201
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Maimaitiyiming Y, Wang QQ, Hsu CH, Naranmandura H. Arsenic induced epigenetic changes and relevance to treatment of acute promyelocytic leukemia and beyond. Toxicol Appl Pharmacol 2020; 406:115212. [PMID: 32882258 DOI: 10.1016/j.taap.2020.115212] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/18/2020] [Accepted: 08/22/2020] [Indexed: 12/13/2022]
Abstract
Epigenetic alterations regulate gene expression without changes in the DNA sequence. It is well-demonstrated that aberrant epigenetic changes contribute to the leukemogenesis of acute promyelocytic leukemia (APL). Arsenic trioxide (ATO) is one of the most common drugs used in the frontline treatment of APL that act through targeting and destabilizing the PML/RARα oncofusion protein. ATO together with all-trans retinoic acid (ATRA) lead to durable remission of more than 90% non-high-risk APL patients, turning APL treatment into a paradigm of oncoprotein targeted cure. Although relapse and drug resistance in APL are yet to be resolved in the clinic, epigenetic machineries might hold the key to address this issue. Further, ATO also showed promising anticancer activities against a variety of malignancies, but its application is particularly restricted due to limited understanding of the mechanism. Thus, a thorough understanding of epigenetic mechanism behind anti-leukemic effects of ATO would benefit the development of ATO-based anticancer strategy. Role of ATRA on APL associated epigenetic alterations has been extensively studied and reviewed. Recently, accumulating evidence suggest that ATO also induces some epigenetic changes that might favor APL eradication. In this article, we comprehensively discuss arsenic induced epigenetic changes and its relevance in APL treatment and beyond, so as to provide novel insights into overcoming arsenic resistance in APL and promote application of this drug to other malignancies.
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Affiliation(s)
- Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, Department of Public Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Qian Qian Wang
- Department of Hematology of First Affiliated Hospital, Department of Public Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Chih-Hung Hsu
- Department of Public Health, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, Department of Public Health, Zhejiang University School of Medicine, Hangzhou, China.
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202
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Probst AV, Desvoyes B, Gutierrez C. Similar yet critically different: the distribution, dynamics and function of histone variants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5191-5204. [PMID: 32392582 DOI: 10.1093/jxb/eraa230] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/06/2020] [Indexed: 05/23/2023]
Abstract
Organization of the genetic information into chromatin plays an important role in the regulation of all DNA template-based reactions. The incorporation of different variant versions of the core histones H3, H2A, and H2B, or the linker histone H1 results in nucleosomes with unique properties. Histone variants can differ by only a few amino acids or larger protein domains and their incorporation may directly affect nucleosome stability and higher order chromatin organization or indirectly influence chromatin function through histone variant-specific binding partners. Histone variants employ dedicated histone deposition machinery for their timely and locus-specific incorporation into chromatin. Plants have evolved specific histone variants with unique expression patterns and features. In this review, we discuss our current knowledge on histone variants in Arabidopsis, their mode of deposition, variant-specific post-translational modifications, and genome-wide distribution, as well as their role in defining different chromatin states.
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Affiliation(s)
- Aline V Probst
- Université Clermont Auvergne, CNRS, Inserm, GReD, Clermont-Ferrand, France
| | - Bénédicte Desvoyes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, Spain
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203
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Neganova ME, Klochkov SG, Aleksandrova YR, Aliev G. Histone modifications in epigenetic regulation of cancer: Perspectives and achieved progress. Semin Cancer Biol 2020; 83:452-471. [PMID: 32814115 DOI: 10.1016/j.semcancer.2020.07.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
Epigenetic changes associated with histone modifications play an important role in the emergence and maintenance of the phenotype of various cancer types. In contrast to direct mutations in the main DNA sequence, these changes are reversible, which makes the development of inhibitors of enzymes of post-translational histone modifications one of the most promising strategies for the creation of anticancer drugs. To date, a wide variety of histone modifications have been found that play an important role in the regulation of chromatin state, gene expression, and other nuclear events. This review examines the main features of the most common and studied epigenetic histone modifications with a proven role in the pathogenesis of a wide range of malignant neoplasms: acetylation / deacetylation and methylation / demethylation of histone proteins, as well as the role of enzymes of the HAT / HDAC and HMT / HDMT families in the development of oncological pathologies. The data on the relationship between histone modifications and certain types of cancer are presented and discussed. Special attention is devoted to the consideration of various strategies for the development of epigenetic inhibitors. The main directions of the development of inhibitors of histone modifications are analyzed and effective strategies for their creation are identified and discussed. The most promising strategy is the use of multitarget drugs, which will affect multiple molecular targets of cancer. A critical analysis of the current status of approved epigenetic anticancer drugs has also been performed.
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Affiliation(s)
- Margarita E Neganova
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Sergey G Klochkov
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Yulia R Aleksandrova
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Gjumrakch Aliev
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation.,I. M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Str., Moscow, 119991, Russian Federation.,Laboratory of Cellular Pathology, Federal State Budgetary Institution «Research Institute of Human Morphology», 3, Tsyurupy Str., Moscow, 117418, Russian Federation.,GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX, 78229, USA.
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204
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Climent-Cantó P, Carbonell A, Tatarski M, Reina O, Bujosa P, Font-Mateu J, Bernués J, Beato M, Azorín F. The embryonic linker histone dBigH1 alters the functional state of active chromatin. Nucleic Acids Res 2020; 48:4147-4160. [PMID: 32103264 PMCID: PMC7192587 DOI: 10.1093/nar/gkaa122] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/30/2020] [Accepted: 02/25/2020] [Indexed: 11/13/2022] Open
Abstract
Linker histones H1 are principal chromatin components, whose contribution to the epigenetic regulation of chromatin structure and function is not fully understood. In metazoa, specific linker histones are expressed in the germline, with female-specific H1s being normally retained in the early-embryo. Embryonic H1s are present while the zygotic genome is transcriptionally silent and they are replaced by somatic variants upon activation, suggesting a contribution to transcriptional silencing. Here we directly address this question by ectopically expressing dBigH1 in Drosophila S2 cells, which lack dBigH1. We show that dBigH1 binds across chromatin, replaces somatic dH1 and reduces nucleosome repeat length (NRL). Concomitantly, dBigH1 expression down-regulates gene expression by impairing RNApol II binding and histone acetylation. These effects depend on the acidic N-terminal ED-domain of dBigH1 since a truncated form lacking this domain binds across chromatin and replaces dH1 like full-length dBigH1, but it does not affect NRL either transcription. In vitro reconstitution experiments using Drosophila preblastodermic embryo extracts corroborate these results. Altogether these results suggest that the negatively charged N-terminal tail of dBigH1 alters the functional state of active chromatin compromising transcription.
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Affiliation(s)
- Paula Climent-Cantó
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain.,Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Albert Carbonell
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain.,Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Milos Tatarski
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain.,Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Paula Bujosa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain.,Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jofre Font-Mateu
- Centre de Regulació Genòmica (CRG). The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jordi Bernués
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain.,Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Miguel Beato
- Centre de Regulació Genòmica (CRG). The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain.,Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
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205
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Woods DC, Wereszczynski J. Elucidating the influence of linker histone variants on chromatosome dynamics and energetics. Nucleic Acids Res 2020; 48:3591-3604. [PMID: 32128577 PMCID: PMC7144933 DOI: 10.1093/nar/gkaa121] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/23/2022] Open
Abstract
Linker histones are epigenetic regulators that bind to nucleosomes and alter chromatin structures and dynamics. Biophysical studies have revealed two binding modes in the linker histone/nucleosome complex, the chromatosome, where the linker histone is either centered on or askew from the dyad axis. Each has been posited to have distinct effects on chromatin, however the molecular and thermodynamic mechanisms that drive them and their dependence on linker histone compositions remain poorly understood. We present molecular dynamics simulations of chromatosomes with the globular domain of two linker histone variants, generic H1 (genGH1) and H1.0 (GH1.0), to determine how their differences influence chromatosome structures, energetics and dynamics. Results show that both unbound linker histones adopt a single compact conformation. Upon binding, DNA flexibility is reduced, resulting in increased chromatosome compaction. While both variants enthalpically favor on-dyad binding, energetic benefits are significantly higher for GH1.0, suggesting that GH1.0 is more capable than genGH1 of overcoming the large entropic reduction required for on-dyad binding which helps rationalize experiments that have consistently demonstrated GH1.0 in on-dyad states but that show genGH1 in both locations. These simulations highlight the thermodynamic basis for different linker histone binding motifs, and details their physical and chemical effects on chromatosomes.
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Affiliation(s)
- Dustin C Woods
- Department of Chemistry and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jeff Wereszczynski
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, USA
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206
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Wahab S, Saettone A, Nabeel-Shah S, Dannah N, Fillingham J. Exploring the Histone Acetylation Cycle in the Protozoan Model Tetrahymena thermophila. Front Cell Dev Biol 2020; 8:509. [PMID: 32695779 PMCID: PMC7339932 DOI: 10.3389/fcell.2020.00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic histone acetylation cycle is composed of three classes of proteins, histone acetyltransferases (HATs) that add acetyl groups to lysine amino acids, bromodomain (BRD) containing proteins that are one of the most characterized of several protein domains that recognize acetyl-lysine (Kac) and effect downstream function, and histone deacetylases (HDACs) that catalyze the reverse reaction. Dysfunction of selected proteins of these three classes is associated with human disease such as cancer. Additionally, the HATs, BRDs, and HDACs of fungi and parasitic protozoa present potential drug targets. Despite their importance, the function and mechanisms of HATs, BRDs, and HDACs and how they relate to chromatin remodeling (CR) remain incompletely understood. Tetrahymena thermophila (Tt) provides a highly tractable single-celled free-living protozoan model for studying histone acetylation, featuring a massively acetylated somatic genome, a property that was exploited in the identification of the first nuclear/type A HAT Gcn5 in the 1990s. Since then, Tetrahymena remains an under-explored model for the molecular analysis of HATs, BRDs, and HDACs. Studies of HATs, BRDs, and HDACs in Tetrahymena have the potential to reveal the function of HATs and BRDs relevant to both fundamental eukaryotic biology and to the study of disease mechanisms in parasitic protozoa.
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Affiliation(s)
| | | | | | | | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
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207
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Christophorou N, She W, Long J, Hurel A, Beaubiat S, Idir Y, Tagliaro-Jahns M, Chambon A, Solier V, Vezon D, Grelon M, Feng X, Bouché N, Mézard C. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLoS Genet 2020; 16:e1008894. [PMID: 32598340 PMCID: PMC7351236 DOI: 10.1371/journal.pgen.1008894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 07/10/2020] [Accepted: 05/29/2020] [Indexed: 12/17/2022] Open
Abstract
Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells. In sexually reproducing organisms, each parent transmits one and only one copy of each chromosome to their progeny via their packaging in haploid gametes. To ensure the proper transmission of the chromosomes, pairs of homologous chromosomes must associate and exchange genetic information (also called reciprocal recombination) during a special division called meiosis that lead to the formation of the gametes. The recombination process is highly controlled in terms of number and localization of the events along the chromosomes. Disruption of this control may cause an inappropriate transmission of the chromosomes in the gametes leading to abnormal chromosome numbers in the offspring which is usually deleterious. In the plant Arabidopis thaliana, we show that when the pathway modifying proteins through ubiquitination/neddylation is impaired, the number of reciprocal recombination events is maintained but they are delocalized toward the ends of the chromosomes and some chromosomes do not exchange material. We also detected changes of patterns for DNA methylation, an epigenetic modification localised on DNA cytosines. Furthermore, we demonstrate that the methylation of cytosines is not causal to the localization change of meiotic recombination events.
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Affiliation(s)
- Nicolas Christophorou
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Wenjing She
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Jincheng Long
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Aurélie Hurel
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Sébastien Beaubiat
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Yassir Idir
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Marina Tagliaro-Jahns
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Aurélie Chambon
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Victor Solier
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Daniel Vezon
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Mathilde Grelon
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Nicolas Bouché
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France
- * E-mail: (NB); (CM)
| | - Christine Mézard
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France
- * E-mail: (NB); (CM)
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208
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Maruyama H, Prieto EI, Nambu T, Mashimo C, Kashiwagi K, Okinaga T, Atomi H, Takeyasu K. Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis. Front Microbiol 2020; 11:1247. [PMID: 32655523 PMCID: PMC7325993 DOI: 10.3389/fmicb.2020.01247] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/15/2020] [Indexed: 12/15/2022] Open
Abstract
Archaeal species encode a variety of distinct lineage-specific chromosomal proteins. We have previously shown that in Thermococcus kodakarensis, histone, Alba, and TrmBL2 play distinct roles in chromosome organization. Although our understanding of individual archaeal chromosomal proteins has been advancing, how archaeal chromosomes are folded into higher-order structures and how they are regulated are largely unknown. Here, we investigated the primary and higher-order structures of archaeal chromosomes from different archaeal lineages. Atomic force microscopy of chromosome spreads out of Thermoplasma acidophilum and Pyrobaculum calidifontis cells revealed 10-nm fibers and 30–40-nm globular structures, suggesting the occurrence of higher-order chromosomal folding. Our results also indicated that chromosome compaction occurs toward the stationary phase. Micrococcal nuclease digestion indicated that fundamental structural units of the chromosome exist in T. acidophilum and T. kodakarensis but not in P. calidifontis or Sulfolobus solfataricus. In vitro reconstitution showed that, in T. acidophilum, the bacterial HU protein homolog HTa formed a 6-nm fiber by wrapping DNA, and that Alba was responsible for the formation of the 10-nm fiber by binding along the DNA without wrapping. Remarkably, Alba could form different higher-order complexes with histone or HTa on DNA in vitro. Mass spectrometry detected HTa and Rad50 in the T. acidophilum chromosome but not in other species. A putative transcriptional regulator of the AsnC/Lrp family (Pcal_1183) was detected on the P. calidifontis chromosome, but not on that of other species studied. Putative membrane-associated proteins were detected in the chromosomes of the three archaeal species studied, including T. acidophilum, P. calidifontis, and T. kodakarensis. Collectively, our data show that Archaea use different combinations of proteins to achieve chromosomal architecture and functional regulation.
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Affiliation(s)
- Hugo Maruyama
- Department of Bacteriology, Osaka Dental University, Hirakata, Japan
| | - Eloise I Prieto
- National Institute of Molecular Biology and Biotechnology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Takayuki Nambu
- Department of Bacteriology, Osaka Dental University, Hirakata, Japan
| | - Chiho Mashimo
- Department of Bacteriology, Osaka Dental University, Hirakata, Japan
| | - Kosuke Kashiwagi
- Department of Fixed Prosthodontics, Osaka Dental University, Hirakata, Japan
| | - Toshinori Okinaga
- Department of Bacteriology, Osaka Dental University, Hirakata, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kunio Takeyasu
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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209
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H1 linker histones silence repetitive elements by promoting both histone H3K9 methylation and chromatin compaction. Proc Natl Acad Sci U S A 2020; 117:14251-14258. [PMID: 32513732 DOI: 10.1073/pnas.1920725117] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nearly 50% of mouse and human genomes are composed of repetitive sequences. Transcription of these sequences is tightly controlled during development to prevent genomic instability, inappropriate gene activation and other maladaptive processes. Here, we demonstrate an integral role for H1 linker histones in silencing repetitive elements in mouse embryonic stem cells. Strong H1 depletion causes a profound de-repression of several classes of repetitive sequences, including major satellite, LINE-1, and ERV. Activation of repetitive sequence transcription is accompanied by decreased H3K9 trimethylation of repetitive sequence chromatin. H1 linker histones interact directly with Suv39h1, Suv39h2, and SETDB1, the histone methyltransferases responsible for H3K9 trimethylation of chromatin within these regions, and stimulate their activity toward chromatin in vitro. However, we also implicate chromatin compaction mediated by H1 as an additional, dominant repressive mechanism for silencing of repetitive major satellite sequences. Our findings elucidate two distinct, H1-mediated pathways for silencing heterochromatin.
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210
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Teif VB, Gould TJ, Clarkson CT, Boyd L, Antwi EB, Ishaque N, Olins AL, Olins DE. Linker histone epitopes are hidden by in situ higher-order chromatin structure. Epigenetics Chromatin 2020; 13:26. [PMID: 32505195 PMCID: PMC7276084 DOI: 10.1186/s13072-020-00345-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 05/13/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone H1 is the most mobile histone in the cell nucleus. Defining the positions of H1 on chromatin in situ, therefore, represents a challenge. Immunoprecipitation of formaldehyde-fixed and sonicated chromatin, followed by DNA sequencing (xChIP-seq), is traditionally the method for mapping histones onto DNA elements. But since sonication fragmentation precedes ChIP, there is a consequent loss of information about chromatin higher-order structure. Here, we present a new method, xxChIP-seq, employing antibody binding to fixed intact in situ chromatin, followed by extensive washing, a second fixation, sonication and immunoprecipitation. The second fixation is intended to prevent the loss of specifically bound antibody during washing and subsequent sonication and to prevent antibody shifting to epitopes revealed by the sonication process. In many respects, xxChIP-seq is comparable to immunostaining microscopy, which also involves interaction of the primary antibody with fixed and permeabilized intact cells. The only epitopes displayed after immunostaining are the "exposed" epitopes, not "hidden" by the fixation of chromatin higher-order structure. Comparison of immunoprecipitated fragments between xChIP-seq versus xxChIP-seq should indicate which epitopes become inaccessible with fixation and identify their associated DNA elements. RESULTS We determined the genomic distribution of histone variants H1.2 and H1.5 in human myeloid leukemia cells HL-60/S4 and compared their epitope exposure by both xChIP-seq and xxChIP-seq, as well as high-resolution microscopy, illustrating the influences of preserved chromatin higher-order structure in situ. We found that xChIP and xxChIP H1 signals are in general negatively correlated, with differences being more pronounced near active regulatory regions. Among the intriguing observations, we find that transcription-related regions and histone PTMs (i.e., enhancers, promoters, CpG islands, H3K4me1, H3K4me3, H3K9ac, H3K27ac and H3K36me3) exhibit significant deficiencies (depletions) in H1.2 and H1.5 xxChIP-seq reads, compared to xChIP-seq. These observations suggest the existence of in situ transcription-related chromatin higher-order structures stabilized by formaldehyde. CONCLUSION Comparison of H1 xxChIP-seq to H1 xChIP-seq allows the development of hypotheses on the chromosomal localization of (stabilized) higher-order structure, indicated by the generation of "hidden" H1 epitopes following formaldehyde crosslinking. Changes in H1 epitope exposure surrounding averaged chromosomal binding sites or epigenetic modifications can also indicate whether these sites have chromatin higher-order structure. For example, comparison between averaged active or inactive promoter regions suggests that both regions can acquire stabilized higher-order structure with hidden H1 epitopes. However, the H1 xChIP-seq comparison cannot define their differences. Application of the xxChIP-seq versus H1 xChIP-seq method is particularly relevant to chromatin-associated proteins, such as linker histones, that play dynamic roles in establishing chromatin higher-order structure.
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Affiliation(s)
- Vladimir B Teif
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
| | - Travis J Gould
- Department of Physics & Astronomy, Bates College, Lewiston, ME, USA
| | | | - Logan Boyd
- Department of Physics & Astronomy, Bates College, Lewiston, ME, USA.,StarBird Technologies, LLC, Brunswick, ME, USA
| | - Enoch B Antwi
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Molecular and Cellular Engineering, Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, Freiburg im Breisgau, 79104 , Germany
| | - Naveed Ishaque
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, Berlin, 10178 , Germany
| | - Ada L Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME, 04103, USA
| | - Donald E Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME, 04103, USA.
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211
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Hayakawa K, Tani R, Nishitani K, Tanaka S. Linker histone variant H1T functions as a chromatin de-condenser on genic regions. Biochem Biophys Res Commun 2020; 528:685-690. [PMID: 32513538 DOI: 10.1016/j.bbrc.2020.05.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/16/2020] [Indexed: 10/24/2022]
Abstract
Linker histone H1 is mainly localized in the linker DNA region, between two nucleosome cores, and regulates chromatin structures linking gene expression. There are 11 variants in histone H1, and each variant has unique functions. Our previous study demonstrates that one of the H1 variants, H1T is mainly localized in the nucleolus and targets the rDNA repeat region. Moreover, H1T condenses the chromatin structures on rDNA to repress pre-rRNA expression. Although H1T is partially localized in the nucleoplasm area, the functions of H1T in the non-repeat genic region are unclear. In this study, we aimed to identify the target loci and the role of H1T in the genic region. Chromatin immunoprecipitation sequencing analysis showed that H1T is localized around the transcriptional start site and the chromatin structures of the region were relaxed. H1T knockdown and overexpression experiments revealed that H1T induced chromatin de-condensation and was associated with the increased expression of target genes. Moreover, we observed H1T co-localization with transcriptional factor SPZ1 on the genic region. Collectively, H1T has opposing roles in the genic region and in rDNA repeats; H1T functions to facilitate chromatin relaxation linked gene activation.
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Affiliation(s)
- Koji Hayakawa
- Department of Toxicology, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan; Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Ruiko Tani
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kenta Nishitani
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Satoshi Tanaka
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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212
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Sridhar A, Orozco M, Collepardo-Guevara R. Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1. Nucleic Acids Res 2020; 48:5318-5331. [PMID: 32356891 PMCID: PMC7261198 DOI: 10.1093/nar/gkaa285] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/02/2020] [Accepted: 04/14/2020] [Indexed: 12/18/2022] Open
Abstract
Intrinsically disordered proteins are crucial elements of chromatin heterogenous organization. While disorder in the histone tails enables a large variation of inter-nucleosome arrangements, disorder within the chromatin-binding proteins facilitates promiscuous binding to a wide range of different molecular targets, consistent with structural heterogeneity. Among the partially disordered chromatin-binding proteins, the H1 linker histone influences a myriad of chromatin characteristics including compaction, nucleosome spacing, transcription regulation, and the recruitment of other chromatin regulating proteins. Although it is now established that the long C-terminal domain (CTD) of H1 remains disordered upon nucleosome binding and that such disorder favours chromatin fluidity, the structural behaviour and thereby the role/function of the N-terminal domain (NTD) within chromatin is yet unresolved. On the basis of microsecond-long parallel-tempering metadynamics and temperature-replica exchange atomistic molecular dynamics simulations of different H1 NTD subtypes, we demonstrate that the NTD is completely unstructured in solution but undergoes an important disorder-to-order transition upon nucleosome binding: it forms a helix that enhances its DNA binding ability. Further, we show that the helical propensity of the H1 NTD is subtype-dependent and correlates with the experimentally observed binding affinity of H1 subtypes, suggesting an important functional implication of this disorder-to-order transition.
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Affiliation(s)
- Akshay Sridhar
- Maxwell Centre, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Modesto Orozco
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri i Reixac, 19, 08028 Barcelona, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, Av. Diagonal 647. 08028 Barcelona, Spain
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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213
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Abstract
DNA-replication machinery introduces intertwining and supercoiling of DNA strands as it traverses the double helix, which could impede replication and compromise genome stability. A new study in Cell shows that the intrinsic physical properties of chromatin fibers dictate how torsional stress is partitioned to minimize these risks and facilitate DNA replication.
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214
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Gerlitz G. The Emerging Roles of Heterochromatin in Cell Migration. Front Cell Dev Biol 2020; 8:394. [PMID: 32528959 PMCID: PMC7266953 DOI: 10.3389/fcell.2020.00394] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/29/2020] [Indexed: 12/17/2022] Open
Abstract
Cell migration is a key process in health and disease. In the last decade an increasing attention is given to chromatin organization in migrating cells. In various types of cells induction of migration leads to a global increase in heterochromatin levels. Heterochromatin is required for optimal cell migration capabilities, since various interventions with heterochromatin formation impeded the migration rate of numerous cell types. Heterochromatin supports the migration process by affecting both the mechanical properties of the nucleus as well as the genetic processes taking place within it. Increased heterochromatin levels elevate nuclear rigidity in a manner that allows faster cell migration in 3D environments. Condensed chromatin and a more rigid nucleus may increase nuclear durability to shear stress and prevent DNA damage during the migration process. In addition, heterochromatin reorganization in migrating cells is important for induction of migration-specific transcriptional plan together with inhibition of many other unnecessary transcriptional changes. Thus, chromatin organization appears to have a key role in the cellular migration process.
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Affiliation(s)
- Gabi Gerlitz
- Department of Molecular Biology and Ariel Center for Applied Cancer Research, Faculty of Life Sciences, Ariel University, Ariel, Israel
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215
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Saloura V, Vougiouklakis T, Bao R, Kim S, Baek S, Zewde M, Bernard B, Burkitt K, Nigam N, Izumchenko E, Dohmae N, Hamamoto R, Nakamura Y. WHSC1 monomethylates histone H1 and induces stem-cell like features in squamous cell carcinoma of the head and neck. Neoplasia 2020; 22:283-293. [PMID: 32497898 PMCID: PMC7265065 DOI: 10.1016/j.neo.2020.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 12/17/2022] Open
Abstract
Squamous cell carcinoma of the head and neck (SCCHN) is a malignancy with poor outcomes, thus novel therapies are urgently needed. We recently showed that WHSC1 is necessary for the viability of SCCHN cells through H3K36 di-methylation. Here, we report the identification of its novel substrate, histone H1, and that WHSC1-mediated H1.4K85 mono-methylation may enhance stemness features in SCCHN cells. To identify proteins interacting with WHSC1 in SCCHN cells, WHSC1 immunoprecipitation and mass spectrometry identified H1 as a WHSC1-interacting candidate. In vitro methyltransferase assays showed that WHSC1 mono-methylates H1 at K85. We generated an H1K85 mono-methylation-specific antibody and confirmed that this methylation occurs in vivo. Sphere formation assays using SCC-35 cells stably expressing either wild-type (FLAG-H1.4-WT) or mutated (FLAG-H1.4K85A) vector with lysine 85 to alanine substitution which is not methylated, indicated a higher number of spheres in SCC-35 cells expressing the wild type than those with the mutant vector. SCC-35 cells expressing the wild type H1.4 proliferated faster than those expressing the mutated vector. RNA sequencing, RT-PCR and Western blotting of the FLAG-H1.4-WT or FLAG-H1.4K85A SCC-35 cells revealed that OCT4 levels were higher in wild type compared to mutant cells. These results were reproduced in SCC-35 cells genetically modified with CRISPR to express H1.4K85R. Chromatin immunoprecipitation showed that FLAG-H1.4K85A had decreased occupancy in the OCT4 gene compared to FLAG-H1.4-WT. This study supports that WHSC1 mono-methylates H1.4 at K85, it induces transcriptional activation of OCT4 and stemness features in SCCHN cells, providing rationale to target H1.4K85 mono-methylation through WHSC1 in SCCHN.
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Affiliation(s)
- Vassiliki Saloura
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA.
| | | | - Riyue Bao
- Center for Research Bioinformatics, University of Chicago, Chicago, USA; Department of Pediatrics, University of Chicago, Chicago, USA
| | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, USA
| | - Makda Zewde
- Department of Medicine, University of Chicago, Chicago, USA
| | - Benjamin Bernard
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Kyunghee Burkitt
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Nupur Nigam
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | | | | | | | - Yusuke Nakamura
- Department of Medicine, University of Chicago, Chicago, USA; Department of Surgery, University of Chicago, Chicago, USA
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216
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Zhao Y, Cortes-Huerto R, Kremer K, Rudzinski JF. Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model. J Phys Chem B 2020; 124:4097-4113. [PMID: 32345021 PMCID: PMC7246978 DOI: 10.1021/acs.jpcb.0c01949] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Intrinsically
disordered proteins (IDPs) play an important role
in an array of biological processes but present a number of fundamental
challenges for computational modeling. Recently, simple polymer models
have regained popularity for interpreting the experimental characterization
of IDPs. Homopolymer theory provides a strong foundation for understanding
generic features of phenomena ranging from single-chain conformational
dynamics to the properties of entangled polymer melts, but is difficult
to extend to the copolymer context. This challenge is magnified for
proteins due to the variety of competing interactions and large deviations
in side-chain properties. In this work, we apply a simple physics-based
coarse-grained model for describing largely disordered conformational
ensembles of peptides, based on the premise that sampling sterically
forbidden conformations can compromise the faithful description of
both static and dynamical properties. The Hamiltonian of the employed
model can be easily adjusted to investigate the impact of distinct
interactions and sequence specificity on the randomness of the resulting
conformational ensemble. In particular, starting with a bead–spring-like
model and then adding more detailed interactions one by one, we construct
a hierarchical set of models and perform a detailed comparison of
their properties. Our analysis clarifies the role of generic attractions,
electrostatics, and side-chain sterics, while providing a foundation
for developing efficient models for IDPs that retain an accurate description
of the hierarchy of conformational dynamics, which is nontrivially
influenced by interactions with surrounding proteins and solvent molecules.
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Affiliation(s)
- Yani Zhao
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | | | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Joseph F Rudzinski
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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217
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Myers CG, Olins DE, Olins AL, Schlick T. Mesoscale Modeling of Nucleosome-Binding Antibody PL2-6: Mono- versus Bivalent Chromatin Complexes. Biophys J 2020; 118:2066-2076. [PMID: 31668748 PMCID: PMC7202932 DOI: 10.1016/j.bpj.2019.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/25/2019] [Accepted: 08/15/2019] [Indexed: 12/28/2022] Open
Abstract
Interactions of chromatin with bivalent immunoglobin nucleosome-binding antibodies and their monovalent (papain-derived) antigen-binding fragment analogs are useful probes for examining chromatin conformational states. To help interpret antibody-chromatin interactions and explore how antibodies might compete for interactions with chromatin components, we incorporate coarse-grained PL2-6 antibody modeling into our mesoscale chromatin model. We analyze interactions and fiber structures for the antibody-chromatin complexes in open and condensed chromatin, with and without H1 linker histone (LH). Despite minimal and transient interactions at physiological salt, we capture significant differences in antibody-chromatin complex configurations in open fibers, with more intense interactions between the bivalent antibody and chromatin compared to monovalent antigen-binding fragments. For these open chromatin fiber morphologies, antibody binding to histone tails is increased and compaction is greater for bivalent compared to monovalent and antibody-free systems. Differences between monovalent and bivalent binding result from antibody competition with internal chromatin fiber components (nucleosome core and linker DNA) for histone tail (H3, H4, H2A, H2B) interactions. This antibody competition for tail contacts reduces tail-core and tail-linker interactions and increases tail-antibody interactions. Such internal structural changes in open fibers resemble mechanisms of LH condensation, driven by charge screening and entropy changes. For condensed fibers at physiological salt, the three systems are much more similar overall, but some subtle tail interaction differences can be noted. Adding LH results in less-dramatic changes for all systems, except that the bivalent complex at physiological salt shows cooperative effects between LH and the antibodies in condensing chromatin fibers. Such dynamic interactions that depend on the internal structure and complex-stabilizing interactions within the chromatin fiber have implications for gene regulation and other chromatin complexes such as with LH, remodeling proteins, and small molecular chaperones that bind and modulate chromatin structure.
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Affiliation(s)
| | - Donald E Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, Maine
| | - Ada L Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, Maine
| | - Tamar Schlick
- Department of Chemistry, New York University, New York, New York; Courant Institute of Mathematical Sciences, New York University, New York, New York; New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai, China.
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218
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Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis. Nat Commun 2020; 11:1886. [PMID: 32312999 PMCID: PMC7170881 DOI: 10.1038/s41467-020-15809-5] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/30/2020] [Indexed: 02/08/2023] Open
Abstract
In higher eukaryotes, heterochromatin is mainly composed of transposable elements (TEs) silenced by epigenetic mechanisms. But, the silencing of certain heterochromatin-associated TEs is disrupted by heat stress. By comparing genome-wide high-resolution chromatin packing patterns under normal or heat conditions obtained through Hi-C analysis, we show here that heat stress causes global rearrangement of the 3D genome in Arabidopsis thaliana. Contacts between pericentromeric regions and distal chromosome arms, as well as proximal intra-chromosomal interactions along the chromosomes, are enhanced. However, interactions within pericentromeres and those between distal intra-chromosomal regions are decreased. Many inter-chromosomal interactions, including those within the KNOT, are also reduced. Furthermore, heat activation of TEs exhibits a high correlation with the reduction of chromosomal interactions involving pericentromeres, the KNOT, the knob, and the upstream and downstream flanking regions of the activated TEs. Together, our results provide insights into the relationship between TE activation and 3D genome reorganization.
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219
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Kumar A, Kono H. Heterochromatin protein 1 (HP1): interactions with itself and chromatin components. Biophys Rev 2020; 12:387-400. [PMID: 32144738 PMCID: PMC7242596 DOI: 10.1007/s12551-020-00663-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/23/2020] [Indexed: 12/12/2022] Open
Abstract
Isoforms of heterochromatin protein 1 (HP1) have been known to perform a multitude of functions ranging from gene silencing, gene activation to cell cycle regulation, and cell differentiation. This functional diversity arises from the dissimilarities coded in protein sequence which confers different biophysical and biochemical properties to individual structural elements of HP1 and thereby different behavior and interaction patterns. Hence, an understanding of various interactions of the structural elements of HP1 will be of utmost importance to better elucidate chromatin dynamics in its presence. In this review, we have gathered available information about interactions of HP1 both within and with itself as well as with chromatin elements. Also, the possible implications of these interactions are discussed.
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Affiliation(s)
- Amarjeet Kumar
- Molecular Modelling and Simulation (MMS) Group, Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), Kizugawa, Kyoto, 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modelling and Simulation (MMS) Group, Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), Kizugawa, Kyoto, 619-0215, Japan.
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220
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Chikhirzhina EV, Starkova TY, Polyanichko AM. The Role of Linker Histones in Chromatin Structural Organization. 2. Interaction with DNA and Nuclear Proteins. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920020049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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221
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Shakya A, Park S, Rana N, King JT. Liquid-Liquid Phase Separation of Histone Proteins in Cells: Role in Chromatin Organization. Biophys J 2020; 118:753-764. [PMID: 31952807 PMCID: PMC7002979 DOI: 10.1016/j.bpj.2019.12.022] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/26/2019] [Accepted: 12/18/2019] [Indexed: 11/23/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) of proteins and nucleic acids has emerged as an important phenomenon in membraneless intracellular organization. We demonstrate that the linker histone H1 condenses into liquid-like droplets in the nuclei of HeLa cells. The droplets, observed during the interphase of the cell cycle, are colocalized with DNA-dense regions indicative of heterochromatin. In vitro, H1 readily undergoes LLPS with both DNA and nucleosomes of varying lengths but does not phase separate in the absence of DNA. The nucleosome core particle maintains its structural integrity inside the droplets, as demonstrated by FRET. Unexpectedly, H2A also forms droplets in the presence of DNA and nucleosomes in vitro, whereas the other core histones precipitate. The phase diagram of H1 with nucleosomes is invariant to the nucleosome length at physiological salt concentration, indicating that H1 is capable of partitioning large segments of DNA into liquid-like droplets. Of the proteins tested (H1, core histones, and the heterochromatin protein HP1α), this property is unique to H1. In addition, free nucleotides promote droplet formation of H1 nucleosome in a nucleotide-dependent manner, with droplet formation being most favorable with ATP. Although LLPS of HP1α is known to contribute to the organization of heterochromatin, our results indicate that H1 also plays a role. Based on our study, we propose that H1 and DNA act as scaffolds for phase-separated heterochromatin domains.
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Affiliation(s)
- Anisha Shakya
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, Republic of Korea.
| | - Seonyoung Park
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, Republic of Korea; Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Neha Rana
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, Republic of Korea; Department of Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - John T King
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, Republic of Korea.
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222
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Öztürk MA, De M, Cojocaru V, Wade RC. Chromatosome Structure and Dynamics from Molecular Simulations. Annu Rev Phys Chem 2020; 71:101-119. [PMID: 32017651 DOI: 10.1146/annurev-physchem-071119-040043] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromatosomes are fundamental units of chromatin structure that are formed when a linker histone protein binds to a nucleosome. The positioning of the linker histone on the nucleosome influences the packing of chromatin. Recent simulations and experiments have shown that chromatosomes adopt an ensemble of structures that differ in the geometry of the linker histone-nucleosome interaction. In this article we review the application of Brownian, Monte Carlo, and molecular dynamics simulations to predict the structure of linker histone-nucleosome complexes, to study the binding mechanisms involved, and to predict how this binding affects chromatin fiber structure. These simulations have revealed the sensitivityof the chromatosome structure to variations in DNA and linker histone sequence, as well as to posttranslational modifications, thereby explaining the structural variability observed in experiments. We propose that a concerted application of experimental and computational approaches will reveal the determinants of chromatosome structural variability and how it impacts chromatin packing.
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Affiliation(s)
- Mehmet Ali Öztürk
- Centre for Biological Signalling Studies (BIOSS) and Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany;
| | - Madhura De
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany; .,Department of Biophysics of Macromolecules, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; .,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Vlad Cojocaru
- In Silico Biomolecular Structure and Dynamics, Hubrecht Institute, 3584 CT Utrecht, The Netherlands; .,Computational Structural Biology Group, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany; .,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany
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223
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Abstract
The tumor suppressor phosphatase and tension homolog (PTEN) is frequently mutated in human cancers, and it functions in multiple ways to safeguard cells from tumorigenesis. In the cytoplasm, PTEN antagonizes the PI3K/AKT pathway and suppresses cellular proliferation and survival. In the nucleus, PTEN is indispensable for the maintenance of genomic stability. In addition, PTEN loss leads to extensive changes in gene expression at the transcriptional level. The linker histone H1, generally considered as a transcriptional repressor, binds to the nucleosome to form a structure named the chromatosome. The dynamics between H1 and chromatin play an important role in determining gene expression. Here, we summarize the current understanding of roles of PTEN in controlling chromatin dynamics and global gene expression, which is crucial function of nuclear PTEN. We will also introduce the recent discovery of the PTEN family members and their functions.
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Affiliation(s)
- Jingyi Yang
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yuxin Yin
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
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224
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Mu W, Provaznik J, Hackert T, Zöller M. Tspan8-Tumor Extracellular Vesicle-Induced Endothelial Cell and Fibroblast Remodeling Relies on the Target Cell-Selective Response. Cells 2020; 9:cells9020319. [PMID: 32013145 PMCID: PMC7072212 DOI: 10.3390/cells9020319] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/17/2020] [Accepted: 01/26/2020] [Indexed: 12/12/2022] Open
Abstract
Tumor cell-derived extracellular vesicles (TEX) expressing tetraspanin Tspan8-alpha4/beta1 support angiogenesis. Tspan8-alpha6/beta4 facilitates lung premetastatic niche establishment. TEX-promoted target reprogramming is still being disputed, we explored rat endothelial cell (EC) and lung fibroblast (Fb) mRNA and miRNA profile changes after coculture with TEX. TEX were derived from non-metastatic BSp73AS (AS) or metastatic BSp73ASML (ASML) rat tumor lines transfected with Tspan8 (AS-Tspan8) or Tspan8-shRNA (ASML-Tspan8kd). mRNA was analyzed by deep sequencing and miRNA by array analysis of EC and Fb before and after coculture with TEX. EC and Fb responded more vigorously to AS-Tspan8- than AS-TEX. Though EC and Fb responses differed, both cell lines predominantly responded to membrane receptor activation with upregulation and activation of signaling molecules and transcription factors. Minor TEX-initiated changes in the miRNA profile relied, at least partly, on long noncoding RNA (lncRNA) that also affected chromosome organization and mRNA processing. These analyses uncovered three important points. TEX activate target cell autonomous programs. Responses are initiated by TEX targeting units and are target cell-specific. The strong TEX-promoted lncRNA impact reflects lncRNA shuttling and location-dependent distinct activities. These informations urge for an in depth exploration on the mode of TEX-initiated target cell-specific remodeling including, as a major factor, lncRNA.
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Affiliation(s)
- Wei Mu
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Department of General, Visceral and Transplantation Surgery, Pancreas Section, University of Heidelberg, 69120 Heidelberg, Germany
- Correspondence: (W.M.); (M.Z.); Tel.: +86-021-6384-6590 (W.M.); +49-6221-484-730 (M.Z.)
| | - Jan Provaznik
- EMBL Genomics Core Facility, 69117 Heidelberg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, Pancreas Section, University of Heidelberg, 69120 Heidelberg, Germany
| | - Margot Zöller
- Department of General, Visceral and Transplantation Surgery, Pancreas Section, University of Heidelberg, 69120 Heidelberg, Germany
- Correspondence: (W.M.); (M.Z.); Tel.: +86-021-6384-6590 (W.M.); +49-6221-484-730 (M.Z.)
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225
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Nucleus-specific linker histones Hho1 and Mlh1 form distinct protein interactions during growth, starvation and development in Tetrahymena thermophila. Sci Rep 2020; 10:168. [PMID: 31932604 PMCID: PMC6957481 DOI: 10.1038/s41598-019-56867-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023] Open
Abstract
Chromatin organization influences most aspects of gene expression regulation. The linker histone H1, along with the core histones, is a key component of eukaryotic chromatin. Despite its critical roles in chromatin structure and function and gene regulation, studies regarding the H1 protein-protein interaction networks, particularly outside of Opisthokonts, are limited. The nuclear dimorphic ciliate protozoan Tetrahymena thermophila encodes two distinct nucleus-specific linker histones, macronuclear Hho1 and micronuclear Mlh1. We used a comparative proteomics approach to identify the Hho1 and Mlh1 protein-protein interaction networks in Tetrahymena during growth, starvation, and sexual development. Affinity purification followed by mass spectrometry analysis of the Hho1 and Mlh1 proteins revealed a non-overlapping set of co-purifying proteins suggesting that Tetrahymena nucleus-specific linker histones are subject to distinct regulatory pathways. Furthermore, we found that linker histones interact with distinct proteins under the different stages of the Tetrahymena life cycle. Hho1 and Mlh1 co-purified with several Tetrahymena-specific as well as conserved interacting partners involved in chromatin structure and function and other important cellular pathways. Our results suggest that nucleus-specific linker histones might be subject to nucleus-specific regulatory pathways and are dynamically regulated under different stages of the Tetrahymena life cycle.
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226
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DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts. Mol Cell 2020; 77:310-323.e7. [DOI: 10.1016/j.molcel.2019.10.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 08/26/2019] [Accepted: 10/10/2019] [Indexed: 12/12/2022]
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227
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Legoff L, D’Cruz SC, Tevosian S, Primig M, Smagulova F. Transgenerational Inheritance of Environmentally Induced Epigenetic Alterations during Mammalian Development. Cells 2019; 8:cells8121559. [PMID: 31816913 PMCID: PMC6953051 DOI: 10.3390/cells8121559] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 12/11/2022] Open
Abstract
Genetic studies traditionally focus on DNA as the molecule that passes information on from parents to their offspring. Changes in the DNA code alter heritable information and can more or less severely affect the progeny's phenotype. While the idea that information can be inherited between generations independently of the DNA's nucleotide sequence is not new, the outcome of recent studies provides a mechanistic foundation for the concept. In this review, we attempt to summarize our current knowledge about the transgenerational inheritance of environmentally induced epigenetic changes. We focus primarily on studies using mice but refer to other species to illustrate salient points. Some studies support the notion that there is a somatic component within the phenomenon of epigenetic inheritance. However, here, we will mostly focus on gamete-based processes and the primary molecular mechanisms that are thought to contribute to epigenetic inheritance: DNA methylation, histone modifications, and non-coding RNAs. Most of the rodent studies published in the literature suggest that transgenerational epigenetic inheritance through gametes can be modulated by environmental factors. Modification and redistribution of chromatin proteins in gametes is one of the major routes for transmitting epigenetic information from parents to the offspring. Our recent studies provide additional specific cues for this concept and help better understand environmental exposure influences fitness and fidelity in the germline. In summary, environmental cues can induce parental alterations and affect the phenotypes of offspring through gametic epigenetic inheritance. Consequently, epigenetic factors and their heritability should be considered during disease risk assessment.
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Affiliation(s)
- Louis Legoff
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)—UMR_S 1085, F-35000 Rennes, France; (L.L.); (S.C.D.); (M.P.)
| | - Shereen Cynthia D’Cruz
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)—UMR_S 1085, F-35000 Rennes, France; (L.L.); (S.C.D.); (M.P.)
| | - Sergei Tevosian
- University of Florida, Department of Physiological Sciences Box 100144, 1333 Center Drive, Gainesville, FL 32610, USA;
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)—UMR_S 1085, F-35000 Rennes, France; (L.L.); (S.C.D.); (M.P.)
| | - Fatima Smagulova
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)—UMR_S 1085, F-35000 Rennes, France; (L.L.); (S.C.D.); (M.P.)
- Correspondence:
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228
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Perišić O, Portillo-Ledesma S, Schlick T. Sensitive effect of linker histone binding mode and subtype on chromatin condensation. Nucleic Acids Res 2019; 47:4948-4957. [PMID: 30968131 PMCID: PMC6547455 DOI: 10.1093/nar/gkz234] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/14/2022] Open
Abstract
The complex role of linker histone (LH) on chromatin compaction regulation has been highlighted by recent discoveries of the effect of LH binding variability and isoforms on genome structure and function. Here we examine the effect of two LH variants and variable binding modes on the structure of chromatin fibers. Our mesoscale modeling considers oligonucleosomes with H1C and H1E, bound in three different on and off-dyad modes, and spanning different LH densities (0.5–1.6 per nucleosome), over a wide range of physiologically relevant nucleosome repeat lengths (NRLs). Our studies reveal an LH-variant and binding-mode dependent heterogeneous ensemble of fiber structures with variable packing ratios, sedimentation coefficients, and persistence lengths. For maximal compaction, besides dominantly interacting with parental DNA, LHs must have strong interactions with nonparental DNA and promote tail/nonparental core interactions. An off-dyad binding of H1E enables both; others compromise compaction for bendability. We also find that an increase of LH density beyond 1 is best accommodated in chromatosomes with one on-dyad and one off-dyad LH. We suggest that variable LH binding modes and concentrations are advantageous, allowing tunable levels of chromatin condensation and DNA accessibility/interactions. Thus, LHs add another level of epigenetic regulation of chromatin.
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Affiliation(s)
- Ognjen Perišić
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA
| | - Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA.,Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA.,New York University ECNU - Center for Computational Chemistry at NYU Shanghai, 3663 North Zhongshan Road, Shanghai, 200062, China
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229
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Zhang S, Deng T, Tang W, He B, Furusawa T, Ambs S, Bustin M. Epigenetic regulation of REX1 expression and chromatin binding specificity by HMGNs. Nucleic Acids Res 2019; 47:4449-4461. [PMID: 30838422 DOI: 10.1093/nar/gkz161] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 12/16/2022] Open
Abstract
HMGN proteins localize to chromatin regulatory sites and modulate the cell-type specific transcription profile; however, the molecular mechanism whereby these ubiquitous nucleosome binding proteins affect gene expression is not fully understood. Here, we show that HMGNs regulate the expression of Rex1, one of the most highly transcribed genes in mouse embryonic stem cells (ESCs), by recruiting the transcription factors NANOG, OCT4 and SOX2 to an ESC-specific super enhancer located in the 5' region of Rex1. HMGNs facilitate the establishment of an epigenetic landscape characteristic of active chromatin and enhancer promoter interactions, as seen by chromatin conformation capture. Loss of HMGNs alters the local epigenetic profile, increases histone H1 occupancy, decreases transcription factors binding and reduces enhancer promoter interactions, thereby downregulating, but not abolishing Rex1 expression. ChIP-seq analyses show high colocalization of HMGNs and of REX1, a zinc finger protein, at promoters and enhancers. Loss of HMGNs preferentially reduces the specific binding of REX1 to these chromatin regulatory sites. Thus, HMGNs affects both the expression and the chromatin binding specificity of REX1. We suggest that HMGNs affect cell-type specific gene expression by modulating the binding specificity of transcription factors to chromatin.
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Affiliation(s)
- Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Bing He
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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230
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Abstract
Supplemental Digital Content is available in the text. If unifying principles could be revealed for how the same genome encodes different eukaryotic cells and for how genetic variability and environmental input are integrated to impact cardiovascular health, grand challenges in basic cell biology and translational medicine may succumb to experimental dissection. A rich body of work in model systems has implicated chromatin-modifying enzymes, DNA methylation, noncoding RNAs, and other transcriptome-shaping factors in adult health and in the development, progression, and mitigation of cardiovascular disease. Meanwhile, deployment of epigenomic tools, powered by next-generation sequencing technologies in cardiovascular models and human populations, has enabled description of epigenomic landscapes underpinning cellular function in the cardiovascular system. This essay aims to unpack the conceptual framework in which epigenomes are studied and to stimulate discussion on how principles of chromatin function may inform investigations of cardiovascular disease and the development of new therapies.
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Affiliation(s)
- Manuel Rosa-Garrido
- From the Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles
| | - Douglas J Chapski
- From the Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles
| | - Thomas M Vondriska
- From the Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles.
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231
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Sun M, Zhang J. Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells. PLoS Genet 2019; 15:e1008389. [PMID: 31525198 PMCID: PMC6762216 DOI: 10.1371/journal.pgen.1008389] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/26/2019] [Accepted: 08/28/2019] [Indexed: 12/31/2022] Open
Abstract
Gene expression is subject to stochastic noise, but to what extent and by which means such stochastic variations are coordinated among different genes are unclear. We hypothesize that neighboring genes on the same chromosome co-fluctuate in expression because of their common chromatin dynamics, and verify it at the genomic scale using allele-specific single-cell RNA-sequencing data of mouse cells. Unexpectedly, the co-fluctuation extends to genes that are over 60 million bases apart. We provide evidence that this long-range effect arises in part from chromatin co-accessibilities of linked loci attributable to three-dimensional proximity, which is much closer intra-chromosomally than inter-chromosomally. We further show that genes encoding components of the same protein complex tend to be chromosomally linked, likely resulting from natural selection for intracellular among-component dosage balance. These findings have implications for both the evolution of genome organization and optimal design of synthetic genomes in the face of gene expression noise.
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Affiliation(s)
- Mengyi Sun
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
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232
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Li Y, Li Z, Dong L, Tang M, Zhang P, Zhang C, Cao Z, Zhu Q, Chen Y, Wang H, Wang T, Lv D, Wang L, Zhao Y, Yang Y, Wang H, Zhang H, Roeder RG, Zhu WG. Histone H1 acetylation at lysine 85 regulates chromatin condensation and genome stability upon DNA damage. Nucleic Acids Res 2019; 46:7716-7730. [PMID: 29982688 PMCID: PMC6125638 DOI: 10.1093/nar/gky568] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/14/2018] [Indexed: 12/22/2022] Open
Abstract
Linker histone H1 has a key role in maintaining higher order chromatin structure and genome stability, but how H1 functions in these processes is elusive. Here, we report that acetylation of lysine 85 (K85) within the H1 globular domain is a critical post-translational modification that regulates chromatin organization. H1K85 is dynamically acetylated by the acetyltransferase PCAF in response to DNA damage, and this effect is counterbalanced by the histone deacetylase HDAC1. Notably, an acetylation-mimic mutation of H1K85 (H1K85Q) alters H1 binding to the nucleosome and leads to condensed chromatin as a result of increased H1 binding to core histones. In addition, H1K85 acetylation promotes heterochromatin protein 1 (HP1) recruitment to facilitate chromatin compaction. Consequently, H1K85 mutation leads to genomic instability and decreased cell survival upon DNA damage. Together, our data suggest a novel model whereby H1K85 acetylation regulates chromatin structure and preserves chromosome integrity upon DNA damage.
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Affiliation(s)
- Yinglu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Zhiming Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Liping Dong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Tang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ping Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chaohua Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ziyang Cao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Qian Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Yongcan Chen
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China.,Peking University-Tsinghua University Center for Life Sciences, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Tianzhuo Wang
- Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing 100191, China
| | - Danyu Lv
- Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing 100191, China
| | - Lina Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ying Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yang Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Haiying Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Hongquan Zhang
- Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing 100191, China
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wei-Guo Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China.,Peking University-Tsinghua University Center for Life Sciences, Beijing 100871, China
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233
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Burkardt DD, Zachariou A, Loveday C, Allen CL, Amor DJ, Ardissone A, Banka S, Bourgois A, Coubes C, Cytrynbaum C, Faivre L, Marion G, Horton R, Kotzot D, Lay‐Son G, Lees M, Low K, Luk H, Mark P, McConkie‐Rosell A, McDonald M, Pappas J, Phillipe C, Shears D, Skotko B, Stewart F, Stewart H, Temple IK, Mau‐Them FT, Verdugo RA, Weksberg R, Zarate YA, Graham JM, Tatton‐Brown K. HIST1H1E
heterozygous protein‐truncating variants cause a recognizable syndrome with intellectual disability and distinctive facial gestalt: A study to clarify the HIST1H1E syndrome phenotype in 30 individuals. Am J Med Genet A 2019; 179:2049-2055. [DOI: 10.1002/ajmg.a.61321] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 07/25/2019] [Accepted: 07/27/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Deepika D'Cunha Burkardt
- Center for Human Genetics,University Hospitals Rainbow Babies and Children, Department of genetics, Case Western Reserve University Cleveland Ohio
| | | | | | | | - David J. Amor
- Department of PaediatricsThe Royal Children's Hospital, Murdoch Children's Research Institute, University of Melbourne Parkville Victoria Australia
| | - Anna Ardissone
- Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Lombardia Italy
| | - Siddharth Banka
- Faculty of Biology, Medicine and Health, Division of Evolution and Genomic Sciences, School of Biological SciencesUniversity of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation Trust, Health Innovation Manchester Manchester UK
| | | | | | - Cheryl Cytrynbaum
- Division of Clinical and Metabolic GeneticsThe Hospital for Sick Children Toronto Ontario Canada
| | | | - Gerard Marion
- Service de GénétiqueCentre Hospitalier Universitaire de Caen Normandie Caen France
| | - Rachel Horton
- University Hospital Southampton NHS Foundation Trust Southampton UK
| | - Dieter Kotzot
- Division of Clinical Genetics, Department of PediatricsParacelsus Medical University Salzburg Salzburg Austria
| | - Guillermo Lay‐Son
- División de PediatríaPontificia Universidad Católica de Chile Santiago Chile
| | - Melissa Lees
- Clinical Genetics DepartmentGreat Ormond Street Hospital for Children NHS Foundation Trust London UK
| | - Karen Low
- Clinical GeneticsSt Michaels Hospital, University Hospitals Bristol Bristol UK
| | - Ho‐Ming Luk
- Department of HealthClinical Genetic Service Hong Kong Hong Kong
| | - Paul Mark
- Spectrum Health Division of Medical Genetics Grand Rapids Michigan
| | - Allyn McConkie‐Rosell
- Division of Medical Genetics, Department of PediatricsDuke University Medical Genetics Durham North Carolina
| | - Marie McDonald
- Division of Medical Genetics, Department of PediatricsDuke University Medical Genetics Durham North Carolina
| | - John Pappas
- Human Genetics ProgramUniversity School of Medicine New York New York USA
| | - Christophe Phillipe
- UF Innovation en Diagnostic Génomique des Maladies RaresCHU Dijon Bourgogne, INSERM UMR1231 GAD Dijon France
| | | | - Brian Skotko
- Division of Medical Genetics and Genomics, Department of PediatricsMassachusetts General Hospital, Harvard Medical School Boston Massachusetts
| | | | - Helen Stewart
- Clinical GeneticsOxford University Hospitals NHS Foundation Trust, Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre Oxford UK
| | - I Karen. Temple
- Faculty of MedicineWessex Clinical Genetics Service, University Hospital Southampton, University of Southampton Southampton UK
| | - Frederic T. Mau‐Them
- UF D'innovation en Génétique Moléculaire, Plateau Technique de Biologie, Centre Hospitalier Universitaire de Dijon, FHU TRANSLAD Dijon France
| | | | - Rosanna Weksberg
- Division of Clinical and Metabolic GeneticsThe Hospital for Sick Children Toronto Ontario Canada
| | - Yuri A. Zarate
- Section of Genetics and MetabolismArkansas Children's Hospital Little Rock Arkansas
| | - John M. Graham
- Medical GeneticsCedars‐Sinai Medical Center Los Angeles California
| | - Katrina Tatton‐Brown
- Institute of Cancer Research London UK
- South West Thames Regional Genetics ServiceSt George's University Hospitals NHS Foundation Trust London UK
- St George's University of London London UK
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234
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Rutowicz K, Lirski M, Mermaz B, Teano G, Schubert J, Mestiri I, Kroteń MA, Fabrice TN, Fritz S, Grob S, Ringli C, Cherkezyan L, Barneche F, Jerzmanowski A, Baroux C. Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis. Genome Biol 2019; 20:157. [PMID: 31391082 PMCID: PMC6685187 DOI: 10.1186/s13059-019-1767-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/21/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function. Well studied in animals, little is known about the evolution of H1 function in other eukaryotic lineages for instance plants. Notably, in the model plant Arabidopsis, while H1 is known to influence heterochromatin and DNA methylation, its contribution to transcription, molecular, and cytological chromatin organization remains elusive. RESULTS We provide a multi-scale functional study of Arabidopsis linker histones. We show that H1-deficient plants are viable yet show phenotypes in seed dormancy, flowering time, lateral root, and stomata formation-complemented by either or both of the major variants. H1 depletion also impairs pluripotent callus formation. Fine-scale chromatin analyses combined with transcriptome and nucleosome profiling reveal distinct roles of H1 on hetero- and euchromatin: H1 is necessary to form heterochromatic domains yet dispensable for silencing of most transposable elements; H1 depletion affects nucleosome density distribution and mobility in euchromatin, spatial arrangement of nanodomains, histone acetylation, and methylation. These drastic changes affect moderately the transcription but reveal a subset of H1-sensitive genes. CONCLUSIONS H1 variants have a profound impact on the molecular and spatial (nuclear) chromatin organization in Arabidopsis with distinct roles in euchromatin and heterochromatin and a dual causality on gene expression. Phenotypical analyses further suggest the novel possibility that H1-mediated chromatin organization may contribute to the epigenetic control of developmental and cellular transitions.
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Affiliation(s)
- Kinga Rutowicz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Maciej Lirski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Benoît Mermaz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
- Department of Molecular, Cellular & Developmental Biology, Yale University, 352a Osborn memorial laboratories, New Haven, CT, 06511, USA
| | - Gianluca Teano
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Jasmin Schubert
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Imen Mestiri
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Magdalena A Kroteń
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089, Warsaw, Poland
| | - Tohnyui Ndinyanka Fabrice
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Simon Fritz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Stefan Grob
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Christoph Ringli
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Lusik Cherkezyan
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Fredy Barneche
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Andrzej Jerzmanowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Célia Baroux
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland.
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235
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Ying H, Ying B, Zhang J, Kong D. Sirt1 modulates H3 phosphorylation and facilitates osteosarcoma cell autophagy. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:3374-3381. [PMID: 31390921 DOI: 10.1080/21691401.2019.1648280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hongliang Ying
- Department of Orthopaedics, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Boda Ying
- Department of Joint Surgery of Orthopaedic Center, The Second Hospital of Jilin University, Changchun, China
| | - Jinrui Zhang
- Department of Orthopaedics, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Daliang Kong
- Department of Orthopaedics, China-Japan Union Hospital of Jilin University, Changchun, China
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236
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Portillo-Ledesma S, Schlick T. Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019; 10. [PMID: 34046090 DOI: 10.1002/wcms.1434] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromatin structure, dynamics, and function are being intensely investigated by a variety of methods, including microscopy, X-ray diffraction, nuclear magnetic resonance, biochemical crosslinking, chromosome conformation capture, and computation. A range of experimental techniques combined with modeling is clearly valuable to help interpret experimental data and, importantly, generate configurations and mechanisms related to the 3D organization and function of the genome. Contact maps, in particular, as obtained by a variety of chromosome conformation capture methods, are of increasing interest due to their implications on genome structure and regulation on many levels. In this perspective, using seven examples from our group's studies, we illustrate how molecular modeling can help interpret such experimental data. Specifically, we show how computed contact maps related to experimental systems can be used to explain structures of nucleosomes, chromatin higher-order folding, domain segregation mechanisms, gene organization, and the effect on chromatin structure of external and internal fiber parameters, such as nucleosome positioning, presence of nucleosome free regions, histone posttranslational modifications, and linker histone binding. We argue that such computations on multiple spatial and temporal scales will be increasingly important for the integration of genomic, epigenomic, and biophysical data on chromatin structure and related cellular processes.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, New York, 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, New York, 10003, USA.,Courant Institute of Mathematical Sciences, New York University, 251 Mercer St, New York, New York, 10012, USA.,New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Room 340, Geography Building, 3663 North Zhongshan Road, Shanghai, 200062, China
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237
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Abstract
Physical access to DNA is a highly dynamic property of chromatin that plays an essential role in establishing and maintaining cellular identity. The organization of accessible chromatin across the genome reflects a network of permissible physical interactions through which enhancers, promoters, insulators and chromatin-binding factors cooperatively regulate gene expression. This landscape of accessibility changes dynamically in response to both external stimuli and developmental cues, and emerging evidence suggests that homeostatic maintenance of accessibility is itself dynamically regulated through a competitive interplay between chromatin-binding factors and nucleosomes. In this Review, we examine how the accessible genome is measured and explore the role of transcription factors in initiating accessibility remodelling; our goal is to illustrate how chromatin accessibility defines regulatory elements within the genome and how these epigenetic features are dynamically established to control gene expression.
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Affiliation(s)
- Sandy L Klemm
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Zohar Shipony
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg BioHub, San Francisco, CA, USA.
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238
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Kang CL, Qi B, Cai QQ, Fu LS, Yang Y, Tang C, Zhu P, Chen QW, Pan J, Chen MH, Wu XZ. LncRNA AY promotes hepatocellular carcinoma metastasis by stimulating ITGAV transcription. Am J Cancer Res 2019; 9:4421-4436. [PMID: 31285770 PMCID: PMC6599657 DOI: 10.7150/thno.32854] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 05/21/2019] [Indexed: 01/11/2023] Open
Abstract
Rationale: Tumor metastasis is the main cause for cancer-related death. However, the driving molecules of metastasis remain largely unknown. Here, we aim to identify long non-coding RNAs (lncRNAs) critical for human hepatocellular carcinoma (HCC) metastasis. Methods: Microarrays were used to screen a comprehensive set of lncRNAs with differential expression profiles in sulfatide-treated cells. Mass spectrometry, protein arrays, and RNA pull-down experiments were used to identify proteins that interacted with lncRNA. Epigenetic analysis was used to study lncRNA-mediated regulation mechanisms. Results: We identified lncRNA AY927503 (AY) as a metastasis-associated molecule that was highly expressed in human hepatocellular carcinoma (HCC) and correlated with metastatic events and poor prognosis in patients with HCC. AY promoted HCC cell migration, stemness, 5-fluorouracil resistance, and metastasis in mice. However, knockdown of integrin αV (ITGAV) abolished AY-stimulated migration, cell viability in HCC cells or tube formation. AY strongly promoted ITGAV transcription and αVβ3 expression by interacting with the ITGAV promoter specifically and stimulating its activity. AY was identified to interact with histone 1FX (H1FX), but deletion of the central domain of AY (AY∆371-522) abolished H1FX binding and ITGAV promoter stimulation. AY significantly enriched H3K4Me3 and acH3K9/14 but reduced H3K27Me3 and H1FX occupancy on the ITGAV promoter, which remodeled chromatin structures for RNA polymerase II recruitment. Knockdown of H1FX abrogated ITGAV transcription stimulated by AY. Conclusions: Our findings suggested that lncRNA AY promoted HCC metastasis via induction of chromatin modification for ITGAV transcription as a pioneer factor and was a potential molecular signature for metastasis or poor prognosis in patients with HCC.
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239
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The High Mobility Group A1 (HMGA1) Chromatin Architectural Factor Modulates Nuclear Stiffness in Breast Cancer Cells. Int J Mol Sci 2019; 20:ijms20112733. [PMID: 31167352 PMCID: PMC6600462 DOI: 10.3390/ijms20112733] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/28/2022] Open
Abstract
Plasticity is an essential condition for cancer cells to invade surrounding tissues. The nucleus is the most rigid cellular organelle and it undergoes substantial deformations to get through environmental constrictions. Nuclear stiffness mostly depends on the nuclear lamina and chromatin, which in turn might be affected by nuclear architectural proteins. Among these is the HMGA1 (High Mobility Group A1) protein, a factor that plays a causal role in neoplastic transformation and that is able to disentangle heterochromatic domains by H1 displacement. Here we made use of atomic force microscopy to analyze the stiffness of breast cancer cellular models in which we modulated HMGA1 expression to investigate its role in regulating nuclear plasticity. Since histone H1 is the main modulator of chromatin structure and HMGA1 is a well-established histone H1 competitor, we correlated HMGA1 expression and cellular stiffness with histone H1 expression level, post-translational modifications, and nuclear distribution. Our results showed that HMGA1 expression level correlates with nuclear stiffness, is associated to histone H1 phosphorylation status, and alters both histone H1 chromatin distribution and expression. These data suggest that HMGA1 might promote chromatin relaxation through a histone H1-mediated mechanism strongly impacting on the invasiveness of cancer cells.
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240
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Lai X, Stigliani A, Vachon G, Carles C, Smaczniak C, Zubieta C, Kaufmann K, Parcy F. Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants. MOLECULAR PLANT 2019; 12:743-763. [PMID: 30447332 DOI: 10.1016/j.molp.2018.10.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/20/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Transcription factors (TFs) are key cellular components that control gene expression. They recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to specific regions of the genome where they can recruit transcriptional co-factors and/or chromatin regulators to fine-tune spatiotemporal gene regulation. Therefore, the identification of TFBSs in genomic sequences and their subsequent quantitative modeling is of crucial importance for understanding and predicting gene expression. Here, we review how TFBSs can be determined experimentally, how the TFBS models can be constructed in silico, and how they can be optimized by taking into account features such as position interdependence within TFBSs, DNA shape, and/or by introducing state-of-the-art computational algorithms such as deep learning methods. In addition, we discuss the integration of context variables into the TFBS modeling, including nucleosome positioning, chromatin states, methylation patterns, 3D genome architectures, and TF cooperative binding, in order to better predict TF binding under cellular contexts. Finally, we explore the possibilities of combining the optimized TFBS model with technological advances, such as targeted TFBS perturbation by CRISPR, to better understand gene regulation, evolution, and plant diversity.
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Affiliation(s)
- Xuelei Lai
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
| | - Arnaud Stigliani
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Gilles Vachon
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Cristel Carles
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Cezary Smaczniak
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Chloe Zubieta
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - François Parcy
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
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241
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Huang M, Huang J, Zheng Y, Sun Q. Histone acetyltransferase inhibitors: An overview in synthesis, structure-activity relationship and molecular mechanism. Eur J Med Chem 2019; 178:259-286. [PMID: 31195169 DOI: 10.1016/j.ejmech.2019.05.078] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 02/05/2023]
Abstract
Acetylation, a key component in post-translational modification regulated by HATs and HDACs, is relevant to many crucial cellular contexts in organisms. Based on crucial pharmacophore patterns and the structure of targeted proteins, HAT inhibitors are designed and modified for higher affinity and better bioactivity. However, there are still some challenges, such as cell permeability, selectivity, toxicity and synthetic availability, which limit the improvement of HAT inhibitors. So far, only few HAT inhibitors have been approved for commercialization, indicating the urgent need for more successful and effective structure-based drug design and synthetic strategies. Here, we summarized three classes of HAT inhibitors based on their sources and structural scaffolds, emphasizing on their synthetic methods and structure-activity relationships and molecular mechanisms, hoping to facilitate the development and further application of HAT inhibitors.
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Affiliation(s)
- Mengyuan Huang
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Jiangkun Huang
- Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yongcheng Zheng
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Qiu Sun
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
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242
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He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife 2019; 8:42530. [PMID: 31135340 PMCID: PMC6594752 DOI: 10.7554/elife.42530] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/26/2019] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell - vegetative cell (VC) - of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.
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Affiliation(s)
- Shengbo He
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Martin Vickers
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Jingyi Zhang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
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243
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Brunk CF, Martin WF. Archaeal Histone Contributions to the Origin of Eukaryotes. Trends Microbiol 2019; 27:703-714. [PMID: 31076245 DOI: 10.1016/j.tim.2019.04.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/01/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022]
Abstract
The eukaryotic lineage arose from bacterial and archaeal cells that underwent a symbiotic merger. At the origin of the eukaryote lineage, the bacterial partner contributed genes, metabolic energy, and the building blocks of the endomembrane system. What did the archaeal partner donate that made the eukaryotic experiment a success? The archaeal partner provided the potential for complex information processing. Archaeal histones were crucial in that regard by providing the basic functional unit with which eukaryotes organize DNA into nucleosomes, exert epigenetic control of gene expression, transcribe genes with CCAAT-box promoters, and a manifest cell cycle with condensed chromosomes. While mitochondrial energy lifted energetic constraints on eukaryotic protein production, histone-based chromatin organization paved the path to eukaryotic genome complexity, a critical hurdle en route to the evolution of complex cells.
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Affiliation(s)
- Clifford F Brunk
- Department of Ecology and Evolutionary Biology and Molecular Biology Institute University of California Los Angeles, Los Angeles, USA
| | - William F Martin
- Institute of Molecular Evolution Heinrich-Heine-Universitaet Duesseldorf, Dusseldorf, Germany.
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244
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Disordered domains in chromatin-binding proteins. Essays Biochem 2019; 63:147-156. [PMID: 30940742 DOI: 10.1042/ebc20180068] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 02/08/2023]
Abstract
Chromatin comprises proteins, DNA and RNA, and its function is to condense and package the genome in a way that allows the necessary transactions such as transcription, replication and repair to occur in a highly organised and regulated manner. The packaging of chromatin is often thought of in a hierarchical fashion starting from the most basic unit of DNA packaging, the nucleosome, to the condensation of nucleosomal 'beads on a string' by linker histones to form the 30-nm fibre and eventually large chromatin domains. However, a picture of a more heterogeneous, dynamic and liquid-like assembly is emerging, in which intrinsically disordered proteins (IDPs) and proteins containing intrinsically disordered regions (IDRs) play a central role. Disorder features at all levels of chromatin organisation, from the histone tails, which are sites of extensive post-translational modification (PTM) that change the fate of the underlying genomic information, right through to transcription hubs, and the recently elucidated roles of IDPs and IDRs in the condensation of large regions of the genome through liquid-liquid phase separation.
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245
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Starkova TY, Artamonova TO, Ermakova VV, Chikhirzhina EV, Khodorkovskii MA, Tomilin AN. The Profile of Post-translational Modifications of Histone H1 in Chromatin of Mouse Embryonic Stem Cells. Acta Naturae 2019; 11:82-91. [PMID: 31413884 PMCID: PMC6643340 DOI: 10.32607/20758251-2019-11-2-82-91] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Indexed: 01/10/2023] Open
Abstract
Linker histone H1 is one of the main chromatin proteins which plays an important role in organizing eukaryotic DNA into a compact structure. There is data indicating that cell type-specific post-translational modifications of H1 modulate chromatin activity. Here, we compared histone H1 variants from NIH/3T3, mouse embryonic fibroblasts (MEFs), and mouse embryonic stem (ES) cells using matrix-assisted laser desorption/ ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR-MS). We found significant differences in the nature and positions of the post-translational modifications (PTMs) of H1.3-H1.5 variants in ES cells compared to differentiated cells. For instance, methylation of K75 in the H1.2-1.4 variants; methylation of K108, K148, K151, K152 K154, K155, K160, K161, K179, and K185 in H1.1, as well as of K168 in H1.2; phosphorylation of S129, T146, T149, S159, S163, and S180 in H1.1, T180 in H1.2, and T155 in H1.3 were identified exclusively in ES cells. The H1.0 and H1.2 variants in ES cells were characterized by an enhanced acetylation and overall reduced expression levels. Most of the acetylation sites of the H1.0 and H1.2 variants from ES cells were located within their C-terminal tails known to be involved in the stabilization of the condensed chromatin. These data may be used for further studies aimed at analyzing the functional role played by the revealed histone H1 PTMs in the self-renewal and differentiation of pluripotent stem cells.
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Affiliation(s)
- T. Yu. Starkova
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Biology of Stem Cells, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - T. O. Artamonova
- Peter the Great St.Petersburg Polytechnic University, Politekhnicheskaya Str. 29, St. Petersburg, 195251 , Russia
| | - V. V. Ermakova
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Biology of Stem Cells, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - E. V. Chikhirzhina
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Biology of Stem Cells, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - M. A. Khodorkovskii
- Peter the Great St.Petersburg Polytechnic University, Politekhnicheskaya Str. 29, St. Petersburg, 195251 , Russia
| | - A. N. Tomilin
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Biology of Stem Cells, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
- Saint Petersburg State University, 13B Universitetskaya Emb., St. Petersburg, 199034, Russia
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246
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Chromatin structures condensed by linker histones. Essays Biochem 2019; 63:75-87. [DOI: 10.1042/ebc20180056] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/14/2023]
Abstract
Abstract
In eukaryotic cells, genomic DNA exists in the form of chromatin through association with histone proteins, which consist of four core histone (H2A, H2B, H3, and H4) families and one linker histone (H1) family. The core histones bind to DNA to form the nucleosome, the recurring structural unit of chromatin. The linker histone binds to the nucleosome to form the next structural unit of chromatin, the chromatosome, which occurs dominantly in metazoans. Linker histones also play an essential role in condensing chromatin to form higher order structures. Unlike the core histones in the formation of the nucleosome, the role of linker histone in the formation of the chromatosome and high-order chromatin structure is not well understood. Nevertheless, exciting progress in the structural studies of chromatosomes and nucleosome arrays condensed by linker histones has been made in the last several years. In this mini-review, we discuss these recent experimental results and provide some perspectives for future studies.
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247
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Shimada M, Chen WY, Nakadai T, Onikubo T, Guermah M, Rhodes D, Roeder RG. Gene-Specific H1 Eviction through a Transcriptional Activator→p300→NAP1→H1 Pathway. Mol Cell 2019; 74:268-283.e5. [PMID: 30902546 DOI: 10.1016/j.molcel.2019.02.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 01/07/2019] [Accepted: 02/12/2019] [Indexed: 02/03/2023]
Abstract
Linker histone H1 has been correlated with transcriptional inhibition, but the mechanistic basis of the inhibition and its reversal during gene activation has remained enigmatic. We report that H1-compacted chromatin, reconstituted in vitro, blocks transcription by abrogating core histone modifications by p300 but not activator and p300 binding. Transcription from H1-bound chromatin is elicited by the H1 chaperone NAP1, which is recruited in a gene-specific manner through direct interactions with activator-bound p300 that facilitate core histone acetylation (by p300) and concomitant eviction of H1 and H2A-H2B. An analysis in B cells confirms the strong dependency on NAP1-mediated H1 eviction for induction of the silent CD40 gene and further demonstrates that H1 eviction, seeded by activator-p300-NAP1-H1 interactions, is propagated over a CCCTC-binding factor (CTCF)-demarcated region through a distinct mechanism that also involves NAP1. Our results confirm direct transcriptional inhibition by H1 and establish a gene-specific H1 eviction mechanism through an activator→p300→NAP1→H1 pathway.
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Affiliation(s)
- Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wei-Yi Chen
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA; Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan; Cancer Progression Research Center, National Yang-Ming University, Taipei 112, Taiwan
| | - Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Takashi Onikubo
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Mohamed Guermah
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Daniela Rhodes
- NTU Institute of Structural Biology and School of Biological Sciences, Nanyang Technological University, Singapore 636921, Singapore
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
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248
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Ivic N, Potocnjak M, Solis-Mezarino V, Herzog F, Bilokapic S, Halic M. Fuzzy Interactions Form and Shape the Histone Transport Complex. Mol Cell 2019; 73:1191-1203.e6. [PMID: 30824373 PMCID: PMC6436938 DOI: 10.1016/j.molcel.2019.01.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/01/2018] [Accepted: 01/22/2019] [Indexed: 01/27/2023]
Abstract
Protein transport into the nucleus is mediated by transport receptors. Import of highly charged proteins, such as histone H1 and ribosomal proteins, requires a dimer of two transport receptors. In this study, we determined the cryo-EM structure of the Imp7:Impβ:H1.0 complex, showing that the two importins form a cradle that accommodates the linker histone. The H1.0 globular domain is bound to Impβ, whereas the acidic loops of Impβ and Imp7 chaperone the positively charged C-terminal tail. Although it remains disordered, the H1 tail serves as a zipper that closes and stabilizes the structure through transient non-specific interactions with importins. Moreover, we found that the GGxxF and FxFG motifs in the Imp7 C-terminal tail are essential for Imp7:Impβ dimerization and H1 import, resembling importin interaction with nucleoporins, which, in turn, promote complex disassembly. The architecture of many other complexes might be similarly defined by rapidly exchanging electrostatic interactions mediated by disordered regions. Importin 7 and Importin β form a cradle to chaperone and transport histone H1 Transient and non-specific electrostatic interactions form and shape the complex The H1 tail serves as a zipper that closes and stabilizes Imp7:Impβ:H1 FxFG motifs in nucleoporins facilitate RanGTP-dependent disassembly of the complex
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Affiliation(s)
- Nives Ivic
- Gene Center Munich and Department of Biochemistry, Ludwig Maximilian University of Munich, 81377 Munich, Germany; Department of Physical Chemistry, Rudjer Boskovic Institute, 10000 Zagreb, Croatia
| | - Mia Potocnjak
- Gene Center Munich and Department of Biochemistry, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Victor Solis-Mezarino
- Gene Center Munich and Department of Biochemistry, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Franz Herzog
- Gene Center Munich and Department of Biochemistry, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Silvija Bilokapic
- Gene Center Munich and Department of Biochemistry, Ludwig Maximilian University of Munich, 81377 Munich, Germany; Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Mario Halic
- Gene Center Munich and Department of Biochemistry, Ludwig Maximilian University of Munich, 81377 Munich, Germany; Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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249
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The Roles of Human DNA Methyltransferases and Their Isoforms in Shaping the Epigenome. Genes (Basel) 2019; 10:genes10020172. [PMID: 30813436 PMCID: PMC6409524 DOI: 10.3390/genes10020172] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/16/2019] [Accepted: 02/19/2019] [Indexed: 12/20/2022] Open
Abstract
A DNA sequence is the hard copy of the human genome and it is a driving force in determining the physiological processes in an organism. Concurrently, the chemical modification of the genome and its related histone proteins is dynamically involved in regulating physiological processes and diseases, which overall constitutes the epigenome network. Among the various forms of epigenetic modifications, DNA methylation at the C-5 position of cytosine in the cytosine–guanine (CpG) dinucleotide is one of the most well studied epigenetic modifications. DNA methyltransferases (DNMTs) are a family of enzymes involved in generating and maintaining CpG methylation across the genome. In mammalian systems, DNA methylation is performed by DNMT1 and DNMT3s (DNMT3A and 3B). DNMT1 is predominantly involved in the maintenance of DNA methylation during cell division, while DNMT3s are involved in establishing de novo cytosine methylation and maintenance in both embryonic and somatic cells. In general, all DNMTs require accessory proteins, such as ubiquitin-like containing plant homeodomain (PHD) and really interesting new gene (RING) finger domain 1 (UHRF1) or DNMT3-like (DNMT3L), for their biological function. This review mainly focuses on the role of DNMT3B and its isoforms in de novo methylation and maintenance of DNA methylation, especially with respect to their role as an accessory protein.
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250
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Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub. Proc Natl Acad Sci U S A 2019; 116:4955-4962. [PMID: 30718394 DOI: 10.1073/pnas.1816424116] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Gene expression is orchestrated at the structural level by nucleosome positioning, histone tail acetylation, and linker histone (LH) binding. Here, we integrate available data on nucleosome positioning, nucleosome-free regions (NFRs), acetylation islands, and LH binding sites to "fold" in silico the 55-kb HOXC gene cluster and investigate the role of each feature on the gene's folding. The gene cluster spontaneously forms a dynamic connection hub, characterized by hierarchical loops which accommodate multiple contacts simultaneously and decrease the average distance between promoters by ∼100 nm. Contact probability matrices exhibit "stripes" near promoter regions, a feature associated with transcriptional regulation. Interestingly, while LH proteins alone decrease long-range contacts and acetylation alone increases transient contacts, combined LH and acetylation produce long-range contacts. Thus, our work emphasizes how chromatin architecture is coordinated strongly by epigenetic factors and opens the way for nucleosome resolution models incorporating epigenetic modifications to understand and predict gene activity.
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