proliferation, and sensitivity to taxanes and oxaliplatin. Together, our results reveal that BRG1 phosphorylation drives tumor malignancy by inhibiting the functions of SWI/SNF complex in chromatin activation, thereby promoting expression of various cancer-related proteins. SIGNIFICANCE: For the first time we demonstrated that the mutation on Ser1452 phosphorylation site of BRG1, a component of SWI/SNF chromatin remodeling complex, changed protein and phosphoprotein levels of linker histone H1s, binding competitor of histone H1s, and histone methylase/demethylase involved in the heterochromatic histone modifications to promote the chromatin inactivation. In phosphorylation-mimic mutant, significant decrease of various cancer-related proteins as well as migration, proliferation, and sensitivity to specific antitumor agents were detected. Our results reveal that BRG1 phosphorylation drives tumor malignancy by inhibiting the functions of SWI/SNF complex in chromatin activation, thereby promoting expression of various cancer-related proteins.
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Affiliation(s)
- Ayuko Kimura
- Advanced Medical Research Center, Yokohama City University and Graduate School of Medical Life Science, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Graduate School of Health Science, Gunma Paz University, Tonyamachi 1-7-1, Takasaki City, Gunma 370-0006, Japan.
| | - Noriaki Arakawa
- Advanced Medical Research Center, Yokohama City University and Graduate School of Medical Life Science, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki, Tonomachi 3-25-26, Kawasaki-ku, Kawasaki City, Kanagawa 210-9501, Japan
| | - Hiroyuki Kagawa
- Advanced Medical Research Center, Yokohama City University and Graduate School of Medical Life Science, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University and Graduate School of Medical Life Science, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Hisashi Hirano
- Advanced Medical Research Center, Yokohama City University and Graduate School of Medical Life Science, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Graduate School of Health Science, Gunma Paz University, Tonyamachi 1-7-1, Takasaki City, Gunma 370-0006, Japan
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10
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Huang D, Li Q, Sun X, Sun X, Tang Y, Qu Y, Liu D, Yu T, Li G, Tong T, Zhang Y. CRL4 DCAF8 dependent opposing stability control over the chromatin remodeler LSH orchestrates epigenetic dynamics in ferroptosis. Cell Death Differ 2021; 28:1593-1609. [PMID: 33288900 PMCID: PMC8166945 DOI: 10.1038/s41418-020-00689-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 01/28/2023] Open
Abstract
Despite the emerging evidence on ferroptosis implicated in diverse pathologies, molecular linkage between oxidative inducers and chromatin as epigenetic memory carrier for its propagation remains elusive. Here, we report the identification of two WD40 proteins DCAF8 and WDR76 as substrate adapter and molecular inhibitor respectively of the Cullin-4 RING ubiquitin ligase (CRL4) system for stability control of chromatin remodeler LSH. Degradation analysis and CRL4-DCAF8 complex reconstitution demonstrate that CRL4DCAF8 is a bona fide E3 ligase for LSH. In contrast, WDR76 antagonizes DCAF8-targeted LSH proteolysis through competitive inhibition of the holo-CRL4DCAF8-LSH complex assembly. Importantly, this opposing regulatory strategy is utilized in lipid hydroperoxide induced ferroptosis, where we identify key redox homeostasis genes significantly regulated by the DCAF8/WDR76/LSH axis through transcriptomic epistasis analysis. This regulation is mechanistically attributed to DNA hydroxymethylation fostered WDR76 interaction with LSH and increased ratio of DCAF8 to WDR76 for antagonistic LSH association accompanying decreased DNA oxidation along with ROS overproduction. Evaluation of epigenetic dynamics at ferroptosis gene promoters reveals linker histone H1- and LSH-associated transcriptional repression is coordinately removed upon lipid peroxidation stress. Together with the phenotypes driven by WDR76 and DCAF8 manipulations, these data identify DCAF8- and WDR76-adapted oxidative damage sensing through DNA hydroxymethylation for LSH degradation control as a crucial nexus in epigenetic regulation of ferroptosis.
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Affiliation(s)
- Daoyuan Huang
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Qian Li
- grid.11135.370000 0001 2256 9319Department of Orthodontics, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, 100081 Beijing, China
| | - Xinpei Sun
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Xiwen Sun
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Yunyi Tang
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Yanan Qu
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Dawei Liu
- grid.11135.370000 0001 2256 9319Department of Orthodontics, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, 100081 Beijing, China
| | - Tingting Yu
- grid.11135.370000 0001 2256 9319Department of Orthodontics, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, 100081 Beijing, China
| | - Guodong Li
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Tanjun Tong
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Yu Zhang
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
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11
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Woods DC, Rodríguez-Ropero F, Wereszczynski J. The Dynamic Influence of Linker Histone Saturation within the Poly-Nucleosome Array. J Mol Biol 2021; 433:166902. [PMID: 33667509 DOI: 10.1016/j.jmb.2021.166902] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 02/08/2023]
Abstract
Linker histones bind to nucleosomes and modify chromatin structure and dynamics as a means of epigenetic regulation. Biophysical studies have shown that chromatin fibers can adopt a plethora of conformations with varying levels of compaction. Linker histone condensation, and its specific binding disposition, has been associated with directly tuning this ensemble of states. However, the atomistic dynamics and quantification of this mechanism remains poorly understood. Here, we present molecular dynamics simulations of octa-nucleosome arrays, based on a cryo-EM structure of the 30-nm chromatin fiber, with and without the globular domains of the H1 linker histone to determine how they influence fiber structures and dynamics. Results show that when bound, linker histones inhibit DNA flexibility and stabilize repeating tetra-nucleosomal units, giving rise to increased chromatin compaction. Furthermore, upon the removal of H1, there is a significant destabilization of this compact structure as the fiber adopts less strained and untwisted states. Interestingly, linker DNA sampling in the octa-nucleosome is exaggerated compared to its mono-nucleosome counterparts, suggesting that chromatin architecture plays a significant role in DNA strain even in the absence of linker histones. Moreover, H1-bound states are shown to have increased stiffness within tetra-nucleosomes, but not between them. This increased stiffness leads to stronger long-range correlations within the fiber, which may result in the propagation of epigenetic signals over longer spatial ranges. These simulations highlight the effects of linker histone binding on the internal dynamics and global structure of poly-nucleosome arrays, while providing physical insight into a mechanism of chromatin compaction.
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Affiliation(s)
- Dustin C Woods
- Department of Chemistry and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, United States
| | - Francisco Rodríguez-Ropero
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, United States
| | - Jeff Wereszczynski
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, United States.
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12
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Lizarraga A, Muñoz D, Strobl-Mazzulla PH, de Miguel N. Toward incorporating epigenetics into regulation of gene expression in the parasite Trichomonas vaginalis. Mol Microbiol 2021; 115:959-967. [PMID: 33599017 DOI: 10.1111/mmi.14704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 02/13/2021] [Indexed: 12/11/2022]
Abstract
Trichomonas vaginalis is an extracellular parasite that colonizes the human urogenital tract, causing a highly prevalent sexually transmitted infection. The parasite must change its transcriptional profile in order to establish and maintain infection. However, few core regulatory elements and transcription factors have been identified to date and little is known about other mechanisms that may control these rapid changes in gene expression during parasite infection. In the last years, epigenetic mechanisms involved in the regulation of gene expression have been gaining major attention in this parasite. In this review, we summarize and discuss the major advances of the last few years with regard to epigenetics (DNA methylation, post-translational histone modifications, and histone variants) in the parasite T. vaginalis. These studies can shed light into our current understanding of this parasite's biology with far-reaching implications for the prognosis and treatment of trichomoniasis.
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Affiliation(s)
- Ayelen Lizarraga
- Laboratorio de Parásitos Anaerobios, Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM, Chascomús, Argentina
| | - Daniela Muñoz
- Laboratorio de Parásitos Anaerobios, Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM, Chascomús, Argentina
| | - Pablo H Strobl-Mazzulla
- Laboratorio de Biología del Desarrollo, Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM, Chascomús, Argentina
| | - Natalia de Miguel
- Laboratorio de Parásitos Anaerobios, Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM, Chascomús, Argentina
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13
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Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR, Bai Y. Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms. Mol Cell 2021; 81:166-182.e6. [PMID: 33238161 PMCID: PMC7796963 DOI: 10.1016/j.molcel.2020.10.038] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/21/2020] [Accepted: 10/27/2020] [Indexed: 12/21/2022]
Abstract
The repeating structural unit of metazoan chromatin is the chromatosome, a nucleosome bound to a linker histone, H1. There are 11 human H1 isoforms with diverse cellular functions, but how they interact with the nucleosome remains elusive. Here, we determined the cryoelectron microscopy (cryo-EM) structures of chromatosomes containing 197 bp DNA and three different human H1 isoforms, respectively. The globular domains of all three H1 isoforms bound to the nucleosome dyad. However, the flanking/linker DNAs displayed substantial distinct dynamic conformations. Nuclear magnetic resonance (NMR) and H1 tail-swapping cryo-EM experiments revealed that the C-terminal tails of the H1 isoforms mainly controlled the flanking DNA orientations. We also observed partial ordering of the core histone H2A C-terminal and H3 N-terminal tails in the chromatosomes. Our results provide insights into the structures and dynamics of the chromatosomes and have implications for the structure and function of chromatin.
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Affiliation(s)
- Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seyit Kale
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey
| | - Tara Fox
- Center of Macromolecular Microscopy, National Cancer Institute, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Htet Khant
- Center of Macromolecular Microscopy, National Cancer Institute, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Natalia de Val
- Center of Macromolecular Microscopy, National Cancer Institute, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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14
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Site-Specific Phosphorylation of Histone H1.4 Is Associated with Transcription Activation. Int J Mol Sci 2020; 21:ijms21228861. [PMID: 33238524 PMCID: PMC7700352 DOI: 10.3390/ijms21228861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 01/05/2023] Open
Abstract
Core histone variants, such as H2A.X and H3.3, serve specialized roles in chromatin processes that depend on the genomic distributions and amino acid sequence differences of the variant proteins. Modifications of these variants alter interactions with other chromatin components and thus the protein’s functions. These inferences add to the growing arsenal of evidence against the older generic view of those linker histones as redundant repressors. Furthermore, certain modifications of specific H1 variants can confer distinct roles. On the one hand, it has been reported that the phosphorylation of H1 results in its release from chromatin and the subsequent transcription of HIV-1 genes. On the other hand, recent evidence indicates that phosphorylated H1 may in fact be associated with active promoters. This conflict suggests that different H1 isoforms and modified versions of these variants are not redundant when together but may play distinct functional roles. Here, we provide the first genome-wide evidence that when phosphorylated, the H1.4 variant remains associated with active promoters and may even play a role in transcription activation. Using novel, highly specific antibodies, we generated the first genome-wide view of the H1.4 isoform phosphorylated at serine 187 (pS187-H1.4) in estradiol-inducible MCF7 cells. We observe that pS187-H1.4 is enriched primarily at the transcription start sites (TSSs) of genes activated by estradiol treatment and depleted from those that are repressed. We also show that pS187-H1.4 associates with ‘early estrogen response’ genes and stably interacts with RNAPII. Based on the observations presented here, we propose that phosphorylation at S187 by CDK9 represents an early event required for gene activation. This event may also be involved in the release of promoter-proximal polymerases to begin elongation by interacting directly with the polymerase or other parts of the transcription machinery. Although we focused on estrogen-responsive genes, taking into account previous evidence of H1.4′s enrichment of promoters of pluripotency genes, and its involvement with rDNA activation, we propose that H1.4 phosphorylation for gene activation may be a more global observation.
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15
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Woods DC, Wereszczynski J. Elucidating the influence of linker histone variants on chromatosome dynamics and energetics. Nucleic Acids Res 2020; 48:3591-3604. [PMID: 32128577 PMCID: PMC7144933 DOI: 10.1093/nar/gkaa121] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/23/2022] Open
Abstract
Linker histones are epigenetic regulators that bind to nucleosomes and alter chromatin structures and dynamics. Biophysical studies have revealed two binding modes in the linker histone/nucleosome complex, the chromatosome, where the linker histone is either centered on or askew from the dyad axis. Each has been posited to have distinct effects on chromatin, however the molecular and thermodynamic mechanisms that drive them and their dependence on linker histone compositions remain poorly understood. We present molecular dynamics simulations of chromatosomes with the globular domain of two linker histone variants, generic H1 (genGH1) and H1.0 (GH1.0), to determine how their differences influence chromatosome structures, energetics and dynamics. Results show that both unbound linker histones adopt a single compact conformation. Upon binding, DNA flexibility is reduced, resulting in increased chromatosome compaction. While both variants enthalpically favor on-dyad binding, energetic benefits are significantly higher for GH1.0, suggesting that GH1.0 is more capable than genGH1 of overcoming the large entropic reduction required for on-dyad binding which helps rationalize experiments that have consistently demonstrated GH1.0 in on-dyad states but that show genGH1 in both locations. These simulations highlight the thermodynamic basis for different linker histone binding motifs, and details their physical and chemical effects on chromatosomes.
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Affiliation(s)
- Dustin C Woods
- Department of Chemistry and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jeff Wereszczynski
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, USA
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16
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Rutowicz K, Lirski M, Mermaz B, Teano G, Schubert J, Mestiri I, Kroteń MA, Fabrice TN, Fritz S, Grob S, Ringli C, Cherkezyan L, Barneche F, Jerzmanowski A, Baroux C. Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis. Genome Biol 2019; 20:157. [PMID: 31391082 PMCID: PMC6685187 DOI: 10.1186/s13059-019-1767-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/21/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function. Well studied in animals, little is known about the evolution of H1 function in other eukaryotic lineages for instance plants. Notably, in the model plant Arabidopsis, while H1 is known to influence heterochromatin and DNA methylation, its contribution to transcription, molecular, and cytological chromatin organization remains elusive. RESULTS We provide a multi-scale functional study of Arabidopsis linker histones. We show that H1-deficient plants are viable yet show phenotypes in seed dormancy, flowering time, lateral root, and stomata formation-complemented by either or both of the major variants. H1 depletion also impairs pluripotent callus formation. Fine-scale chromatin analyses combined with transcriptome and nucleosome profiling reveal distinct roles of H1 on hetero- and euchromatin: H1 is necessary to form heterochromatic domains yet dispensable for silencing of most transposable elements; H1 depletion affects nucleosome density distribution and mobility in euchromatin, spatial arrangement of nanodomains, histone acetylation, and methylation. These drastic changes affect moderately the transcription but reveal a subset of H1-sensitive genes. CONCLUSIONS H1 variants have a profound impact on the molecular and spatial (nuclear) chromatin organization in Arabidopsis with distinct roles in euchromatin and heterochromatin and a dual causality on gene expression. Phenotypical analyses further suggest the novel possibility that H1-mediated chromatin organization may contribute to the epigenetic control of developmental and cellular transitions.
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Affiliation(s)
- Kinga Rutowicz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Maciej Lirski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Benoît Mermaz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
- Department of Molecular, Cellular & Developmental Biology, Yale University, 352a Osborn memorial laboratories, New Haven, CT, 06511, USA
| | - Gianluca Teano
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Jasmin Schubert
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Imen Mestiri
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Magdalena A Kroteń
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089, Warsaw, Poland
| | - Tohnyui Ndinyanka Fabrice
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Simon Fritz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Stefan Grob
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Christoph Ringli
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Lusik Cherkezyan
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Fredy Barneche
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Andrzej Jerzmanowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Célia Baroux
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland.
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17
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Abstract
Physical access to DNA is a highly dynamic property of chromatin that plays an essential role in establishing and maintaining cellular identity. The organization of accessible chromatin across the genome reflects a network of permissible physical interactions through which enhancers, promoters, insulators and chromatin-binding factors cooperatively regulate gene expression. This landscape of accessibility changes dynamically in response to both external stimuli and developmental cues, and emerging evidence suggests that homeostatic maintenance of accessibility is itself dynamically regulated through a competitive interplay between chromatin-binding factors and nucleosomes. In this Review, we examine how the accessible genome is measured and explore the role of transcription factors in initiating accessibility remodelling; our goal is to illustrate how chromatin accessibility defines regulatory elements within the genome and how these epigenetic features are dynamically established to control gene expression.
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Affiliation(s)
- Sandy L Klemm
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Zohar Shipony
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg BioHub, San Francisco, CA, USA.
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18
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Glaich O, Leader Y, Lev Maor G, Ast G. Histone H1.5 binds over splice sites in chromatin and regulates alternative splicing. Nucleic Acids Res 2019; 47:6145-6159. [PMID: 31076740 PMCID: PMC6614845 DOI: 10.1093/nar/gkz338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 04/17/2019] [Accepted: 04/27/2019] [Indexed: 12/11/2022] Open
Abstract
Chromatin organization and epigenetic markers influence splicing, though the magnitudes of these effects and the mechanisms are largely unknown. Here, we demonstrate that linker histone H1.5 influences mRNA splicing. We observed that linker histone H1.5 binds DNA over splice sites of short exons in human lung fibroblasts (IMR90 cells). We found that association of H1.5 with these splice sites correlated with the level of inclusion of alternatively spliced exons. Exons marked by H1.5 had more RNA polymerase II (RNAP II) stalling near the 3' splice site than did exons not associated with H1.5. In cells depleted of H1.5, we showed that the inclusion of five exons evaluated decreased and that RNAP II levels over these exons were also reduced. Our findings indicate that H1.5 is involved in regulation of splice site selection and alternative splicing, a function not previously demonstrated for linker histones.
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Affiliation(s)
- Ohad Glaich
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Yodfat Leader
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Galit Lev Maor
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
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19
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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] [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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20
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Öztürk MA, Cojocaru V, Wade RC. Toward an Ensemble View of Chromatosome Structure: A Paradigm Shift from One to Many. Structure 2018; 26:1050-1057. [PMID: 29937356 DOI: 10.1016/j.str.2018.05.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/31/2018] [Accepted: 05/15/2018] [Indexed: 11/29/2022]
Abstract
There is renewed interest in linker histone (LH)-nucleosome binding and how LHs influence eukaryotic DNA compaction. For a long time, the goal was to uncover "the structure of the chromatosome," but recent studies of LH-nucleosome complexes have revealed an ensemble of structures. Notably, the reconstituted LH-nucleosome complexes used in experiments rarely correspond to the sequence combinations present in organisms. For a full understanding of the determinants of the distribution of the chromatosome structural ensemble, studies must include a complete description of the sequences and experimental conditions used, and be designed to enable systematic evaluation of sequence and environmental effects.
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Affiliation(s)
- Mehmet Ali Öztürk
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany; The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Heidelberg University, 69120 Heidelberg, Germany
| | - Vlad Cojocaru
- Computational Structural Biology Laboratory, Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, 48149 Münster, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.
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21
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Dong S, Xia T, Yang Y, Lin S, Mao L. Bioaccumulation of 14C-Labeled Graphene in an Aquatic Food Chain through Direct Uptake or Trophic Transfer. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:541-549. [PMID: 29265813 DOI: 10.1021/acs.est.7b04339] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The growing applications of graphene materials warrant a careful evaluation of their environmental fate in aquatic food webs. Escherichia coli (Bacteria), Tetrahymena thermophila (protozoa), Daphnia magna (zooplankton), and Danio rerio (vertebrate) were used to build aquatic food chains to investigate the waterborne uptake and trophic transfer of 14C-labeled graphene. Body burden factor (BBF) and trophic transfer factor (TTF) were analyzed for each organism and food chain to assess the bioaccumulation and biomagnification of graphene. The test organisms have high potential of accumulating graphene via direct uptake from culture medium with log-transformed BBF (log BBF) values of 3.66, 5.1, 3.9, and 1.62 for each organism, respectively. In the food chain from E. coli to T. thermophila, the calculated TTFs of 0.2 to 8.6 indicate the high trophic transfer potential in this aquatic food chain. However, the TTFs calculated for the food chain from T. thermophila to D. magna and from D. magna to D. rerio are much lower than 1, indicating that biomagnification was unlikely to occur in these food chains. Body burden measured for dietary uptake by T. thermophila, D. magna, and D. rerio are higher than that via waterborne exposure in a similar nominal concentration, respectively, indicating that trophic transfer is a nonnegligible route for the bioaccumulation of graphene in organisms.
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Affiliation(s)
- Shipeng Dong
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing 210093, China
| | - Tian Xia
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
- Division of NanoMedicine, Department of Medicine, University of California , Los Angeles 90095, United States
| | - Yu Yang
- Department of Civil & Environmental Engineering, University of Nevada , Reno 89557, United States
| | - Sijie Lin
- College of Environmental Science & Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University , Shanghai 200092, China
| | - Liang Mao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing 210093, China
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22
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Izquierdo-Bouldstridge A, Bustillos A, Bonet-Costa C, Aribau-Miralbés P, García-Gomis D, Dabad M, Esteve-Codina A, Pascual-Reguant L, Peiró S, Esteller M, Murtha M, Millán-Ariño L, Jordan A. Histone H1 depletion triggers an interferon response in cancer cells via activation of heterochromatic repeats. Nucleic Acids Res 2017; 45:11622-11642. [PMID: 28977426 PMCID: PMC5714221 DOI: 10.1093/nar/gkx746] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/15/2017] [Indexed: 12/21/2022] Open
Abstract
Histone H1 has seven variants in human somatic cells and contributes to chromatin compaction and transcriptional regulation. Knock-down (KD) of each H1 variant in breast cancer cells results in altered gene expression and proliferation differently in a variant specific manner with H1.2 and H1.4 KDs being most deleterious. Here we show combined depletion of H1.2 and H1.4 has a strong deleterious effect resulting in a strong interferon (IFN) response, as evidenced by an up-regulation of many IFN-stimulated genes (ISGs) not seen in individual nor in other combinations of H1 variant KDs. Although H1 participates to repress ISG promoters, IFN activation upon H1.2 and H1.4 KD is mainly generated through the activation of the IFN response by cytosolic nucleic acid receptors and IFN synthesis, and without changes in histone modifications at induced ISG promoters. H1.2 and H1.4 co-KD also promotes the appearance of accessibility sites genome wide and, particularly, at satellites and other repeats. The IFN response may be triggered by the expression of noncoding RNA generated from heterochromatic repeats or endogenous retroviruses upon H1 KD. In conclusion, redundant H1-mediated silencing of heterochromatin is important to maintain cell homeostasis and to avoid an unspecific IFN response.
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Affiliation(s)
| | - Alberto Bustillos
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Catalonia 08028, Spain
| | - Carles Bonet-Costa
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Catalonia 08028, Spain
| | | | - Daniel García-Gomis
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Catalonia 08028, Spain
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia 08003, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia 08003, Spain
| | | | - Sandra Peiró
- Vall d'Hebron Institute of Oncology, Barcelona, Catalonia 08035, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia 08028, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Catalonia 08028, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08028, Spain
| | - Matthew Murtha
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia 08028, Spain
| | - Lluís Millán-Ariño
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Catalonia 08028, Spain
| | - Albert Jordan
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Catalonia 08028, Spain
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23
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Qiao J, Xu J, Bo T, Wang W. Micronucleus-specific histone H1 is required for micronuclear chromosome integrity in Tetrahymena thermophila. PLoS One 2017; 12:e0187475. [PMID: 29095884 PMCID: PMC5667856 DOI: 10.1371/journal.pone.0187475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 10/19/2017] [Indexed: 02/02/2023] Open
Abstract
Histone H1 molecules play a key role in establishing and maintaining higher order chromatin structures. They can bind to linker DNA entering and exiting the nucleosome and regulate transcriptional activity. Tetrahymena thermophila has two histone H1, namely, macronuclear histone H1 and micronuclear histone H1 (Mlh1). Mlh1 is specifically localized at micronuclei during growth and starvation stages. Moreover, Mlh1 is localized around micronuclei and forms a specific structure during the conjugation stage. It co-localizes partially with spindle apparatus during micronuclear meiosis. Analysis of MLH1 knock-out revealed that Mlh1 was required for the micronuclear integrity and development during conjugation stage. Overexpression of Mlh1 led to abnormal conjugation progression. RT-PCR analysis indicated that the expression level of HMGB3 increased in ΔMLH1 strains, while the expression level of MLH1 increased in ΔHMGB3 cells during conjugation. These results indicate that micronuclear integrity and sexual development require normal expression level of Mlh1 and that HmgB3 and Mlh1 may functionally compensate each other in regulating micronuclear structure in T. thermophila.
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Affiliation(s)
- Juxia Qiao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi, China
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi, China
- College of Life Science, Shanxi University, Taiyuan, Shanxi, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong, China
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi, China
- * E-mail:
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24
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Feng L, Wang G, Hamilton EP, Xiong J, Yan G, Chen K, Chen X, Dui W, Plemens A, Khadr L, Dhanekula A, Juma M, Dang HQ, Kapler GM, Orias E, Miao W, Liu Y. A germline-limited piggyBac transposase gene is required for precise excision in Tetrahymena genome rearrangement. Nucleic Acids Res 2017; 45:9481-9502. [PMID: 28934495 PMCID: PMC5766162 DOI: 10.1093/nar/gkx652] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/15/2017] [Indexed: 12/20/2022] Open
Abstract
Developmentally programmed genome rearrangement accompanies differentiation of the silent germline micronucleus into the transcriptionally active somatic macronucleus in the ciliated protozoan Tetrahymena thermophila. Internal eliminated sequences (IES) are excised, followed by rejoining of MAC-destined sequences, while fragmentation occurs at conserved chromosome breakage sequences, generating macronuclear chromosomes. Some macronuclear chromosomes, referred to as non-maintained chromosomes (NMC), are lost soon after differentiation. Large NMC contain genes implicated in development-specific roles. One such gene encodes the domesticated piggyBac transposase TPB6, required for heterochromatin-dependent precise excision of IES residing within exons of functionally important genes. These conserved exonic IES determine alternative transcription products in the developing macronucleus; some even contain free-standing genes. Examples of precise loss of some exonic IES in the micronucleus and retention of others in the macronucleus of related species suggest an evolutionary analogy to introns. Our results reveal that germline-limited sequences can encode genes with specific expression patterns and development-related functions, which may be a recurring theme in eukaryotic organisms experiencing programmed genome rearrangement during germline to soma differentiation.
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Affiliation(s)
- Lifang Feng
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.,Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Eileen P Hamilton
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Guanxiong Yan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Kai Chen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao Chen
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wen Dui
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amber Plemens
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lara Khadr
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arjune Dhanekula
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mina Juma
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hung Quang Dang
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Geoffrey M Kapler
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Eduardo Orias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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25
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Izzo A, Ziegler-Birling C, Hill PWS, Brondani L, Hajkova P, Torres-Padilla ME, Schneider R. Dynamic changes in H1 subtype composition during epigenetic reprogramming. J Cell Biol 2017; 216:3017-3028. [PMID: 28794128 PMCID: PMC5626532 DOI: 10.1083/jcb.201611012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 05/30/2017] [Accepted: 07/07/2017] [Indexed: 12/13/2022] Open
Abstract
In mammals, the histone H1 family includes five somatic replication-dependent (H1.1–H1.5) and two replication-independent (H1.10 and H1.0) subtypes. Izzo et al. analyze the contributions of all somatic H1 subtypes to the chromatin landscape during reprogramming in preimplantation embryo and primordial germ cell development. In mammals, histone H1 consists of a family of related proteins, including five replication-dependent (H1.1–H1.5) and two replication-independent (H1.10 and H1.0) subtypes, all expressed in somatic cells. To systematically study the expression and function of H1 subtypes, we generated knockin mouse lines in which endogenous H1 subtypes are tagged. We focused on key developmental periods when epigenetic reprogramming occurs: early mouse embryos and primordial germ cell development. We found that dynamic changes in H1 subtype expression and localization are tightly linked with chromatin remodeling and might be crucial for transitions in chromatin structure during reprogramming. Although all somatic H1 subtypes are present in the blastocyst, each stage of preimplantation development is characterized by a different combination of H1 subtypes. Similarly, the relative abundance of somatic H1 subtypes can distinguish male and female chromatin upon sex differentiation in developing germ cells. Overall, our data provide new insights into the chromatin changes underlying epigenetic reprogramming. We suggest that distinct H1 subtypes may mediate the extensive chromatin remodeling occurring during epigenetic reprogramming and that they may be key players in the acquisition of cellular totipotency and the establishment of specific cellular states.
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Affiliation(s)
- Annalisa Izzo
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Céline Ziegler-Birling
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Peter W S Hill
- Hammersmith Hospital Campus, Medical Research Council London Institute of Medical Sciences, London, England, UK.,Institute of Clinical Sciences, Hammersmith Hospital Campus, Imperial College Faculty of Medicine, London, England, UK
| | - Lydia Brondani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Petra Hajkova
- Hammersmith Hospital Campus, Medical Research Council London Institute of Medical Sciences, London, England, UK.,Institute of Clinical Sciences, Hammersmith Hospital Campus, Imperial College Faculty of Medicine, London, England, UK
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Neuherberg, Germany .,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany .,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
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26
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Histone Acetylation, Not Stoichiometry, Regulates Linker Histone Binding in Saccharomyces cerevisiae. Genetics 2017; 207:347-355. [PMID: 28739661 DOI: 10.1534/genetics.117.1132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 07/12/2017] [Indexed: 12/27/2022] Open
Abstract
Linker histones play a fundamental role in shaping chromatin structure, but how their interaction with chromatin is regulated is not well understood. In this study, we used a combination of genetic and genomic approaches to explore the regulation of linker histone binding in the yeast, Saccharomyces cerevisiae We found that increased expression of Hho1, the yeast linker histone, resulted in a severe growth defect, despite only subtle changes in chromatin structure. Further, this growth defect was rescued by mutations that increase histone acetylation. Consistent with this, genome-wide analysis of linker histone occupancy revealed an inverse correlation with histone tail acetylation in both yeast and mouse embryonic stem cells. Collectively, these results suggest that histone acetylation negatively regulates linker histone binding in S. cerevisiae and other organisms and provide important insight into how chromatin structure is regulated and maintained to both facilitate and repress transcription.
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27
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Ye X, Feng C, Gao T, Mu G, Zhu W, Yang Y. Linker Histone in Diseases. Int J Biol Sci 2017; 13:1008-1018. [PMID: 28924382 PMCID: PMC5599906 DOI: 10.7150/ijbs.19891] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/30/2017] [Indexed: 01/21/2023] Open
Abstract
The linker histone is a protein that binds with the nucleosome, which is generally considered to achieve chromatin condensation in the nucleus. Accumulating evidences suggest that the linker histone is essential in the pathogenesis of several diseases. In this review, we briefly introduce the current knowledge of the linker histone, including its structure, characteristics and functions. Also, we move forward to present the advances of the linker histone's association with certain diseases, such as cancer, Alzheimer's disease, infection, male infertility and aberrant immunity situations, focusing on the alteration of the linker histone under certain pathological conditions and its role in developing each disease.
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Affiliation(s)
- Xin Ye
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xueyuan Road, Beijing 100191, China
| | - ChuanLin Feng
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xueyuan Road, Beijing 100191, China
| | - Tian Gao
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xueyuan Road, Beijing 100191, China
| | - Guanqun Mu
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xueyuan Road, Beijing 100191, China
| | - Weiguo Zhu
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xueyuan Road, Beijing 100191, China
| | - Yang Yang
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xueyuan Road, Beijing 100191, China
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28
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Kowalski A, Pałyga J. Modulation of chromatin function through linker histone H1 variants. Biol Cell 2016; 108:339-356. [PMID: 27412812 DOI: 10.1111/boc.201600007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 07/08/2016] [Accepted: 07/08/2016] [Indexed: 12/30/2022]
Abstract
In this review, the structural aspects of linker H1 histones are presented as a background for characterization of the factors influencing their function in animal and human chromatin. The action of H1 histone variants is largely determined by dynamic alterations of their intrinsically disordered tail domains, posttranslational modifications and allelic diversification. The interdependent effects of these factors can establish dynamic histone H1 states that may affect the organization and function of chromatin regions.
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Affiliation(s)
- Andrzej Kowalski
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
| | - Jan Pałyga
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
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29
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A Small Number of Residues Can Determine if Linker Histones Are Bound On or Off Dyad in the Chromatosome. J Mol Biol 2016; 428:3948-3959. [PMID: 27558112 DOI: 10.1016/j.jmb.2016.08.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/16/2016] [Accepted: 08/17/2016] [Indexed: 11/20/2022]
Abstract
Linker histones bind to the nucleosome and regulate the structure and function of chromatin. We have previously shown that the globular domains of chicken H5 and Drosophila H1 linker histones bind to the nucleosome with on- or off-dyad modes, respectively. To explore the determinant for the distinct binding modes, we investigated the binding of a mutant globular domain of H5 to the nucleosome. This mutant, termed GH5_pMut, includes substitutions of five globular domain residues of H5 with the corresponding residues in the globular domain of Drosophila H1. The residues at these five positions play important roles in nucleosome binding by either H5 or Drosophila H1. NMR and spin-labeling experiments showed that GH5_pMut bound to the nucleosome off the dyad. We further found that the nucleosome array condensed by either the GH5_pMut or the globular domain of Drosophila H1 displayed a similar sedimentation coefficient, whereas the same nucleosome array condensed by the wild-type globular domain of H5 showed a much larger sedimentation coefficient. Moreover, NMR and spin-labeling results from the study of the nucleosome in complex with the full-length human linker histone H1.0, whose globular domain shares high sequence conservation with the corresponding globular domain of H5, are consistent with an on-dyad binding mode. Taken together, our results suggest that a small number of residues in the globular domain of a linker histone can control its binding location on the nucleosome and higher-order chromatin structure.
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30
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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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31
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Fang H, Wei S, Lee TH, Hayes JJ. Chromatin structure-dependent conformations of the H1 CTD. Nucleic Acids Res 2016; 44:9131-9141. [PMID: 27365050 PMCID: PMC5100576 DOI: 10.1093/nar/gkw586] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/20/2016] [Indexed: 12/17/2022] Open
Abstract
Linker histones are an integral component of chromatin but how these proteins promote assembly of chromatin fibers and higher order structures and regulate gene expression remains an open question. Using Förster resonance energy transfer (FRET) approaches we find that association of a linker histone with oligonucleosomal arrays induces condensation of the intrinsically disordered H1 CTD in a manner consistent with adoption of a defined fold or ensemble of folds in the bound state. However, H1 CTD structure when bound to nucleosomes in arrays is distinct from that induced upon H1 association with mononucleosomes or bare double stranded DNA. Moreover, the H1 CTD becomes more condensed upon condensation of extended nucleosome arrays to the contacting zig-zag form found in moderate salts, but does not detectably change during folding to fully compacted chromatin fibers. We provide evidence that linker DNA conformation is a key determinant of H1 CTD structure and that constraints imposed by neighboring nucleosomes cause linker DNAs to adopt distinct trajectories in oligonucleosomes compared to H1-bound mononucleosomes. Finally, inter-molecular FRET between H1s within fully condensed nucleosome arrays suggests a regular spatial arrangement for the H1 CTD within the 30 nm chromatin fiber.
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Affiliation(s)
- He Fang
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Sijie Wei
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tae-Hee Lee
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
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32
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Staneva D, Georgieva M, Miloshev G. Kluyveromyces lactis genome harbours a functional linker histone encoding gene. FEMS Yeast Res 2016; 16:fow034. [PMID: 27189369 DOI: 10.1093/femsyr/fow034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2016] [Indexed: 11/14/2022] Open
Abstract
Linker histones are essential components of chromatin in eukaryotes. Through interactions with linker DNA and nucleosomes they facilitate folding and maintenance of higher-order chromatin structures and thus delicately modulate gene activity. The necessity of linker histones in lower eukaryotes appears controversial and dubious. Genomic data have shown that Schizosaccharomyces pombe does not possess genes encoding linker histones while Kluyveromyces lactis has been reported to have a pseudogene. Regarding this controversy, we have provided the first direct experimental evidence for the existence of a functional linker histone gene, KlLH1, in K. lactis genome. Sequencing of KlLH1 from both genomic DNA and copy DNA confirmed the presence of an intact open reading frame. Transcription and splicing of the KlLH1 sequence as well as translation of its mRNA have been studied. In silico analysis revealed homology of KlLH1p to the histone H1/H5 protein family with predicted three domain structure characteristic for the linker histones of higher eukaryotes. This strongly proves that the yeast K. lactis does indeed possess a functional linker histone gene thus entailing the evolutionary preservation and significance of linker histones. The nucleotide sequences of KlLH1 are deposited in the GenBank under accession numbers KT826576, KT826577 and KT826578.
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Affiliation(s)
- Dessislava Staneva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
| | - Milena Georgieva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
| | - George Miloshev
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
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33
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Niu Y, Shao Z, Wang H, Yang J, Zhang F, Luo Y, Xu L, Ding Y, Zhao L. LASP1-S100A11 axis promotes colorectal cancer aggressiveness by modulating TGFβ/Smad signaling. Sci Rep 2016; 6:26112. [PMID: 27181092 PMCID: PMC4867635 DOI: 10.1038/srep26112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/26/2016] [Indexed: 01/05/2023] Open
Abstract
LIM and SH3 protein 1(LASP1) can promote colorectal cancer (CRC) progression and metastasis, but the mechanism remains unclear. Here, we show that LASP1 interacts with S100 calcium binding protein A11(S100A11) and enhances its expression in CRC. LASP1-S100A11 axis is essential for TGFβ-mediated epithelial-mesenchymal transition (EMT) and cell aggressive phenotype. Clinically, S100A11 is overexpressed in CRC tissues and localized in both the cytoplasm and the nucleus of CRC cells. Overexpression of S100A11 in cytoplasmic and nuclear subcellular compartments is associated with tumor metastasis and poor prognosis of CRC patients. Introduction of cytoplasmic and nuclear S100A11 promotes aggressive phenotypes of CRC cells in vitro as well as growth and metastasis of CRC xenografts, whereas suppressing S100A11 abrogates these effects. Furthermore, we identify flotillin-1 (FLOT1) and histone H1 as downstream factors for cytoplasmic and nuclear pathway of S100A11, which are required for LASP1-S100A11 axis-mediated EMT and CRC progression. These findings indicate S100A11, combined with LASP1, plays a critical role in promoting CRC metastasis via its subcellular effectors, FLOT1 and histone H1.
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Affiliation(s)
- Ya Niu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ziyun Shao
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hui Wang
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiaqi Yang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Feifei Zhang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yuhao Luo
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Lijun Xu
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yanqing Ding
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Liang Zhao
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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Kalashnikova AA, Rogge RA, Hansen JC. Linker histone H1 and protein-protein interactions. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:455-61. [PMID: 26455956 PMCID: PMC4775371 DOI: 10.1016/j.bbagrm.2015.10.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 09/21/2015] [Accepted: 10/05/2015] [Indexed: 01/11/2023]
Abstract
Linker histones H1 are ubiquitous chromatin proteins that play important roles in chromatin compaction, transcription regulation, nucleosome spacing and chromosome spacing. H1 function in DNA and chromatin structure stabilization is well studied and established. The current paradigm of linker histone mode of function considers all other cellular roles of linker histones to be a consequence from H1 chromatin compaction and repression. Here we review the multiple processes regulated by linker histones and the emerging importance of protein interactions in H1 functioning. We propose a new paradigm which explains the multi functionality of linker histones through linker histones protein interactions as a way to directly regulate recruitment of proteins to chromatin.
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Affiliation(s)
- Anna A Kalashnikova
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Ryan A Rogge
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA.
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35
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Millán-Ariño L, Izquierdo-Bouldstridge A, Jordan A. Specificities and genomic distribution of somatic mammalian histone H1 subtypes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:510-9. [DOI: 10.1016/j.bbagrm.2015.10.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 11/15/2022]
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36
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Pan C, Fan Y. Role of H1 linker histones in mammalian development and stem cell differentiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:496-509. [PMID: 26689747 DOI: 10.1016/j.bbagrm.2015.12.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/09/2015] [Accepted: 12/09/2015] [Indexed: 12/19/2022]
Abstract
H1 linker histones are key chromatin architectural proteins facilitating the formation of higher order chromatin structures. The H1 family constitutes the most heterogeneous group of histone proteins, with eleven non-allelic H1 variants in mammals. H1 variants differ in their biochemical properties and exhibit significant sequence divergence from one another, yet most of them are highly conserved during evolution from mouse to human. H1 variants are differentially regulated during development and their cellular compositions undergo dramatic changes in embryogenesis, gametogenesis, tissue maturation and cellular differentiation. As a group, H1 histones are essential for mouse development and proper stem cell differentiation. Here we summarize our current knowledge on the expression and functions of H1 variants in mammalian development and stem cell differentiation. Their diversity, sequence conservation, complex expression and distinct functions suggest that H1s mediate chromatin reprogramming and contribute to the large variations and complexity of chromatin structure and gene expression in the mammalian genome.
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Affiliation(s)
- Chenyi Pan
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA; The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Yuhong Fan
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA; The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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37
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Liao R, Mizzen CA. Interphase H1 phosphorylation: Regulation and functions in chromatin. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:476-85. [PMID: 26657617 DOI: 10.1016/j.bbagrm.2015.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/25/2022]
Abstract
Many metazoan cell types differentially express multiple non-allelic amino acid sequence variants of histone H1. Although early work revealed that H1 variants, collectively, are phosphorylated during interphase and mitosis, differences between individual H1 variants in the sites they possess for mitotic and interphase phosphorylation have been elucidated only relatively recently. Here, we review current knowledge on the regulation and function of interphase H1 phosphorylation, with a particular emphasis on how differences in interphase phosphorylation among the H1 variants of mammalian cells may enable them to have differential effects on transcription and other chromatin processes.
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Affiliation(s)
- Ruiqi Liao
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, USA
| | - Craig A Mizzen
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, USA; Institute for Genomic Biology, University of Illinois at Urbana Champaign, USA.
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38
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Parseghian MH. What is the role of histone H1 heterogeneity? A functional model emerges from a 50 year mystery. AIMS BIOPHYSICS 2015; 2:724-772. [PMID: 31289748 PMCID: PMC6615755 DOI: 10.3934/biophy.2015.4.724] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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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39
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Bednar J, Hamiche A, Dimitrov S. H1-nucleosome interactions and their functional implications. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:436-43. [PMID: 26477489 DOI: 10.1016/j.bbagrm.2015.10.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 01/13/2023]
Abstract
Linker histones are three domain proteins and consist of a structured (globular) domain, flanked by two likely non-structured NH2- and COOH-termini. The binding of the linker histones to the nucleosome was characterized by different methods in solution. Apparently, the globular domain interacts with the linker DNA and the nucleosome dyad, while the binding of the large and rich in lysines COOH-terminus results in "closing" the linker DNA of the nucleosome and the formation of the "stem" structure. What is the mode of binding of the linker histones within the chromatin fiber remains still elusive. Nonetheless, it is clear that linker histones are essential for both the assembly and maintenance of the condensed chromatin fiber. Interestingly, linker histones are post-translationally modified and how this affects both their binding to chromatin and functions is now beginning to emerge. In addition, linker histones are highly mobile in vivo, but not in vitro. No explanation of this finding is reported for the moment. The higher mobility of the linker histones should, however, have strong impact on their function. Linker histones plays an important role in gene expression regulation and other chromatin related process and their function is predominantly regulated by their posttranslational modifications. However, the detailed mechanism how the linker histones do function remains still not well understood despite numerous efforts. Here we will summarize and analyze the data on the linker histone binding to the nucleosome and the chromatin fiber and will discuss its functional consequences.
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Affiliation(s)
- Jan Bednar
- Université de Grenoble Alpes/CNRS, Laboratoire Interdisciplinaire de Physique, UMR 5588, 140 rue de la Physique, B.P. 87, St. Martin d'Heres, F-38402, France.
| | - Ali Hamiche
- Equipe labellisée Ligue contre le Cancer, Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UDS, CNRS, INSERM, 1 rue Laurent Fries, B.P. 10142, 67404 Illkirch Cedex, France
| | - Stefan Dimitrov
- INSERM/UJF, Institut Albert Bonniot, U823, Site Santé-BP 170, 38042 Grenoble Cedex 9, France
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40
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Hergeth SP, Schneider R. The H1 linker histones: multifunctional proteins beyond the nucleosomal core particle. EMBO Rep 2015; 16:1439-53. [PMID: 26474902 DOI: 10.15252/embr.201540749] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/14/2015] [Indexed: 12/21/2022] Open
Abstract
The linker histone H1 family members are a key component of chromatin and bind to the nucleosomal core particle around the DNA entry and exit sites. H1 can stabilize both nucleosome structure and higher-order chromatin architecture. In general, H1 molecules consist of a central globular domain with more flexible tail regions at both their N- and C-terminal ends. The existence of multiple H1 subtypes and a large variety of posttranslational modifications brings about a considerable degree of complexity and makes studying this protein family challenging. Here, we review recent progress in understanding the function of linker histones and their subtypes beyond their role as merely structural chromatin components. We summarize current findings on the role of H1 in heterochromatin formation, transcriptional regulation and embryogenesis with a focus on H1 subtypes and their specific modifications.
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Affiliation(s)
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, Inserm U964, Université de Strasbourg, Illkirch, France
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41
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Histone H1: Lessons from Drosophila. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:526-32. [PMID: 26361208 DOI: 10.1016/j.bbagrm.2015.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/28/2015] [Accepted: 09/02/2015] [Indexed: 01/02/2023]
Abstract
Eukaryotic genomes are structured in the form of chromatin with the help of a set of five small basic proteins, the histones. Four of them are highly conserved through evolution, form the basic unit of the chromatin, the nucleosome, and have been intensively studied and are well characterized. The fifth histone, histone H1, adds to this basic structure through its interaction at the entry/exit site of DNA in the nucleosome and makes an essential contribution to the higher order folding of the chromatin fiber. Histone H1 is the less conserved histone and the less known of them. Though for long time considered as a general repressor of gene expression, recent studies in Drosophila have rejected this view and have contributed to uncover important functions on genome stability and development. Here we present some of the most recent data obtained in the Drosophila model system and discuss how the lessons learnt in these studies compare and could be applied to all other eukaryotes.
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42
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Izzo A, Schneider R. The role of linker histone H1 modifications in the regulation of gene expression and chromatin dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:486-95. [PMID: 26348411 DOI: 10.1016/j.bbagrm.2015.09.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/07/2015] [Accepted: 09/02/2015] [Indexed: 12/27/2022]
Abstract
BACKGROUND Linker histone H1 is a structural component of chromatin. It exists as a family of related proteins known as variants and/or subtypes. H1.1, H1.2, H1.3, H1.4 and H1.5 are present in most somatic cells, whereas other subtypes are mainly expressed in more specialized cells. SCOPE OF REVIEW H1 subtypes have been shown to have unique functions in chromatin structure and dynamics. This can occur at least in part via specific post-translational modifications of distinct H1 subtypes. However, while core histone modifications have been extensively studied, our knowledge of H1 modifications and their molecular functions has remained for a long time limited to phosphorylation. In this review we discuss the current state of knowledge of linker histone H1 modifications and where possible highlight functional differences in the modifications of distinct H1 subtypes. MAJOR CONCLUSIONS AND GENERAL SIGNIFICANCE H1 histones are intensely post-translationally modified. These modifications are located in the N- and C-terminal tails as well as within the globular domain. Recently, advanced mass spectrometrical analysis revealed a large number of novel histone H1 subtype specific modification sites and types. H1 modifications include phosphorylation, acetylation, methylation, ubiquitination, and ADP ribosylation. They are involved in the regulation of all aspects of linker histone functions, however their mechanism of action is often only poorly understood. Therefore systematic functional characterization of H1 modifications will be necessary in order to better understand their role in gene regulation as well as in higher-order chromatin structure and dynamics.
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Affiliation(s)
- Annalisa Izzo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67404 Illkirch, France
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67404 Illkirch, France.
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Abstract
Linker histones bind to the nucleosome and regulate the structure of chromatin and gene expression. Despite more than three decades of effort, the structural basis of nucleosome recognition by linker histones remains elusive. Here, we report the crystal structure of the globular domain of chicken linker histone H5 in complex with the nucleosome at 3.5 Å resolution, which is validated using nuclear magnetic resonance spectroscopy. The globular domain sits on the dyad of the nucleosome and interacts with both DNA linkers. Our structure integrates results from mutation analyses and previous cross-linking and fluorescence recovery after photobleach experiments, and it helps resolve the long debate on structural mechanisms of nucleosome recognition by linker histones. The on-dyad binding mode of the H5 globular domain is different from the recently reported off-dyad binding mode of Drosophila linker histone H1. We demonstrate that linker histones with different binding modes could fold chromatin to form distinct higher-order structures.
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44
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Brush GS. Evidence that histone H1 is dispensable for proper meiotic recombination in budding yeast. BMC Res Notes 2015; 8:275. [PMID: 26122007 PMCID: PMC4486124 DOI: 10.1186/s13104-015-1246-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/17/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone H1, referred to as the linker histone, associates with the nucleosome core particle. While there is indication that the budding yeast version of histone H1 (Hho1) contributes to regulation of chromatin structure and certain chromatin-related processes, such as DNA double-strand break repair, cells lacking Hho1 are healthy and display subtle phenotypes. A recent report has revealed that Hho1 is required for optimal sporulation. The studies described here were conducted to determine whether Hho1 influences meiotic recombination, an event that occurs during sporulation, involves generation and repair of DNA double-strand breaks, and is critical for spore viability. FINDINGS Through tetrad analysis, cells with or without Hho1 were compared for meiotic reciprocal recombination events within several chromosome XV intervals. Parameters investigated included crossover frequency (genetic map distance) and crossover interference. No significant differences were detected between the two cell types. In agreement with earlier studies, spore viability was not affected by Hho1 absence. CONCLUSION These data suggest that complete absence of Hho1 from chromatin does not affect reciprocal recombination between homologous chromosomes during meiosis. Therefore, the basal level of Hho1 that remains after its reported depletion early in meiosis is unlikely to be important for regulating recombination. Furthermore, the subsequent accumulation of Hho1 as the haploid products mature does not appear to be crucial for spore viability.
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Affiliation(s)
- George S Brush
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA. .,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA.
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45
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Glycation of H1 Histone by 3-Deoxyglucosone: Effects on Protein Structure and Generation of Different Advanced Glycation End Products. PLoS One 2015; 10:e0130630. [PMID: 26121680 PMCID: PMC4487796 DOI: 10.1371/journal.pone.0130630] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/21/2015] [Indexed: 11/19/2022] Open
Abstract
Advanced glycation end products (AGEs) culminate from the non-enzymatic reaction between a free carbonyl group of a reducing sugar and free amino group of proteins. 3-deoxyglucosone (3-DG) is one of the dicarbonyl species that rapidly forms several protein-AGE complexes that are believed to be involved in the pathogenesis of several diseases, particularly diabetic complications. In this study, the generation of AGEs (Nε-carboxymethyl lysine and pentosidine) by 3-DG in H1 histone protein was characterized by evaluating extent of side chain modification (lysine and arginine) and formation of Amadori products as well as carbonyl contents using several physicochemical techniques. Results strongly suggested that 3-DG is a potent glycating agent that forms various intermediates and AGEs during glycation reactions and affects the secondary structure of the H1 protein. Structural changes and AGE formation may influence the function of H1 histone and compromise chromatin structures in cases of secondary diabetic complications.
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46
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Cutter AR, Hayes JJ. A brief review of nucleosome structure. FEBS Lett 2015; 589:2914-22. [PMID: 25980611 DOI: 10.1016/j.febslet.2015.05.016] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 04/29/2015] [Accepted: 05/05/2015] [Indexed: 12/23/2022]
Abstract
The nucleosomal subunit organization of chromatin provides a multitude of functions. Nucleosomes elicit an initial ∼7-fold linear compaction of genomic DNA. They provide a critical mechanism for stable repression of genes and other DNA-dependent activities by restricting binding of trans-acting factors to cognate DNA sequences. Conversely they are engineered to be nearly meta-stable and disassembled (and reassembled) in a facile manner to allow rapid access to the underlying DNA during processes such as transcription, replication and DNA repair. Nucleosomes protect the genome from DNA damaging agents and provide a lattice onto which a myriad of epigenetic signals are deposited. Moreover, vast strings of nucleosomes provide a framework for assembly of the chromatin fiber and higher-order chromatin structures. Thus, in order to provide a foundation for understanding these functions, we present a review of the basic elements of nucleosome structure and stability, including the association of linker histones.
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Affiliation(s)
- Amber R Cutter
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, United States
| | - Jeffrey J Hayes
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, United States.
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47
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Bailly A, Perrin A, Bou Malhab LJ, Pion E, Larance M, Nagala M, Smith P, O'Donohue MF, Gleizes PE, Zomerdijk J, Lamond AI, Xirodimas DP. The NEDD8 inhibitor MLN4924 increases the size of the nucleolus and activates p53 through the ribosomal-Mdm2 pathway. Oncogene 2015; 35:415-26. [PMID: 25867069 DOI: 10.1038/onc.2015.104] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 02/10/2015] [Accepted: 03/03/2015] [Indexed: 12/19/2022]
Abstract
The ubiquitin-like molecule NEDD8 is essential for viability, growth and development, and is a potential target for therapeutic intervention. We found that the small molecule inhibitor of NEDDylation, MLN4924, alters the morphology and increases the surface size of the nucleolus in human and germline cells of Caenorhabditis elegans in the absence of nucleolar fragmentation. SILAC proteomics and monitoring of rRNA production, processing and ribosome profiling shows that MLN4924 changes the composition of the nucleolar proteome but does not inhibit RNA Pol I transcription. Further analysis demonstrates that MLN4924 activates the p53 tumour suppressor through the RPL11/RPL5-Mdm2 pathway, with characteristics of nucleolar stress. The study identifies the nucleolus as a target of inhibitors of NEDDylation and provides a mechanism for p53 activation upon NEDD8 inhibition. It also indicates that targeting the nucleolar proteome without affecting nucleolar transcription initiates the required signalling events for the control of cell cycle regulators.
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Affiliation(s)
- A Bailly
- Centre de Recherche de Biochimie Macromoléculaire-UMR 5237, CNRS, Montpellier, France
| | - A Perrin
- Centre de Recherche de Biochimie Macromoléculaire-UMR 5237, CNRS, Montpellier, France
| | - L J Bou Malhab
- Centre de Recherche de Biochimie Macromoléculaire-UMR 5237, CNRS, Montpellier, France
| | - E Pion
- Centre de Recherche de Biochimie Macromoléculaire-UMR 5237, CNRS, Montpellier, France
| | - M Larance
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland/UK
| | - M Nagala
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland/UK
| | - P Smith
- Millennium Pharmaceuticals Inc., Cambridge, MA, USA
| | - M-F O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, UMR CNRS 5099, Bâtiment IBCG, Toulouse, France
| | - P-E Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, UMR CNRS 5099, Bâtiment IBCG, Toulouse, France
| | - J Zomerdijk
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland/UK
| | - A I Lamond
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland/UK
| | - D P Xirodimas
- Centre de Recherche de Biochimie Macromoléculaire-UMR 5237, CNRS, Montpellier, France
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48
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Mayor R, Izquierdo-Bouldstridge A, Millán-Ariño L, Bustillos A, Sampaio C, Luque N, Jordan A. Genome distribution of replication-independent histone H1 variants shows H1.0 associated with nucleolar domains and H1X associated with RNA polymerase II-enriched regions. J Biol Chem 2015; 290:7474-91. [PMID: 25645921 DOI: 10.1074/jbc.m114.617324] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Unlike core histones, the linker histone H1 family is more evolutionarily diverse, and many organisms have multiple H1 variants or subtypes. In mammals, the H1 family includes seven somatic H1 variants; H1.1 to H1.5 are expressed in a replication-dependent manner, whereas H1.0 and H1X are replication-independent. Using ChIP-sequencing data and cell fractionation, we have compared the genomic distribution of H1.0 and H1X in human breast cancer cells, in which we previously observed differential distribution of H1.2 compared with the other subtypes. We have found H1.0 to be enriched at nucleolus-associated DNA repeats and chromatin domains, whereas H1X is associated with coding regions, RNA polymerase II-enriched regions, and hypomethylated CpG islands. Further, H1X accumulates within constitutive or included exons and retained introns and toward the 3' end of expressed genes. Inducible H1X knockdown does not affect cell proliferation but dysregulates a subset of genes related to cell movement and transport. In H1X-depleted cells, the promoters of up-regulated genes are not occupied specifically by this variant, have a lower than average H1 content, and, unexpectedly, do not form an H1 valley upon induction. We conclude that H1 variants are not distributed evenly across the genome and may participate with some specificity in chromatin domain organization or gene regulation.
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Affiliation(s)
- Regina Mayor
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Andrea Izquierdo-Bouldstridge
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Lluís Millán-Ariño
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Alberto Bustillos
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Cristina Sampaio
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Neus Luque
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Albert Jordan
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
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49
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Liu J, Wang H, Ma F, Xu D, Chang Y, Zhang J, Wang J, Zhao M, Lin C, Huang C, Qian H, Zhan Q. MTA1 regulates higher-order chromatin structure and histone H1-chromatin interaction in-vivo. Mol Oncol 2015; 9:218-35. [PMID: 25205035 PMCID: PMC5528677 DOI: 10.1016/j.molonc.2014.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/04/2014] [Accepted: 08/18/2014] [Indexed: 11/27/2022] Open
Abstract
In the current study, for the first time, we found that metastasis-associated gene 1 (MTA1) was a higher-order chromatin structure organizer that decondenses the interphase chromatin and mitotic chromosomes. MTA1 interacts dynamically with nucleosomes during the cell cycle progression, prominently contributing to the mitotic chromatin/chromosome structure transitions at both prophase and telophase. We showed that the decondensation of interphase chromatin by MTA1 was independent of Mi-2 chromatin remodeling activity. H1 was reported to stabilize the compact higher-order chromatin structure through its interaction with DNA. Our data showed that MTA1 caused a reduced H1-chromatin interaction in-vivo. Moreover, the dynamic MTA1-chromatin interaction in the cell cycle contributed to the periodical H1-chromatin interaction, which in turn modulated chromatin/chromosome transitions. Although MTA1 drove a global decondensation of chromatin structure, it changed the expression of only a small proportion of genes. After MTA1 overexpression, the up-regulated genes were distributed in clusters along with down-regulated genes on chromosomes at parallel frequencies.
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Affiliation(s)
- Jian Liu
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China; Medical Research Center, Beijing ChaoYang Hospital, Capital Medical University, Beijing 100020, China
| | - Haijuan Wang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Fei Ma
- Department of Medical Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, State Key Laboratory of Molecular Oncology, Beijing 100021, China
| | - Dongkui Xu
- Department of Abdominal Surgery, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, State Key Laboratory of Molecular Oncology, Beijing 100021, China
| | - Yanan Chang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Jinlong Zhang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Jia Wang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Mei Zhao
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Chen Lin
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Changzhi Huang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China.
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China.
| | - Qimin Zhan
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China.
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50
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Wang W, Wang Y, Du Y, Zhao Z, Zhu X, Jiang X, Shu Z, Yin Y, Li X. Overexpression of Camellia sinensis H1 histone gene confers abiotic stress tolerance in transgenic tobacco. PLANT CELL REPORTS 2014; 33:1829-41. [PMID: 25063323 DOI: 10.1007/s00299-014-1660-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/07/2014] [Accepted: 07/14/2014] [Indexed: 05/08/2023]
Abstract
KEY MESSAGE Overexpression of CsHis in tobacco promoted chromatin condensation, but did not affect the phenotype. It also conferred tolerance to low-temperature, high-salinity, ABA, drought and oxidative stress in transgenic tobacco. H1 histone, as a major structural protein of higher-order chromatin, is associated with stress responses in plants. Here, we describe the functions of the Camellia sinensis H1 Histone gene (CsHis) to illustrate its roles in plant responses to stresses. Subcellular localization and prokaryotic expression assays showed that the CsHis protein is localized in the nucleus, and its molecular size is approximately 22.5 kD. The expression levels of CsHis in C. sinensis leaves under various conditions were investigated by qRT-PCR, and the results indicated that CsHis was strongly induced by various abiotic stresses such as low-temperature, high-salinity, ABA, drought and oxidative stress. Overexpression of CsHis in tobacco (Nicotiana tabacum) promoted chromatin condensation, while there were almost no changes in the growth and development of transgenic tobacco plants. Phylogenetic analysis showed that CsHis belongs to the H1C and H1D variants of H1 histones, which are stress-induced variants and not the key variants required for growth and development. Stress tolerance analysis indicated that the transgenic tobacco plants exhibited higher tolerance than the WT plants upon exposure to various abiotic stresses; the transgenic plants displayed reduced wilting and senescence and exhibited greater net photosynthetic rate (Pn), stomatal conductance (Gs) and maximal photochemical efficiency (Fv/Fm) values. All the above results suggest that CsHis is a stress-induced gene and that its overexpression improves the tolerance to various abiotic stresses in the transgenic tobacco plants, possibly through the maintenance of photosynthetic efficiency.
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Affiliation(s)
- Weidong Wang
- Tea Science Research Institute, Nanjing Agricultural University, Nanjing, 210095, China,
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