101
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Leicher R, Osunsade A, Chua GNL, Faulkner SC, Latham AP, Watters JW, Nguyen T, Beckwitt EC, Christodoulou-Rubalcava S, Young PG, Zhang B, David Y, Liu S. Single-stranded nucleic acid binding and coacervation by linker histone H1. Nat Struct Mol Biol 2022; 29:463-471. [PMID: 35484234 PMCID: PMC9117509 DOI: 10.1038/s41594-022-00760-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/14/2022] [Indexed: 02/04/2023]
Abstract
The H1 linker histone family is the most abundant group of eukaryotic chromatin-binding proteins. However, their contribution to chromosome structure and function remains incompletely understood. Here we use single-molecule fluorescence and force microscopy to directly visualize the behavior of H1 on various nucleic acid and nucleosome substrates. We observe that H1 coalesces around single-stranded DNA generated from tension-induced DNA duplex melting. Using a droplet fusion assay controlled by optical tweezers, we find that single-stranded nucleic acids mediate the formation of gel-like H1 droplets, whereas H1-double-stranded DNA and H1-nucleosome droplets are more liquid-like. Molecular dynamics simulations reveal that multivalent and transient engagement of H1 with unpaired DNA strands drives their enhanced phase separation. Using eGFP-tagged H1, we demonstrate that inducing single-stranded DNA accumulation in cells causes an increase in H1 puncta that are able to fuse. We further show that H1 and Replication Protein A occupy separate nuclear regions, but that H1 colocalizes with the replication factor Proliferating Cell Nuclear Antigen, particularly after DNA damage. Overall, our results provide a refined perspective on the diverse roles of H1 in genome organization and maintenance, and indicate its involvement at stalled replication forks.
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Affiliation(s)
- Rachel Leicher
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Adewola Osunsade
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Gabriella N L Chua
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Sarah C Faulkner
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John W Watters
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Tuan Nguyen
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
- Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Emily C Beckwitt
- Laboratory of DNA Replication, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | | | - Paul G Young
- Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA.
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA.
- Tri-Institutional MD-PhD Program, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, USA.
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA.
- Tri-Institutional MD-PhD Program, New York, NY, USA.
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102
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Etier A, Dumetz F, Chéreau S, Ponts N. Post-Translational Modifications of Histones Are Versatile Regulators of Fungal Development and Secondary Metabolism. Toxins (Basel) 2022; 14:toxins14050317. [PMID: 35622565 PMCID: PMC9145779 DOI: 10.3390/toxins14050317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 02/04/2023] Open
Abstract
Chromatin structure is a major regulator of DNA-associated processes, such as transcription, DNA repair, and replication. Histone post-translational modifications, or PTMs, play a key role on chromatin dynamics. PTMs are involved in a wide range of biological processes in eukaryotes, including fungal species. Their deposition/removal and their underlying functions have been extensively investigated in yeasts but much less in other fungi. Nonetheless, the major role of histone PTMs in regulating primary and secondary metabolisms of filamentous fungi, including human and plant pathogens, has been pinpointed. In this review, an overview of major identified PTMs and their respective functions in fungi is provided, with a focus on filamentous fungi when knowledge is available. To date, most of these studies investigated histone acetylations and methylations, but the development of new methodologies and technologies increasingly allows the wider exploration of other PTMs, such as phosphorylation, ubiquitylation, sumoylation, and acylation. Considering the increasing number of known PTMs and the full range of their possible interactions, investigations of the subsequent Histone Code, i.e., the biological consequence of the combinatorial language of all histone PTMs, from a functional point of view, are exponentially complex. Better knowledge about histone PTMs would make it possible to efficiently fight plant or human contamination, avoid the production of toxic secondary metabolites, or optimize the industrial biosynthesis of certain beneficial compounds.
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103
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Gurova K. Can aggressive cancers be identified by the "aggressiveness" of their chromatin? Bioessays 2022; 44:e2100212. [PMID: 35452144 DOI: 10.1002/bies.202100212] [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] [Received: 09/07/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/15/2022]
Abstract
Phenotypic plasticity is a crucial feature of aggressive cancer, providing the means for cancer progression. Stochastic changes in tumor cell transcriptional programs increase the chances of survival under any condition. I hypothesize that unstable chromatin permits stochastic transitions between transcriptional programs in aggressive cancers and supports non-genetic heterogeneity of tumor cells as a basis for their adaptability. I present a mechanistic model for unstable chromatin which includes destabilized nucleosomes, mobile chromatin fibers and random enhancer-promoter contacts, resulting in stochastic transcription. I suggest potential markers for "unsettled" chromatin in tumors associated with poor prognosis. Although many of the characteristics of unstable chromatin have been described, they were mostly used to explain changes in the transcription of individual genes. I discuss approaches to evaluate the role of unstable chromatin in non-genetic tumor cell heterogeneity and suggest using the degree of chromatin instability and transcriptional noise in tumor cells to predict cancer aggressiveness.
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Affiliation(s)
- Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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104
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Burge N, Thuma JL, Hong ZZ, Jamison KB, Ottesen JJ, Poirier MG. H1.0 C Terminal Domain Is Integral for Altering Transcription Factor Binding within Nucleosomes. Biochemistry 2022; 61:625-638. [PMID: 35377618 PMCID: PMC9022651 DOI: 10.1021/acs.biochem.2c00001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 02/24/2022] [Indexed: 12/25/2022]
Abstract
The linker histone H1 is a highly prevalent protein that compacts chromatin and regulates DNA accessibility and transcription. However, the mechanisms behind H1 regulation of transcription factor (TF) binding within nucleosomes are not well understood. Using in vitro fluorescence assays, we positioned fluorophores throughout human H1 and the nucleosome, then monitored the distance changes between H1 and the histone octamer, H1 and nucleosomal DNA, or nucleosomal DNA and the histone octamer to monitor the H1 movement during TF binding. We found that H1 remains bound to the nucleosome dyad, while the C terminal domain (CTD) releases the linker DNA during nucleosome partial unwrapping and TF binding. In addition, mutational studies revealed that a small 16 amino acid region at the beginning of the H1 CTD is largely responsible for altering nucleosome wrapping and regulating TF binding within nucleosomes. We then investigated physiologically relevant post-translational modifications (PTMs) in human H1 by preparing fully synthetic H1 using convergent hybrid phase native chemical ligation. Both individual PTMs and combinations of phosphorylation and citrullination of H1 had no detectable influence on nucleosome binding and nucleosome wrapping, and had only a minor impact on H1 regulation of TF occupancy within nucleosomes. This suggests that these H1 PTMs function by other mechanisms. Our results highlight the importance of the H1 CTD, in particular, the first 16 amino acids, in regulating nucleosome linker DNA dynamics and TF binding within the nucleosome.
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Affiliation(s)
- Nathaniel
L. Burge
- Ohio
State Biochemistry Program, The Ohio State
University, Columbus, Ohio 43210, United States
| | - Jenna L. Thuma
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ziyong Z. Hong
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Kevin B. Jamison
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jennifer J. Ottesen
- Ohio
State Biochemistry Program, The Ohio State
University, Columbus, Ohio 43210, United States
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Michael G. Poirier
- Ohio
State Biochemistry Program, The Ohio State
University, Columbus, Ohio 43210, United States
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
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105
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Serna-Pujol N, Salinas-Pena M, Mugianesi F, Le Dily F, Marti-Renom MA, Jordan A. Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion. Nucleic Acids Res 2022; 50:3892-3910. [PMID: 35380694 PMCID: PMC9023279 DOI: 10.1093/nar/gkac226] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022] Open
Abstract
Up to seven members of the histone H1 family may contribute to chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down of multiple H1 variants deregulates many genes, promotes the appearance of genome-wide accessibility sites and triggers an interferon response via activation of heterochromatic repeats. However, how these changes in the expression profile relate to the re-distribution of H1 variants as well as to genome conformational changes have not been yet studied. Here, we combined ChIP-seq of five endogenous H1 variants with Chromosome Conformation Capture analysis in wild-type and H1.2/H1.4 knock-down T47D cells. The results indicate that H1 variants coexist in the genome in two large groups depending on the local GC content and that their distribution is robust with respect to H1 depletion. Despite the small changes in H1 variants distribution, knock-down of H1 translated into more isolated but de-compacted chromatin structures at the scale of topologically associating domains (TADs). Such changes in TAD structure correlated with a coordinated gene expression response of their resident genes. This is the first report describing simultaneous profiling of five endogenous H1 variants and giving functional evidence of genome topology alterations upon H1 depletion in human cancer cells.
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Affiliation(s)
- Núria Serna-Pujol
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, 08028 Spain
| | - Mónica Salinas-Pena
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, 08028 Spain
| | - Francesca Mugianesi
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - François Le Dily
- Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain.,Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain.,Pompeu Fabra University, Doctor Aiguader 88, Barcelona 08003, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Albert Jordan
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, 08028 Spain
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106
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Nothof SA, Magdinier F, Van-Gils J. Chromatin Structure and Dynamics: Focus on Neuronal Differentiation and Pathological Implication. Genes (Basel) 2022; 13:genes13040639. [PMID: 35456445 PMCID: PMC9029427 DOI: 10.3390/genes13040639] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Chromatin structure is an essential regulator of gene expression. Its state of compaction contributes to the regulation of genetic programs, in particular during differentiation. Epigenetic processes, which include post-translational modifications of histones, DNA methylation and implication of non-coding RNA, are powerful regulators of gene expression. Neurogenesis and neuronal differentiation are spatio-temporally regulated events that allow the formation of the central nervous system components. Here, we review the chromatin structure and post-translational histone modifications associated with neuronal differentiation. Studying the impact of histone modifications on neuronal differentiation improves our understanding of the pathophysiological mechanisms of chromatinopathies and opens up new therapeutic avenues. In addition, we will discuss techniques for the analysis of histone modifications on a genome-wide scale and the pathologies associated with the dysregulation of the epigenetic machinery.
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Affiliation(s)
- Sophie A. Nothof
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Frédérique Magdinier
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Julien Van-Gils
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
- Reference Center AD SOOR, AnDDI-RARE, Inserm U 1211, Medical Genetics Department, Bordeaux University, Center Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France
- Correspondence:
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107
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Reece AS, Hulse GK. Geotemporospatial and causal inferential epidemiological overview and survey of USA cannabis, cannabidiol and cannabinoid genotoxicity expressed in cancer incidence 2003-2017: part 1 - continuous bivariate analysis. Arch Public Health 2022; 80:99. [PMID: 35354487 PMCID: PMC8966217 DOI: 10.1186/s13690-022-00811-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 01/29/2022] [Indexed: 01/07/2023] Open
Abstract
Background The genotoxic and cancerogenic impacts of population-wide cannabinoid exposure remains an open but highly salient question. The present report examines these issues from a continuous bivariate perspective with subsequent reports continuing categorical and detailed analyses. Methods Age-standardized state census incidence of 28 cancer types (including “All (non-skin) Cancer”) was sourced using SEER*Stat software from Centres for Disease Control and National Cancer Institute across US states 2001–2017. It was joined with drug exposure data from the nationally representative National Survey of Drug Use and Health conducted annually by the Substance Abuse and Mental Health Services Administration 2003–2017, response rate 74.1%. Cannabinoid data was from Federal seizure data. Income and ethnicity data sourced from the US Census Bureau. Data was processed in R. Results Nineteen thousand eight hundred seventy-seven age-standardized cancer rates were returned. Based on these rates and state populations this equated to 51,623,922 cancer cases over an aggregated population 2003–2017 of 124,896,418,350. Regression lines were charted for cancer-substance exposures for cigarettes, alcohol use disorder (AUD), cannabis, THC, cannabidiol, cannabichromene, cannabinol and cannabigerol. In this substance series positive trends were found for 14, 9, 6, 9, 12, 6, 9 and 7 cancers; with largest minimum E-Values (mEV) of 1.76 × 109, 4.67 × 108, 2.74 × 104, 4.72, 2.34 × 1018, 2.74 × 1017, 1.90 × 107, 5.05 × 109; and total sum of exponents of mEV of 34, 32, 13, 0, 103, 58, 25, 31 indicating that cannabidiol followed by cannabichromene are the most strongly implicated in environmental carcinogenesis. Breast cancer was associated with tobacco and all cannabinoids (from mEV = 3.53 × 109); “All Cancer” (non-skin) linked with cannabidiol (mEV = 1.43 × 1011); pediatric AML linked with cannabis (mEV = 19.61); testicular cancer linked with THC (mEV = 1.33). Cancers demonstrating elevated mEV in association with THC were: thyroid, liver, pancreas, AML, breast, oropharynx, CML, testis and kidney. Cancers demonstrating elevated mEV in relation to cannabidiol: prostate, bladder, ovary, all cancers, colorectum, Hodgkins, brain, Non-Hodgkins lymphoma, esophagus, breast and stomach. Conclusion Data suggest that cannabinoids including THC and cannabidiol are important community carcinogens exceeding the effects of tobacco or alcohol. Testicular, (prostatic) and ovarian tumours indicate mutagenic corruption of the germline in both sexes; pediatric tumourigenesis confirms transgenerational oncogenesis; quantitative criteria implying causality are fulfilled. Supplementary Information The online version contains supplementary material available at 10.1186/s13690-022-00811-8.
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Affiliation(s)
- Albert Stuart Reece
- Division of Psychiatry, University of Western Australia, Crawley, WA, 6009, Australia. .,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, 6027, Australia. .,, Brisbane, Australia.
| | - Gary Kenneth Hulse
- Division of Psychiatry, University of Western Australia, Crawley, WA, 6009, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, 6027, Australia
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108
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Rekvig OP. The Anti-DNA Antibodies: Their Specificities for Unique DNA Structures and Their Unresolved Clinical Impact-A System Criticism and a Hypothesis. Front Immunol 2022; 12:808008. [PMID: 35087528 PMCID: PMC8786728 DOI: 10.3389/fimmu.2021.808008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is diagnosed and classified by criteria, or by experience, intuition and traditions, and not by scientifically well-defined etiology(ies) or pathogenicity(ies). One central criterion and diagnostic factor is founded on theoretical and analytical approaches based on our imperfect definition of the term “The anti-dsDNA antibody”. “The anti-dsDNA antibody” holds an archaic position in SLE as a unique classification criterium and pathogenic factor. In a wider sense, antibodies to unique transcriptionally active or silent DNA structures and chromatin components may have individual and profound nephritogenic impact although not considered yet – not in theoretical nor in descriptive or experimental contexts. This hypothesis is contemplated here. In this analysis, our state-of-the-art conception of these antibodies is probed and found too deficient with respect to their origin, structural DNA specificities and clinical/pathogenic impact. Discoveries of DNA structures and functions started with Miescher’s Nuclein (1871), via Chargaff, Franklin, Watson and Crick, and continues today. The discoveries have left us with a DNA helix that presents distinct structures expressing unique operations of DNA. All structures are proven immunogenic! Unique autoimmune antibodies are described against e.g. ssDNA, elongated B DNA, bent B DNA, Z DNA, cruciform DNA, or individual components of chromatin. In light of the massive scientific interest in anti-DNA antibodies over decades, it is an unexpected observation that the spectrum of DNA structures has been known for decades without being implemented in clinical immunology. This leads consequently to a critical analysis of historical and contemporary evidence-based data and of ignored and one-dimensional contexts and hypotheses: i.e. “one antibody - one disease”. In this study radical viewpoints on the impact of DNA and chromatin immunity/autoimmunity are considered and discussed in context of the pathogenesis of lupus nephritis.
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Affiliation(s)
- Ole Petter Rekvig
- Section of Autoimmunity, Fürst Medical Laboratory, Oslo, Norway.,Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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109
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Zhang S, Postnikov Y, Lobanov A, Furusawa T, Deng T, Bustin M. H3K27ac nucleosomes facilitate HMGN localization at regulatory sites to modulate chromatin binding of transcription factors. Commun Biol 2022; 5:159. [PMID: 35197580 PMCID: PMC8866397 DOI: 10.1038/s42003-022-03099-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 02/01/2022] [Indexed: 11/09/2022] Open
Abstract
Nucleosomes containing acetylated H3K27 are a major epigenetic mark of active chromatin and identify cell-type specific chromatin regulatory regions which serve as binding sites for transcription factors. Here we show that the ubiquitous nucleosome binding proteins HMGN1 and HMGN2 bind preferentially to H3K27ac nucleosomes at cell-type specific chromatin regulatory regions. HMGNs bind directly to the acetylated nucleosome; the H3K27ac residue and linker DNA facilitate the preferential binding of HMGNs to the modified nucleosomes. Loss of HMGNs increases the levels of H3K27me3 and the histone H1 occupancy at enhancers and promoters and alters the interaction of transcription factors with chromatin. These experiments indicate that the H3K27ac epigenetic mark enhances the interaction of architectural protein with chromatin regulatory sites and identify determinants that facilitate the localization of HMGN proteins at regulatory sites to modulate cell-type specific gene expression.
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Affiliation(s)
- Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Yuri Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Maryland, MD, USA
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
- Cell Translation Laboratory, NCATS, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA.
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110
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Mondello P, Ansell SM, Nowakowski GS. Immune Epigenetic Crosstalk Between Malignant B Cells and the Tumor Microenvironment in B Cell Lymphoma. Front Genet 2022; 13:826594. [PMID: 35237302 PMCID: PMC8883034 DOI: 10.3389/fgene.2022.826594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/24/2022] [Indexed: 12/22/2022] Open
Abstract
Epigenetic reprogramming is a hallmark of lymphomagenesis, however its role in reshaping the tumor microenvironment is still not well understood. Here we review the most common chromatin modifier mutations in B cell lymphoma and their effect on B cells as well as on T cell landscape. We will also discuss precision therapy strategies to reverse their aberrant signaling by targeting mutated proteins or counterbalance epigenetic mechanisms.
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111
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Pillay LC, Nekati L, Makhwitine PJ, Ndlovu SI. Epigenetic Activation of Silent Biosynthetic Gene Clusters in Endophytic Fungi Using Small Molecular Modifiers. Front Microbiol 2022; 13:815008. [PMID: 35237247 PMCID: PMC8882859 DOI: 10.3389/fmicb.2022.815008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/19/2022] [Indexed: 11/29/2022] Open
Abstract
The discovery of silent biosynthetic gene clusters (BGCs) in fungi provides unlimited prospects to harness the secondary metabolites encoded by gene clusters for various applications, including pharmaceuticals. Amplifying these prospects is the new interest in exploring fungi living in the extremes, such as those associated with plants (fungal endophytes). Fungal species in endosymbiosis relationship with plants are recognized as the future factories of clinically relevant agents since discovering that they can produce similar metabolites as their plant host. The endophytes produce these compounds in natural environments as a defense mechanism against pathogens that infect the plant host or as a strategy for mitigating competitors. The signaling cascades leading to the expression of silent biosynthetic gene clusters in the natural environment remain unknown. Lack of knowledge on regulatory circuits of biosynthetic gene clusters limits the ability to exploit them in the laboratory. They are often silent and require tailor-designed strategies for activation. Epigenetic modification using small molecular compounds that alter the chromatin network, leading to the changes in secondary metabolites profile, has achieved considerable success. This review aims to comprehensively analyze the secondary metabolite profiles expressed after treatment with various epigenetic modifiers. We first describe the regulatory circuits governing the expression of secondary metabolites in fungi. Following this, we provide a detailed review of the small molecular modifiers, their mechanism(s) of action, and the diverse chemistries resulting from epigenetic modification. We further show that genetic deletion or epigenetic inhibition of histone deacetylases does not always lead to the overexpression or induction of silent secondary metabolites. Instead, the response is more complex and often leads to differential expression of secondary metabolites. Finally, we propose using this strategy as an initial screening tool to dereplicate promising fungal species.
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112
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Shukla S, Agarwal P, Kumar A. Disordered regions tune order in chromatin organization and function. Biophys Chem 2022; 281:106716. [PMID: 34844028 DOI: 10.1016/j.bpc.2021.106716] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins or hybrid proteins with ordered domains and disordered regions (both collectively designated as IDP(R)s) defy the well-established structure-function paradigm due to their ability to perform multiple biological functions even in the absence of a well-defined 3D structure. IDP(R)s have a unique ability to exist as a functional heterogeneous ensemble, where they adopt multiple thermodynamically stable conformations with low energy barriers between states. The resultant structural plasticity or conformational adaptability provides them with a high functional diversity and ease of regulation. Hence, IDP(R)s are highly efficient biological machinery to mediate intricate cellular functions such as signaling, gene expression, and assembly of complex structures. One such structure is the nucleoprotein complex known as Chromatin. Interestingly, the proteins involved in shaping up the structure and function of chromatin are abundant in disordered regions, which serve more than just as mere flexible linkers. The disordered regions are involved in crucial processes such as gene expression regulation, chromatin architecture maintenance, and liquid-liquid phase separation initiation. This review is an attempt to explore the advantages and the functional and regulatory roles of intrinsic disorder in several Chromatin Associated Proteins from a mechanistic standpoint.
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Affiliation(s)
- Shivangi Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Prakhar Agarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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113
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Lai S, Jia J, Cao X, Zhou PK, Gao S. Molecular and Cellular Functions of the Linker Histone H1.2. Front Cell Dev Biol 2022; 9:773195. [PMID: 35087830 PMCID: PMC8786799 DOI: 10.3389/fcell.2021.773195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 01/14/2023] Open
Abstract
Linker histone H1.2, which belongs to the linker histone family H1, plays a crucial role in the maintenance of the stable higher-order structures of chromatin and nucleosomes. As a critical part of chromatin structure, H1.2 has an important function in regulating chromatin dynamics and participates in multiple other cellular processes as well. Recent work has also shown that linker histone H1.2 regulates the transcription levels of certain target genes and affects different processes as well, such as cancer cell growth and migration, DNA duplication and DNA repair. The present work briefly summarizes the current knowledge of linker histone H1.2 modifications. Further, we also discuss the roles of linker histone H1.2 in the maintenance of genome stability, apoptosis, cell cycle regulation, and its association with disease.
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Affiliation(s)
- Shuting Lai
- Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, China.,Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jin Jia
- Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China.,School of Medicine, University of South China, Hengyang, China
| | - Xiaoyu Cao
- Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China.,School of Life Sciences, Hebei University, Baoding, China
| | - Ping-Kun Zhou
- Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, China.,Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Shanshan Gao
- Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
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114
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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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115
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Martinsen JH, Saar D, Fernandes CB, Schuler B, Bugge K, Kragelund BB. Structure, Dynamics and Stability of the Globular Domain of Human Linker Histone H1.0 and the Role of Positive Charges. Protein Sci 2022; 31:918-932. [PMID: 35066947 PMCID: PMC8927875 DOI: 10.1002/pro.4281] [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: 11/04/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 11/25/2022]
Abstract
Linker histone H1 (H1) is an abundant chromatin‐binding protein that acts as an epigenetic regulator binding to nucleosomes and altering chromatin structures and dynamics. Nonetheless, the mechanistic details of its function remain poorly understood. Recent work suggest that the number and position of charged side chains on the globular domain (GD) of H1 influence chromatin structure and hence gene repression. Here, we solved the solution structure of the unbound GD of human H1.0, revealing that the structure is almost completely unperturbed by complex formation, except for a loop connecting two antiparallel β‐strands. We further quantified the role of the many positive charges of the GD for its structure and conformational stability through the analysis of 11 charge variants. We find that modulating the number of charges has little effect on the structure, but the stability is affected, resulting in a difference in melting temperature of 26 K between GD of net charge +5 versus +13. This result suggests that the large number of positive charges on H1‐GDs have evolved for function rather than structure and high stability. The stabilization of the GD upon binding to DNA can thus be expected to have a pronounced electrostatic component, a contribution that is amenable to modulation by posttranslational modifications, especially acetylation and phosphorylation. PDB Code(s): 6hq1;
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Affiliation(s)
- Jacob H Martinsen
- REPIN and the Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Ole Maaloes Vej 5, DK-.2200, Copenhagen N, Denmark
| | - Daniel Saar
- REPIN and the Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Ole Maaloes Vej 5, DK-.2200, Copenhagen N, Denmark
| | - Catarina B Fernandes
- REPIN and the Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Ole Maaloes Vej 5, DK-.2200, Copenhagen N, Denmark
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.,Department of Physics, Winterthurerstrasse 190, 8057 University of Zurich, Zurich, Switzerland
| | - Katrine Bugge
- REPIN and the Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Ole Maaloes Vej 5, DK-.2200, Copenhagen N, Denmark
| | - Birthe B Kragelund
- REPIN and the Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Ole Maaloes Vej 5, DK-.2200, Copenhagen N, Denmark
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116
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Ito K, Takizawa T. Nuclear Architecture in the Nervous System. Results Probl Cell Differ 2022; 70:419-442. [PMID: 36348117 DOI: 10.1007/978-3-031-06573-6_15] [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] [Indexed: 06/16/2023]
Abstract
Neurons and glial cells in the nervous system exhibit different gene expression programs for neural development and function. These programs are controlled by the epigenetic regulatory layers in the nucleus. The nucleus is a well-organized subcellular organelle that includes chromatin, the nuclear lamina, and nuclear bodies. These subnuclear components operate together as epigenetic regulators of neural development and function and are collectively called the nuclear architecture. In the nervous system, dynamic rearrangement of the nuclear architecture has been observed in each cell type, especially in neurons, allowing for their specialized functions, including learning and memory formation. Although the importance of nuclear architecture has been debated for decades, the paradigm has been changing rapidly, owing to the development of new technologies. Here, we reviewed the latest studies on nuclear geometry, nuclear bodies, and heterochromatin compartments, as well as summarized recent novel insights regarding radial positioning, chromatin condensation, and chromatin interaction between genes and cis-regulatory elements.
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Affiliation(s)
- Kenji Ito
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, Pennsylvania, USA
| | - Takumi Takizawa
- Department of Pediatrics, Gunma University Graduate School of Medicine, Maebashi, Japan.
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117
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Amigo R, Farkas C, Gidi C, Hepp MI, Cartes N, Tarifeño E, Workman JL, Gutiérrez JL. The linker histone Hho1 modulates the activity of ATP-dependent chromatin remodeling complexes. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194781. [PMID: 34963628 DOI: 10.1016/j.bbagrm.2021.194781] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 11/30/2021] [Accepted: 12/12/2021] [Indexed: 02/07/2023]
Abstract
Diverse factors play roles in chromatin dynamics, including linker proteins. Among them are high mobility group (HMG) box family proteins and linker histones. In the yeast Saccharomyces cerevisiae, Hmo1 has been identified as an HMG-box protein. This protein displays properties that are in agreement with this allocation. However, a number of studies have postulated that Hmo1 functions as a linker histone in yeast. On the other hand, when discovered, the Hho1 protein was identified as a linker histone. While multiple studies support this classification, some findings point to characteristics of Hho1 that are dissimilar to those commonly assigned to linker histones. In order to better understand the roles played by Hmo1 and Hho1 in chromatin dynamics and transcriptional regulation, we performed several analyses directly comparing these two proteins. Our analyses of genome-wide binding profiles support the belonging of Hmo1 to the HMGB family and Hho1 to the linker histones family. Interestingly, by performing protein-protein interaction analyses we found that both Hmo1 and Hho1 display physical interaction with the ATP-dependent chromatin remodeling complexes RSC, ISW1a and SWI/SNF. Moreover, by carrying out nucleosome remodeling assays, we found that both proteins stimulate the activity of the ISW1a complex. However, in the case of RSC, Hmo1 and Hho1 displayed differential properties, with Hho1 mainly showing an inhibitory effect. Our results are in agreement with the opposite roles played by RSC and ISW1a in chromatin dynamics and transcriptional regulation, and expand the view for the roles played by Hho1 and linker histones.
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Affiliation(s)
- Roberto Amigo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Carlos Farkas
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Cristian Gidi
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Matias I Hepp
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Natalia Cartes
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Estefanía Tarifeño
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E 50(th) Street, Kansas City, MO 64110, USA
| | - José L Gutiérrez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile.
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118
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Soshnev AA, Allis CD, Cesarman E, Melnick AM. Histone H1 Mutations in Lymphoma: A Link(er) between Chromatin Organization, Developmental Reprogramming, and Cancer. Cancer Res 2021; 81:6061-6070. [PMID: 34580064 PMCID: PMC8678342 DOI: 10.1158/0008-5472.can-21-2619] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022]
Abstract
Aberrant cell fate decisions due to transcriptional misregulation are central to malignant transformation. Histones are the major constituents of chromatin, and mutations in histone-encoding genes are increasingly recognized as drivers of oncogenic transformation. Mutations in linker histone H1 genes were recently identified as drivers of peripheral lymphoid malignancy. Loss of H1 in germinal center B cells results in widespread chromatin decompaction, redistribution of core histone modifications, and reactivation of stem cell-specific transcriptional programs. This review explores how linker histones and mutations therein regulate chromatin structure, highlighting reciprocal relationships between epigenetic circuits, and discusses the emerging role of aberrant three-dimensional chromatin architecture in malignancy.
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Affiliation(s)
- Alexey A Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York.
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Ari M Melnick
- Division of Hematology & Medical Oncology, Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York.
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119
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Cai Q, Gan C, Tang C, Wu H, Gao J. Mechanism and Therapeutic Opportunities of Histone Modifications in Chronic Liver Disease. Front Pharmacol 2021; 12:784591. [PMID: 34887768 PMCID: PMC8650224 DOI: 10.3389/fphar.2021.784591] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/08/2021] [Indexed: 02/05/2023] Open
Abstract
Chronic liver disease (CLD) represents a global health problem, accounting for the heavy burden of disability and increased health care utilization. Epigenome alterations play an important role in the occurrence and progression of CLD. Histone modifications, which include acetylation, methylation, and phosphorylation, represent an essential part of epigenetic modifications that affect the transcriptional activity of genes. Different from genetic mutations, histone modifications are plastic and reversible. They can be modulated pharmacologically without changing the DNA sequence. Thus, there might be chances to establish interventional solutions by targeting histone modifications to reverse CLD. Here we summarized the roles of histone modifications in the context of alcoholic liver disease (ALD), metabolic associated fatty liver disease (MAFLD), viral hepatitis, autoimmune liver disease, drug-induced liver injury (DILI), and liver fibrosis or cirrhosis. The potential targets of histone modifications for translation into therapeutics were also investigated. In prospect, high efficacy and low toxicity drugs that are selectively targeting histone modifications are required to completely reverse CLD and prevent the development of liver cirrhosis and malignancy.
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Affiliation(s)
- Qiuyu Cai
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Can Gan
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Chengwei Tang
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Wu
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Jinhang Gao
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
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120
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Lynch KL, Dillon MR, Bat-Erdene M, Lewis HC, Kaai RJ, Arnold EA, Avgousti DC. A viral histone-like protein exploits antagonism between linker histones and HMGB proteins to obstruct the cell cycle. Curr Biol 2021; 31:5227-5237.e7. [PMID: 34666003 DOI: 10.1016/j.cub.2021.09.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/30/2021] [Accepted: 09/17/2021] [Indexed: 11/17/2022]
Abstract
Virus infection necessarily requires redirecting cellular resources toward viral progeny production. Adenovirus encodes the histone-like protein VII, which causes catastrophic global reorganization of host chromatin to promote virus infection. Protein VII recruits the family of high mobility group box (HMGB) proteins to chromatin along with the histone chaperone SET. As a consequence of this recruitment, we find that protein VII causes chromatin depletion of several linker histone H1 isoforms. The relationship between linker histone H1 and the functionally opposite HMGB proteins is critical for higher-order chromatin structure. However, the physiological consequences of perturbing this relationship are largely unknown. Here, we employ complementary systems in Saccharomyces cerevisiae and human cells to demonstrate that adenovirus protein VII disrupts the H1-HMGB balance to obstruct the cell cycle. We find that protein VII causes an accumulation of G2/M cells both in yeast and human systems, underscoring the high conservation of this chromatin vulnerability. In contrast, adenovirus E1A and E1B proteins are well established to override cell cycle regulation and promote transformation of human cells. Strikingly, we find that protein VII obstructs the cell cycle, even in the presence of E1A and E1B. We further show that, in a protein-VII-deleted infection, several cell cycle markers are regulated differently compared to wild-type infection, supporting our model that protein VII plays an integral role in hijacking cell cycle regulation during infection. Together, our results demonstrate that protein VII targets H1-HMGB1 antagonism to obstruct cell cycle progression, revealing an unexpected chromatin vulnerability exploited for viral benefit.
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Affiliation(s)
- Kelsey L Lynch
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Melanie R Dillon
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Mongoljin Bat-Erdene
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Hannah C Lewis
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA; Molecular & Cellular Biology in Seattle, Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Robin J Kaai
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA; Molecular & Cellular Biology in Seattle, Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Edward A Arnold
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA; Microbiology Graduate Program, University of Washington, 1705 NE Pacific Street, Box 357735, Seattle, WA 98195, USA
| | - Daphne C Avgousti
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA; Molecular & Cellular Biology in Seattle, Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA; Microbiology Graduate Program, University of Washington, 1705 NE Pacific Street, Box 357735, Seattle, WA 98195, USA.
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121
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Sheban D, Shani T, Maor R, Aguilera-Castrejon A, Mor N, Oldak B, Shmueli MD, Eisenberg-Lerner A, Bayerl J, Hebert J, Viukov S, Chen G, Kacen A, Krupalnik V, Chugaeva V, Tarazi S, Rodríguez-delaRosa A, Zerbib M, Ulman A, Masarwi S, Kupervaser M, Levin Y, Shema E, David Y, Novershtern N, Hanna JH, Merbl Y. SUMOylation of linker histone H1 drives chromatin condensation and restriction of embryonic cell fate identity. Mol Cell 2021; 82:106-122.e9. [PMID: 34875212 DOI: 10.1016/j.molcel.2021.11.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022]
Abstract
The fidelity of the early embryonic program is underlined by tight regulation of the chromatin. Yet, how the chromatin is organized to prohibit the reversal of the developmental program remains unclear. Specifically, the totipotency-to-pluripotency transition marks one of the most dramatic events to the chromatin, and yet, the nature of histone alterations underlying this process is incompletely characterized. Here, we show that linker histone H1 is post-translationally modulated by SUMO2/3, which facilitates its fixation onto ultra-condensed heterochromatin in embryonic stem cells (ESCs). Upon SUMOylation depletion, the chromatin becomes de-compacted and H1 is evicted, leading to totipotency reactivation. Furthermore, we show that H1 and SUMO2/3 jointly mediate the repression of totipotent elements. Lastly, we demonstrate that preventing SUMOylation on H1 abrogates its ability to repress the totipotency program in ESCs. Collectively, our findings unravel a critical role for SUMOylation of H1 in facilitating chromatin repression and desolation of the totipotent identity.
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Affiliation(s)
- Daoud Sheban
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tom Shani
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Roey Maor
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Nofar Mor
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Bernardo Oldak
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Merav D Shmueli
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Jonathan Bayerl
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jakob Hebert
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Sergey Viukov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Guoyun Chen
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Assaf Kacen
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Vladislav Krupalnik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Valeriya Chugaeva
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shadi Tarazi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Mirie Zerbib
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Ulman
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Solaiman Masarwi
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Meital Kupervaser
- De Botton Institute for Protein Profiling, INCPM, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yishai Levin
- De Botton Institute for Protein Profiling, INCPM, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Noa Novershtern
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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122
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Aksenova AY, Zhuk AS, Lada AG, Zotova IV, Stepchenkova EI, Kostroma II, Gritsaev SV, Pavlov YI. Genome Instability in Multiple Myeloma: Facts and Factors. Cancers (Basel) 2021; 13:5949. [PMID: 34885058 PMCID: PMC8656811 DOI: 10.3390/cancers13235949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.
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Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna S. Zhuk
- International Laboratory “Computer Technologies”, ITMO University, 197101 St. Petersburg, Russia;
| | - Artem G. Lada
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA;
| | - Irina V. Zotova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Ivan I. Kostroma
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Sergey V. Gritsaev
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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123
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Herman AB, Occean JR, Sen P. Epigenetic dysregulation in cardiovascular aging and disease. THE JOURNAL OF CARDIOVASCULAR AGING 2021; 1. [PMID: 34790973 PMCID: PMC8594871 DOI: 10.20517/jca.2021.16] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cardiovascular disease (CVD) is the leading cause of mortality and morbidity for all sexes, racial and ethnic groups. Age, and its associated physiological and pathological consequences, exacerbate CVD incidence and progression, while modulation of biological age with interventions track with cardiovascular health. Despite the strong link between aging and CVD, surprisingly few studies have directly investigated heart failure and vascular dysfunction in aged models and subjects. Nevertheless, strong correlations have been found between heart disease, atherosclerosis, hypertension, fibrosis, and regeneration efficiency with senescent cell burden and its proinflammatory sequelae. In agreement, senotherapeutics have had success in reducing the detrimental effects in experimental models of cardiovascular aging and disease. Aside from senotherapeutics, cellular reprogramming strategies targeting epigenetic enzymes remain an unexplored yet viable option for reversing or delaying CVD. Epigenetic alterations comprising local and global changes in DNA and histone modifications, transcription factor binding, disorganization of the nuclear lamina, and misfolding of the genome are hallmarks of aging. Limited studies in the aging cardiovascular system of murine models or human patient samples have identified strong correlations between the epigenome, age, and senescence. Here, we compile the findings in published studies linking epigenetic changes to CVD and identify clear themes of epigenetic deregulation during aging. Pending direct investigation of these general mechanisms in aged tissues, this review predicts that future work will establish epigenetic rejuvenation as a potent method to delay CVD.
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Affiliation(s)
- Allison B Herman
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - James R Occean
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
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124
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Bonitto K, Sarathy K, Atai K, Mitra M, Coller HA. Is There a Histone Code for Cellular Quiescence? Front Cell Dev Biol 2021; 9:739780. [PMID: 34778253 PMCID: PMC8586460 DOI: 10.3389/fcell.2021.739780] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/17/2021] [Indexed: 12/14/2022] Open
Abstract
Many of the cells in our bodies are quiescent, that is, temporarily not dividing. Under certain physiological conditions such as during tissue repair and maintenance, quiescent cells receive the appropriate stimulus and are induced to enter the cell cycle. The ability of cells to successfully transition into and out of a quiescent state is crucial for many biological processes including wound healing, stem cell maintenance, and immunological responses. Across species and tissues, transcriptional, epigenetic, and chromosomal changes associated with the transition between proliferation and quiescence have been analyzed, and some consistent changes associated with quiescence have been identified. Histone modifications have been shown to play a role in chromatin packing and accessibility, nucleosome mobility, gene expression, and chromosome arrangement. In this review, we critically evaluate the role of different histone marks in these processes during quiescence entry and exit. We consider different model systems for quiescence, each of the most frequently monitored candidate histone marks, and the role of their writers, erasers and readers. We highlight data that support these marks contributing to the changes observed with quiescence. We specifically ask whether there is a quiescence histone “code,” a mechanism whereby the language encoded by specific combinations of histone marks is read and relayed downstream to modulate cell state and function. We conclude by highlighting emerging technologies that can be applied to gain greater insight into the role of a histone code for quiescence.
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Affiliation(s)
- Kenya Bonitto
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kirthana Sarathy
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kaiser Atai
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Mithun Mitra
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Hilary A Coller
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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125
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Yu X, Li M, Guo C, Wu Y, Zhao L, Shi Q, Song J, Song B. Therapeutic Targeting of Cancer: Epigenetic Homeostasis. Front Oncol 2021; 11:747022. [PMID: 34765551 PMCID: PMC8576334 DOI: 10.3389/fonc.2021.747022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
A large number of studies have revealed that epigenetics plays an important role in cancer development. However, the currently-developed epigenetic drugs cannot achieve a stable curative effect. Thus, it may be necessary to redefine the role of epigenetics in cancer development. It has been shown that embryonic development and tumor development share significant similarities in terms of biological behavior and molecular expression patterns, and epigenetics may be the link between them. Cell differentiation is likely a manifestation of epigenetic homeostasis at the cellular level. In this article, we introduced the importance of epigenetic homeostasis in cancer development and analyzed the shortcomings of current epigenetic treatment regimens. Understanding the dynamic process of epigenetic homeostasis in organ development can help us characterize cancer according to its differentiation stages, explore new targets for cancer treatment, and improve the clinical prognosis of patients with cancer.
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Affiliation(s)
- Xiaoyuan Yu
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Menglu Li
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Chunyan Guo
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuesheng Wu
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Li Zhao
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Qinying Shi
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Jianbo Song
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Bin Song
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
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126
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To export, or not to export: how nuclear export factor variants resolve Piwi's dilemma. Biochem Soc Trans 2021; 49:2073-2079. [PMID: 34643228 DOI: 10.1042/bst20201171] [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: 03/29/2021] [Revised: 09/06/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022]
Abstract
Piwi-interacting RNAs (piRNAs) defend animal gonads by guiding PIWI-clade Argonaute proteins to silence transposons. The nuclear Piwi/piRNA complexes confer transcriptional repression of transposons, which is accompanied with heterochromatin formation at target loci. On the other hand, piRNA clusters, genomic loci that transcribe piRNA precursors composed of transposon fragments, are often recognized by piRNAs to define their heterochromatic identity. Therefore, Piwi/piRNA complexes must resolve this conundrum of silencing transposons while allowing the expression of piRNA precursors, at least in Drosophila germlines. This review is focused on recent advances how the piRNA pathway deals with this genetic conflict.
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127
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Dai S, Qu L, Li J, Chen Y. Toward a mechanistic understanding of DNA binding by forkhead transcription factors and its perturbation by pathogenic mutations. Nucleic Acids Res 2021; 49:10235-10249. [PMID: 34551426 PMCID: PMC8501956 DOI: 10.1093/nar/gkab807] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 01/12/2023] Open
Abstract
Forkhead box (FOX) proteins are an evolutionarily conserved family of transcription factors that play numerous regulatory roles in eukaryotes during developmental and adult life. Dysfunction of FOX proteins has been implicated in a variety of human diseases, including cancer, neurodevelopment disorders and genetic diseases. The FOX family members share a highly conserved DNA-binding domain (DBD), which is essential for DNA recognition, binding and function. Since the first FOX structure was resolved in 1993, >30 FOX structures have been reported to date. It is clear now that the structure and DNA recognition mechanisms vary among FOX members; however, a systematic review on this aspect is lacking. In this manuscript, we present an overview of the mechanisms by which FOX transcription factors bind DNA, including protein structures, DNA binding properties and disease-causing mutations. This review should enable a better understanding of FOX family transcription factors for basic researchers and clinicians.
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Affiliation(s)
- Shuyan Dai
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Linzhi Qu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jun Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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128
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Huang J, Dong J, Qu LJ. From birth to function: Male gametophyte development in flowering plants. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102118. [PMID: 34625367 PMCID: PMC9039994 DOI: 10.1016/j.pbi.2021.102118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/13/2021] [Accepted: 08/25/2021] [Indexed: 05/08/2023]
Abstract
Male germline development in flowering plants involves two distinct and successive phases, microsporogenesis and microgametogenesis, which involve one meiosis followed by two rounds of mitosis. Many aspects of distinctions after mitosis between the vegetative cell and the male germ cells are seen, from morphology to structure, and the differential functions of the two cell types in the male gametophyte are differentially needed and required for double fertilization. The two sperm cells, carriers of the hereditary substances, depend on the vegetative cell/pollen tube to be delivered to the female gametophyte for double fertilization. Thus, the intercellular communication and coordinated activity within the male gametophyte probably represent the most subtle regulation in flowering plants to guarantee the success of reproduction. This review will focus on what we have known about the differentiation process and the functional diversification of the vegetative cell and the male germ cell, the most crucial cell types for plant fertility and crop production.
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Affiliation(s)
- Jiaying Huang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China; Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA; Department of Plant Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08901, USA
| | - Juan Dong
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA; Department of Plant Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08901, USA.
| | - Li-Jia Qu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China; The National Plant Gene Research Center (Beijing), Beijing 100101, People's Republic of China.
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129
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Kato K, Kawaguchi A, Nagata K. Template activating factor-I epigenetically regulates the TERT transcription in human cancer cells. Sci Rep 2021; 11:17726. [PMID: 34489496 PMCID: PMC8421516 DOI: 10.1038/s41598-021-97009-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 08/19/2021] [Indexed: 11/09/2022] Open
Abstract
Telomere, the terminus of linear chromosome in eukaryotes, is composed of specific repeat DNA which is mainly synthesized by a protein complex called telomerase. The maintenance of telomere DNA is important for unlimited proliferative capacity of cancer cells. The telomerase activity is controlled by the expression level of telomerase reverse transcriptase (TERT), a catalytic unit of telomerase, in some species including human. Therefore, to reveal the regulatory mechanisms of the transcription of TERT gene is important for understanding the tumor development. We found that template activating factor-I (TAF-I), a multifunctional nuclear protein, is involved in the transcriptional activation of TERT for the maintenance of telomere DNA in HeLa cells. TAF-I maintains the histone H3 modifications involved in transcriptional activation and hypomethylated cytosines in CpG dinucleotides around the transcription start site (TSS) in the TERT gene locus. Collectively, TAF-I is involved in the maintenance of telomere DNA through the regulation of TERT transcription, then consequently the occurrence and/or recurrence of cancer cells.
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Affiliation(s)
- Kohsuke Kato
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan.
| | - Atsushi Kawaguchi
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan.,Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Kyosuke Nagata
- Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.
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130
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Shen CH, Allan J. MNase Digestion Protection Patterns of the Linker DNA in Chromatosomes. Cells 2021; 10:cells10092239. [PMID: 34571888 PMCID: PMC8469290 DOI: 10.3390/cells10092239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/16/2022] Open
Abstract
The compact nucleosomal structure limits DNA accessibility and regulates DNA-dependent cellular activities. Linker histones bind to nucleosomes and compact nucleosomal arrays into a higher-order chromatin structure. Recent developments in high throughput technologies and structural computational studies provide nucleosome positioning at a high resolution and contribute to the information of linker histone location within a chromatosome. However, the precise linker histone location within the chromatin fibre remains unclear. Using monomer extension, we mapped core particle and chromatosomal positions over a core histone-reconstituted, 1.5 kb stretch of DNA from the chicken adult β-globin gene, after titration with linker histones and linker histone globular domains. Our results show that, although linker histone globular domains and linker histones display a wide variation in their binding affinity for different positioned nucleosomes, they do not alter nucleosome positions or generate new nucleosome positions. Furthermore, the extra ~20 bp of DNA protected in a chromatosome is usually symmetrically distributed at each end of the core particle, suggesting linker histones or linker histone globular domains are located close to the nucleosomal dyad axis.
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Affiliation(s)
- Chang-Hui Shen
- Biology Department, College of Staten Island, City University of New York, 2800 Victory Boulevard, Staten Island, NY 10314, USA
- Biochemistry and Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY 10016, USA
- Institute for Macromolecular Assemblies, City University of New York, New York, NY 10031, USA
- Correspondence: ; Tel.: +1-718-982-3998; Fax: +1-718-982-3852
| | - James Allan
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK;
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131
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Nuclear import of histones. Biochem Soc Trans 2021; 48:2753-2767. [PMID: 33300986 PMCID: PMC7752055 DOI: 10.1042/bst20200572] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/30/2020] [Accepted: 11/13/2020] [Indexed: 12/14/2022]
Abstract
The transport of histones from the cytoplasm to the nucleus of the cell, through the nuclear membrane, is a cellular process that regulates the supply of new histones in the nucleus and is key for DNA replication and transcription. Nuclear import of histones is mediated by proteins of the karyopherin family of nuclear transport receptors. Karyopherins recognize their cargos through linear motifs known as nuclear localization/export sequences or through folded domains in the cargos. Karyopherins interact with nucleoporins, proteins that form the nuclear pore complex, to promote the translocation of their cargos into the nucleus. When binding to histones, karyopherins not only function as nuclear import receptors but also as chaperones, protecting histones from non-specific interactions in the cytoplasm, in the nuclear pore and possibly in the nucleus. Studies have also suggested that karyopherins might participate in histones deposition into nucleosomes. In this review we describe structural and biochemical studies from the last two decades on how karyopherins recognize and transport the core histone proteins H3, H4, H2A and H2B and the linker histone H1 from the cytoplasm to the nucleus, which karyopherin is the major nuclear import receptor for each of these histones, the oligomeric state of histones during nuclear import and the roles of post-translational modifications, histone-chaperones and RanGTP in regulating these nuclear import pathways.
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132
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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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133
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Shimohira T, Niimi H, Ohsugi Y, Tsuchiya Y, Morita K, Yoshida S, Hatasa M, Shiba T, Kadokura H, Yokose S, Katagiri S, Iwata T, Aoki A. Low-Level Erbium-Doped Yttrium Aluminum Garnet Laser Irradiation Induced Alteration of Gene Expression in Osteogenic Cells from Rat Calvariae. PHOTOBIOMODULATION PHOTOMEDICINE AND LASER SURGERY 2021; 39:566-577. [PMID: 34339325 DOI: 10.1089/photob.2020.4958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Objective: The aim of this study was to investigate the effect of low-level erbium-doped yttrium aluminum garnet (Er:YAG) laser irradiation on gene expression in osteogenic cells from rat calvariae. Background: Previous studies showed beneficial effects of laser irradiation on bone-related cells. However, few studies have examined the gene expression alteration by laser irradiation on osteogenic cells in a calcified condition. Materials and methods: Osteogenic cells were prepared by culturing rat calvarial osteoblast-like cells in osteoinductive medium for 21 days. The cells at the bottom of the culture dish were irradiated with Er:YAG laser (wavelength: 2.94 μm, energy density: 3.1 and 8.2 J/cm2) positioned at distance of 25 cm. Lactate dehydrogenase (LDH) assay of the irradiated cells was performed. After screening for genes related to bone formation, mechanotransduction, and thermal effect by quantitative polymerase chain reaction (qPCR), gene expression at 3 h after 3.1 J/cm2 irradiation was comprehensively analyzed using microarray. Results: No dramatical increase in surface temperature and LDH activities after laser irradiation were observed. Sost expression was significantly reduced at 3 h after 3.1 J/cm2 irradiation. Bcar1 and Hspa1a expression was significantly increased following 8.2 J/cm2 irradiation. Microarray analysis identified 116 differentially expressed genes. Gene set enrichment analysis showed enrichment of histone H3-K9 methylation and modification gene sets. Conclusions: Er:YAG laser irradiation, especially at 3.1 J/cm2, showed positive effect on the expression of genes related to bone formation in osteogenic cells, without inducing significant cell damage. These findings may represent critical mechanisms of early bone formation after Er:YAG laser irradiation.
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Affiliation(s)
- Tsuyoshi Shimohira
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hiromi Niimi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yujin Ohsugi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yosuke Tsuchiya
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kazuki Morita
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Sumiko Yoshida
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masahiro Hatasa
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hiroshi Kadokura
- Division of Endodontic and Operative Dentistry, Department of Restorative and Biomaterials Sciences, School of Dentistry, Meikai University, Saitama, Japan
| | - Satoshi Yokose
- Division of Endodontic and Operative Dentistry, Department of Restorative and Biomaterials Sciences, School of Dentistry, Meikai University, Saitama, Japan
| | - Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Akira Aoki
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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134
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Hai R, He L, Shu G, Yin G. Characterization of Histone Deacetylase Mechanisms in Cancer Development. Front Oncol 2021; 11:700947. [PMID: 34395273 PMCID: PMC8360675 DOI: 10.3389/fonc.2021.700947] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/05/2021] [Indexed: 02/01/2023] Open
Abstract
Over decades of studies, accumulating evidence has suggested that epigenetic dysregulation is a hallmark of tumours. Post-translational modifications of histones are involved in tumour pathogenesis and development mainly by influencing a broad range of physiological processes. Histone deacetylases (HDACs) and histone acetyltransferases (HATs) are pivotal epigenetic modulators that regulate dynamic processes in the acetylation of histones at lysine residues, thereby influencing transcription of oncogenes and tumour suppressor genes. Moreover, HDACs mediate the deacetylation process of many nonhistone proteins and thus orchestrate a host of pathological processes, such as tumour pathogenesis. In this review, we elucidate the functions of HDACs in cancer.
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Affiliation(s)
- Rihan Hai
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China.,School of Basic Medical Sciences, Central South University, Changsha, China
| | - Liuer He
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China.,School of Basic Medical Sciences, Central South University, Changsha, China
| | - Guang Shu
- School of Basic Medical Sciences, Central South University, Changsha, China
| | - Gang Yin
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
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135
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Bjarnason S, Ruidiaz SF, McIvor J, Mercadante D, Heidarsson PO. Protein intrinsic disorder on a dynamic nucleosomal landscape. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:295-354. [PMID: 34656332 DOI: 10.1016/bs.pmbts.2021.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The complex nucleoprotein landscape of the eukaryotic cell nucleus is rich in dynamic proteins that lack a stable three-dimensional structure. Many of these intrinsically disordered proteins operate directly on the first fundamental level of genome compaction: the nucleosome. Here we give an overview of how disordered interactions with and within nucleosomes shape the dynamics, architecture, and epigenetic regulation of the genetic material, controlling cellular transcription patterns. We highlight experimental and computational challenges in the study of protein disorder and illustrate how integrative approaches are increasingly unveiling the fine details of nuclear interaction networks. We finally dissect sequence properties encoded in disordered regions and assess common features of disordered nucleosome-binding proteins. As drivers of many critical biological processes, disordered proteins are integral to a comprehensive molecular view of the dynamic nuclear milieu.
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Affiliation(s)
- Sveinn Bjarnason
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland
| | - Sarah F Ruidiaz
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland
| | - Jordan McIvor
- School of Chemical Science, University of Auckland, Auckland, New Zealand
| | - Davide Mercadante
- School of Chemical Science, University of Auckland, Auckland, New Zealand.
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland.
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136
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DNA sequence-dependent positioning of the linker histone in a nucleosome: A single-pair FRET study. Biophys J 2021; 120:3747-3763. [PMID: 34293303 DOI: 10.1016/j.bpj.2021.07.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/25/2021] [Accepted: 07/13/2021] [Indexed: 01/01/2023] Open
Abstract
Linker histones (LHs) bind to nucleosomes with their globular domain (gH) positioned in either an on- or an off-dyad binding mode. Here, we study the effect of the linker DNA (L-DNA) sequence on the binding of a full-length LH, Xenopus laevis H1.0b, to a Widom 601 nucleosome core particle (NCP) flanked by two 40 bp long L-DNA arms, by single-pair FRET spectroscopy. We varied the sequence of the 11 bp of L-DNA adjoining the NCP on either side, making the sequence either A-tract, purely GC, or mixed with 64% AT. The labeled gH consistently exhibited higher FRET efficiency with the labeled L-DNA containing the A-tract than that with the pure-GC stretch, even when the stretches were swapped. However, it did not exhibit higher FRET efficiency with the L-DNA containing 64% AT-rich mixed DNA when compared to the pure-GC stretch. We explain our observations with a model that shows that the gH binds on dyad and that two arginines mediate recognition of the A-tract via its characteristically narrow minor groove. To investigate whether this on-dyad minor groove-based recognition was distinct from previously identified off-dyad major groove-based recognition, a nucleosome was designed with A-tracts on both the L-DNA arms. One A-tract was complementary to thymine and the other to deoxyuridine. The major groove of the thymine-tract was lined with methyl groups that were absent from the major groove of the deoxyuridine tract. The gH exhibited similar FRET for both these A-tracts, suggesting that it does not interact with the thymine methyl groups exposed on the major groove. Our observations thus complement previous studies that suggest that different LH isoforms may employ different ways of recognizing AT-rich DNA and A-tracts. This adaptability may enable the LH to universally compact scaffold-associated regions and constitutive heterochromatin, which are rich in such sequences.
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137
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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138
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Changes in Chromatin Organization Eradicate Cellular Stress Resilience to UVA/B Light and Induce Premature Aging. Cells 2021; 10:cells10071755. [PMID: 34359924 PMCID: PMC8304177 DOI: 10.3390/cells10071755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/10/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
Complex interactions among DNA and nuclear proteins maintain genome organization and stability. The nuclear proteins, particularly the histones, organize, compact, and preserve the stability of DNA, but also allow its dynamic reorganization whenever the nuclear processes require access to it. Five histone classes exist and they are evolutionarily conserved among eukaryotes. The linker histones are the fifth class and over time, their role in chromatin has been neglected. Linker histones interact with DNA and the other histones and thus sustain genome stability and nuclear organization. Saccharomyces cerevisiae is a brilliant model for studying linker histones as the gene for it is a single-copy and is non-essential. We, therefore, created a linker histone-free yeast strain using a knockout of the relevant gene and traced the way cells age chronologically. Here we present our results demonstrating that the altered chromatin dynamics during the chronological lifespan of the yeast cells with a mutation in ARP4 (the actin-related protein 4) and without the gene HHO1 for the linker histone leads to strong alterations in the gene expression profiles of a subset of genes involved in DNA repair and autophagy. The obtained results further prove that the yeast mutants have reduced survival upon UVA/B irradiation possibly due to the accelerated decompaction of chromatin and impaired proliferation. Our hypothesis posits that the higher-order chromatin structure and the interactions among chromatin proteins are crucial for the maintenance of chromatin organization during chronological aging under optimal and UVA-B stress conditions.
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139
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Adhireksan Z, Sharma D, Lee PL, Bao Q, Padavattan S, Shum WK, Davey GE, Davey CA. Engineering nucleosomes for generating diverse chromatin assemblies. Nucleic Acids Res 2021; 49:e52. [PMID: 33590100 PMCID: PMC8136823 DOI: 10.1093/nar/gkab070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/09/2021] [Accepted: 02/04/2021] [Indexed: 01/01/2023] Open
Abstract
Structural characterization of chromatin is challenging due to conformational and compositional heterogeneity in vivo and dynamic properties that limit achievable resolution in vitro. Although the maximum resolution for solving structures of large macromolecular assemblies by electron microscopy has recently undergone profound increases, X-ray crystallographic approaches may still offer advantages for certain systems. One such system is compact chromatin, wherein the crystalline state recapitulates the crowded molecular environment within the nucleus. Here we show that nucleosomal constructs with cohesive-ended DNA can be designed that assemble into different types of circular configurations or continuous fibers extending throughout crystals. We demonstrate the utility of the method for characterizing nucleosome compaction and linker histone binding at near-atomic resolution but also advance its application for tackling further problems in chromatin structural biology and for generating novel types of DNA nanostructures. We provide a library of cohesive-ended DNA fragment expression constructs and a strategy for engineering DNA-based nanomaterials with a seemingly vast potential variety of architectures and histone chemistries.
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Affiliation(s)
- Zenita Adhireksan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Deepti Sharma
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Phoi Leng Lee
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Qiuye Bao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Sivaraman Padavattan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Wayne K Shum
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Gabriela E Davey
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Curt A Davey
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
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140
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Wang Y, Iwamori T, Kaneko T, Iida H, Iwamori N. Comparative distributions of RSBN1 and methylated histone H4 Lysine 20 in the mouse spermatogenesis. PLoS One 2021; 16:e0253897. [PMID: 34185806 PMCID: PMC8241091 DOI: 10.1371/journal.pone.0253897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/16/2021] [Indexed: 12/15/2022] Open
Abstract
During spermatogenesis, nuclear architecture of male germ cells is dynamically changed and epigenetic modifications, in particular methylation of histones, highly contribute to its regulation as well as differentiation of male germ cells. Although several methyltransferases and demethylases for histone H3 are involved in the regulation of spermatogenesis, roles of either histone H4 lysine 20 (H4K20) methyltransferases or H4K20 demethylases during spermatogenesis still remain to be elucidated. Recently, RSBN1 which is a testis-specific gene expressed in round spermatids was identified as a demethylase for dimethyl H4K20. In this study, therefore, we confirm the demethylase function of RSBN1 and compare distributions between RSBN1 and methylated H4K20 in the seminiferous tubules. Unlike previous report, expression analyses for RSBN1 reveal that RSBN1 is not a testis-specific gene and is expressed not only in round spermatids but also in elongated spermatids. In addition, RSBN1 can demethylate not only dimethyl H4K20 but also trimethyl H4K20 and could convert both dimethyl H4K20 and trimethyl H4K20 into monomethyl H4K20. When distribution pattern of RSBN1 in the seminiferous tubule is compared to that of methylated H4K20, both dimethyl H4K20 and trimethyl H4K20 but not monomethyl H4K20 are disappeared from RSBN1 positive germ cells, suggesting that testis-specific distribution patterns of methylated H4K20 might be constructed by RSBN1. Thus, novel expression and function of RSBN1 could be useful to comprehend epigenetic regulation during spermatogenesis.
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Affiliation(s)
- Youtao Wang
- Laboratory of Zoology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka-shi, Fukuoka, Japan
| | - Tokuko Iwamori
- Laboratory of Zoology, Graduate School of Agriculture, Kyushu University, Fukuoka-shi, Fukuoka, Japan
| | - Takane Kaneko
- Laboratory of Zoology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka-shi, Fukuoka, Japan
- Laboratory of Zoology, Graduate School of Agriculture, Kyushu University, Fukuoka-shi, Fukuoka, Japan
| | - Hiroshi Iida
- Laboratory of Zoology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka-shi, Fukuoka, Japan
- Laboratory of Zoology, Graduate School of Agriculture, Kyushu University, Fukuoka-shi, Fukuoka, Japan
| | - Naoki Iwamori
- Laboratory of Zoology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka-shi, Fukuoka, Japan
- Laboratory of Zoology, Graduate School of Agriculture, Kyushu University, Fukuoka-shi, Fukuoka, Japan
- * E-mail:
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141
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Rudnizky S, Khamis H, Ginosar Y, Goren E, Melamed P, Kaplan A. Extended and dynamic linker histone-DNA Interactions control chromatosome compaction. Mol Cell 2021; 81:3410-3421.e4. [PMID: 34192510 DOI: 10.1016/j.molcel.2021.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
Chromatosomes play a fundamental role in chromatin regulation, but a detailed understanding of their structure is lacking, partially due to their complex dynamics. Using single-molecule DNA unzipping with optical tweezers, we reveal that linker histone interactions with DNA are remarkably extended, with the C-terminal domain binding both DNA linkers as far as approximately ±140 bp from the dyad. In addition to a symmetrical compaction of the nucleosome core governed by globular domain contacts at the dyad, the C-terminal domain compacts the nucleosome's entry and exit. These interactions are dynamic, exhibit rapid binding and dissociation, are sensitive to phosphorylation of a specific residue, and are crucial to determining the symmetry of the chromatosome's core. Extensive unzipping of the linker DNA, which mimics its invasion by motor proteins, shifts H1 into an asymmetric, off-dyad configuration and triggers nucleosome decompaction, highlighting the plasticity of the chromatosome structure and its potential regulatory role.
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Affiliation(s)
- Sergei Rudnizky
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Hadeel Khamis
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel; Faculty of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Yuval Ginosar
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Efrat Goren
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel; Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel; Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel.
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142
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Milpied P, Gandhi AK, Cartron G, Pasqualucci L, Tarte K, Nadel B, Roulland S. Follicular lymphoma dynamics. Adv Immunol 2021; 150:43-103. [PMID: 34176559 DOI: 10.1016/bs.ai.2021.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Follicular lymphoma (FL) is an indolent yet challenging disease. Despite a generally favorable response to immunochemotherapy regimens, a fraction of patients does not respond or relapses early with unfavorable prognosis. For the vast majority of those who initially respond, relapses will repeatedly occur with increasing refractoriness to available treatments. Addressing the clinical challenges in FL warrants deep understanding of the nature of treatment-resistant FL cells seeding relapses, and of the biological basis of early disease progression. Great progress has been made in the last decade in the description and interrogation of the (epi)genomic landscape of FL cells, of their major dependency to the tumor microenvironment (TME), and of the stepwise lymphomagenesis process, from healthy to subclinical disease and to overt FL. A new picture is emerging, in which an ever-evolving tumor-TME duo sparks a complex and multilayered clonal and functional heterogeneity, blurring the discovery of prognostic biomarkers, patient stratification and reliable designs of risk-adapted treatments. Novel technological approaches allowing to decipher both tumor and TME heterogeneity at the single-cell level are beginning to unravel unsuspected cell dynamics and plasticity of FL cells. The upcoming drawing of a comprehensive functional picture of FL within its ecosystem holds great promise to address the unmet medical needs of this complex lymphoma.
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Affiliation(s)
- Pierre Milpied
- Aix Marseille University, CNRS, INSERM, CIML, Marseille, France
| | - Anita K Gandhi
- Translational Medicine, Bristol Myers Squibb, Summit, NJ, United States
| | - Guillaume Cartron
- Department of Hematology, Centre Hospitalier Universitaire Montpellier, UMR-CNRS 5535, Montpellier, France
| | - Laura Pasqualucci
- Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York City, NY, United States
| | - Karin Tarte
- INSERM U1236, Univ Rennes, EFS Bretagne, CHU Rennes, Rennes, France
| | - Bertrand Nadel
- Aix Marseille University, CNRS, INSERM, CIML, Marseille, France.
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143
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Jeong KY, Park M. Poly adenosine diphosphate-ribosylation, a promising target for colorectal cancer treatment. World J Gastrointest Oncol 2021. [PMID: 34163574 DOI: 10.4251/wjgo.v13.i6.574.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The development of colorectal cancer (CRC) can result from changes in a variety of cellular systems within the tumor microenvironment. Particularly, it is primarily associated with genomic instability that is the gradual accumulation of genetic and epigenetic changes consisting of a characteristic set of mutations crucial for pathways in CRC progression. Based on this background, the potential to focus on poly [adenosine diphosphate (ADP)-ribose] polymerase (PARP)-1 and poly-ADP ribosylation (PARylation) as the main causes of malignant formation of CRC may be considered. One of the important functions of PARP-1 and PARylation is its deoxyribonucleic acid (DNA) repair function, which plays a pivotal role in the DNA damage response and prevention of DNA damage maintaining the redox homeostasis involved in the regulation of oxidation and superoxide. PARP-1 and PARylation can also alter epigenetic markers and chromatin structure involved in transcriptional regulation for the oncogenes or tumor suppressor genes by remodeling histone and chromatin enzymes. Given the high importance of these processes in CRC, it can be considered that PARP-1 and PARylation are at the forefront of the pathological changes required for CRC progression. Therefore, this review addresses the current molecular biological features for understanding the multifactorial function of PARP-1 and PARylation in CRC related to the aforementioned roles; furthermore, it presents a summary of recent approaches with PARP-1 inhibition in non-clinical and clinical studies targeting CRC. This understanding could help embrace the importance of targeting PARP-1 and PARylation in the treatment of CRC, which may present the potential to identify various research topics that can be challenged both non-clinically and clinically.
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Affiliation(s)
- Keun-Yeong Jeong
- Research and Development, Metimedi Pharmaceuticals, Incheon 22006, South Korea.
| | - Minhee Park
- Research and Development, Metimedi Pharmaceuticals, Incheon 22006, South Korea
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144
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Jeong KY, Park M. Poly adenosine diphosphate-ribosylation, a promising target for colorectal cancer treatment. World J Gastrointest Oncol 2021; 13:574-588. [PMID: 34163574 PMCID: PMC8204356 DOI: 10.4251/wjgo.v13.i6.574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/22/2021] [Accepted: 05/08/2021] [Indexed: 02/06/2023] Open
Abstract
The development of colorectal cancer (CRC) can result from changes in a variety of cellular systems within the tumor microenvironment. Particularly, it is primarily associated with genomic instability that is the gradual accumulation of genetic and epigenetic changes consisting of a characteristic set of mutations crucial for pathways in CRC progression. Based on this background, the potential to focus on poly [adenosine diphosphate (ADP)-ribose] polymerase (PARP)-1 and poly-ADP ribosylation (PARylation) as the main causes of malignant formation of CRC may be considered. One of the important functions of PARP-1 and PARylation is its deoxyribonucleic acid (DNA) repair function, which plays a pivotal role in the DNA damage response and prevention of DNA damage maintaining the redox homeostasis involved in the regulation of oxidation and superoxide. PARP-1 and PARylation can also alter epigenetic markers and chromatin structure involved in transcriptional regulation for the oncogenes or tumor suppressor genes by remodeling histone and chromatin enzymes. Given the high importance of these processes in CRC, it can be considered that PARP-1 and PARylation are at the forefront of the pathological changes required for CRC progression. Therefore, this review addresses the current molecular biological features for understanding the multifactorial function of PARP-1 and PARylation in CRC related to the aforementioned roles; furthermore, it presents a summary of recent approaches with PARP-1 inhibition in non-clinical and clinical studies targeting CRC. This understanding could help embrace the importance of targeting PARP-1 and PARylation in the treatment of CRC, which may present the potential to identify various research topics that can be challenged both non-clinically and clinically.
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Affiliation(s)
- Keun-Yeong Jeong
- Research and Development, Metimedi Pharmaceuticals, Incheon 22006, South Korea
| | - Minhee Park
- Research and Development, Metimedi Pharmaceuticals, Incheon 22006, South Korea
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145
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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: 17] [Impact Index Per Article: 5.7] [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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146
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Zhao B, Xi Y, Kim J, Sung S. Chromatin architectural proteins regulate flowering time by precluding gene looping. SCIENCE ADVANCES 2021; 7:eabg3097. [PMID: 34117065 PMCID: PMC8195489 DOI: 10.1126/sciadv.abg3097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/28/2021] [Indexed: 05/03/2023]
Abstract
Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC A genome-wide study revealed that this family preferentially binds to the 5' and 3' ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5' to 3' gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.
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Affiliation(s)
- Bo Zhao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yanpeng Xi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Junghyun Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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147
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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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148
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Shintomi K, Hirano T. Guiding functions of the C-terminal domain of topoisomerase IIα advance mitotic chromosome assembly. Nat Commun 2021; 12:2917. [PMID: 34006877 PMCID: PMC8131626 DOI: 10.1038/s41467-021-23205-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/20/2021] [Indexed: 12/21/2022] Open
Abstract
Topoisomerase II (topo II) is one of the six proteins essential for mitotic chromatid reconstitution in vitro. It is not fully understood, however, mechanistically how this enzyme regulates this process. In an attempt to further refine the reconstitution assay, we have found that chromosomal binding of Xenopus laevis topo IIα is sensitive to buffer conditions and depends on its C-terminal domain (CTD). Enzymological assays using circular DNA substrates supports the idea that topo IIα first resolves inter-chromatid entanglements to drive individualization and then generates intra-chromatid entanglements to promote thickening. Importantly, only the latter process requires the CTD. By using frog egg extracts, we also show that the CTD contributes to proper formation of nucleosome-depleted chromatids by competing with a linker histone for non-nucleosomal DNA. Our results demonstrate that topo IIα utilizes its CTD to deliver the enzymatic core to crowded environments created during mitotic chromatid assembly, thereby fine-tuning this process. Topoisomerase IIα (topo IIα) is critical for mitotic chromatid assembly. Here the authors report a refinement of the mitotic chromatid reconstitution assay and provide novel insights into the C-terminal domain (CTD) of topo IIα.
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Affiliation(s)
| | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama, Japan.
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149
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Scourzic L, Salataj E, Apostolou E. Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies. Front Immunol 2021; 12:669881. [PMID: 34054841 PMCID: PMC8160312 DOI: 10.3389/fimmu.2021.669881] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Proper lymphopoiesis and immune responses depend on the spatiotemporal control of multiple processes, including gene expression, DNA recombination and cell fate decisions. High-order 3D chromatin organization is increasingly appreciated as an important regulator of these processes and dysregulation of genomic architecture has been linked to various immune disorders, including lymphoid malignancies. In this review, we present the general principles of the 3D chromatin topology and its dynamic reorganization during various steps of B and T lymphocyte development and activation. We also discuss functional interconnections between architectural, epigenetic and transcriptional changes and introduce major key players of genomic organization in B/T lymphocytes. Finally, we present how alterations in architectural factors and/or 3D genome organization are linked to dysregulation of the lymphopoietic transcriptional program and ultimately to hematological malignancies.
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Affiliation(s)
| | | | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
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150
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Dionne O, Corbin F. An "Omic" Overview of Fragile X Syndrome. BIOLOGY 2021; 10:433. [PMID: 34068266 PMCID: PMC8153138 DOI: 10.3390/biology10050433] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/01/2021] [Accepted: 05/08/2021] [Indexed: 01/16/2023]
Abstract
Fragile X syndrome (FXS) is a neurodevelopmental disorder associated with a wide range of cognitive, behavioral and medical problems. It arises from the silencing of the fragile X mental retardation 1 (FMR1) gene and, consequently, in the absence of its encoded protein, FMRP (fragile X mental retardation protein). FMRP is a ubiquitously expressed and multifunctional RNA-binding protein, primarily considered as a translational regulator. Pre-clinical studies of the past two decades have therefore focused on this function to relate FMRP's absence to the molecular mechanisms underlying FXS physiopathology. Based on these data, successful pharmacological strategies were developed to rescue fragile X phenotype in animal models. Unfortunately, these results did not translate into humans as clinical trials using same therapeutic approaches did not reach the expected outcomes. These failures highlight the need to put into perspective the different functions of FMRP in order to get a more comprehensive understanding of FXS pathophysiology. This work presents a review of FMRP's involvement on noteworthy molecular mechanisms that may ultimately contribute to various biochemical alterations composing the fragile X phenotype.
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Affiliation(s)
- Olivier Dionne
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke and Centre de Recherche du CHUS, CIUSSS de l’Estrie-CHUS, Sherbrooke, QC J1H 5H4, Canada;
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