1
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Özdemir C, Purkey LR, Sanchez A, Miller KM. PARticular MARks: Histone ADP-ribosylation and the DNA damage response. DNA Repair (Amst) 2024; 140:103711. [PMID: 38924925 DOI: 10.1016/j.dnarep.2024.103711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/04/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
Cellular and molecular responses to DNA damage are highly orchestrated and dynamic, acting to preserve the maintenance and integrity of the genome. Histone proteins bind DNA and organize the genome into chromatin. Post-translational modifications of histones have been shown to play an essential role in orchestrating the chromatin response to DNA damage by regulating the DNA damage response pathway. Among the histone modifications that contribute to this intricate network, histone ADP-ribosylation (ADPr) is emerging as a pivotal component of chromatin-based DNA damage response (DDR) pathways. In this review, we survey how histone ADPr is regulated to promote the DDR and how it impacts chromatin and other histone marks. Recent advancements have revealed histone ADPr effects on chromatin structure and the regulation of DNA repair factor recruitment to DNA lesions. Additionally, we highlight advancements in technology that have enabled the identification and functional validation of histone ADPr in cells and in response to DNA damage. Given the involvement of DNA damage and epigenetic regulation in human diseases including cancer, these findings have clinical implications for histone ADPr, which are also discussed. Overall, this review covers the involvement of histone ADPr in the DDR and highlights potential future investigations aimed at identifying mechanisms governed by histone ADPr that participate in the DDR, human diseases, and their treatments.
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Affiliation(s)
- Cem Özdemir
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Laura R Purkey
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
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2
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Takeuchi H, Nagahara S, Higashiyama T, Berger F. The Chaperone NASP Contributes to de Novo Deposition of the Centromeric Histone Variant CENH3 in Arabidopsis Early Embryogenesis. PLANT & CELL PHYSIOLOGY 2024; 65:1135-1148. [PMID: 38597891 PMCID: PMC11287212 DOI: 10.1093/pcp/pcae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/01/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
The centromere is an essential chromosome region where the kinetochore is formed to control equal chromosome distribution during cell division. The centromere-specific histone H3 variant CENH3 (also called CENP-A) is a prerequisite for the kinetochore formation. Since CENH3 evolves rapidly, associated factors, including histone chaperones mediating the deposition of CENH3 on the centromere, are thought to act through species-specific amino acid sequences. The functions and interaction networks of CENH3 and histone chaperons have been well-characterized in animals and yeasts. However, molecular mechanisms involved in recognition and deposition of CENH3 are still unclear in plants. Here, we used a swapping strategy between domains of CENH3 of Arabidopsis thaliana and the liverwort Marchantia polymorpha to identify specific regions of CENH3 involved in targeting the centromeres and interacting with the general histone H3 chaperone, nuclear autoantigenic sperm protein (NASP). CENH3's LoopN-α1 region was necessary and sufficient for the centromere targeting in cooperation with the α2 region and was involved in interaction with NASP in cooperation with αN, suggesting a species-specific CENH3 recognition. In addition, by generating an Arabidopsis nasp knock-out mutant in the background of a fully fertile GFP-CENH3/cenh3-1 line, we found that NASP was implicated for de novo CENH3 deposition after fertilization and thus for early embryo development. Our results imply that the NASP mediates the supply of CENH3 in the context of the rapidly evolving centromere identity in land plants.
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Affiliation(s)
- Hidenori Takeuchi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Aichi 464-8601, Japan
- Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Shiori Nagahara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Aichi 464-8601, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna 1030, Austria
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3
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Wu ZP, Bloom KS, Forest MG, Cao XZ. Transient crosslinking controls the condensate formation pathway within chromatin networks. Phys Rev E 2024; 109:L042401. [PMID: 38755828 PMCID: PMC11137846 DOI: 10.1103/physreve.109.l042401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/26/2024] [Indexed: 05/18/2024]
Abstract
The network structure of densely packed chromatin within the nucleus of eukaryotic cells acts in concert with nonequilibrium processes. Using statistical physics simulations, we explore the control provided by transient crosslinking of the chromatin network by structural-maintenance-of-chromosome (SMC) proteins over (i) the physical properties of the chromatin network and (ii) condensate formation of embedded molecular species. We find that the density and lifetime of transient SMC crosslinks regulate structural relaxation modes and tune the sol-vs-gel state of the chromatin network, which imparts control over the kinetic pathway to condensate formation. Specifically, lower density, shorter-lived crosslinks induce sollike networks and a droplet-fusion pathway, whereas higher density, longer-lived crosslinks induce gellike networks and an Ostwald-ripening pathway.
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Affiliation(s)
- Zong-Pei Wu
- Department of Physics at Xiamen University, Xiamen 361005, P.R. China
| | - Kerry S. Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - M. Gregory Forest
- Departments of Mathematics, Applied Physical Sciences and Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xue-Zheng Cao
- Department of Physics at Xiamen University, Xiamen 361005, P.R. China
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4
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Whiwon L, Salma S, Daniel A, Stephanie L, Marc C, Cherith S, Abby T, Angela S, Robin H, Yvonne B. Patient-facing digital tools for delivering genetic services: a systematic review. J Med Genet 2023; 60:1-10. [PMID: 36137613 DOI: 10.1136/jmg-2022-109085] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/19/2022] [Indexed: 01/24/2023]
Abstract
This study systematically reviewed the literature on the impact of digital genetics tools on patient care and system efficiencies. MEDLINE and Embase were searched for articles published between January 2010 and March 2021. Studies evaluating the use of patient-facing digital tools in the context of genetic service delivery were included. Two reviewers screened and extracted patient-reported and system-focused outcomes from each study. Data were synthesised using a descriptive approach. Of 3226 unique studies identified, 87 were included. A total of 70 unique digital tools were identified. As a result of using digital tools, 84% of studies reported a positive outcome in at least one of the following patient outcomes: knowledge, psychosocial well-being, behavioural/management changes, family communication, decision-making or level of engagement. Digital tools improved workflow and efficiency for providers and reduced the amount of time they needed to spend with patients. However, we identified a misalignment between study purpose and patient-reported outcomes measured and a lack of tools that encompass the entire genetic counselling and testing trajectory. Given increased demand for genetic services and the shift towards virtual care, this review provides evidence that digital tools can be used to efficiently deliver patient-centred care. Future research should prioritise development, evaluation and implementation of digital tools that can support the entire patient trajectory across a range of clinical settings. PROSPERO registration numberCRD42020202862.
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Affiliation(s)
- Lee Whiwon
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Shickh Salma
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Assamad Daniel
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Luca Stephanie
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Clausen Marc
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Somerville Cherith
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Tafler Abby
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Shaw Angela
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Hayeems Robin
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Bombard Yvonne
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
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5
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Tessadori F, Duran K, Knapp K, Fellner M, Smithson S, Beleza Meireles A, Elting MW, Waisfisz Q, O’Donnell-Luria A, Nowak C, Douglas J, Ronan A, Brunet T, Kotzaeridou U, Svihovec S, Saenz MS, Thiffault I, Del Viso F, Devine P, Rego S, Tenney J, van Haeringen A, Ruivenkamp CA, Koene S, Robertson SP, Deshpande C, Pfundt R, Verbeek N, van de Kamp JM, Weiss JM, Ruiz A, Gabau E, Banne E, Pepler A, Bottani A, Laurent S, Guipponi M, Bijlsma E, Bruel AL, Sorlin A, Willis M, Powis Z, Smol T, Vincent-Delorme C, Baralle D, Colin E, Revencu N, Calpena E, Wilkie AO, Chopra M, Cormier-Daire V, Keren B, Afenjar A, Niceta M, Terracciano A, Specchio N, Tartaglia M, Rio M, Barcia G, Rondeau S, Colson C, Bakkers J, Mace PD, Bicknell LS, van Haaften G, van Haaften G. Recurrent de novo missense variants across multiple histone H4 genes underlie a neurodevelopmental syndrome. Am J Hum Genet 2022; 109:750-758. [PMID: 35202563 PMCID: PMC9069069 DOI: 10.1016/j.ajhg.2022.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/03/2022] [Indexed: 12/12/2022] Open
Abstract
Chromatin is essentially an array of nucleosomes, each of which consists of the DNA double-stranded fiber wrapped around a histone octamer. This organization supports cellular processes such as DNA replication, DNA transcription, and DNA repair in all eukaryotes. Human histone H4 is encoded by fourteen canonical histone H4 genes, all differing at the nucleotide level but encoding an invariant protein. Here, we present a cohort of 29 subjects with de novo missense variants in six H4 genes (H4C3, H4C4, H4C5, H4C6, H4C9, and H4C11) identified by whole-exome sequencing and matchmaking. All individuals present with neurodevelopmental features of intellectual disability and motor and/or gross developmental delay, while non-neurological features are more variable. Ten amino acids are affected, six recurrently, and are all located within the H4 core or C-terminal tail. These variants cluster to specific regions of the core H4 globular domain, where protein-protein interactions occur with either other histone subunits or histone chaperones. Functional consequences of the identified variants were evaluated in zebrafish embryos, which displayed abnormal general development, defective head organs, and reduced body axis length, providing compelling evidence for the causality of the reported disorder(s). While multiple developmental syndromes have been linked to chromatin-associated factors, missense-bearing histone variants (e.g., H3 oncohistones) are only recently emerging as a major cause of pathogenicity. Our findings establish a broader involvement of H4 variants in developmental syndromes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gijs van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 Utrecht, the Netherlands.
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He Y, Lawrimore J, Cook D, Van Gorder EE, De Larimat SC, Adalsteinsson D, Forest MG, Bloom K. Statistical mechanics of chromosomes: in vivo and in silico approaches reveal high-level organization and structure arise exclusively through mechanical feedback between loop extruders and chromatin substrate properties. Nucleic Acids Res 2020; 48:11284-11303. [PMID: 33080019 PMCID: PMC7672462 DOI: 10.1093/nar/gkaa871] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 11/14/2022] Open
Abstract
The revolution in understanding higher order chromosome dynamics and organization derives from treating the chromosome as a chain polymer and adapting appropriate polymer-based physical principles. Using basic principles, such as entropic fluctuations and timescales of relaxation of Rouse polymer chains, one can recapitulate the dominant features of chromatin motion observed in vivo. An emerging challenge is to relate the mechanical properties of chromatin to more nuanced organizational principles such as ubiquitous DNA loops. Toward this goal, we introduce a real-time numerical simulation model of a long chain polymer in the presence of histones and condensin, encoding physical principles of chromosome dynamics with coupled histone and condensin sources of transient loop generation. An exact experimental correlate of the model was obtained through analysis of a model-matching fluorescently labeled circular chromosome in live yeast cells. We show that experimentally observed chromosome compaction and variance in compaction are reproduced only with tandem interactions between histone and condensin, not from either individually. The hierarchical loop structures that emerge upon incorporation of histone and condensin activities significantly impact the dynamic and structural properties of chromatin. Moreover, simulations reveal that tandem condensin–histone activity is responsible for higher order chromosomal structures, including recently observed Z-loops.
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Affiliation(s)
- Yunyan He
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Diana Cook
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - David Adalsteinsson
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - M Gregory Forest
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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7
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Rai LS, Singha R, Sanchez H, Chakraborty T, Chand B, Bachellier-Bassi S, Chowdhury S, d’Enfert C, Andes DR, Sanyal K. The Candida albicans biofilm gene circuit modulated at the chromatin level by a recent molecular histone innovation. PLoS Biol 2019; 17:e3000422. [PMID: 31398188 PMCID: PMC6703697 DOI: 10.1371/journal.pbio.3000422] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/21/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023] Open
Abstract
Histone H3 and its variants regulate gene expression but the latter are absent in most ascomycetous fungi. Here, we report the identification of a variant histone H3, which we have designated H3VCTG because of its exclusive presence in the CTG clade of ascomycetes, including Candida albicans, a human pathogen. C. albicans grows both as single yeast cells and hyphal filaments in the planktonic mode of growth. It also forms a three-dimensional biofilm structure in the host as well as on human catheter materials under suitable conditions. H3VCTG null (hht1/hht1) cells of C. albicans are viable but produce more robust biofilms than wild-type cells in both in vitro and in vivo conditions. Indeed, a comparative transcriptome analysis of planktonic and biofilm cells reveals that the biofilm circuitry is significantly altered in H3VCTG null cells. H3VCTG binds more efficiently to the promoters of many biofilm-related genes in the planktonic cells than during biofilm growth, whereas the binding of the core canonical histone H3 on the corresponding promoters largely remains unchanged. Furthermore, biofilm defects associated with master regulators, namely, biofilm and cell wall regulator 1 (Bcr1), transposon enhancement control 1 (Tec1), and non-dityrosine 80 (Ndt80), are significantly rescued in cells lacking H3VCTG. The occupancy of the transcription factor Bcr1 at its cognate promoter binding sites was found to be enhanced in the absence of H3VCTG in the planktonic form of growth resulting in enhanced transcription of biofilm-specific genes. Further, we demonstrate that co-occurrence of valine and serine at the 31st and 32nd positions in H3VCTG, respectively, is essential for its function. Taken together, we show that even in a unicellular organism, differential gene expression patterns are modulated by the relative occupancy of the specific histone H3 type at the chromatin level. A variant histone H3 specific to the CTG clade of ascomycete fungi modulates the expression of the majority of the biofilm genes in the human pathogen Candida albicans by binding differentially to biofilm-relevant gene promoters.
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Affiliation(s)
- Laxmi Shanker Rai
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, USC2019 INRA, Paris, France
| | - Rima Singha
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Hiram Sanchez
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Tanmoy Chakraborty
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Bipin Chand
- Genotypic Technology Private Limited, Bangalore, India
| | | | - Shantanu Chowdhury
- GNR Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Christophe d’Enfert
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, USC2019 INRA, Paris, France
| | - David R. Andes
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- * E-mail:
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8
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He H, Hu Z, Xiao H, Zhou F, Yang B. The tale of histone modifications and its role in multiple sclerosis. Hum Genomics 2018; 12:31. [PMID: 29933755 PMCID: PMC6013900 DOI: 10.1186/s40246-018-0163-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/08/2018] [Indexed: 02/08/2023] Open
Abstract
Epigenetics defines the persistent modifications of gene expression in a manner that does not involve the corresponding alterations in DNA sequences. It includes modifications of DNA nucleotides, nucleosomal remodeling, and post-translational modifications (PTMs). It is becoming evident that PTMs which act singly or in combination to form “histone codes” orchestrate the chromatin structure and dynamic functions. PTMs of histone tails have been demonstrated to influence numerous biological developments, as well as disease onset and progression. Multiple sclerosis (MS) is an autoimmune inflammatory demyelinating and neurodegenerative disease of the central nervous system, of which the precise pathophysiological mechanisms remain to be fully elucidated. There is a wealth of emerging evidence that epigenetic modifications may confer risk for MS, which provides new insights into MS. Histone PTMs, one of the key events that regulate gene activation, seem to play a prominent role in the epigenetic mechanism of MS. In this review, we summarize recent studies in our understanding of the epigenetic language encompassing histone, with special emphasis on histone acetylation and histone lysine methylation, two of the best characterized histone modifications. We also discuss how the current studies address histone acetylation and histone lysine methylation influencing pathophysiology of MS and how future studies could be designed to establish optimized therapeutic strategies for MS.
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Affiliation(s)
- Hui He
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China
| | - Zhiping Hu
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China
| | - Han Xiao
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China
| | - Fangfang Zhou
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China
| | - Binbin Yang
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China.
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9
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Shukla A, Bhargava P. Regulation of tRNA gene transcription by the chromatin structure and nucleosome dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:295-309. [PMID: 29313808 DOI: 10.1016/j.bbagrm.2017.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 01/19/2023]
Abstract
The short, non-coding genes transcribed by the RNA polymerase (pol) III, necessary for survival of a cell, need to be repressed under the stress conditions in vivo. The pol III-transcribed genes have adopted several novel chromatin-based regulatory mechanisms to their advantage. In the budding yeast, the sub-nucleosomal size tRNA genes are found in the nucleosome-free regions, flanked by positioned nucleosomes at both the ends. With their chromosomes-wide distribution, all tRNA genes have a different chromatin context. A single nucleosome dynamics controls the accessibility of the genes for transcription. This dynamics operates under the influence of several chromatin modifiers in a gene-specific manner, giving the scope for differential regulation of even the isogenes within a tRNA gene family. The chromatin structure around the pol III-transcribed genes provides a context conducive for steady-state transcription as well as gene-specific transcriptional regulation upon signaling from the environmental cues. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
- Ashutosh Shukla
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Uppal Road, Hyderabad 500007, India
| | - Purnima Bhargava
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Uppal Road, Hyderabad 500007, India.
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10
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Ors A, Papin C, Favier B, Roulland Y, Dalkara D, Ozturk M, Hamiche A, Dimitrov S, Padmanabhan K. Histone H3.3 regulates mitotic progression in mouse embryonic fibroblasts. Biochem Cell Biol 2017; 95:491-499. [DOI: 10.1139/bcb-2016-0190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
H3.3 is a histone variant that marks transcription start sites as well as telomeres and heterochromatic sites on the genome. The presence of H3.3 is thought to positively correlate with the transcriptional status of its target genes. Using a conditional genetic strategy against H3.3B, combined with short hairpin RNAs against H3.3A, we essentially depleted all H3.3 gene expression in mouse embryonic fibroblasts. Following nearly complete loss of H3.3 in the cells, our transcriptomic analyses show very little impact on global gene expression or on the localization of histone variant H2A.Z. Instead, fibroblasts displayed slower cell growth and an increase in cell death, coincident with large-scale chromosome misalignment in mitosis and large polylobed or micronuclei in interphase cells. Thus, we conclude that H3.3 may have an important under-explored additional role in chromosome segregation, nuclear structure, and the maintenance of genome integrity.
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Affiliation(s)
- Aysegul Ors
- Université de Grenoble Alpes, Institute for Advanced Biosciences, INSERM U1209/CNRS 5309, 38700 La Tronche, France
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, 06800 Ankara, Turkey
| | - Christophe Papin
- Université de Strasbourg, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), CNRS, INSERM, Equipe labélisée Ligue contre le Cancer, 1 rue Laurent Fries, B.P. 10142, 67404 Illkirch Cedex, France
| | - Bertrand Favier
- Université de Grenoble Alpes, Team GREPI, Etablissement Français du Sang, EA 7408, BP35, 38701 La Tronche, France
| | - Yohan Roulland
- Université de Grenoble Alpes, Institute for Advanced Biosciences, INSERM U1209/CNRS 5309, 38700 La Tronche, France
| | - Defne Dalkara
- Université de Grenoble Alpes, Institute for Advanced Biosciences, INSERM U1209/CNRS 5309, 38700 La Tronche, France
| | - Mehmet Ozturk
- Izmir Biomedicine and Genome Center, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey
| | - Ali Hamiche
- Université de Strasbourg, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), CNRS, INSERM, Equipe labélisée Ligue contre le Cancer, 1 rue Laurent Fries, B.P. 10142, 67404 Illkirch Cedex, France
| | - Stefan Dimitrov
- Université de Grenoble Alpes, Institute for Advanced Biosciences, INSERM U1209/CNRS 5309, 38700 La Tronche, France
| | - Kiran Padmanabhan
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole normale supérieur de Lyon, Université Claude Bernard Lyon 1, 46 Allée d’Italie, F-69364 Lyon, France
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11
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Silva PES, Godinho MH. Helical Microfilaments with Alternating Imprinted Intrinsic Curvatures. Macromol Rapid Commun 2017; 38. [DOI: 10.1002/marc.201600700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 12/14/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Pedro Emanuel Santos Silva
- Departmento de Física/I3N - Universidade de Aveiro; Campus Universitario de Santiago; 3810-193 Aveiro Portugal
- Departamento de Ciência dos Materiais and CENIMAT/I3N Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; 2829-516 Caparica Portugal
| | - Maria Helena Godinho
- Departamento de Ciência dos Materiais and CENIMAT/I3N Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; 2829-516 Caparica Portugal
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12
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Önder Ö, Sidoli S, Carroll M, Garcia BA. Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations. Expert Rev Proteomics 2016; 12:499-517. [PMID: 26400466 DOI: 10.1586/14789450.2015.1084231] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chromatin biology and epigenetics are scientific fields that are rapid expanding due to their fundamental role in understanding cell development, heritable characters and progression of diseases. Histone post-translational modifications (PTMs) are major regulators of the epigenetic machinery due to their ability to modulate gene expression, DNA repair and chromosome condensation. Large-scale strategies based on mass spectrometry have been impressively improved in the last decade, so that global changes of histone PTM abundances are quantifiable with nearly routine proteomics analyses and it is now possible to determine combinatorial patterns of modifications. Presented here is an overview of the most utilized and newly developed proteomics strategies for histone PTM characterization and a number of case studies where epigenetic mechanisms have been comprehensively characterized. Moreover, a number of current epigenetic therapies are illustrated, with an emphasis on cancer.
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Affiliation(s)
- Özlem Önder
- a 1 Division of Hematology and Oncology, Philadelphia, 19104, USA.,b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simone Sidoli
- b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Martin Carroll
- a 1 Division of Hematology and Oncology, Philadelphia, 19104, USA
| | - Benjamin A Garcia
- b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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13
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Sadakierska-Chudy A, Kostrzewa RM, Filip M. A comprehensive view of the epigenetic landscape part I: DNA methylation, passive and active DNA demethylation pathways and histone variants. Neurotox Res 2014; 27:84-97. [PMID: 25362550 PMCID: PMC4286137 DOI: 10.1007/s12640-014-9497-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/07/2014] [Accepted: 10/16/2014] [Indexed: 12/31/2022]
Abstract
In multicellular organisms, all the cells are genetically identical but turn genes on or off at the right time to promote differentiation into specific cell types. The regulation of higher-order chromatin structure is essential for genome-wide reprogramming and for tissue-specific patterns of gene expression. The complexity of the genome is regulated by epigenetic mechanisms, which act at the level of DNA, histones, and nucleosomes. Epigenetic machinery is involved in many biological processes, including genomic imprinting, X-chromosome inactivation, heterochromatin formation, and transcriptional regulation, as well as DNA damage repair. In this review, we summarize the recent understanding of DNA methylation, cytosine derivatives, active and passive demethylation pathways as well as histone variants. DNA methylation is one of the well-characterized epigenetic signaling tools. Cytosine methylation of promoter regions usually represses transcription but methylation in the gene body may have a positive correlation with gene expression. The attachment of a methyl group to cytosine residue in the DNA sequence is catalyzed by enzymes of the DNA methyltransferase family. Recent studies have shown that the Ten-Eleven translocation family enzymes are involved in stepwise oxidation of 5-methylcytosine, creating new cytosine derivatives including 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine. Additionally, histone variants into nucleosomes create another strategy to regulate the structure and function of chromatin. The replacement of canonical histones with specialized histone variants regulates accessibility of DNA, and thus may affect multiple biological processes, such as replication, transcription, DNA repair, and play a role in various disorders such as cancer.
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Affiliation(s)
- Anna Sadakierska-Chudy
- Laboratory of Drug Addiction Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna Street 12, 31-343, Kraków, Poland,
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14
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Regulation of ISWI chromatin remodelling activity. Chromosoma 2014; 123:91-102. [PMID: 24414837 DOI: 10.1007/s00412-013-0447-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 11/20/2013] [Accepted: 11/25/2013] [Indexed: 12/22/2022]
Abstract
The packaging of the eukaryotic genome into chromatin facilitates the storage of the genetic information within the nucleus, but prevents the access to the underlying DNA sequences. Structural changes in chromatin are mediated by several mechanisms. Among them, ATP-dependent remodelling complexes belonging to ISWI family provides one of the best examples that eukaryotic cells evolved to finely regulate these changes. ISWI-containing complexes use the energy derived from ATP hydrolysis to rearrange nucleosomes on chromatin in order to favour specific nuclear reactions. The combination of regulatory nuclear factors associated with the ATPase subunit as well as its modulation by specific histone modifications, specializes the nuclear function of each ISWI-containing complex. Here we review the different ways by which ISWI enzymatic activity can be modulated and regulated in the nucleus of eukaryotic cells.
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Epigenetic regulation of transcription by RNA polymerase III. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1015-25. [DOI: 10.1016/j.bbagrm.2013.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 05/11/2013] [Accepted: 05/15/2013] [Indexed: 01/11/2023]
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16
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Hoeijmakers WAM, Salcedo-Amaya AM, Smits AH, Françoijs KJ, Treeck M, Gilberger TW, Stunnenberg HG, Bártfai R. H2A.Z/H2B.Z double-variant nucleosomes inhabit the AT-rich promoter regions of the Plasmodium falciparum genome. Mol Microbiol 2013; 87:1061-73. [PMID: 23320541 PMCID: PMC3594968 DOI: 10.1111/mmi.12151] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2013] [Indexed: 02/06/2023]
Abstract
Histone variants are key components of the epigenetic code and evolved to perform specific functions in transcriptional regulation, DNA repair, chromosome segregation and other fundamental processes. Although variants for histone H2A and H3 are found throughout the eukaryotic kingdom, variants of histone H2B and H4 are rarely encountered. H2B.Z is one of those rare H2B variants and is apicomplexan-specific. Here we show that in Plasmodium falciparum H2B.Z localizes to euchromatic intergenic regions throughout intraerythrocytic development and together with H2A.Z forms a double-variant nucleosome subtype. These nucleosomes are enriched in promoters over 3′ intergenic regions and their occupancy generally correlates with the strength of the promoter, but not with its temporal activity. Remarkably, H2B.Z occupancy levels exhibit a clear correlation with the base-composition of the underlying DNA, raising the intriguing possibility that the extreme AT content of the intergenic regions within the Plasmodium genome might be instructive for histone variant deposition. In summary, our data show that the H2A.Z/H2B.Z double-variant nucleosome demarcates putative regulatory regions of the P. falciparum epigenome and likely provides a scaffold for dynamic regulation of gene expression in this deadly human pathogen.
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Affiliation(s)
- Wieteke A M Hoeijmakers
- Department of Molecular Biology, Radboud University, Nijmegen Centre for Molecular Life Sciences, Nijmegen 6525GA, the Netherlands
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17
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Kumari S, Swaminathan A, Chatterjee S, Senapati P, Boopathi R, Kundu TK. Chromatin organization, epigenetics and differentiation: an evolutionary perspective. Subcell Biochem 2013; 61:3-35. [PMID: 23150244 DOI: 10.1007/978-94-007-4525-4_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Genome packaging is a universal phenomenon from prokaryotes to higher mammals. Genomic constituents and forces have however, travelled a long evolutionary route. Both DNA and protein elements constitute the genome and also aid in its dynamicity. With the evolution of organisms, these have experienced several structural and functional changes. These evolutionary changes were made to meet the challenging scenario of evolving organisms. This review discusses in detail the evolutionary perspective and functionality gain in the phenomena of genome organization and epigenetics.
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Affiliation(s)
- Sujata Kumari
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit (MBGU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Post, Bangalore, 560064, India
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18
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Abstract
Histones are the protein components of chromatin and are important for its organization and compaction. Although core histones are exclusively expressed during S phase of the cell cycle, there exist variants of canonical histones that are expressed throughout the cell cycle. These histone variants are often deposited at defined regions of the genome and they play important roles in a variety of cellular processes, such as transcription regulation, heterochromatin formation and DNA repair. In this chapter, we will focus on several histone variants that have been linked to transcription regulation, and highlight their physical and functional features that facilitate their activities in this context.
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Affiliation(s)
- Cindy Law
- Ontario Cancer Institute, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
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19
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Verdaasdonk JS, Gardner R, Stephens AD, Yeh E, Bloom K. Tension-dependent nucleosome remodeling at the pericentromere in yeast. Mol Biol Cell 2012; 23:2560-70. [PMID: 22593210 PMCID: PMC3386219 DOI: 10.1091/mbc.e11-07-0651] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Dynamics of histones under tension in the pericentromere depends on RSC and ISW2 chromatin remodeling. The underlying pericentromeric chromatin forms a platform that is required to maintain kinetochore structure when under spindle-based tension. Nucleosome positioning is important for the structural integrity of chromosomes. During metaphase the mitotic spindle exerts physical force on pericentromeric chromatin. The cell must adjust the pericentromeric chromatin to accommodate the changing tension resulting from microtubule dynamics to maintain a stable metaphase spindle. Here we examine the effects of spindle-based tension on nucleosome dynamics by measuring the histone turnover of the chromosome arm and the pericentromere during metaphase in the budding yeast Saccharomyces cerevisiae. We find that both histones H2B and H4 exhibit greater turnover in the pericentromere during metaphase. Loss of spindle-based tension by treatment with the microtubule-depolymerizing drug nocodazole or compromising kinetochore function results in reduced histone turnover in the pericentromere. Pericentromeric histone dynamics are influenced by the chromatin-remodeling activities of STH1/NPS1 and ISW2. Sth1p is the ATPase component of the Remodels the Structure of Chromatin (RSC) complex, and Isw2p is an ATP-dependent DNA translocase member of the Imitation Switch (ISWI) subfamily of chromatin-remodeling factors. The balance between displacement and insertion of pericentromeric histones provides a mechanism to accommodate spindle-based tension while maintaining proper chromatin packaging during mitosis.
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Affiliation(s)
- Jolien S Verdaasdonk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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20
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Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. PLoS One 2012; 7:e35269. [PMID: 22529998 PMCID: PMC3329448 DOI: 10.1371/journal.pone.0035269] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 03/13/2012] [Indexed: 12/20/2022] Open
Abstract
Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts. Our data represent the most comprehensive dinoflagellate EST data set to date. This study provides a comprehensive resource to further analyze the genetic makeup, metabolic capacities, and gene repertoire of Symbiodinium and dinoflagellates. Overall, our findings indicate that Symbiodinium possesses some unique characteristics, in particular the transcriptional regulation in Symbiodinium may differ from the currently known mechanisms of eukaryotic gene regulation.
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21
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ATP-independent cooperative binding of yeast Isw1a to bare and nucleosomal DNA. PLoS One 2012; 7:e31845. [PMID: 22359636 PMCID: PMC3281020 DOI: 10.1371/journal.pone.0031845] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 01/13/2012] [Indexed: 12/26/2022] Open
Abstract
Among chromatin remodeling factors, the ISWI family displays a nucleosome-enhanced ATPase activity coupled to DNA translocation. While these enzymes are known to bind to DNA, their activity has not been fully characterized. Here we use TEM imaging and single molecule manipulation to investigate the interaction between DNA and yeast Isw1a. We show that Isw1a displays a highly cooperative ATP-independent binding to and bridging between DNA segments. Under appropriate tension, rare single nucleation events can sometimes be observed and loop DNA with a regular step. These nucleation events are often followed by binding of successive complexes bridging between nearby DNA segments in a zipper-like fashion, as confirmed by TEM observations. On nucleosomal substrates, we show that the specific ATP-dependent remodeling activity occurs in the context of cooperative Isw1a complexes bridging extranucleosomal DNA. Our results are interpreted in the context of the recently published partial structure of Isw1a and support its acting as a “protein ruler” (with possibly more than one tick).
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22
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Gräff J, Kim D, Dobbin MM, Tsai LH. Epigenetic regulation of gene expression in physiological and pathological brain processes. Physiol Rev 2011; 91:603-49. [PMID: 21527733 DOI: 10.1152/physrev.00012.2010] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Over the past decade, it has become increasingly obvious that epigenetic mechanisms are an integral part of a multitude of brain functions that range from the development of the nervous system over basic neuronal functions to higher order cognitive processes. At the same time, a substantial body of evidence has surfaced indicating that several neurodevelopmental, neurodegenerative, and neuropsychiatric disorders are in part caused by aberrant epigenetic modifications. Because of their inherent plasticity, such pathological epigenetic modifications are readily amenable to pharmacological interventions and have thus raised justified hopes that the epigenetic machinery provides a powerful new platform for therapeutic approaches against these diseases. In this review, we give a detailed overview of the implication of epigenetic mechanisms in both physiological and pathological brain processes and summarize the state-of-the-art of "epigenetic medicine" where applicable. Despite, or because of, these new and exciting findings, it is becoming apparent that the epigenetic machinery in the brain is highly complex and intertwined, which underscores the need for more refined studies to disentangle brain-region and cell-type specific epigenetic codes in a given environmental condition. Clearly, the brain contains an epigenetic "hotspot" with a unique potential to not only better understand its most complex functions, but also to treat its most vicious diseases.
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Affiliation(s)
- Johannes Gräff
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
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23
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Mahapatra S, Dewari PS, Bhardwaj A, Bhargava P. Yeast H2A.Z, FACT complex and RSC regulate transcription of tRNA gene through differential dynamics of flanking nucleosomes. Nucleic Acids Res 2011; 39:4023-34. [PMID: 21266479 PMCID: PMC3105386 DOI: 10.1093/nar/gkq1286] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
FACT complex is involved in elongation and ensures fidelity in the initiation step of transcription by RNA polymerase (pol) II. Histone variant H2A.Z is found in nucleosomes at the 5'-end of many genes. We report here H2A.Z-chaperone activity of the yeast FACT complex on the short, nucleosome-free, non-coding, pol III-transcribed yeast tRNA genes. On a prototype gene, yeast SUP4, chromatin remodeler RSC and FACT regulate its transcription through novel mechanisms, wherein the two gene-flanking nucleosomes containing H2A.Z, play different roles. Nhp6, which ensures transcription fidelity and helps load yFACT onto the gene flanking nucleosomes, has inhibitory role. RSC maintains a nucleosome abutting the gene terminator downstream, which results in reduced transcription rate in active state while H2A.Z probably helps RSC in keeping the gene nucleosome-free and serves as stress-sensor. All these factors maintain an epigenetic state which allows the gene to return quickly from repressed to active state and tones down the expression from the active SUP4 gene, required probably to maintain the balance in cellular tRNA pool.
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Affiliation(s)
- Sahasransu Mahapatra
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India
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24
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Wiedemann SM, Mildner SN, Bönisch C, Israel L, Maiser A, Matheisl S, Straub T, Merkl R, Leonhardt H, Kremmer E, Schermelleh L, Hake SB. Identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y. ACTA ACUST UNITED AC 2010; 190:777-91. [PMID: 20819935 PMCID: PMC2935562 DOI: 10.1083/jcb.201002043] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The expression of a new histone variant H3.Y increases during cellular stress to regulate cell cycle progression and gene expression. Nucleosomal incorporation of specialized histone variants is an important mechanism to generate different functional chromatin states. Here, we describe the identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y. Their messenger RNAs are found in certain human cell lines, in addition to several normal and malignant human tissues. In keeping with their primate specificity, H3.X and H3.Y are detected in different brain regions. Transgenic H3.X and H3.Y proteins are stably incorporated into chromatin in a similar fashion to the known H3 variants. Importantly, we demonstrate biochemically and by mass spectrometry that endogenous H3.Y protein exists in vivo, and that stress stimuli, such as starvation and cellular density, increase the abundance of H3.Y-expressing cells. Global transcriptome analysis revealed that knockdown of H3.Y affects cell growth and leads to changes in the expression of many genes involved in cell cycle control. Thus, H3.Y is a novel histone variant involved in the regulation of cellular responses to outside stimuli.
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Affiliation(s)
- Sonja M Wiedemann
- Adolf-Butenandt-Institute, Department of Molecular Biology, Ludwig Maximilians University of Munich, 80336 Munich, Germany
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25
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Nashun B, Yukawa M, Liu H, Akiyama T, Aoki F. Changes in the nuclear deposition of histone H2A variants during pre-implantation development in mice. Development 2010; 137:3785-94. [PMID: 20943707 DOI: 10.1242/dev.051805] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Histone H2A has several variants, and changes in chromatin composition associated with their replacement might involve chromatin structure remodeling. We examined the dynamics of the canonical histone H2A and its three variants, H2A.X, H2A.Z and macroH2A, in the mouse during oogenesis and pre-implantation development when genome remodeling occurs. Immunocytochemistry with specific antibodies revealed that, although H2A and all variants were deposited in the nuclei of full-grown oocytes, only histone H2A.X was abundant in the pronuclei of one-cell embryos after fertilization, in contrast with the low abundance of histone H2A and the absence of H2A.Z. The decline in H2A and the depletion of H2A.Z and macroH2A after fertilization were confirmed using Flag epitope-tagged H2A, H2A.Z and macroH2A transgenic mouse lines. Microinjection experiments with mRNA encoding the Flag-tagged proteins revealed a similar pattern of nuclear incorporation of the H2A variants. Fusion protein experiments using H2A, H2A.Z and macroH2A fused with the C-terminal 23 amino acids of H2A.X showed that the C-terminal amino acids of H2A.X function specifically to target this variant histone into chromatin in embryos after fertilization and that the absence of H2A.Z and macroH2A from the chromatin is required for normal development. These results suggest that global changes in the composition of histone H2A variants in chromatin play a role in genome remodeling after fertilization.
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Affiliation(s)
- Buhe Nashun
- Department of Integrated Biosciences, Graduate school of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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26
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Cong P, Luo Y, Bao W, Hu S. Genomic organization and promoter analysis of the Trichomonas vaginalis core histone gene families. Parasitol Int 2010; 59:29-34. [DOI: 10.1016/j.parint.2009.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 08/23/2009] [Accepted: 08/25/2009] [Indexed: 11/25/2022]
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28
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Lavelle C. Forces and torques in the nucleus: chromatin under mechanical constraints. Biochem Cell Biol 2009; 87:307-22. [PMID: 19234543 DOI: 10.1139/o08-123] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Genomic DNA in eukaryotic cells is organized in discrete chromosome territories, each consisting of a single huge hierarchically supercoiled nucleosomal fiber. Through dynamic changes in structure, resulting from chemical modifications and mechanical constraints imposed by numerous factors in vivo, chromatin plays a critical role in the regulation of DNA metabolism processes, including replication and transcription. Indeed, DNA-translocating enzymes, such as polymerases, produce physical constraints that chromatin has to overcome. Recent techniques, in particular single-molecule micromanipulation, have allowed precise quantization of forces and torques at work in the nucleus and have greatly improved our understanding of chromatin behavior under physiological mechanical constraints. These new biophysical approaches should enable us to build realistic mechanistic models and progressively specify the ad hoc and hazy "because of chromatin structure" argument often used to interpret experimental studies of biological function in the context of chromatin.
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29
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Hansen DF, Zhou Z, Feng H, Miller Jenkins LM, Bai Y, Kay LE. Binding kinetics of histone chaperone Chz1 and variant histone H2A.Z-H2B by relaxation dispersion NMR spectroscopy. J Mol Biol 2009; 387:1-9. [PMID: 19385041 PMCID: PMC2768378 DOI: 10.1016/j.jmb.2009.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The genome of eukaryotic cells is packed into a compact structure called chromatin that consists of DNA as well as histone and non-histone proteins. Histone chaperones associate with histone proteins and play important roles in the assembly of chromatin structure and transport of histones in the cell. The recently discovered histone chaperone Chz1 associates with the variant histone H2A.Z of budding yeast and plays a critical role in the exchange of the canonical histone pair H2A-H2B for the variant H2A.ZH2B. Here, we present an NMR approach that provides accurate estimates for the rates of association and dissociation of Chz1 and H2A.Z-H2B. The methodology exploits the fact that in a 1:1 mixture of Chz1 and H2A.Z-H2B, the small amounts of unbound proteins that are invisible in spectra produce line broadening of signals from the complex that can be quantified in terms of the thermodynamics and kinetics of the exchange process. The dissociation rate constant measured, 22 +/- 2 s(-1), provides an upper bound for the rate of transfer of H2A.Z-H2B to the chromatin remodeling complex, and the faster-than-diffusion association rate, 10(8) +/- 10(7) M(-1) s(-1), establishes the importance of attractive electrostatic interactions that form the chaperone-histone complex.
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Affiliation(s)
- D Flemming Hansen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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30
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Reid G, Gallais R, Métivier R. Marking time: the dynamic role of chromatin and covalent modification in transcription. Int J Biochem Cell Biol 2008; 41:155-63. [PMID: 18805503 DOI: 10.1016/j.biocel.2008.08.028] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 08/19/2008] [Accepted: 08/19/2008] [Indexed: 12/31/2022]
Abstract
The expression of genes subject to strict regulation can be a highly dynamic, cyclical process that sequentially achieves and then limits transcription. Kinetic investigations of the estrogen responsive pS2 (TFF1) promoter, to determine the occupancy of factors or the occurrence of covalent marks on chromatin, have provided the most comprehensive picture of the complexity of transcriptional cycling to date. Cycles are initiated by the assembly of intermediate transcription factors that in turn provoke conscription of the basal transcription machinery. These events then achieve activation of the polymerase II complex, which is subsequently followed by limitation of productivity through the action of repressive complexes. This latter phase resets the target promoter, through acting on chromatin structure, such that a subsequent cycle can be initiated. In consequence, transcription is dependent upon cis-acting elements (DNA and nucleosomes) that either interact with or are modified by trans-acting factors. Induced local structural changes to chromatin encompassing regulatory elements of gene promoters include alteration of the positional phasing of nucleosomes, substitution by variant histones, post-translational modification of nucleosomes, changes in the methylation of CpG dinucleotides and breaks in the sugar-phosphate backbone of DNA. A primary function of covalent modification of chromatin may be to drive a sequential progression of reversible interactions that achieve and regulate gene expression.
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Affiliation(s)
- George Reid
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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31
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Hadnagy A, Beaulieu R, Balicki D. Histone tail modifications and noncanonical functions of histones: perspectives in cancer epigenetics. Mol Cancer Ther 2008; 7:740-8. [PMID: 18413789 DOI: 10.1158/1535-7163.mct-07-2284] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Over the past few years, the histone deacetylase (HDAC) inhibitors have occupied an important place in the effort to develop novel, but less toxic, anticancer therapy. HDAC inhibitors block HDACs, which are the enzymes responsible for histone deacetylation, and therefore they modulate gene expression. The cellular effects of HDAC inhibitors include growth arrest and the induction of differentiation. Early successes in cancer therapeutics obtained using these drugs alone or in combination with other anticancer drugs emphasize the important place of posttranslational modifications of histones in cancer therapy. Histone tail modifications along with DNA methylation are the most studied epigenetic events related to cancer progression. Moreover, extranuclear functions of histones have also been described. Because HDAC inhibitors block HDACs and thereby increase histone acetylation, we propose a model wherein exogenous acetylated histones or other related acetylated proteins that are introduced into the nucleus become HDAC substrates and thereby compete with endogenous histones for HDACs. This competition may lead to the increased acetylation of the endogenous histones, as in the case of HDAC inhibitor therapy. Moreover, other mechanisms of action, such as binding to chromatin and modulating gene expression, are also possible for exogenously introduced histones.
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Affiliation(s)
- Annamaria Hadnagy
- Research Centre and Department of Medicine, Hôtel-Dieu du Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada
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Bönisch C, Nieratschker SM, Orfanos NK, Hake SB. Chromatin proteomics and epigenetic regulatory circuits. Expert Rev Proteomics 2008; 5:105-19. [PMID: 18282127 DOI: 10.1586/14789450.5.1.105] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Many phenotypic changes of eukaryotic cells due to changes in gene expression depend on alterations in chromatin structure. Processes involved in the alteration of chromatin are diverse and include post-translational modifications of histone proteins, incorporation of specific histone variants, methylation of DNA and ATP-dependent chromatin remodeling. Interconnected with these processes are the localization of chromatin domains within the nuclear architecture and the appearance of various classes of noncoding regulatory RNAs. Recent experiments underscore the role of these processes in influencing diverse biological functions. However, the evidence to date implies the importance of an interplay of all these chromatin-changing functions, generating an epigenetic regulatory circuit that is still not well understood.
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Affiliation(s)
- Clemens Bönisch
- Adolf-Butenandt-Institute & Center for Integrated Protein Science Munich (CIPSM), Department of Molecular Biology, Ludwig-Maximilians University, Schillerstr. 44, 80336 Munich, Germany.
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Arimbasseri AG, Bhargava P. Chromatin structure and expression of a gene transcribed by RNA polymerase III are independent of H2A.Z deposition. Mol Cell Biol 2008; 28:2598-607. [PMID: 18268003 PMCID: PMC2293117 DOI: 10.1128/mcb.01953-07] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 12/04/2007] [Accepted: 02/04/2008] [Indexed: 01/09/2023] Open
Abstract
The genes transcribed by RNA polymerase III (Pol III) generally have intragenic promoter elements. One of them, the yeast U6 snRNA (SNR6) gene is activated in vitro by a positioned nucleosome between its intragenic box A and extragenic, downstream box B separated by approximately 200 bp. We demonstrate here that the in vivo chromatin structure of the gene region is characterized by the presence of an array of positioned nucleosomes, with only one of them in the 5' end of the gene having a regulatory role. A positioned nucleosome present between boxes A and B in vivo does not move when the gene is repressed due to nutritional deprivation. In contrast, the upstream nucleosome which covers the TATA box under repressed conditions is shifted approximately 50 bp further upstream by the ATP-dependent chromatin remodeler RSC upon activation. It is marked with the histone variant H2A.Z and H4K16 acetylation in active state. In the absence of H2A.Z, the chromatin structure of the gene does not change, suggesting that H2A.Z is not required for establishing the active chromatin structure. These results show that the chromatin structure directly participates in regulation of a Pol III-transcribed gene under different states of its activity in vivo.
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Hanai K, Furuhashi H, Yamamoto T, Akasaka K, Hirose S. RSF governs silent chromatin formation via histone H2Av replacement. PLoS Genet 2008; 4:e1000011. [PMID: 18454204 PMCID: PMC2265536 DOI: 10.1371/journal.pgen.1000011] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Accepted: 01/25/2008] [Indexed: 12/20/2022] Open
Abstract
Human remodeling and spacing factor (RSF) consists of a heterodimer of Rsf-1 and hSNF2H, a counterpart of Drosophila ISWI. RSF possesses not only chromatin remodeling activity but also chromatin assembly activity in vitro. While no other single factor can execute the same activities as RSF, the biological significance of RSF remained unknown. To investigate the in vivo function of RSF, we generated a mutant allele of Drosophila Rsf-1 (dRsf-1). The dRsf-1 mutant behaved as a dominant suppressor of position effect variegation. In dRsf-1 mutant, the levels of histone H3K9 dimethylation and histone H2A variant H2Av were significantly reduced in an euchromatic region juxtaposed with heterochromatin. Furthermore, using both genetic and biochemical approaches, we demonstrate that dRsf-1 interacts with H2Av and the H2Av-exchanging machinery Tip60 complex. These results suggest that RSF contributes to histone H2Av replacement in the pathway of silent chromatin formation. As DNA is packaged into chromatin in the nucleus, every DNA transaction requires alteration of the chromatin structure. RSF, a heterodimer of Rsf-1 and ISWI/SNF2H, is a unique chromatin remodeling factor that can assemble regularly spaced nucleosome arrays without the aid of histone chaperons, but its biological function is not clear. Using Drosophila melanogaster as a model organism, we investigated the in vivo role of RSF in gene expression. The loss of RSF function reduces the levels of histone variant H2Av and histone H3-K9 methylation, and suppresses silencing of transcription in an euchromatic region neighboring the centromeric heterochromatin. We also observed that Rsf-1 interacts with histone H2Av and the H2Av-exchanging machinery Tip60 complex. Based on these findings, we propose that RSF plays a role in silent chromatin formation by promoting histone H2Av replacement.
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Affiliation(s)
- Kazuma Hanai
- Department of Developmental Genetics, National Institute of Genetics, Shizuoka-ken, Japan
- Department of Mathematical and Life Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hirofumi Furuhashi
- Department of Developmental Genetics, National Institute of Genetics, Shizuoka-ken, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Koji Akasaka
- Misaki Marine Biological Station, Graduate School of Science, The University of Tokyo, Miura, Kanagawa, Japan
| | - Susumu Hirose
- Department of Developmental Genetics, National Institute of Genetics, Shizuoka-ken, Japan
- * E-mail:
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A phosphorylated subpopulation of the histone variant macroH2A1 is excluded from the inactive X chromosome and enriched during mitosis. Proc Natl Acad Sci U S A 2008; 105:1533-8. [PMID: 18227505 DOI: 10.1073/pnas.0711632105] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Histone variants play an important role in numerous biological processes through changes in nucleosome structure and stability and possibly through mechanisms influenced by posttranslational modifications unique to a histone variant. The family of histone H2A variants includes members such as H2A.Z, the DNA damage-associated H2A.X, macroH2A (mH2A), and H2ABbd (Barr body-deficient). Here, we have undertaken the challenge to decipher the posttranslational modification-mediated "histone code" of mH2A, a variant generally associated with certain forms of condensed chromatin such as the inactive X chromosome in female mammals. By using female human cells as a source of mH2A, endogenous mH2A was purified and analyzed by mass spectrometry. Although mH2A is in low abundance compared with conventional histones, we identified a phosphorylation site, S137ph, which resides within the "hinge" region of mH2A. This lysine-rich hinge is an approximately 30-aa stretch between the H2A and macro domains, proposed to bind nucleic acids. A specific antibody to S137ph was raised; by using this reagent, S137 phosphorylation was found to be present in both male and female cells and on both splice variants of the mH2A1 gene. Although mH2A is generally enriched on the inactive X chromosome in female cells, mH2AS137ph is excluded from this heterochromatic structure. Thus, a phosphorylated subpopulation of mH2A appears to play a unique role in chromatin regulation beyond X inactivation. We provide evidence that S137ph is enriched in mitosis, suggestive of a role in the regulation of mH2A posttranslational modifications throughout the cell cycle.
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Abstract
Two-dimensional (2D) polyacrylamide gel electrophoresis (PAGE) systems employing combinations of acetic acid/urea (AU), acetic acid/urea/Triton X-100 (AUT) and sodium dodecyl sulfate (SDS) gel formulations are uniquely effective for resolution of histone variants and their modified derivatives. Coupled with Western transfer methods using modification-specific antibodies and recent advances in mass spectrometry, 2D PAGE emerges as a versatile tool for histone purification and analysis. This chapter describes 2D PAGE gel systems appropriate for histone proteins, including detailed procedures for designing, running, and staining gels. Methods for electrophoretic transfer of histones from AUTxSDS and AUTxAU 2D gels are described and evaluated. Alternatively, methods are provided for obtaining highly purified protein samples from fixed and stained gels via electroelution of proteins from specific gel spots.
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Affiliation(s)
- George R Green
- Department of Pharmaceutical Sciences, Mercer University College of Pharmacy and Health Sciences, Atlanta, GA, USA
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Vijayalakshmi M, Shivashankar GV, Sowdhamini R. Simulations of SIN Mutations and Histone Variants in Human Nucleosomes Reveal Altered Protein-DNA and Core Histone Interactions. J Biomol Struct Dyn 2007; 25:207-218. [DOI: 10.1080/07391102.2007.10507170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Pusarla RH, Vinayachandran V, Bhargava P. Nucleosome positioning in relation to nucleosome spacing and DNA sequence-specific binding of a protein. FEBS J 2007; 274:2396-410. [PMID: 17419736 DOI: 10.1111/j.1742-4658.2007.05775.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Nucleosome positioning is an important mechanism for the regulation of eukaryotic gene expression. Folding of the chromatin fiber can influence nucleosome positioning, whereas similar electrostatic mechanisms govern the nucleosome repeat length and chromatin fiber folding in vitro. The position of the nucleosomes is directed either by the DNA sequence or by the boundaries created due to the binding of certain trans-acting factors to their target sites in the DNA. Increasing ionic strength results in an increase in nucleosome spacing on the chromatin assembled by the S-190 extract of Drosophila embryos. In this study, a mutant lac repressor protein R3 was used to find the mechanisms of nucleosome positioning on a plasmid with three R3-binding sites. With increasing ionic strength in the presence of R3, the number of positioned nucleosomes in the chromatin decreased, whereas the internucleosomal spacings of the positioned nucleosomes in a single register did not change. The number of the positioned nucleosomes in the chromatin assembled in vitro over different plasmid DNAs with 1-3 lac operators changed with the relative position and number of the R3-binding sites. We found that in the presence of R3, nucleosomes were positioned in the salt gradient method of the chromatin assembly, even in the absence of a nucleosome-positioning sequence. Our results show that nucleosome-positioning mechanisms are dominant, as the nucleosomes can be positioned even in the absence of regular spacing mechanisms. The protein-generated boundaries are more effective when more than one binding site is present with a minimum distance of approximately 165 bp, greater than the nucleosome core DNA length, between them.
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Razin SV, Iarovaia OV, Sjakste N, Sjakste T, Bagdoniene L, Rynditch AV, Eivazova ER, Lipinski M, Vassetzky YS. Chromatin domains and regulation of transcription. J Mol Biol 2007; 369:597-607. [PMID: 17466329 DOI: 10.1016/j.jmb.2007.04.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 03/27/2007] [Accepted: 04/02/2007] [Indexed: 12/20/2022]
Abstract
Compartmentalization and compaction of DNA in the nucleus is the characteristic feature of eukaryotic cells. A fully extended DNA molecule has to be compacted 100,000 times to fit within the nucleus. At the same time it is critical that various DNA regions remain accessible for interaction with regulatory factors and transcription/replication factories. This puzzle is solved at the level of DNA packaging in chromatin that occurs in several steps: rolling of DNA onto nucleosomes, compaction of nucleosome fiber with formation of the so-called 30 nm fiber, and folding of the latter into the giant (50-200 kbp) loops, fixed onto the protein skeleton, the nuclear matrix. The general assumption is that DNA folding in the cell nucleus cannot be uniform. It has been known for a long time that a transcriptionally active chromatin fraction is more sensitive to nucleases; this was interpreted as evidence for the less tight compaction of this fraction. In this review we summarize the latest results on structure of transcriptionally active chromatin and the mechanisms of transcriptional regulation in the context of chromatin dynamics. In particular the significance of histone modifications and the mechanisms controlling dynamics of chromatin domains are discussed as well as the significance of spatial organization of the genome for functioning of distant regulatory elements.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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41
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Jamai A, Imoberdorf RM, Strubin M. Continuous histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication. Mol Cell 2007; 25:345-55. [PMID: 17289583 DOI: 10.1016/j.molcel.2007.01.019] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 10/17/2006] [Accepted: 01/19/2007] [Indexed: 11/21/2022]
Abstract
We investigated the dynamics of histone-DNA interactions in yeast by using inducible forms of epitope-tagged histones H2B and H3. Chromatin assembly of newly synthesized histones was assessed by chromatin immunoprecipitation in G1-arrested cells to prevent replication-coupled histone incorporation. We find that while histone deposition within a subtelomeric region is strictly linked to DNA replication, histone H2B is continuously incorporated at the promoter and coding regions of both transcriptionally active and inactive loci. In contrast, incorporation of histone H3 occurs only at active genes, being predominant at the promoter and showing a dynamics along the gene that inversely correlates with the average nucleosomal density. Similar results were obtained with N-terminally truncated H2B and H3 variants. We infer that replication-independent incorporation of H2B and H3 are distinct events, each occurring independently of the histone tail, and that nucleosome loss at active promoters reflects a dynamic equilibrium between histone deposition and dissociation.
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Affiliation(s)
- Adil Jamai
- Department of Microbiology and Molecular Medicine, University Medical Centre, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
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42
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Johnson AB, Barton MC. Hypoxia-induced and stress-specific changes in chromatin structure and function. Mutat Res 2007; 618:149-62. [PMID: 17292925 PMCID: PMC1924842 DOI: 10.1016/j.mrfmmm.2006.10.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2006] [Accepted: 10/27/2006] [Indexed: 11/16/2022]
Abstract
Cellular adaptation to stress relies on specific, regulated responses to evoke changes in gene expression. Stresses such as hypoxia, heat shock, oxidative stress and DNA-damage activate signaling cascades that ultimately lead to either induction or repression of stress-responsive genes. In this review, we concentrate on the mechanisms by which stress-induced signaling promotes alterations in chromatin structure, whether the read-out is activation or repression of transcription. Specific alterations in chromatin are highly regulated and dictated by the type of imposed stress. Our primary focus is on the types of chromatin alterations that occur under hypoxic conditions, which exist within a majority of tumors, and to compare these to changes in chromatin structure that occur in response to a wide variety of cellular stresses.
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Affiliation(s)
| | - Michelle Craig Barton
- *Address correspondence to: Michelle Craig Barton, Dept. of Biochemistry and Molecular Biology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Box 1000, Houston, TX 77030. Phone: 713-834-6268, Fax: 713-834-6271,
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43
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D'Alessio AC, Szyf M. Epigenetic tête-à-tête: the bilateral relationship between chromatin modifications and DNA methylation. Biochem Cell Biol 2007; 84:463-76. [PMID: 16936820 DOI: 10.1139/o06-090] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The epigenome, which comprises chromatin, associated proteins, and the pattern of covalent modification of DNA by methylation, sets up and maintains gene expression programs. It was originally believed that DNA methylation was the dominant reaction in determining the chromatin structure. However, emerging data suggest that chromatin can affect DNA methylation in both directions, triggering either de novo DNA methylation or demethylation. These events are particularly important for the understanding of cellular transformation, which requires a coordinated change in gene expression profiles. While genetic alterations can explain some of the changes, the important role of epigenetic reprogramming is becoming more and more evident. Cancer cells exhibit a paradoxical coexistence of global loss of DNA methylation with regional hypermethylation.
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Affiliation(s)
- Ana C D'Alessio
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
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Su X, Jacob NK, Amunugama R, Lucas DM, Knapp AR, Ren C, Davis ME, Marcucci G, Parthun MR, Byrd JC, Fishel RA, Freitas MA. Liquid chromatography mass spectrometry profiling of histones. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 850:440-54. [PMID: 17254850 PMCID: PMC2694509 DOI: 10.1016/j.jchromb.2006.12.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 12/08/2006] [Accepted: 12/17/2006] [Indexed: 11/25/2022]
Abstract
Here we describe the use of reverse-phase liquid chromatography mass spectrometry (RPLC-MS) to simultaneously characterize variants and post-translationally modified isoforms for each histone. The analysis of intact proteins significantly reduces the time of sample preparation and simplifies data interpretation. LC-MS analysis and peptide mass mapping have previously been applied to identify histone proteins and to characterize their post-translational modifications. However, these studies provided limited characterization of both linker histones and core histones. The current LC-MS analysis allows for the simultaneous observation of all histone PTMs and variants (both replacement and bulk histones) without further enrichment, which will be valuable in comparative studies. Protein identities were verified by the analysis of histone H2A species using RPLC fractionation, AU-PAGE separation and nano-LC-MS/MS.
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Affiliation(s)
- Xiaodan Su
- Department of Chemistry, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Naduparambil K. Jacob
- Department of Molecular Virology, Immunology, and Medical Genetics; Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Ravindra Amunugama
- Department of Molecular Virology, Immunology, and Medical Genetics; Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - David M. Lucas
- Department of Internal Medicine, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Amy R. Knapp
- Department of Molecular and Cellular Biochemistry, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Chen Ren
- Department of Chemistry, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Melanie E. Davis
- Department of Internal Medicine, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Guido Marcucci
- Department of Internal Medicine, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Mark R. Parthun
- Department of Molecular and Cellular Biochemistry, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - John C. Byrd
- Department of Internal Medicine, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Richard A. Fishel
- Department of Molecular Virology, Immunology, and Medical Genetics; Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Michael A. Freitas
- Department of Molecular Virology, Immunology, and Medical Genetics; Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
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Garcia BA, Hake SB, Diaz RL, Kauer M, Morris SA, Recht J, Shabanowitz J, Mishra N, Strahl BD, Allis CD, Hunt DF. Organismal differences in post-translational modifications in histones H3 and H4. J Biol Chem 2006; 282:7641-55. [PMID: 17194708 DOI: 10.1074/jbc.m607900200] [Citation(s) in RCA: 248] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Post-translational modifications (PTMs) of histones play an important role in many cellular processes, notably gene regulation. Using a combination of mass spectrometric and immunobiochemical approaches, we show that the PTM profile of histone H3 differs significantly among the various model organisms examined. Unicellular eukaryotes, such as Saccharomyces cerevisiae (yeast) and Tetrahymena thermophila (Tet), for example, contain more activation than silencing marks as compared with mammalian cells (mouse and human), which are generally enriched in PTMs more often associated with gene silencing. Close examination reveals that many of the better-known modified lysines (Lys) can be either methylated or acetylated and that the overall modification patterns become more complex from unicellular eukaryotes to mammals. Additionally, novel species-specific H3 PTMs from wild-type asynchronously grown cells are also detected by mass spectrometry. Our results suggest that some PTMs are more conserved than previously thought, including H3K9me1 and H4K20me2 in yeast and H3K27me1, -me2, and -me3 in Tet. On histone H4, methylation at Lys-20 showed a similar pattern as H3 methylation at Lys-9, with mammals containing more methylation than the unicellular organisms. Additionally, modification profiles of H4 acetylation were very similar among the organisms examined.
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Affiliation(s)
- Benjamin A Garcia
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, USA
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Okada T, Singh MB, Bhalla PL. Histone H3 variants in male gametic cells of lily and H3 methylation in mature pollen. PLANT MOLECULAR BIOLOGY 2006; 62:503-12. [PMID: 16915513 DOI: 10.1007/s11103-006-9036-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 06/21/2006] [Indexed: 05/08/2023]
Abstract
Histones are vital structural proteins of chromatin that influence its dynamics and function. The tissue-specific expression of histone variants has been shown to regulate the expression of specific genes and genomic stability in animal systems. Here we report on the characterization of five histone H3 variants expressed in Lilium generative cell. The gcH3 and leH3 variants show unique sequence diversity by lacking a conserved lysine residue at position 9 (H3K9). The gH3 shares conserved structural features with centromeric H3 of Arabidopsis. The gH3 variant gene is strongly expressed in generative cells and gH3 histone is incorporated in to generative cell chromatin. The lysine residue of H3 at position 4 (H3K4) is highly methylated in the nuclei of generative cells of mature pollen, while methylation of H3K4 is low in vegetative cell nuclei. Taken together, these results suggest that male gametic cells of Lilium have unique chromatin state and histone H3 variants and their methylation might be involved in gene regulation of male gametic cells.
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Affiliation(s)
- Takashi Okada
- Plant Molecular Biology and Biotechnology laboratory, Australian Research Council Centre of Excellence for Integrative Legume Research, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Poirier R, Lemaire I, Lemaire S. Characterization, localization and possible anti-inflammatory function of rat histone H4 mRNA variants. FEBS J 2006; 273:4360-73. [PMID: 16939626 DOI: 10.1111/j.1742-4658.2006.05444.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Two histone H4 mRNA variants, H4-v.1 and histogranin mRNAs, were detected in the rat genome and measured in various tissues and isolated alveolar macrophages. Medium to high levels of both mRNAs were present in the liver, adrenal glands, thymus, bone marrow and alveolar macrophages. H4-v.1 cDNA contained an open reading frame that coded for unmodified whole histone H4, whereas histogranin cDNA lacked the first ATG codon and contained an open reading frame that coded for modified (Thr89) H4-(84-102). The two genes displayed a sequence homologous (> 80%) to the open reading frame of core H4 somatic (H4s) and H4 germinal (H4g) and their variant nature was supported by the absence of histone consensus palindromic and purine-rich sequences in the proximal 3'UTR, and the presence of a polyadenylation signal in the distal 3'UTR and of specific upstream transcription factor-binding sites. H4-v.1 and histogranin transcripts, but not H4s transcript, were selectively induced by lipopolysaccharide and/or interferon gamma in alveolar macrophages. In vitro transcription/translation experiments with H4-v.1 and histogranin cDNA pCMV constructs produced peptides with the molecular mass (2 kDa) of the alternative histone H4 translation product which, like synthetic H4-(86-100) and [Thr89]H4-(86-100) or rat histogranin, inhibited lipopolysaccharide-induced prostaglandin E(2) release from rat alveolar macrophages. The synthetic peptides also inhibited the secretion of the CXC chemokine interleukin-8 (GRO/CINC-1) in response to lipopolysaccharide. The presence of H4-v.1 and histogranin mRNAs in tissues wherein immune reactions take place and the inhibitory effects of their translation products on prostaglandin E(2) and interkeukin-8 secretion by activated alveolar macrophages suggest an anti-inflammatory function.
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Affiliation(s)
- René Poirier
- Department of Cellular and Molecular Medicine, University of Ottawa, Canada
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49
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Bernstein E, Hake SB. The nucleosome: a little variation goes a long wayThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process. Biochem Cell Biol 2006; 84:505-17. [PMID: 16936823 DOI: 10.1139/o06-085] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Changes in the overall structure of chromatin are essential for the proper regulation of cellular processes, including gene activation and silencing, DNA repair, chromosome segregation during mitosis and meiosis, X chromosome inactivation in female mammals, and chromatin compaction during apoptosis. Such alterations of the chromatin template occur through at least 3 interrelated mechanisms: post-translational modifications of histones, ATP-dependent chromatin remodeling, and the incorporation (or replacement) of specialized histone variants into chromatin. Of these mechanisms, the exchange of variants into and out of chromatin is the least well understood. However, the exchange of conventional histones for variant histones has distinct and profound consequences within the cell. This review focuses on the growing number of mammalian histone variants, their particular biological functions and unique features, and how they may affect the structure of the nucleosome. We propose that a given nucleosome might not consist of heterotypic variants, but rather, that only specific histone variants come together to form a homotypic nucleosome, a hypothesis that we refer to as the nucleosome code. Such nucleosomes might in turn participate in marking specific chromatin domains that may contribute to epigenetic inheritance.
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Affiliation(s)
- Emily Bernstein
- Laboratory of Chromatin Biology, The Rockefeller University, Box 78, 1230 York Avenue, NY, NY 10021, USA
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50
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Hake SB, Allis CD. Histone H3 variants and their potential role in indexing mammalian genomes: the "H3 barcode hypothesis". Proc Natl Acad Sci U S A 2006; 103:6428-35. [PMID: 16571659 PMCID: PMC1564199 DOI: 10.1073/pnas.0600803103] [Citation(s) in RCA: 313] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In the history of science, provocative but, at times, controversial ideas have been put forward to explain basic problems that confront and intrigue the scientific community. These hypotheses, although often not correct in every detail, lead to increased discussion that ultimately guides experimental tests of the principal concepts and produce valuable insights into long-standing questions. Here, we present a hypothesis, the "H3 barcode hypothesis." Hopefully, our ideas will evoke critical discussion and new experimental approaches that bear on general topics, such as nuclear architecture, epigenetic memory, and cell-fate choice. Our hypothesis rests on the central concept that mammalian histone H3 variants (H3.1, H3.2, and H3.3), although remarkably similar in amino acid sequence, exhibit distinct posttranslational "signatures" that create different chromosomal domains or territories, which, in turn, influence epigenetic states during cellular differentiation and development. Although we restrict our comments to H3 variants in mammals, we expect that the more general concepts presented here will apply to other histone variant families in organisms that employ them.
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Affiliation(s)
- Sandra B Hake
- Laboratory of Chromatin Biology, The Rockefeller University, Box 78, 1230 York Avenue, New York, NY 10021, USA.
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