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González-Alvarez ME, Inyang I, Keating AF. Exposure to 7,12-dimethylbenz[a]anthracene impacts ovarian DNA damage sensing and repair proteins differently in lean and obese female mice and weight loss may mitigate obesity-induced ovarian dysfunction. Toxicol Appl Pharmacol 2024; 486:116930. [PMID: 38626870 DOI: 10.1016/j.taap.2024.116930] [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: 02/29/2024] [Revised: 03/28/2024] [Accepted: 04/10/2024] [Indexed: 05/21/2024]
Abstract
Obesity impairs oocyte quality, fertility, pregnancy maintenance, and is associated with offspring birth defects. The model ovotoxicant, 7,12-dimethylbenz[a]anthracene (DMBA), causes ovarian DNA damage and follicle loss. Both DMBA-induced chemical biotransformation and the DNA damage response are partially attenuated in obese relative to lean female mice but whether weight loss could improve the DNA damage response to DMBA exposure has not been explored. Thus, at six weeks of age, C57BL/6 J female mice were divided in three groups: 1) Lean (L; n = 20) fed a chow diet for 12 weeks, 2) obese (O; n = 20) fed a high fat high sugar (HFHS) diet for 12 weeks and, 3) slim-down (S; n = 20). The S group was fed with HFHS diet for 7 weeks until attaining a higher body relative to L mice on week 7.5 and switched to a chow diet for 5 weeks to achieve weight loss. Mice then received either corn oil (CT) or DMBA (D; 1 mg/kg) for 7 d via intraperitoneal injection (n = 10/treatment). Obesity increased (P < 0.05) kidney and spleen weight, and DMBA decreased uterine weight (P < 0.05). Ovarian weight was reduced (P < 0.05) in S mice, but DMBA exposure increased ovary weight in the S mice. LC-MS/MS identified 18, 64, and 7 ovarian proteins as altered (P < 0.05) by DMBA in the L, S and O groups, respectively. In S and O mice, 24 and 8 proteins differed, respectively, from L mice. These findings support weight loss as a strategy to modulate the ovarian genotoxicant response.
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Affiliation(s)
| | - Imaobong Inyang
- Department of Animal Science, Iowa State University, United States of America
| | - Aileen F Keating
- Department of Animal Science, Iowa State University, United States of America.
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2
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Singh R, Rathore AS, Dilnashin H, Keshri PK, Gupta NK, Prakash SAS, Zahra W, Singh S, Singh SP. HAT and HDAC: Enzyme with Contradictory Action in Neurodegenerative Diseases. Mol Neurobiol 2024:10.1007/s12035-024-04115-6. [PMID: 38587698 DOI: 10.1007/s12035-024-04115-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 03/08/2024] [Indexed: 04/09/2024]
Abstract
In view of the increasing risk of neurodegenerative diseases, epigenetics plays a fundamental role in the field of neuroscience. Several modifications have been studied including DNA methylation, histone acetylation, histone phosphorylation, etc. Histone acetylation and deacetylation regulate gene expression, and the regular activity of histone acetyltransferases (HATs) and histone deacetylases (HDACs) provides regulatory stages for gene expression and cell cycle. Imbalanced homeostasis in these enzymes causes a detrimental effect on neurophysiological function. Intriguingly, epigenetic remodelling via histone acetylation in certain brain areas has been found to play a key role in the neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease. It has been demonstrated that a number of HATs have a role in crucial brain processes such regulating neuronal plasticity and memory formation. The most recent therapeutic methods involve the use of small molecules known as histone deacetylase (HDAC) inhibitors that antagonize HDAC activity thereby increase acetylation levels in order to prevent the loss of HAT function in neurodegenerative disorders. The target specificity of the HDAC inhibitors now in use raises concerns about their applicability, despite the fact that this strategy has demonstrated promising therapeutic outcomes. The aim of this review is to summarize the cross-linking between histone modification and its regulation in the pathogenesis of neurological disorders. Furthermore, these findings also support the notion of new pharmacotherapies that target particular areas of the brain using histone deacetylase inhibitors.
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Affiliation(s)
- Richa Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi-221005 (U.P.), India
| | - Aaina Singh Rathore
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi-221005 (U.P.), India
| | - Hagera Dilnashin
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi-221005 (U.P.), India
| | - Priyanka Kumari Keshri
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi-221005 (U.P.), India
| | - Nitesh Kumar Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi-221005 (U.P.), India
| | - Singh Ankit Satya Prakash
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi-221005 (U.P.), India
| | - Walia Zahra
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi-221005 (U.P.), India
| | - Shekhar Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi-221005 (U.P.), India
| | - Surya Pratap Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi-221005 (U.P.), India.
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3
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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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Song L, Soomro MA, Wang L, Song Y, Hu G. Identification and functional analysis of histone 1.2-like in red sea bream (Pagrus major). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 138:104529. [PMID: 36087785 DOI: 10.1016/j.dci.2022.104529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Histone H1 acts as an essential chromatin component and participates in the formation of higher chromatin structures together with core histones. In addition, H1 also has important functions in physiological processes such as gene expression regulation, DNA repair, and the immune response. In this study, the histone homologous protein Pm-H1.2-like was identified from the transcriptome database of Pagrus major we studied previously. Conservatism of evolution was investigated by sequence alignment and phylogenetic analysis. Transcripts of Pm-H1.2-like were detected in P. major tissues. The highest expression level was found in gill and skin tissues. Consistent with the data from the transcriptome database, we observed that the expression of Pm-H1.2-like was rapidly induced in nonspecific cytotoxic cells (NCCs) infected with inactivated Vibrio anguillarum. Gene silencing of Pm-H1.2-like by RNAi significantly suppressed the expression of NK-lysin and GZMB in NCCs at 12 h after pathogen stimulation, but had no significant effect on IFN-γ expression. Next, we obtained the fusion proteins rPm-H1.2-like and rPm-H1.2-like (36-80) through prokaryotic expression. ELISA showed that rPm-H1.2-like bound to oligonucleotide (ODN) in a concentration-dependent manner, while no binding activity of rPm-H1.2-like (36-80) with ODN was observed. This study confirmed that Pm-H1.2-like actively participates in the immune response of NCCs to bacterial infection, deepening the understanding of the immune features of histone H1 in fish.
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Affiliation(s)
- Lianfei Song
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Maqsood Ahmed Soomro
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Lingshu Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Yuting Song
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Guobin Hu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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5
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The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response. Genes (Basel) 2022; 14:genes14010112. [PMID: 36672853 PMCID: PMC9859207 DOI: 10.3390/genes14010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
The functioning of the eukaryotic cell genome is mediated by sophisticated protein-nucleic-acid complexes, whose minimal structural unit is the nucleosome. After the damage to genomic DNA, repair proteins need to gain access directly to the lesion; therefore, the initiation of the DNA damage response inevitably leads to local chromatin reorganisation. This review focuses on the possible involvement of PARP1, as well as proteins acting nucleosome compaction, linker histone H1 and non-histone chromatin protein HMGB1. The polymer of ADP-ribose is considered the main regulator during the development of the DNA damage response and in the course of assembly of the correct repair complex.
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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: 4] [Impact Index Per Article: 2.0] [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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Jacob C, Kitagawa A, Signoretti C, Dzieciatkowska M, D'Alessandro A, Gupte A, Hossain S, D'Addario CA, Gupte R, Gupte SA. Mediterranean G6PD variant mitigates expression of DNA methyltransferases and right heart pressure in experimental model of pulmonary hypertension. J Biol Chem 2022; 298:102691. [PMID: 36372233 PMCID: PMC9731845 DOI: 10.1016/j.jbc.2022.102691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation potentially contributes to the pathogenesis of pulmonary hypertension (PH). However, the role of DNA methyltransferases (DNMTs: 1, 3a, and 3b), the epigenetic writers, in modulating DNA methylation observed in PH remains elusive. Our objective was to determine DNMT activity and expression in the lungs of experimental rat models of PH. Because the activity of DNMTs is metabolically driven, another objective was to determine the role of glucose-6-phosphate dehydrogenase (G6PD) in regulating DNMT expression and activity in the lungs of novel loss-of-function Mediterranean G6PD variant (G6PDS188F) rats. As outlined for modeling PH, rats injected with sugen5416 (SU) were placed in a hypoxia (Hx) chamber set at 10% oxygen for 3 weeks and then returned to normoxia (Nx) for 5 weeks (SU/Hx/Nx). Rats kept in atmospheric oxygen and treated with SU were used as controls. We assessed the activity and expression of DNMTs in the lungs of rats exposed to SU/Hx/Nx. WT rats exposed to SU/Hx/Nx developed hypertension and exhibited increased DNMT activity and Dnmt1 and Dnmt3b expression. In G6PDS188F rats, which developed less of a SU/Hx/Nx-induced increase in right ventricle pressure and hypertrophy than WT rats, we observed a diminished increase in expression and activity of DNMTs, DNA hypomethylation, increased histone acetylation and methylation, and increased expression of genes encoding NOS3 and SOD2-vascular-protective proteins. Collectively, increased DNMTs contribute to reduced expression of protective genes and to the pathogenesis of SU/Hx/Nx-induced experimental PH. Notably, G6PD regulates the expression of DNMTs and protective proteins in the lungs of hypertensive rats.
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Affiliation(s)
- Christina Jacob
- Department of Pharmacology, New York Medical College, Valhalla, New York, USA
| | - Atsushi Kitagawa
- Department of Pharmacology, New York Medical College, Valhalla, New York, USA
| | | | - Monika Dzieciatkowska
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado Denver - Anschutz Medical Campus, Aurora, Colorado, USA
| | - Angelo D'Alessandro
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado Denver - Anschutz Medical Campus, Aurora, Colorado, USA
| | - Aaditya Gupte
- Department of Pharmacology, New York Medical College, Valhalla, New York, USA
| | - Shakib Hossain
- Department of Pharmacology, New York Medical College, Valhalla, New York, USA
| | | | - Rakhee Gupte
- Department of Pharmacology, New York Medical College, Valhalla, New York, USA
| | - Sachin A Gupte
- Department of Pharmacology, New York Medical College, Valhalla, New York, USA.
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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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9
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Ezazi-Toroghi S, Salarinejad S, Kamkar-Vatanparast M, Mokaberi P, Amiri-Tehranizadeh Z, Saberi MR, Chamani J. Understanding the binding behavior of Malathion with calf thymus DNA by spectroscopic, cell viability and molecular dynamics simulation techniques: binary and ternary systems comparison. J Biomol Struct Dyn 2022; 41:4180-4193. [PMID: 35437091 DOI: 10.1080/07391102.2022.2064914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The interaction between calf thymus DNA (ctDNA) and Malathion in the absence and presence of Histone 1 has been enquired by the means of spectroscopic, viscometry, molecular modeling, and cell viability assay techniques. Malathion is capable of quenching the fluorescence of ct DNA in the absence and presence of H1. The binding constants of Malathion-ctDNA complex in the absence of H1 have been calculated to be 6.62 × 104, 4.31 × 104 and 1.93 × 104 M-1 at 298, 303, and 308 K, respectively that revealed static quenching in complex formation. The observed negative values of enthalpy and entropy changes indicate that the main binding interaction forces were van der Waals force and hydrogen bonding. The binding constant between Malathion and single-stranded ctDNA (ss ctDNA) seemed to be much weaker than that of Malathion and double-stranded ctDNA (ds ctDNA). Furthermore, Malathion can induce detectable alterations in the CD spectrum of ctDNA, along with changes in its viscosity. In the presence of H1, fluorescence quenching of ctDNA-Malathion complex displays dynamic behavior and binding constants were perceived to be 1.66 × 104, 2.93 × 104 and 5.77 × 104 M-1 at 298, 303, and 308 K, respectively. The different of interaction behavior between ctDNA and Malathion in the absence and presence of H1 clearly revealed H1 role in the complex formation and forces change between ctDNA and Malathion. The positive values of enthalpy and entropy changes have suggested that binding process is primarily driven by hydrophobic interactions. The tendency to interact with ss ctDNA, reduced viscosity have designated that the Malathion bound to ctDNA in the presence of H1 is groove binding. The results of molecular docking and molecular dynamics simulation also confirmed potent interactions between Malathion and the macromolecules in the binary and ternary systems.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sara Ezazi-Toroghi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Shadi Salarinejad
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | | | - Parisa Mokaberi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri-Tehranizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Saberi
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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10
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Polymyxin Induces Significant Transcriptomic Perturbations of Cellular Signalling Networks in Human Lung Epithelial Cells. Antibiotics (Basel) 2022; 11:antibiotics11030307. [PMID: 35326770 PMCID: PMC8944768 DOI: 10.3390/antibiotics11030307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Inhaled polymyxins are increasingly used to treat pulmonary infections caused by multidrug-resistant Gram-negative pathogens. We have previously shown that apoptotic pathways, autophagy and oxidative stress are involved in polymyxin-induced toxicity in human lung epithelial cells. In the present study, we employed human lung epithelial cells A549 treated with polymyxin B as a model to elucidate the complex interplay of multiple signalling networks underpinning cellular responses to polymyxin toxicity. Polymyxin B induced toxicity (1.0 mM, 24 h) in A549 cells was assessed by flow cytometry and transcriptomics was performed using microarray. Polymyxin B induced cell death was 19.0 ± 4.2% at 24 h. Differentially expressed genes (DEGs) between the control and polymyxin B treated cells were identified with Student’s t-test. Pathway analysis was conducted with KEGG and Reactome and key hub genes related to polymyxin B induced toxicity were examined using the STRING database. In total we identified 899 DEGs (FDR < 0.01), KEGG and Reactome pathway analyses revealed significantly up-regulated genes related to cell cycle, DNA repair and DNA replication. NF-κB and nucleotide-binding oligomerization domain-like receptor (NOD) signalling pathways were identified as markedly down-regulated genes. Network analysis revealed the top 5 hub genes (i.e., degree) affected by polymyxin B treatment were PLK1(48), CDK20 (46), CCNA2 (42), BUB1 (40) and BUB1B (37). Overall, perturbations of cell cycle, DNA damage and pro-inflammatory NF-κB and NOD-like receptor signalling pathways play key roles in polymyxin-induced toxicity in human lung epithelial cells. Noting that NOD-like receptor signalling represents a group of key sensors for microorganisms and damage in the lung, understanding the mechanism of polymyxin-induced pulmonary toxicity will facilitate the optimisation of polymyxin inhalation therapy in patients.
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11
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Analysis of histone variant constraint and tissue expression suggests five potential novel human disease genes: H2AFY2, H2AFZ, H2AFY, H2AFV, H1F0. Hum Genet 2022; 141:1409-1421. [DOI: 10.1007/s00439-022-02432-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/07/2022] [Indexed: 11/26/2022]
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12
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Morris OM, Torpey JH, Isaacson RL. Intrinsically disordered proteins: modes of binding with emphasis on disordered domains. Open Biol 2021; 11:210222. [PMID: 34610267 PMCID: PMC8492171 DOI: 10.1098/rsob.210222] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Our notions of protein function have long been determined by the protein structure-function paradigm. However, the idea that protein function is dictated by a prerequisite complementarity of shapes at the binding interface is becoming increasingly challenged. Interactions involving intrinsically disordered proteins (IDPs) have indicated a significant degree of disorder present in the bound state, ranging from static disorder to complete disorder, termed 'random fuzziness'. This review assesses the anatomy of an IDP and relates how its intrinsic properties permit promiscuity and allow for the various modes of interaction. Furthermore, a mechanistic overview of the types of disordered domains is detailed, while also relating to a recent example and the kinetic and thermodynamic principles governing its formation.
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Affiliation(s)
- Owen Michael Morris
- Department of Chemistry, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - James Hilary Torpey
- Department of Chemistry, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Rivka Leah Isaacson
- Department of Chemistry, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
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13
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Höllmüller E, Greiner K, Kienle SM, Scheffner M, Marx A, Stengel F. Interactome of Site-Specifically Acetylated Linker Histone H1. J Proteome Res 2021; 20:4443-4451. [PMID: 34351766 DOI: 10.1021/acs.jproteome.1c00396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Linker histone H1 plays a key role in chromatin organization and maintenance, yet our knowledge of the regulation of H1 functions by post-translational modifications is rather limited. In this study, we report on the generation of site-specifically mono- and di-acetylated linker histone H1.2 by genetic code expansion. We used these modified histones to identify and characterize the acetylation-dependent cellular interactome of H1.2 by affinity purification mass spectrometry and show that site-specific acetylation results in overlapping but distinct groups of interacting partners. Among these, we find multiple translational initiation factors and transcriptional regulators such as the NAD+-dependent deacetylase SIRT1, which we demonstrate to act on acetylated H1.2. Taken together, our data suggest that site-specific acetylation of H1.2 plays a role in modulating protein-protein interactions.
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14
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Ko EK, Capell BC. Methyltransferases in the Pathogenesis of Keratinocyte Cancers. Cancers (Basel) 2021; 13:cancers13143402. [PMID: 34298617 PMCID: PMC8304454 DOI: 10.3390/cancers13143402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 12/13/2022] Open
Abstract
Recent evidence suggests that the disruption of gene expression by alterations in DNA, RNA, and histone methylation may be critical contributors to the pathogenesis of keratinocyte cancers (KCs), made up of basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC), which collectively outnumber all other human cancers combined. While it is clear that methylation modifiers are frequently dysregulated in KCs, the underlying molecular and mechanistic changes are only beginning to be understood. Intriguingly, it has recently emerged that there is extensive cross-talk amongst these distinct methylation processes. Here, we summarize and synthesize the latest findings in this space and highlight how these discoveries may uncover novel therapeutic approaches for these ubiquitous cancers.
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Affiliation(s)
- Eun Kyung Ko
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Brian C. Capell
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA;
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence:
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15
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Höllmüller E, Geigges S, Niedermeier ML, Kammer KM, Kienle SM, Rösner D, Scheffner M, Marx A, Stengel F. Site-specific ubiquitylation acts as a regulator of linker histone H1. Nat Commun 2021; 12:3497. [PMID: 34108453 PMCID: PMC8190259 DOI: 10.1038/s41467-021-23636-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 05/03/2021] [Indexed: 01/05/2023] Open
Abstract
Decoding the role of histone posttranslational modifications (PTMs) is key to understand the fundamental process of epigenetic regulation. This is well studied for PTMs of core histones but not for linker histone H1 in general and its ubiquitylation in particular due to a lack of proper tools. Here, we report on the chemical synthesis of site-specifically mono-ubiquitylated H1.2 and identify its ubiquitin-dependent interactome on a proteome-wide scale. We show that site-specific ubiquitylation of H1 at position K64 modulates interactions with deubiquitylating enzymes and the deacetylase SIRT1. Moreover, it affects H1-dependent chromatosome assembly and phase separation resulting in a more open chromatosome conformation generally associated with a transcriptionally active chromatin state. In summary, we propose that site-specific ubiquitylation plays a general regulatory role for linker histone H1. While the role of specific posttranslational modifications (PTMs) is increasingly well understood for core histones, this is not the case for linker histone H1. Here the authors show that site-specific ubiquitylation of H1 results in distinct interactomes, regulates phase separation, and modulates assembly of chromatosomes.
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Affiliation(s)
- Eva Höllmüller
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Simon Geigges
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Marie L Niedermeier
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Kai-Michael Kammer
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Simon M Kienle
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Daniel Rösner
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Martin Scheffner
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Florian Stengel
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
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16
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Oocyte-specific linker histone H1foo interacts with Esrrb to induce chromatin decondensation at specific gene loci. Biochem Biophys Res Commun 2021; 561:165-171. [PMID: 34023782 DOI: 10.1016/j.bbrc.2021.05.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 11/21/2022]
Abstract
Linker histone H1 is mainly localized in the linker DNA region, between two nucleosome cores, and regulates chromatin structures linking gene expression. Mammalian oocytes contain the histone H1foo, a distinct member with low sequence similarity to other members in the H1 histone family. Although, from various previous studies, evidence related to H1foo function in chromatin structures is being accumulated, the distribution of H1foo at the target gene loci in a genome-wide manner and the molecular mechanism of H1foo-dependent chromatin architecture remain unclear. In this study, we aimed to identify the target loci and the physiological factor bound to H1foo at the loci. Chromatin immunoprecipitation sequencing analysis of H1foo-overexpressing mouse embryonic stem cells showed that H1foo is enriched around the transcriptional start sites of genes such as oocyte-specific genes and that the chromatin structures at these regions were relaxed. We demonstrated that H1foo was physiologically bound to the nuclear receptor estrogen-related receptor beta (Esrrb), and Esrrb was necessary for H1foo activity of chromatin decondensation at the target loci. The specific localization and interaction with Esrrb were validated in endogenous H1foo of oocytes. Overall, H1foo induces chromatin decondensation in a locus-specific manner and this function is achieved by interacting with Esrrb.
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17
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Kowalski A. Polymorphism of histone H1.c’ in the population of Muscovy duck (Cairina moschata L.): a link between histone H1.c’ allelic variants and ADP-ribosylation of histone H1 subtypes. THE EUROPEAN ZOOLOGICAL JOURNAL 2021. [DOI: 10.1080/24750263.2021.1912200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Andrzej Kowalski
- Division of Medical Biology, Institute of Biology, Jan Kochanowski University in Kielce, Kielce, Poland
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18
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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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19
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Kowalski A. A survey of human histone H1 subtypes interaction networks: Implications for histones H1 functioning. Proteins 2021; 89:792-810. [PMID: 33550666 DOI: 10.1002/prot.26059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/23/2020] [Accepted: 01/31/2021] [Indexed: 11/08/2022]
Abstract
To show a spectrum of histone H1 subtypes (H1.1-H1.5) activity realized through the protein-protein interactions, data selected from APID resources were processed with sequence-based bioinformatics approaches. Histone H1 subtypes participate in over half a thousand interactions with nuclear and cytosolic proteins (ComPPI database) engaged in the enzymatic activity and binding of nucleic acids and proteins (SIFTER tool). Small-scale networks of H1 subtypes (STRING network) have similar topological parameters (P > .05) which are, however, different for networks hubs between subtype H1.1 and H1.4 and subtype H1.3 and H1.5 (P < .05) (Cytoscape software). Based on enriched GO terms (g:Profiler toolset) of interacting proteins, molecular function and biological process of networks hubs is related to RNA binding and ribosome biogenesis (subtype H1.1 and H1.4), cell cycle and cell division (subtype H1.3 and H1.5) and protein ubiquitination and degradation (subtype H1.2). The residue propensity (BIPSPI predictor) and secondary structures of interacting surfaces (GOR algorithm) as well as a value of equilibrium dissociation constant (ISLAND predictor) indicate that a type of H1 subtypes interactions is transient in term of the stability and medium-strong in relation to the strength of binding. Histone H1 subtypes bind interacting partners in the intrinsic disorder-dependent mode (FoldIndex, PrDOS predictor), according to the coupled folding and binding and mutual synergistic folding mechanism. These results evidence that multifunctional H1 subtypes operate via protein interactions in the networks of crucial cellular processes and, therefore, confirm a new histone H1 paradigm relating to its functioning in the protein-protein interaction networks.
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Affiliation(s)
- Andrzej Kowalski
- Division of Medical Biology, Institute of Biology, Jan Kochanowski University in Kielce, Kielce, Poland
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20
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Kulbay M, Bernier-Parker N, Bernier J. The role of the DFF40/CAD endonuclease in genomic stability. Apoptosis 2021; 26:9-23. [PMID: 33387146 DOI: 10.1007/s10495-020-01649-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 12/18/2022]
Abstract
Maintenance of genomic stability in cells is primordial for cellular integrity and protection against tumor progression. Many factors such as ultraviolet light, oxidative stress, exposure to chemical reagents, particularly mutagens and radiation, can alter the integrity of the genome. Thus, human cells are equipped with many mechanisms that prevent these irreversible lesions in the genome, as DNA repair pathways, cell cycle checkpoints, and telomeric function. These mechanisms activate cellular apoptosis to maintain DNA stability. Emerging studies have proposed a new protein in the maintenance of genomic stability: the DNA fragmentation factor (DFF). The DFF40 is an endonuclease responsible of the oligonucleosomal fragmentation of the DNA during apoptosis. The lack of DFF in renal carcinoma cells induces apoptosis without oligonucleosomal fragmentation, which poses a threat to genetic information transfer between cancerous and healthy cells. In this review, we expose the link between the DFF and genomic instability as the source of disease development.
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Affiliation(s)
- Merve Kulbay
- INRS - Centre Armand-Frappier-Santé-Biotechnologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada.,Department of Medicine, Université de Montréal, 2900 Blvd. Edouard Montpetit, Montreal, QC, Canada
| | - Nathan Bernier-Parker
- Toronto Animal Health Partners Emergency and Specialty Hospital, 1 Scarsdale Road, North York, ON, M3B 2R2, Canada
| | - Jacques Bernier
- INRS - Centre Armand-Frappier-Santé-Biotechnologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada.
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21
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Lyubitelev AV, Kirpichnikov MP, Studitsky VM. The Role of Linker Histones in Carcinogenesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Ponte I, Andrés M, Jordan A, Roque A. Towards understanding the Regulation of Histone H1 Somatic Subtypes with OMICs. J Mol Biol 2020; 433:166734. [PMID: 33279581 DOI: 10.1016/j.jmb.2020.166734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
Histone H1 is involved in the regulation of chromatin higher-order structure and compaction. In humans, histone H1 is a multigene family with seven subtypes differentially expressed in somatic cells. Which are the regulatory mechanisms that determine the variability of the H1 complement is a long-standing biological question regarding histone H1. We have used a new approach based on the integration of OMICs data to address this issue. We have examined the 3D-chromatin structure, the binding of transcription factors (TFs), and the expression of somatic H1 genes in human cell lines, using data from public repositories, such as ENCODE. Analysis of Hi-C, ChIP-seq, and RNA-seq data, have revealed that transcriptional control has a greater impact on H1 regulation than previously thought. Somatic H1 genes located in topologically associated domains (TADs) show higher expression than in boundary regions. H1 genes are targeted by a variable number of transcription factors including cell cycle-related TFs, and tissue-specific TFs, suggesting a fine-tuned, subtype-specific transcriptional control. We describe, for the first time, that all H1 somatic subtypes are under transcriptional co-regulation. The replication-independent subtypes, which are encoded in different chromosomes isolated from other histone genes, are also co-regulated with the rest of the somatic H1 genes, indicating that transcriptional co-regulation extends beyond the histone cluster. Transcriptional control and transcriptional co-regulation explain, at least in part, the variability of H1 complement, the fluctuations of H1 subtypes during development, and also the compensatory effects observed, in model systems, after perturbation of one or more H1 subtypes.
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Affiliation(s)
- Inma Ponte
- Biochemistry and Molecular Biology Department, Bioscience Faculty, Autonomous University of Barcelona, Spain
| | - Marta Andrés
- Biochemistry and Molecular Biology Department, Bioscience Faculty, Autonomous University of Barcelona, Spain
| | - Albert Jordan
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Alicia Roque
- Biochemistry and Molecular Biology Department, Bioscience Faculty, Autonomous University of Barcelona, Spain.
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23
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24
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Teif VB, Gould TJ, Clarkson CT, Boyd L, Antwi EB, Ishaque N, Olins AL, Olins DE. Linker histone epitopes are hidden by in situ higher-order chromatin structure. Epigenetics Chromatin 2020; 13:26. [PMID: 32505195 PMCID: PMC7276084 DOI: 10.1186/s13072-020-00345-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 05/13/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone H1 is the most mobile histone in the cell nucleus. Defining the positions of H1 on chromatin in situ, therefore, represents a challenge. Immunoprecipitation of formaldehyde-fixed and sonicated chromatin, followed by DNA sequencing (xChIP-seq), is traditionally the method for mapping histones onto DNA elements. But since sonication fragmentation precedes ChIP, there is a consequent loss of information about chromatin higher-order structure. Here, we present a new method, xxChIP-seq, employing antibody binding to fixed intact in situ chromatin, followed by extensive washing, a second fixation, sonication and immunoprecipitation. The second fixation is intended to prevent the loss of specifically bound antibody during washing and subsequent sonication and to prevent antibody shifting to epitopes revealed by the sonication process. In many respects, xxChIP-seq is comparable to immunostaining microscopy, which also involves interaction of the primary antibody with fixed and permeabilized intact cells. The only epitopes displayed after immunostaining are the "exposed" epitopes, not "hidden" by the fixation of chromatin higher-order structure. Comparison of immunoprecipitated fragments between xChIP-seq versus xxChIP-seq should indicate which epitopes become inaccessible with fixation and identify their associated DNA elements. RESULTS We determined the genomic distribution of histone variants H1.2 and H1.5 in human myeloid leukemia cells HL-60/S4 and compared their epitope exposure by both xChIP-seq and xxChIP-seq, as well as high-resolution microscopy, illustrating the influences of preserved chromatin higher-order structure in situ. We found that xChIP and xxChIP H1 signals are in general negatively correlated, with differences being more pronounced near active regulatory regions. Among the intriguing observations, we find that transcription-related regions and histone PTMs (i.e., enhancers, promoters, CpG islands, H3K4me1, H3K4me3, H3K9ac, H3K27ac and H3K36me3) exhibit significant deficiencies (depletions) in H1.2 and H1.5 xxChIP-seq reads, compared to xChIP-seq. These observations suggest the existence of in situ transcription-related chromatin higher-order structures stabilized by formaldehyde. CONCLUSION Comparison of H1 xxChIP-seq to H1 xChIP-seq allows the development of hypotheses on the chromosomal localization of (stabilized) higher-order structure, indicated by the generation of "hidden" H1 epitopes following formaldehyde crosslinking. Changes in H1 epitope exposure surrounding averaged chromosomal binding sites or epigenetic modifications can also indicate whether these sites have chromatin higher-order structure. For example, comparison between averaged active or inactive promoter regions suggests that both regions can acquire stabilized higher-order structure with hidden H1 epitopes. However, the H1 xChIP-seq comparison cannot define their differences. Application of the xxChIP-seq versus H1 xChIP-seq method is particularly relevant to chromatin-associated proteins, such as linker histones, that play dynamic roles in establishing chromatin higher-order structure.
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Affiliation(s)
- Vladimir B Teif
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
| | - Travis J Gould
- Department of Physics & Astronomy, Bates College, Lewiston, ME, USA
| | | | - Logan Boyd
- Department of Physics & Astronomy, Bates College, Lewiston, ME, USA.,StarBird Technologies, LLC, Brunswick, ME, USA
| | - Enoch B Antwi
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Molecular and Cellular Engineering, Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, Freiburg im Breisgau, 79104 , Germany
| | - Naveed Ishaque
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, Berlin, 10178 , Germany
| | - Ada L Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME, 04103, USA
| | - Donald E Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME, 04103, USA.
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25
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Hayakawa K, Tani R, Nishitani K, Tanaka S. Linker histone variant H1T functions as a chromatin de-condenser on genic regions. Biochem Biophys Res Commun 2020; 528:685-690. [PMID: 32513538 DOI: 10.1016/j.bbrc.2020.05.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/16/2020] [Indexed: 10/24/2022]
Abstract
Linker histone H1 is mainly localized in the linker DNA region, between two nucleosome cores, and regulates chromatin structures linking gene expression. There are 11 variants in histone H1, and each variant has unique functions. Our previous study demonstrates that one of the H1 variants, H1T is mainly localized in the nucleolus and targets the rDNA repeat region. Moreover, H1T condenses the chromatin structures on rDNA to repress pre-rRNA expression. Although H1T is partially localized in the nucleoplasm area, the functions of H1T in the non-repeat genic region are unclear. In this study, we aimed to identify the target loci and the role of H1T in the genic region. Chromatin immunoprecipitation sequencing analysis showed that H1T is localized around the transcriptional start site and the chromatin structures of the region were relaxed. H1T knockdown and overexpression experiments revealed that H1T induced chromatin de-condensation and was associated with the increased expression of target genes. Moreover, we observed H1T co-localization with transcriptional factor SPZ1 on the genic region. Collectively, H1T has opposing roles in the genic region and in rDNA repeats; H1T functions to facilitate chromatin relaxation linked gene activation.
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Affiliation(s)
- Koji Hayakawa
- Department of Toxicology, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan; Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Ruiko Tani
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kenta Nishitani
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Satoshi Tanaka
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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26
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Chikhirzhina EV, Starkova TY, Polyanichko AM. The Role of Linker Histones in Chromatin Structural Organization. 2. Interaction with DNA and Nuclear Proteins. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920020049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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27
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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 2020; 47:6145-6159. [PMID: 31076740 PMCID: PMC6614845 DOI: 10.1093/nar/gkz338] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [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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Chavez C, Cruz-Becerra G, Fei J, Kassavetis GA, Kadonaga JT. The tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals. eLife 2019; 8:47682. [PMID: 31571581 PMCID: PMC6773438 DOI: 10.7554/elife.47682] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 08/29/2019] [Indexed: 12/21/2022] Open
Abstract
Tardigrades, also known as water bears, are animals that can survive extreme conditions. The tardigrade Ramazzottius varieornatus contains a unique nuclear protein termed Dsup, for damage suppressor, which can increase the resistance of human cells to DNA damage under conditions, such as ionizing radiation or hydrogen peroxide treatment, that generate hydroxyl radicals. Here we find that R. varieornatus Dsup is a nucleosome-binding protein that protects chromatin from hydroxyl radicals. Moreover, a Dsup ortholog from the tardigrade Hypsibius exemplaris similarly binds to nucleosomes and protects DNA from hydroxyl radicals. Strikingly, a conserved region in Dsup proteins exhibits sequence similarity to the nucleosome-binding domain of vertebrate HMGN proteins and is functionally important for nucleosome binding and hydroxyl radical protection. These findings suggest that Dsup promotes the survival of tardigrades under diverse conditions by a direct mechanism that involves binding to nucleosomes and protecting chromosomal DNA from hydroxyl radicals. Tardigrades, also known as water bears and moss piglets, are small animals found in many different environments on land and sea. These animals have the remarkable ability to survive extremes including very low temperatures, high levels of radiation and exposure to chemicals that are harmful to other forms of life. Tardigrades have even been found to survive the harsh conditions of outer space. X-rays are a type of radiation naturally produced by lightning strikes and are also found in cosmic rays from outer space. High doses of X-rays can cause genetic mutations that may lead to serious illness or death. This is because when X-rays come into contact with water they split the water molecules to make particles known as hydroxyl radicals, which in turn damage the DNA inside cells. The genomes of animals and plants are made of DNA, which is packaged into a structure called chromatin. Previous studies identified a protein named Dsup in a tardigrade called Ramazzottius varieornatus that can protect human cells from damage by X-rays. However, it was not known whether Dsup binds directly to chromatin or plays a more indirect role in protecting DNA. Chavez, Cruz-Becerra, Fei, Kassavetis et al. used biochemical approaches to study Dsup. Their experiments revealed that Dsup from R. varieornatus binds to chromatin to protect the DNA from damage by hydroxyl radicals, and that the Dsup protein in another tardigrade species also works in a similar way. Further analysis showed that a region of Dsup that is needed to bind to chromatin is very similar to a region that had been previously found only in chromatin-binding proteins from humans and other vertebrates (animals with backbones). This connection between Dsup and vertebrate chromatin-binding proteins remains a mystery. The new findings about tardigrade Dsup may help researchers develop animal cells that live longer under normal or extreme environmental conditions. In this manner, Dsup could be used to expand the range of applications of cells in biotechnology. It could also increase the effectiveness of current methods, such as the production of some pharmaceuticals, that depend upon the use of cultured cells.
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Affiliation(s)
- Carolina Chavez
- Section of Molecular Biology, University of California, San Diego, San Diego, United States
| | - Grisel Cruz-Becerra
- Section of Molecular Biology, University of California, San Diego, San Diego, United States
| | - Jia Fei
- Section of Molecular Biology, University of California, San Diego, San Diego, United States
| | - George A Kassavetis
- Section of Molecular Biology, University of California, San Diego, San Diego, United States
| | - James T Kadonaga
- Section of Molecular Biology, University of California, San Diego, San Diego, United States
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29
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Flex E, Martinelli S, Van Dijck A, Ciolfi A, Cecchetti S, Coluzzi E, Pannone L, Andreoli C, Radio FC, Pizzi S, Carpentieri G, Bruselles A, Catanzaro G, Pedace L, Miele E, Carcarino E, Ge X, Chijiwa C, Lewis MES, Meuwissen M, Kenis S, Van der Aa N, Larson A, Brown K, Wasserstein MP, Skotko BG, Begtrup A, Person R, Karayiorgou M, Roos JL, Van Gassen KL, Koopmans M, Bijlsma EK, Santen GWE, Barge-Schaapveld DQCM, Ruivenkamp CAL, Hoffer MJV, Lalani SR, Streff H, Craigen WJ, Graham BH, van den Elzen APM, Kamphuis DJ, Õunap K, Reinson K, Pajusalu S, Wojcik MH, Viberti C, Di Gaetano C, Bertini E, Petrucci S, De Luca A, Rota R, Ferretti E, Matullo G, Dallapiccola B, Sgura A, Walkiewicz M, Kooy RF, Tartaglia M. Aberrant Function of the C-Terminal Tail of HIST1H1E Accelerates Cellular Senescence and Causes Premature Aging. Am J Hum Genet 2019; 105:493-508. [PMID: 31447100 DOI: 10.1016/j.ajhg.2019.07.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 07/10/2019] [Indexed: 02/03/2023] Open
Abstract
Histones mediate dynamic packaging of nuclear DNA in chromatin, a process that is precisely controlled to guarantee efficient compaction of the genome and proper chromosomal segregation during cell division and to accomplish DNA replication, transcription, and repair. Due to the important structural and regulatory roles played by histones, it is not surprising that histone functional dysregulation or aberrant levels of histones can have severe consequences for multiple cellular processes and ultimately might affect development or contribute to cell transformation. Recently, germline frameshift mutations involving the C-terminal tail of HIST1H1E, which is a widely expressed member of the linker histone family and facilitates higher-order chromatin folding, have been causally linked to an as-yet poorly defined syndrome that includes intellectual disability. We report that these mutations result in stable proteins that reside in the nucleus, bind to chromatin, disrupt proper compaction of DNA, and are associated with a specific methylation pattern. Cells expressing these mutant proteins have a dramatically reduced proliferation rate and competence, hardly enter into the S phase, and undergo accelerated senescence. Remarkably, clinical assessment of a relatively large cohort of subjects sharing these mutations revealed a premature aging phenotype as a previously unrecognized feature of the disorder. Our findings identify a direct link between aberrant chromatin remodeling, cellular senescence, and accelerated aging.
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Affiliation(s)
- Elisabetta Flex
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, 00161 Italy; Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Simone Martinelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, 00161 Italy
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Edegem, 2650 Belgium; Department of Neurology, Antwerp University Hospital, Edegem, 2650 Belgium
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Serena Cecchetti
- Microscopy Area, Core Facilities, Istituto Superiore di Sanità, Rome, 00161 Italy
| | - Elisa Coluzzi
- Department of Science, University Roma Tre, Rome, 00146 Italy
| | - Luca Pannone
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, 00161 Italy; Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Cristina Andreoli
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161 Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Giovanna Carpentieri
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, 00161 Italy; Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, 00161 Italy
| | | | - Lucia Pedace
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146 Italy
| | - Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146 Italy
| | - Elena Carcarino
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146 Italy; Current affiliation: Cordeliers Research Centre, Inserm 1138, Sorbonne Université, Paris, 75006 France
| | - Xiaoyan Ge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Current affiliation: Department of Genetics and Genomic Sciences, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chieko Chijiwa
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - M E Suzanne Lewis
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Marije Meuwissen
- Department of Medical Genetics, University of Antwerp, Edegem, 2650 Belgium
| | - Sandra Kenis
- Department of Neurology, Antwerp University Hospital, Edegem, 2650 Belgium
| | | | - Austin Larson
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kathleen Brown
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Melissa P Wasserstein
- Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Brian G Skotko
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02114, USA
| | | | | | - Maria Karayiorgou
- Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA
| | - J Louw Roos
- Department of Psychiatry, University of Pretoria, Weskoppies Hospital, Pretoria, 0001 South Africa
| | - Koen L Van Gassen
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, 3508 AB the Netherlands
| | - Marije Koopmans
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, 3508 AB the Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300 RC the Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300 RC the Netherlands
| | | | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300 RC the Netherlands
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300 RC the Netherlands
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brett H Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Daan J Kamphuis
- Departement of Neurology, Reinier de Graaf Ziekenhuis, Delft, 2600 GA the Netherlands
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, 50406 Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, 50406 Estonia
| | - Karit Reinson
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, 50406 Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, 50406 Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, 50406 Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, 50406 Estonia; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Monica H Wojcik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Clara Viberti
- Department of Medical Sciences, University of Turin, Turin, 10126 Italy; Italian Institute for Genomic Medicine, Turin, 10126 Italy
| | - Cornelia Di Gaetano
- Department of Medical Sciences, University of Turin, Turin, 10126 Italy; Italian Institute for Genomic Medicine, Turin, 10126 Italy
| | - Enrico Bertini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Simona Petrucci
- Department of Clinical and Molecular Medicine, Sapienza University, Rome, 00189 Italy; Division of Medical Genetics, Casa Sollievo della Sofferenza Hospital, IRCCS, San Giovanni Rotondo, 71013 Italy
| | - Alessandro De Luca
- Division of Medical Genetics, Casa Sollievo della Sofferenza Hospital, IRCCS, San Giovanni Rotondo, 71013 Italy
| | - Rossella Rota
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146 Italy
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University, Rome, 00161 Italy; Istituto Neuromed, IRCCS, Pozzilli, 86077 Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, 10126 Italy; Italian Institute for Genomic Medicine, Turin, 10126 Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Antonella Sgura
- Department of Science, University Roma Tre, Rome, 00146 Italy
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Current affiliation: National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20892, USA
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Edegem, 2650 Belgium.
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy.
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30
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Chamani E, Ebrahimi R, Khorsandi K, Meshkini A, Zarban A, Sharifzadeh G. In vitro cytotoxicity of polyphenols from Datura innoxia aqueous leaf-extract on human leukemia K562 cells: DNA and nuclear proteins as targets. Drug Chem Toxicol 2019; 43:138-148. [DOI: 10.1080/01480545.2019.1629588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Elham Chamani
- Cardiovascular Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
- Department of Biochemistry, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Roshanak Ebrahimi
- Department of Biochemistry, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Khatereh Khorsandi
- Department of Photodynamic, Medical Laser Research Center, YARA institute, ACECR, Tehran, Iran
| | - Azadeh Meshkini
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Asghar Zarban
- Department of Biochemistry, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Gholamreza Sharifzadeh
- Social Determinants of Health Research Center, Birjand University of Medical Sciences, Birjand, Iran
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31
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Ser Z, Cifani P, Kentsis A. Optimized Cross-Linking Mass Spectrometry for in Situ Interaction Proteomics. J Proteome Res 2019; 18:2545-2558. [PMID: 31083951 DOI: 10.1021/acs.jproteome.9b00085] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recent development of mass spectrometer cleavable protein cross-linkers and algorithms for their spectral identification now permits large-scale cross-linking mass spectrometry (XL-MS). Here, we optimized the use of cleavable disuccinimidyl sulfoxide (DSSO) cross-linker for labeling native protein complexes in live human cells. We applied a generalized linear mixture model to calibrate cross-link peptide-spectra matching (CSM) scores to control the sensitivity and specificity of large-scale XL-MS. Using specific CSM score thresholds to control the false discovery rate, we found that higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) can both be effective for large-scale XL-MS protein interaction mapping. We found that the coverage of protein-protein interaction maps is significantly improved through the use of multiple proteases. In addition, the use of focused sample-specific search databases can be used to improve the specificity of cross-linked peptide spectral matching. Application of this approach to human chromatin labeled in live cells recapitulated known and revealed new protein interactions of nucleosomes and other chromatin-associated complexes in situ. This optimized approach for mapping native protein interactions should be useful for a wide range of biological problems.
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Affiliation(s)
| | | | - Alex Kentsis
- Department of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College , Cornell University , New York , New York 10065 , United States
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32
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Disordered domains in chromatin-binding proteins. Essays Biochem 2019; 63:147-156. [PMID: 30940742 DOI: 10.1042/ebc20180068] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 02/08/2023]
Abstract
Chromatin comprises proteins, DNA and RNA, and its function is to condense and package the genome in a way that allows the necessary transactions such as transcription, replication and repair to occur in a highly organised and regulated manner. The packaging of chromatin is often thought of in a hierarchical fashion starting from the most basic unit of DNA packaging, the nucleosome, to the condensation of nucleosomal 'beads on a string' by linker histones to form the 30-nm fibre and eventually large chromatin domains. However, a picture of a more heterogeneous, dynamic and liquid-like assembly is emerging, in which intrinsically disordered proteins (IDPs) and proteins containing intrinsically disordered regions (IDRs) play a central role. Disorder features at all levels of chromatin organisation, from the histone tails, which are sites of extensive post-translational modification (PTM) that change the fate of the underlying genomic information, right through to transcription hubs, and the recently elucidated roles of IDPs and IDRs in the condensation of large regions of the genome through liquid-liquid phase separation.
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33
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Olins DE, Olins AL. Epichromatin and chromomeres: a 'fuzzy' perspective. Open Biol 2019; 8:rsob.180058. [PMID: 29875200 PMCID: PMC6030114 DOI: 10.1098/rsob.180058] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 05/09/2018] [Indexed: 12/17/2022] Open
Abstract
'Epichromatin', the surface of chromatin beneath the interphase nuclear envelope (NE) or at the surface of mitotic chromosomes, was discovered by immunostaining with a specific bivalent mouse monoclonal anti-nucleosome antibody (mAb PL2-6). 'Chromomeres', punctate chromatin particles approximately 200-300 nm in diameter, identified throughout the interphase chromatin and along mitotic chromosomes, were observed by immunostaining with the monovalent papain-derived Fab fragments of bivalent PL2-6. The specific target for PL2-6 appears to include the nucleosome acidic patch. Thus, within the epichromatin and chromomeric regions, this epitope is 'exposed'. Considering that histones possess unstructured 'tails' (i.e. intrinsically disordered peptide regions, IDPR), our perception of these chromatin regions becomes more 'fuzzy' (less defined). We suggest that epichromatin cationic tails facilitate interactions with anionic components of NE membranes. We also suggest that the unstructured histone tails (especially, histone H1 tails), with their presumed promiscuous binding, establish multivalent binding that stabilizes each chromomere as a unit of chromatin higher order structure. We propose an 'unstructured stability' hypothesis, which postulates that the stability of epichromatin and chromomeres (as well as other nuclear chromatin structures) is a consequence of the collective contributions of numerous weak histone IDPR binding interactions arising from the multivalent nucleosome, analogous to antibody avidity.
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Affiliation(s)
- Donald E Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA
| | - Ada L Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA
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34
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Affiliation(s)
- Kevin Brockers
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Faculty of Biology, LMU, 82152 Martinsried, Germany
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35
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Chaves-Arquero B, Pantoja-Uceda D, Roque A, Ponte I, Suau P, Jiménez MA. A CON-based NMR assignment strategy for pro-rich intrinsically disordered proteins with low signal dispersion: the C-terminal domain of histone H1.0 as a case study. JOURNAL OF BIOMOLECULAR NMR 2018; 72:139-148. [PMID: 30414042 DOI: 10.1007/s10858-018-0213-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/24/2018] [Indexed: 05/23/2023]
Abstract
The C-terminal domain of histone H1.0 (C-H1.0) is involved in DNA binding and is a main determinant of the chromatin condensing properties of histone H1.0. Phosphorylation at the (S/T)-P-X-(K/R) motifs affects DNA binding and is crucial for regulation of C-H1.0 function. Since C-H1.0 is an intrinsically disordered domain, solution NMR is an excellent approach to characterize the effect of phosphorylation on the structural and dynamic properties of C-H1.0. However, its very repetitive, low-amino acid-diverse and Pro-rich sequence, together with the low signal dispersion observed at the 1H-15N HSQC spectra of both non- and tri-phosphorylated C-H1.0 preclude the use of standard 1H-detected assignment strategies. We have achieved an essentially complete assignment of the heavy backbone atoms (15N, 13C' and 13Cα), as well as 1HN and 13Cβ nuclei, of non- and tri-phosphorylated C-H1.0 by applying a novel 13C-detected CON-based strategy. No C-H1.0 region with a clear secondary structure tendency was detected by chemical shift analyses, confirming at residue level that C-H1.0 is disordered in aqueous solution. Phosphorylation only affected the chemical shifts of phosphorylated Thr's, and their adjacent residues. Heteronuclear {1H}-15N NOEs were also essentially equal in the non- and tri-phosphorylated states. Hence, structural tendencies and dynamic properties of C-H1.0 free in aqueous solution are unmodified by phosphorylation. We propose that the assignment strategy used for C-H1.0, which is based on the acquisition of only a few 3D spectra, is an excellent choice for short-lived intrinsically disordered proteins with repetitive sequences.
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Affiliation(s)
- Belén Chaves-Arquero
- Departamento de Química-Física Biológica, Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006, Madrid, Spain
| | - David Pantoja-Uceda
- Departamento de Química-Física Biológica, Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006, Madrid, Spain
| | - Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Inmaculada Ponte
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Pedro Suau
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - M Angeles Jiménez
- Departamento de Química-Física Biológica, Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006, Madrid, Spain.
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36
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Chikhirzhina E, Starkova T, Polyanichko A. The Role of Linker Histones in Chromatin Structural Organization. 1. H1 Family Histones. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918060064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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37
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Kowalski A, Markowski J. Brown Hare's (Lepus europaeus) Histone H1 Variant H1.2 as an Indicator of Anthropogenic Stress. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2018; 75:576-584. [PMID: 29869686 PMCID: PMC6182586 DOI: 10.1007/s00244-018-0540-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 05/21/2018] [Indexed: 05/04/2023]
Abstract
From the liver tissues of brown hare individuals that lived in two various habitats, i.e., the agricultural region with the predominant farms and the industrial area near a metallurgical plant, histones H1 were analyzed to compare their within and between population variability. Furthermore, because agricultural production emits mainly organic pollutants and metallurgical industry is a primarily source of inorganic contaminations, we wanted to check how the brown hare individuals are sensitive for both agents. Among brown hare H1 histones, the histone H1.2 was determined as heterogeneous due to its varied mobility in two-dimensional SDS-polyacrylamide gel. The obtained electrophoretic patterns contained differently moving single spots of histone H1.2 and also its double spots have a similar rate of electrophoretic mobility. Based on this, two homozygous phenotypes (slowly migrating 2a and faster moving 2b) and a heterozygous phenotype (2a2b) was distinguished. The relatively low variable (CV < 0.25) and comparably abundant (p > 0.05) histone H1.2 homozygous phenotypes form a heterozygous phenotype in a similar proportion, at a ratio approximating 0.5. Although the brown hare population originating from agricultural area displayed a slight excess of heterozygous individuals 2a2b (F = - 0.04), it was conformed to the Hardy-Weinberg assumption (χ2 = 0.035, p = 0.853). Compared with this population, a sevenfold reduced frequency of the phenotype 2b and above tenfold increase of a heterozygosity (F = - 0.53) was observed in the brown hare population inhabiting the vicinity of metallurgical plant. Therefore, this population did not fit to the Hardy-Weinberg law (χ2 = 5.65, p = 0.017). Despite the negligible genetic differentiation (FST = 0.026) between brown hare populations inhabiting areas with different anthropogenic pressure, a statistically significant difference in the distribution of their phenotypes (χ2 = 6.01, p = 0.049) and alleles (χ2 = 6.50, p = 0.013) was noted. The collected data confirm that the brown hare species is sensitive for environmental quality and may serve as a good indicator of habitat conditions related to both organic pollution emitted by agricultural activities (PIC = 0.48) and inorganic contamination originating from metallurgical processes (PIC = 0.49). These difference in the environmental quality might be assessed by estimation of genetic variability among the brown hare populations, based on the phenotypes distribution of histone H1 variant H1.2, the protein that was not so far employed as a molecular marker of anthropogenic stress.
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Affiliation(s)
- Andrzej Kowalski
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, Świętokrzyska 15, 25-406, Kielce, Poland.
| | - Janusz Markowski
- Department of Biodiversity Studies, Didactics and Bioeducation, University of Lodz, Banacha 1/3, 90-237, Lodz, Poland
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Yerra VG, Advani A. Histones and heart failure in diabetes. Cell Mol Life Sci 2018; 75:3193-3213. [PMID: 29934664 PMCID: PMC6063320 DOI: 10.1007/s00018-018-2857-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 12/22/2022]
Abstract
Although heart failure is now accepted as being a major long-term complication of diabetes, many of the recent advances in our understanding of the pathobiology of diabetes complications have come about through the study of more traditional microvascular or macrovascular diseases. This has been the case, for example, in the evolving field of the epigenetics of diabetes complications and, in particular, the post-translational modification of histone proteins. However, histone modifications also occur in human heart failure and their perturbation also occurs in diabetic hearts. Here, we review the principal histone modifications and their enzymatic writers and erasers that have been studied to date; we discuss what is currently known about their roles in heart failure and in the diabetic heart; we draw on lessons learned from the studies of microvascular and macrovascular complications; and we speculate that therapeutically manipulating histone modifications may alter the natural history of heart failure in diabetes.
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Affiliation(s)
- Veera Ganesh Yerra
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael's Hospital, 6-151, 61 Queen Street East, Toronto, ON, M5C 2T2, Canada
| | - Andrew Advani
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael's Hospital, 6-151, 61 Queen Street East, Toronto, ON, M5C 2T2, Canada.
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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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40
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Khuong MT, Fei J, Cruz-Becerra G, Kadonaga JT. A simple and versatile system for the ATP-dependent assembly of chromatin. J Biol Chem 2017; 292:19478-19490. [PMID: 28982979 DOI: 10.1074/jbc.m117.815365] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/26/2017] [Indexed: 12/17/2022] Open
Abstract
Chromatin is the natural form of DNA in the eukaryotic nucleus and is the substrate for diverse biological phenomena. The functional analysis of these processes ideally would be carried out with nucleosomal templates that are assembled with customized core histones, DNA sequences, and chromosomal proteins. Here we report a simple, reliable, and versatile method for the ATP-dependent assembly of evenly spaced nucleosome arrays. This minimal chromatin assembly system comprises the Drosophila nucleoplasmin-like protein (dNLP) histone chaperone, the imitation switch (ISWI) ATP-driven motor protein, core histones, template DNA, and ATP. The dNLP and ISWI components were synthesized in bacteria, and each protein could be purified in a single step by affinity chromatography. We show that the dNLP-ISWI system can be used with different DNA sequences, linear or circular DNA, bulk genomic DNA, recombinant or native Drosophila core histones, native human histones, the linker histone H1, the non-histone chromosomal protein HMGN2, and the core histone variants H3.3 and H2A.V. The dNLP-ISWI system should be accessible to a wide range of researchers and enable the assembly of customized chromatin with specifically desired DNA sequences, core histones, and other chromosomal proteins.
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Affiliation(s)
- Mai T Khuong
- From the Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Jia Fei
- From the Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Grisel Cruz-Becerra
- From the Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - James T Kadonaga
- From the Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
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41
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Kowalski A, Knaga S. Evidence on the stability of histone H1.a polymorphic variants during selection in quail. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-145-2017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The goal of this work was to check whether selection for quantitative traits may cause a change in the histone H1 allelic complement and whether it can therefore be considered a modulator of histone H1-dependent chromatin functioning. For this purpose, a fluctuation of histone H1.a polymorphic variants was analyzed among a non-selected (control) quail line and the line selected for a high cholesterol content in the egg yolk. The histone H1.a was found to be polymorphic due to its differential migration rate in the AU-PAGE (acetic acid–urea polyacrylamide gel electrophoresis). Based on this, two H1.a isoforms (H1.a1 and H1.a2) that form three phenotypes (a1, a2 and a1a2) were distinguished in the quail lines tested. A comparably expressed (p > 0. 05) and low relative variable (coefficient of variation, CV < 0. 25) histone H1.a phenotypes were in agreement with Hardy–Weinberg equilibrium (HWE) in both the non-selected (χ2 = 1. 29, p = 0. 25) and selected (χ2 = 1. 9, p = 0. 16) quail line. The similarity among quail lines was assessed based on the equal distribution of histone H1.a phenotypes (χ2 = 1. 63, p = 0. 44) and alleles (χ2 = 0. 018, p = 0. 89) frequency in both quail lines tested. This indicates that selection does not affect the histone H1.a polymorphic variants. The stability of histone H1.a during selection might suggest that likely chromatin processes coupled to the selected trait are not linked to the activity of histone H1.a.
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42
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Tatton-Brown K, Loveday C, Yost S, Clarke M, Ramsay E, Zachariou A, Elliott A, Wylie H, Ardissone A, Rittinger O, Stewart F, Temple IK, Cole T, Mahamdallie S, Seal S, Ruark E, Rahman N. Mutations in Epigenetic Regulation Genes Are a Major Cause of Overgrowth with Intellectual Disability. Am J Hum Genet 2017; 100:725-736. [PMID: 28475857 PMCID: PMC5420355 DOI: 10.1016/j.ajhg.2017.03.010] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/24/2017] [Indexed: 12/04/2022] Open
Abstract
To explore the genetic architecture of human overgrowth syndromes and human growth control, we performed experimental and bioinformatic analyses of 710 individuals with overgrowth (height and/or head circumference ≥+2 SD) and intellectual disability (OGID). We identified a causal mutation in 1 of 14 genes in 50% (353/710). This includes HIST1H1E, encoding histone H1.4, which has not been associated with a developmental disorder previously. The pathogenic HIST1H1E mutations are predicted to result in a product that is less effective in neutralizing negatively charged linker DNA because it has a reduced net charge, and in DNA binding and protein-protein interactions because key residues are truncated. Functional network analyses demonstrated that epigenetic regulation is a prominent biological process dysregulated in individuals with OGID. Mutations in six epigenetic regulation genes—NSD1, EZH2, DNMT3A, CHD8, HIST1H1E, and EED—accounted for 44% of individuals (311/710). There was significant overlap between the 14 genes involved in OGID and 611 genes in regions identified in GWASs to be associated with height (p = 6.84 × 10−8), suggesting that a common variation impacting function of genes involved in OGID influences height at a population level. Increased cellular growth is a hallmark of cancer and there was striking overlap between the genes involved in OGID and 260 somatically mutated cancer driver genes (p = 1.75 × 10−14). However, the mutation spectra of genes involved in OGID and cancer differ, suggesting complex genotype-phenotype relationships. These data reveal insights into the genetic control of human growth and demonstrate that exome sequencing in OGID has a high diagnostic yield.
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Affiliation(s)
- Katrina Tatton-Brown
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK; South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London SW17 0QT, UK
| | - Chey Loveday
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Shawn Yost
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Matthew Clarke
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Emma Ramsay
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Anna Zachariou
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Anna Elliott
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Harriet Wylie
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Anna Ardissone
- Child Neurology Unit, Foundation IRCCS C Besta Neurological Institute, Milan 20133, Italy
| | - Olaf Rittinger
- Landeskrankenanstalten Salzburg, Kinderklinik Department of Pediatrics, Klinische Genetik, Salzburg 5020, Austria
| | - Fiona Stewart
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast BT9 7AB, Northern Ireland
| | - I Karen Temple
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK; Wessex Clinical Genetics Service, University Hospital Southampton NHS Trust, Southampton SO16 6YD, UK
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women's Hospital NHS Foundation Trust and University of Birmingham, Birmingham Health Partners, Birmingham B15 2TG, UK
| | - Shazia Mahamdallie
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Sheila Seal
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Elise Ruark
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Nazneen Rahman
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK; Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK.
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43
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Zhang P, Branson OE, Freitas MA, Parthun MR. Identification of replication-dependent and replication-independent linker histone complexes: Tpr specifically promotes replication-dependent linker histone stability. BMC BIOCHEMISTRY 2016; 17:18. [PMID: 27716023 PMCID: PMC5045598 DOI: 10.1186/s12858-016-0074-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 09/20/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND There are 11 variants of linker histone H1 in mammalian cells. Beyond their shared abilities to stabilize and condense chromatin, the H1 variants have been found to have non-redundant functions, the mechanisms of which are not fully understood. Like core histones, there are both replication-dependent and replication-independent linker histone variants. The histone chaperones and other factors that regulate linker histone dynamics in the cell are largely unknown. In particular, it is not known whether replication-dependent and replication-independent linker histones interact with distinct or common sets of proteins. To better understand linker histone dynamics and assembly, we used chromatography and mass spectrometry approaches to identify proteins that are associated with replication-dependent and replication-independent H1 variants. We then used a variety of in vivo analyses to validate the functional relevance of identified interactions. RESULTS We identified proteins that bind to all linker histone variants and proteins that are specific for only one class of variant. The factors identified include histone chaperones, transcriptional regulators, RNA binding proteins and ribosomal proteins. The nuclear pore complex protein Tpr, which was found to associate with only replication-dependent linker histones, specifically promoted their stability. CONCLUSION Replication-dependent and replication-independent linker histone variants can interact with both common and distinct sets of proteins. Some of these factors are likely to function as histone chaperones while others may suggest novel links between linker histones and RNA metabolism. The nuclear pore complex protein Tpr specifically interacts with histone H1.1 and H1.2 but not H1x and can regulate the stability of these replication-dependent linker histones.
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Affiliation(s)
- Pei Zhang
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210 USA
| | - Owen E. Branson
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210 USA
| | - Michael A. Freitas
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210 USA
| | - Mark R. Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210 USA
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44
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Xu N, Lu X, Kavi H, Emelyanov AV, Bernardo TJ, Vershilova E, Skoultchi AI, Fyodorov DV. BEN domain protein Elba2 can functionally substitute for linker histone H1 in Drosophila in vivo. Sci Rep 2016; 6:34354. [PMID: 27687115 PMCID: PMC5043383 DOI: 10.1038/srep34354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 09/09/2016] [Indexed: 01/20/2023] Open
Abstract
Metazoan linker histones are essential for development and play crucial roles in organization of chromatin, modification of epigenetic states and regulation of genetic activity. Vertebrates express multiple linker histone H1 isoforms, which may function redundantly. In contrast, H1 isoforms are not present in Dipterans, including D. melanogaster, except for an embryo-specific, distantly related dBigH1. Here we show that Drosophila BEN domain protein Elba2, which is expressed in early embryos and was hypothesized to have insulator-specific functions, can compensate for the loss of H1 in vivo. Although the Elba2 gene is not essential, its mutation causes a disruption of normal internucleosomal spacing of chromatin and reduced nuclear compaction in syncytial embryos. Elba2 protein is distributed ubiquitously in polytene chromosomes and strongly colocalizes with H1. In H1-depleted animals, ectopic expression of Elba2 rescues the increased lethality and ameliorates abnormalities of chromosome architecture and heterochromatin functions. We also demonstrate that ectopic expression of BigH1 similarly complements the deficiency of H1 protein. Thus, in organisms that do not express redundant H1 isoforms, the structural and biological functions performed by canonical linker histones in later development, may be shared in early embryos by weakly homologous proteins, such as BigH1, or even unrelated, non-homologous proteins, such as Elba2.
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Affiliation(s)
- Na Xu
- Albert Einstein College of Medicine, Department of Cell Biology, Bronx, NY 10461, USA
| | - Xingwu Lu
- Albert Einstein College of Medicine, Department of Cell Biology, Bronx, NY 10461, USA
| | - Harsh Kavi
- Albert Einstein College of Medicine, Department of Cell Biology, Bronx, NY 10461, USA
| | | | - Travis J. Bernardo
- Albert Einstein College of Medicine, Department of Cell Biology, Bronx, NY 10461, USA
| | - Elena Vershilova
- Albert Einstein College of Medicine, Department of Cell Biology, Bronx, NY 10461, USA
| | - Arthur I. Skoultchi
- Albert Einstein College of Medicine, Department of Cell Biology, Bronx, NY 10461, USA
| | - Dmitry V. Fyodorov
- Albert Einstein College of Medicine, Department of Cell Biology, Bronx, NY 10461, USA
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45
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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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46
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Kowalski A. Nuclear and nucleolar activity of linker histone variant H1.0. Cell Mol Biol Lett 2016; 21:15. [PMID: 28536618 PMCID: PMC5414669 DOI: 10.1186/s11658-016-0014-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/28/2016] [Indexed: 12/31/2022] Open
Abstract
Histone H1.0 belongs to the class of linker histones (H1), although it is substantially distinct from other histone H1 family members. The differences can be observed in the chromosomal location and organization of the histone H1.0 encoding gene, as well as in the length and composition of its amino acid chain. Whereas somatic (H1.1-H1.5) histone H1 variants are synthesized in the cell cycle S-phase, histone H1.0 is synthesized throughout the cell cycle. By replacing somatic H1 variants during cell maturation, histone H1.0 is gradually deposited in low dividing cells and achieves the highest level of expression in the terminally differentiated cells. Compared to other differentiation-specific H1 histone (H5) characteristic for unique tissue and organisms, the distribution of histone H1.0 remains non-specific. Classic investigations emphasize that histone H1.0 is engaged in the organization of nuclear chromatin accounting for formation and maintenance of its nucleosomal and higher-order structure, and thus influences gene expression. However, the recent data confirmed histone H1.0 peculiar localization in the nucleolus and unexpectedly revealed its potential for regulation of nucleolar, RNA-dependent, activity via interaction with other proteins. According to such findings, histone H1.0 participates in the formation of gene-coded information through its control at both transcriptional and translational levels. In order to reappraise the biological significance of histone H1.0, both aspects of its activity are presented in this review.
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Affiliation(s)
- Andrzej Kowalski
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, Świętokrzyska 15, 25-406 Kielce, Poland
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47
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Cutter AR, Hayes JJ. Linker histones: novel insights into structure-specific recognition of the nucleosome. Biochem Cell Biol 2016; 95:171-178. [PMID: 28177778 DOI: 10.1139/bcb-2016-0097] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Linker histones (H1s) are a primary component of metazoan chromatin, fulfilling numerous functions, both in vitro and in vivo, including stabilizing the wrapping of DNA around the nucleosome, promoting folding and assembly of higher order chromatin structures, influencing nucleosome spacing on DNA, and regulating specific gene expression. However, many molecular details of how H1 binds to nucleosomes and recognizes unique structural features on the nucleosome surface remain undefined. Numerous, confounding studies are complicated not only by experimental limitations, but the use of different linker histone isoforms and nucleosome constructions. This review summarizes the decades of research that has resulted in several models of H1 association with nucleosomes, with a focus on recent advances that suggest multiple modes of H1 interaction in chromatin, while highlighting the remaining questions.
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Affiliation(s)
- Amber R Cutter
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.,Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jeffrey J Hayes
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.,Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
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48
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Abstract
By performing high-throughput chromosome conformation capture analyses in embryonic stem cells depleted of the linker histone H1, Geeven and colleagues have uncovered exciting new evidence concerning a role for this histone in modulating three-dimensional genome architecture and chromatin organization. Please see link to Research article: http://www.genomebiology.com/2015/16/1/289
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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. .,Institute of Functional Epigenetics, Helmholtz Zentrum Munich, 85764, Oberschleißheim, Germany.
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49
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Jordan A. Histone H1 in gene expression and development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:429-30. [PMID: 26772994 DOI: 10.1016/j.bbagrm.2016.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Albert Jordan
- Molecular Biology Institute of Barcelona IBMB-CSIC, Department of Molecular Genomics, Scientific Park of Barcelona, Baldiri i Reixac 4, 08028 Barcelona, Catalonia, Spain.
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