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Rogers AM, Neri NR, Chigweshe L, Holmes SG. Histone variant H2A.Z and linker histone H1 influence chromosome condensation in Saccharomyces cerevisiae. Genetics 2024; 226:iyae022. [PMID: 38366024 PMCID: PMC10990423 DOI: 10.1093/genetics/iyae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 10/15/2023] [Accepted: 01/17/2024] [Indexed: 02/18/2024] Open
Abstract
Chromosome condensation is essential for the fidelity of chromosome segregation during mitosis and meiosis. Condensation is associated both with local changes in nucleosome structure and larger-scale alterations in chromosome topology mediated by the condensin complex. We examined the influence of linker histone H1 and variant histone H2A.Z on chromosome condensation in budding yeast cells. Linker histone H1 has been implicated in local and global compaction of chromatin in multiple eukaryotes, but we observe normal condensation of the rDNA locus in yeast strains lacking H1. However, deletion of the yeast HTZ1 gene, coding for variant histone H2A.Z, causes a significant defect in rDNA condensation. Loss of H2A.Z does not change condensin association with the rDNA locus or significantly affect condensin mRNA levels. Prior studies reported that several phenotypes caused by loss of H2A.Z are suppressed by eliminating Swr1, a key component of the SWR complex that deposits H2A.Z in chromatin. We observe that an htz1Δ swr1Δ strain has near-normal rDNA condensation. Unexpectedly, we find that elimination of the linker histone H1 can also suppress the rDNA condensation defect of htz1Δ strains. Our experiments demonstrate that histone H2A.Z promotes chromosome condensation, in part by counteracting activities of histone H1 and the SWR complex.
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Affiliation(s)
- Anna M Rogers
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Nola R Neri
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Lorencia Chigweshe
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Scott G Holmes
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
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2
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Siqueira E, Kim BH, Reser L, Chow R, Delaney K, Esteller M, Ross MM, Shabanowitz J, Hunt DF, Guil S, Ausió J. Analysis of the interplay between MeCP2 and histone H1 during in vitro differentiation of human ReNCell neural progenitor cells. Epigenetics 2023; 18:2276425. [PMID: 37976174 PMCID: PMC10769555 DOI: 10.1080/15592294.2023.2276425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023] Open
Abstract
An immortalized neural cell line derived from the human ventral mesencephalon, called ReNCell, and its MeCP2 knock out were used. With it, we characterized the chromatin compositional transitions undergone during differentiation, with special emphasis on linker histones. While the WT cells displayed the development of dendrites and axons the KO cells did not, despite undergoing differentiation as monitored by NeuN. ReNCell expressed minimal amounts of histone H1.0 and their linker histone complement consisted mainly of histone H1.2, H1.4 and H1.5. The overall level of histone H1 exhibited a trend to increase during the differentiation of MeCP2 KO cells. The phosphorylation levels of histone H1 proteins decreased dramatically during ReNCell's cell differentiation independently of the presence of MeCP2. Immunofluorescence analysis showed that MeCP2 exhibits an extensive co-localization with linker histones. Interestingly, the average size of the nucleus decreased during differentiation but in the MeCP2 KO cells, the smaller size of the nuclei at the start of differentiation increased by almost 40% after differentiation by 8 days (8 DIV). In summary, our data provide a compelling perspective on the dynamic changes of H1 histones during neural differentiation, coupled with the intricate interplay between H1 variants and MeCP2.Abbreviations: ACN, acetonitrile; A230, absorbance at 230 nm; bFGF, basic fibroblast growth factor; CM, chicken erythrocyte histone marker; CNS, central nervous system; CRISPR, clustered regulated interspaced short palindromic repeatsDAPI, 4,'6-diaminidino-2-phenylindole; DIV, days in vitro (days after differentiation is induced); DMEM, Dulbecco's modified Eagle medium; EGF, epidermal growth factor; ESC, embryonic stem cell; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GFAP, glial fibrillary acidic proteinHPLC, high-performance liquid chromatography; IF, immunofluorescence; iPSCs, induced pluripotent stem cells; MAP2, microtubule-associated protein 2; MBD, methyl-binding domain; MeCP2, methyl-CpG binding protein 2; MS, mass spectrometry; NCP, nucleosome core particle; NeuN, neuron nuclear antigen; NPC, neural progenitor cellPAGE, polyacrylamide gel electrophoresis; PBS, phosphate buffered saline; PFA, paraformaldehyde; PTM, posttranslational modification; RP-HPLC, reversed phase HPLC; ReNCells, ReNCells VM; RPLP0, ribosomal protein lateral stalk subunit P0; RT-qPCR, reverse transcription quantitative polymerase-chain reaction; RTT, Rett Syndrome; SDS, sodium dodecyl sulphate; TAD, topologically associating domain; Triple KO, triple knockout.
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Affiliation(s)
- Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- National Council for Scientific and Technological Development (CNPq), Brasilia, Federal District, Brazil
| | - Bo-Hyun Kim
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Larry Reser
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Robert Chow
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Kerry Delaney
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Mark M. Ross
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
- Department of Pathology, University of Virginia, Charlottesville, Virginia, USA
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- GermansTrias i Pujol Health Science Research Institute, Badalona, Barcelona, Catalonia, Spain
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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3
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Sheikh AH, Nawaz K, Tabassum N, Almeida-Trapp M, Mariappan KG, Alhoraibi H, Rayapuram N, Aranda M, Groth M, Hirt H. Linker histone H1 modulates defense priming and immunity in plants. Nucleic Acids Res 2023; 51:4252-4265. [PMID: 36840717 PMCID: PMC10201415 DOI: 10.1093/nar/gkad106] [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: 04/20/2022] [Revised: 01/17/2023] [Accepted: 02/07/2023] [Indexed: 02/26/2023] Open
Abstract
Linker H1 histones play an important role in animal and human pathogenesis, but their function in plant immunity is poorly understood. Here, we analyzed mutants of the three canonical variants of Arabidopsis H1 histones, namely H1.1, H1.2 and H1.3. We observed that double h1.1h1.2 and triple h1.1h1.2h1.3 (3h1) mutants were resistant to Pseudomonas syringae and Botrytis cinerea infections. Transcriptome analysis of 3h1 mutant plants showed H1s play a key role in regulating the expression of early and late defense genes upon pathogen challenge. Moreover, 3h1 mutant plants showed enhanced production of reactive oxygen species and activation of mitogen activated protein kinases upon pathogen-associated molecular pattern (PAMP) treatment. However, 3h1 mutant plants were insensitive to priming with flg22, a well-known bacterial PAMP which induces enhanced resistance in WT plants. The defective defense response in 3h1 upon priming was correlated with altered DNA methylation and reduced global H3K56ac levels. Our data place H1 as a molecular gatekeeper in governing dynamic changes in the chromatin landscape of defense genes during plant pathogen interaction.
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Affiliation(s)
- Arsheed H Sheikh
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Kashif Nawaz
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Naheed Tabassum
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Marilia Almeida-Trapp
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Kiruthiga G Mariappan
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Hanna Alhoraibi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21551Jeddah, Saudi Arabia
| | - Naganand Rayapuram
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Manuel Aranda
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Martin Groth
- Institute of Functional Epigenetics, Helmholtz Munich, 85764Neuherberg, Germany
| | - Heribert Hirt
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
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4
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Zhang L, Cervantes MD, Pan S, Lindsley J, Dabney A, Kapler GM. Transcriptome analysis of the binucleate ciliate Tetrahymena thermophila with asynchronous nuclear cell cycles. Mol Biol Cell 2023; 34:rs1. [PMID: 36475712 PMCID: PMC9930529 DOI: 10.1091/mbc.e22-08-0326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tetrahymena thermophila harbors two functionally and physically distinct nuclei within a shared cytoplasm. During vegetative growth, the "cell cycles" of the diploid micronucleus and polyploid macronucleus are offset. Micronuclear S phase initiates just before cytokinesis and is completed in daughter cells before onset of macronuclear DNA replication. Mitotic micronuclear division occurs mid-cell cycle, while macronuclear amitosis is coupled to cell division. Here we report the first RNA-seq cell cycle analysis of a binucleated ciliated protozoan. RNA was isolated across 1.5 vegetative cell cycles, starting with a macronuclear G1 population synchronized by centrifugal elutriation. Using MetaCycle, 3244 of the 26,000+ predicted genes were shown to be cell cycle regulated. Proteins present in both nuclei exhibit a single mRNA peak that always precedes their macronuclear function. Nucleus-limited genes, including nucleoporins and importins, are expressed before their respective nucleus-specific role. Cyclin D and A/B gene family members exhibit different expression patterns that suggest nucleus-restricted roles. Periodically expressed genes cluster into seven cyclic patterns. Four clusters have known PANTHER gene ontology terms associated with G1/S and G2/M phase. We propose that these clusters encode known and novel factors that coordinate micro- and macronuclear-specific events such as mitosis, amitosis, DNA replication, and cell division.
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Affiliation(s)
- L. Zhang
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,Department of Statistics, Texas A&M University, College Station, TX 77843
| | - M. D. Cervantes
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840
| | - S. Pan
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,Department of Statistics, Texas A&M University, College Station, TX 77843
| | - J. Lindsley
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840
| | - A. Dabney
- Department of Statistics, Texas A&M University, College Station, TX 77843,*Address correspondence to: Geoffrey Kapler (); A. Dabney ()
| | - G. M. Kapler
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,*Address correspondence to: Geoffrey Kapler (); A. Dabney ()
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5
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Foroozani M, Holder DH, Deal RB. Histone Variants in the Specialization of Plant Chromatin. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:149-172. [PMID: 35167758 PMCID: PMC9133179 DOI: 10.1146/annurev-arplant-070221-050044] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The basic unit of chromatin, the nucleosome, is an octamer of four core histone proteins (H2A, H2B, H3, and H4) and serves as a fundamental regulatory unit in all DNA-templated processes. The majority of nucleosome assembly occurs during DNA replication when these core histones are produced en masse to accommodate the nascent genome. In addition, there are a number of nonallelic sequence variants of H2A and H3 in particular, known as histone variants, that can be incorporated into nucleosomes in a targeted and replication-independent manner. By virtue of their sequence divergence from the replication-coupled histones, these histone variants can impart unique properties onto the nucleosomes they occupy and thereby influence transcription and epigenetic states, DNA repair, chromosome segregation, and other nuclear processes in ways that profoundly affect plant biology. In this review, we discuss the evolutionary origins of these variants in plants, their known roles in chromatin, and their impacts on plant development and stress responses. We focus on the individual and combined roles of histone variants in transcriptional regulation within euchromatic and heterochromatic genome regions. Finally, we highlight gaps in our understanding of plant variants at the molecular, cellular, and organismal levels, and we propose new directions for study in the field of plant histone variants.
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Affiliation(s)
| | - Dylan H Holder
- Department of Biology, Emory University, Atlanta, Georgia, USA;
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia, USA;
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6
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Li J, Gao J, Wang R. Control of Chromatin Organization and Chromosome Behavior during the Cell Cycle through Phase Separation. Int J Mol Sci 2021; 22:ijms222212271. [PMID: 34830152 PMCID: PMC8621359 DOI: 10.3390/ijms222212271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 01/02/2023] Open
Abstract
Phase-separated condensates participate in various biological activities. Liquid-liquid phase separation (LLPS) can be driven by collective interactions between multivalent and intrinsically disordered proteins. The manner in which chromatin-with various morphologies and activities-is organized in a complex and small nucleus still remains to be fully determined. Recent findings support the claim that phase separation is involved in the regulation of chromatin organization and chromosome behavior. Moreover, phase separation also influences key events during mitosis and meiosis. This review elaborately dissects how phase separation regulates chromatin and chromosome organization and controls mitotic and meiotic chromosome behavior.
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7
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VCP maintains nuclear size by regulating the DNA damage-associated MDC1-p53-autophagy axis in Drosophila. Nat Commun 2021; 12:4258. [PMID: 34253734 PMCID: PMC8275807 DOI: 10.1038/s41467-021-24556-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 06/24/2021] [Indexed: 12/20/2022] Open
Abstract
The maintenance of constant karyoplasmic ratios suggests that nuclear size has physiological significance. Nuclear size anomalies have been linked to malignant transformation, although the mechanism remains unclear. By expressing dominant-negative TER94 mutants in Drosophila photoreceptors, here we show disruption of VCP (valosin-containing protein, human TER94 ortholog), a ubiquitin-dependent segregase, causes progressive nuclear size increase. Loss of VCP function leads to accumulations of MDC1 (mediator of DNA damage checkpoint protein 1), connecting DNA damage or associated responses to enlarged nuclei. TER94 can interact with MDC1 and decreases MDC1 levels, suggesting that MDC1 is a VCP substrate. Our evidence indicates that MDC1 accumulation stabilizes p53A, leading to TER94K2A-associated nuclear size increase. Together with a previous report that p53A disrupts autophagic flux, we propose that the stabilization of p53A in TER94K2A-expressing cells likely hinders the removal of nuclear content, resulting in aberrant nuclear size increase. Cells maintain a constant cytoplasm to nucleus volume ratio, although the role of DNA damage is not well explored. Here, the authors use Drosophila to connect TER94, the fly homolog of VCP, to disruption of DNA damage repair, leading to ubiquitinated Mu2 protein accumulation and enlarged nuclei.
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8
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Duc C, Thiriet C. Replication-Coupled Chromatin Remodeling: An Overview of Disassembly and Assembly of Chromatin during Replication. Int J Mol Sci 2021; 22:1113. [PMID: 33498649 PMCID: PMC7865951 DOI: 10.3390/ijms22031113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/08/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
The doubling of genomic DNA during the S-phase of the cell cycle involves the global remodeling of chromatin at replication forks. The present review focuses on the eviction of nucleosomes in front of the replication forks to facilitate the passage of replication machinery and the mechanism of replication-coupled chromatin assembly behind the replication forks. The recycling of parental histones as well as the nuclear import and the assembly of newly synthesized histones are also discussed with regard to the epigenetic inheritance.
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Affiliation(s)
| | - Christophe Thiriet
- UFIP UMR-CNRS 6286, Épigénétique et Dynamique de la Chromatine, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes, France;
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9
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Wahab S, Saettone A, Nabeel-Shah S, Dannah N, Fillingham J. Exploring the Histone Acetylation Cycle in the Protozoan Model Tetrahymena thermophila. Front Cell Dev Biol 2020; 8:509. [PMID: 32695779 PMCID: PMC7339932 DOI: 10.3389/fcell.2020.00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic histone acetylation cycle is composed of three classes of proteins, histone acetyltransferases (HATs) that add acetyl groups to lysine amino acids, bromodomain (BRD) containing proteins that are one of the most characterized of several protein domains that recognize acetyl-lysine (Kac) and effect downstream function, and histone deacetylases (HDACs) that catalyze the reverse reaction. Dysfunction of selected proteins of these three classes is associated with human disease such as cancer. Additionally, the HATs, BRDs, and HDACs of fungi and parasitic protozoa present potential drug targets. Despite their importance, the function and mechanisms of HATs, BRDs, and HDACs and how they relate to chromatin remodeling (CR) remain incompletely understood. Tetrahymena thermophila (Tt) provides a highly tractable single-celled free-living protozoan model for studying histone acetylation, featuring a massively acetylated somatic genome, a property that was exploited in the identification of the first nuclear/type A HAT Gcn5 in the 1990s. Since then, Tetrahymena remains an under-explored model for the molecular analysis of HATs, BRDs, and HDACs. Studies of HATs, BRDs, and HDACs in Tetrahymena have the potential to reveal the function of HATs and BRDs relevant to both fundamental eukaryotic biology and to the study of disease mechanisms in parasitic protozoa.
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Affiliation(s)
| | | | | | | | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
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10
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Sridhar A, Orozco M, Collepardo-Guevara R. Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1. Nucleic Acids Res 2020; 48:5318-5331. [PMID: 32356891 PMCID: PMC7261198 DOI: 10.1093/nar/gkaa285] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/02/2020] [Accepted: 04/14/2020] [Indexed: 12/18/2022] Open
Abstract
Intrinsically disordered proteins are crucial elements of chromatin heterogenous organization. While disorder in the histone tails enables a large variation of inter-nucleosome arrangements, disorder within the chromatin-binding proteins facilitates promiscuous binding to a wide range of different molecular targets, consistent with structural heterogeneity. Among the partially disordered chromatin-binding proteins, the H1 linker histone influences a myriad of chromatin characteristics including compaction, nucleosome spacing, transcription regulation, and the recruitment of other chromatin regulating proteins. Although it is now established that the long C-terminal domain (CTD) of H1 remains disordered upon nucleosome binding and that such disorder favours chromatin fluidity, the structural behaviour and thereby the role/function of the N-terminal domain (NTD) within chromatin is yet unresolved. On the basis of microsecond-long parallel-tempering metadynamics and temperature-replica exchange atomistic molecular dynamics simulations of different H1 NTD subtypes, we demonstrate that the NTD is completely unstructured in solution but undergoes an important disorder-to-order transition upon nucleosome binding: it forms a helix that enhances its DNA binding ability. Further, we show that the helical propensity of the H1 NTD is subtype-dependent and correlates with the experimentally observed binding affinity of H1 subtypes, suggesting an important functional implication of this disorder-to-order transition.
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Affiliation(s)
- Akshay Sridhar
- Maxwell Centre, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Modesto Orozco
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri i Reixac, 19, 08028 Barcelona, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, Av. Diagonal 647. 08028 Barcelona, Spain
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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11
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Wesley CC, Mishra S, Levy DL. Organelle size scaling over embryonic development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 9:e376. [PMID: 32003549 DOI: 10.1002/wdev.376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/19/2019] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Cell division without growth results in progressive cell size reductions during early embryonic development. How do the sizes of intracellular structures and organelles scale with cell size and what are the functional implications of such scaling relationships? Model organisms, in particular Caenorhabditis elegans worms, Drosophila melanogaster flies, Xenopus laevis frogs, and Mus musculus mice, have provided insights into developmental size scaling of the nucleus, mitotic spindle, and chromosomes. Nuclear size is regulated by nucleocytoplasmic transport, nuclear envelope proteins, and the cytoskeleton. Regulators of microtubule dynamics and chromatin compaction modulate spindle and mitotic chromosome size scaling, respectively. Developmental scaling relationships for membrane-bound organelles, like the endoplasmic reticulum, Golgi, mitochondria, and lysosomes, have been less studied, although new imaging approaches promise to rectify this deficiency. While models that invoke limiting components and dynamic regulation of assembly and disassembly can account for some size scaling relationships in early embryos, it will be exciting to investigate the contribution of newer concepts in cell biology such as phase separation and interorganellar contacts. With a growing understanding of the underlying mechanisms of organelle size scaling, future studies promise to uncover the significance of proper scaling for cell function and embryonic development, as well as how aberrant scaling contributes to disease. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Early Embryonic Development > Fertilization to Gastrulation Comparative Development and Evolution > Model Systems.
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Affiliation(s)
- Chase C Wesley
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| | - Sampada Mishra
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
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12
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Nucleus-specific linker histones Hho1 and Mlh1 form distinct protein interactions during growth, starvation and development in Tetrahymena thermophila. Sci Rep 2020; 10:168. [PMID: 31932604 PMCID: PMC6957481 DOI: 10.1038/s41598-019-56867-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023] Open
Abstract
Chromatin organization influences most aspects of gene expression regulation. The linker histone H1, along with the core histones, is a key component of eukaryotic chromatin. Despite its critical roles in chromatin structure and function and gene regulation, studies regarding the H1 protein-protein interaction networks, particularly outside of Opisthokonts, are limited. The nuclear dimorphic ciliate protozoan Tetrahymena thermophila encodes two distinct nucleus-specific linker histones, macronuclear Hho1 and micronuclear Mlh1. We used a comparative proteomics approach to identify the Hho1 and Mlh1 protein-protein interaction networks in Tetrahymena during growth, starvation, and sexual development. Affinity purification followed by mass spectrometry analysis of the Hho1 and Mlh1 proteins revealed a non-overlapping set of co-purifying proteins suggesting that Tetrahymena nucleus-specific linker histones are subject to distinct regulatory pathways. Furthermore, we found that linker histones interact with distinct proteins under the different stages of the Tetrahymena life cycle. Hho1 and Mlh1 co-purified with several Tetrahymena-specific as well as conserved interacting partners involved in chromatin structure and function and other important cellular pathways. Our results suggest that nucleus-specific linker histones might be subject to nucleus-specific regulatory pathways and are dynamically regulated under different stages of the Tetrahymena life cycle.
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13
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Gibson BA, Doolittle LK, Schneider MWG, Jensen LE, Gamarra N, Henry L, Gerlich DW, Redding S, Rosen MK. Organization of Chromatin by Intrinsic and Regulated Phase Separation. Cell 2019; 179:470-484.e21. [PMID: 31543265 DOI: 10.1016/j.cell.2019.08.037] [Citation(s) in RCA: 546] [Impact Index Per Article: 109.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/12/2019] [Accepted: 08/21/2019] [Indexed: 02/07/2023]
Abstract
Eukaryotic chromatin is highly condensed but dynamically accessible to regulation and organized into subdomains. We demonstrate that reconstituted chromatin undergoes histone tail-driven liquid-liquid phase separation (LLPS) in physiologic salt and when microinjected into cell nuclei, producing dense and dynamic droplets. Linker histone H1 and internucleosome linker lengths shared across eukaryotes promote phase separation of chromatin, tune droplet properties, and coordinate to form condensates of consistent density in manners that parallel chromatin behavior in cells. Histone acetylation by p300 antagonizes chromatin phase separation, dissolving droplets in vitro and decreasing droplet formation in nuclei. In the presence of multi-bromodomain proteins, such as BRD4, highly acetylated chromatin forms a new phase-separated state with droplets of distinct physical properties, which can be immiscible with unmodified chromatin droplets, mimicking nuclear chromatin subdomains. Our data suggest a framework, based on intrinsic phase separation of the chromatin polymer, for understanding the organization and regulation of eukaryotic genomes.
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Affiliation(s)
- Bryan A Gibson
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lynda K Doolittle
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maximillian W G Schneider
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Liv E Jensen
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nathan Gamarra
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lisa Henry
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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14
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Rutowicz K, Lirski M, Mermaz B, Teano G, Schubert J, Mestiri I, Kroteń MA, Fabrice TN, Fritz S, Grob S, Ringli C, Cherkezyan L, Barneche F, Jerzmanowski A, Baroux C. Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis. Genome Biol 2019; 20:157. [PMID: 31391082 PMCID: PMC6685187 DOI: 10.1186/s13059-019-1767-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/21/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function. Well studied in animals, little is known about the evolution of H1 function in other eukaryotic lineages for instance plants. Notably, in the model plant Arabidopsis, while H1 is known to influence heterochromatin and DNA methylation, its contribution to transcription, molecular, and cytological chromatin organization remains elusive. RESULTS We provide a multi-scale functional study of Arabidopsis linker histones. We show that H1-deficient plants are viable yet show phenotypes in seed dormancy, flowering time, lateral root, and stomata formation-complemented by either or both of the major variants. H1 depletion also impairs pluripotent callus formation. Fine-scale chromatin analyses combined with transcriptome and nucleosome profiling reveal distinct roles of H1 on hetero- and euchromatin: H1 is necessary to form heterochromatic domains yet dispensable for silencing of most transposable elements; H1 depletion affects nucleosome density distribution and mobility in euchromatin, spatial arrangement of nanodomains, histone acetylation, and methylation. These drastic changes affect moderately the transcription but reveal a subset of H1-sensitive genes. CONCLUSIONS H1 variants have a profound impact on the molecular and spatial (nuclear) chromatin organization in Arabidopsis with distinct roles in euchromatin and heterochromatin and a dual causality on gene expression. Phenotypical analyses further suggest the novel possibility that H1-mediated chromatin organization may contribute to the epigenetic control of developmental and cellular transitions.
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Affiliation(s)
- Kinga Rutowicz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Maciej Lirski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Benoît Mermaz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
- Department of Molecular, Cellular & Developmental Biology, Yale University, 352a Osborn memorial laboratories, New Haven, CT, 06511, USA
| | - Gianluca Teano
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Jasmin Schubert
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Imen Mestiri
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Magdalena A Kroteń
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089, Warsaw, Poland
| | - Tohnyui Ndinyanka Fabrice
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Simon Fritz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Stefan Grob
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Christoph Ringli
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Lusik Cherkezyan
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Fredy Barneche
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Andrzej Jerzmanowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Célia Baroux
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland.
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15
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Miloshev G, Staneva D, Uzunova K, Vasileva B, Draganova-Filipova M, Zagorchev P, Georgieva M. Linker histones and chromatin remodelling complexes maintain genome stability and control cellular ageing. Mech Ageing Dev 2018; 177:55-65. [PMID: 30025887 DOI: 10.1016/j.mad.2018.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/06/2018] [Accepted: 07/12/2018] [Indexed: 01/08/2023]
Abstract
Linker histones are major players in chromatin organization and per se are essential players in genome homeostasis. As the fifth class of histone proteins the linker histones not only interact with DNA and core histones but also with other chromatin proteins. These interactions prove to be essential for the higher levels of chromatin organization like chromatin loops, transcription factories and chromosome territories. Our recent results have proved that Saccharomyces cerevisiae linker histone - Hho1p, physically interacts with the actin-related protein 4 (Arp4) and that the abrogation of this interaction through the deletion of the gene for the linker histone in arp4 mutant cells leads to global changes in chromatin compaction. Here, we show that the healthy interaction between the yeast linker histone and Arp4p is critical for maintaining genome stability and for controlling cellular sensitivity to different types of stress. The abolished interaction between the linker histone and Arp4p leads the mutant yeast cells to premature ageing phenotypes. Cells die young and are more sensitive to stress. These results unambiguously prove the role of linker histones and chromatin remodelling in ageing by their cooperation in pertaining higher-order chromatin compaction and thus maintaining genome stability.
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Affiliation(s)
- George Miloshev
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology "Acad. Roumen Tsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Dessislava Staneva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology "Acad. Roumen Tsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Katya Uzunova
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology "Acad. Roumen Tsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Bela Vasileva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology "Acad. Roumen Tsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | | | - Plamen Zagorchev
- Department of Medical Physics and Biophysics, Faculty of Pharmacy, Medical University, Plovdiv, Bulgaria
| | - Milena Georgieva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology "Acad. Roumen Tsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.
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16
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Li Z, Li Y, Tang M, Peng B, Lu X, Yang Q, Zhu Q, Hou T, Li M, Liu C, Wang L, Xu X, Zhao Y, Wang H, Yang Y, Zhu WG. Destabilization of linker histone H1.2 is essential for ATM activation and DNA damage repair. Cell Res 2018; 28:756-770. [PMID: 29844578 PMCID: PMC6028381 DOI: 10.1038/s41422-018-0048-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 04/06/2018] [Accepted: 05/07/2018] [Indexed: 12/22/2022] Open
Abstract
Linker histone H1 is a master regulator of higher order chromatin structure, but its involvement in the DNA damage response and repair is unclear. Here, we report that linker histone H1.2 is an essential regulator of ataxia telangiectasia mutated (ATM) activation. We show that H1.2 protects chromatin from aberrant ATM activation through direct interaction with the ATM HEAT repeat domain and inhibition of MRE11-RAD50-NBS1 (MRN) complex-dependent ATM recruitment. Upon DNA damage, H1.2 undergoes rapid PARP1-dependent chromatin dissociation through poly-ADP-ribosylation (PARylation) of its C terminus and further proteasomal degradation. Inhibition of H1.2 displacement by PARP1 depletion or an H1.2 PARylation-dead mutation compromises ATM activation and DNA damage repair, thus leading to impaired cell survival. Taken together, our findings suggest that linker histone H1.2 functions as a physiological barrier for ATM to target the chromatin, and PARylation-mediated active H1.2 turnover is required for robust ATM activation and DNA damage repair.
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Affiliation(s)
- Zhiming Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yinglu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ming Tang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Bin Peng
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Xiaopeng Lu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Qiaoyan Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Qian Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Tianyun Hou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Meiting Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Chaohua Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Lina Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xingzhi Xu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Ying Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Haiying Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yang Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Wei-Guo Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China.
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17
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Qiao J, Xu J, Bo T, Wang W. Micronucleus-specific histone H1 is required for micronuclear chromosome integrity in Tetrahymena thermophila. PLoS One 2017; 12:e0187475. [PMID: 29095884 PMCID: PMC5667856 DOI: 10.1371/journal.pone.0187475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 10/19/2017] [Indexed: 02/02/2023] Open
Abstract
Histone H1 molecules play a key role in establishing and maintaining higher order chromatin structures. They can bind to linker DNA entering and exiting the nucleosome and regulate transcriptional activity. Tetrahymena thermophila has two histone H1, namely, macronuclear histone H1 and micronuclear histone H1 (Mlh1). Mlh1 is specifically localized at micronuclei during growth and starvation stages. Moreover, Mlh1 is localized around micronuclei and forms a specific structure during the conjugation stage. It co-localizes partially with spindle apparatus during micronuclear meiosis. Analysis of MLH1 knock-out revealed that Mlh1 was required for the micronuclear integrity and development during conjugation stage. Overexpression of Mlh1 led to abnormal conjugation progression. RT-PCR analysis indicated that the expression level of HMGB3 increased in ΔMLH1 strains, while the expression level of MLH1 increased in ΔHMGB3 cells during conjugation. These results indicate that micronuclear integrity and sexual development require normal expression level of Mlh1 and that HmgB3 and Mlh1 may functionally compensate each other in regulating micronuclear structure in T. thermophila.
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Affiliation(s)
- Juxia Qiao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi, China
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi, China
- College of Life Science, Shanxi University, Taiyuan, Shanxi, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong, China
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi, China
- * E-mail:
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18
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Bayona-Feliu A, Casas-Lamesa A, Reina O, Bernués J, Azorín F. Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin. Nat Commun 2017; 8:283. [PMID: 28819201 PMCID: PMC5561251 DOI: 10.1038/s41467-017-00338-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 06/22/2017] [Indexed: 12/01/2022] Open
Abstract
Linker histone H1 is an important structural component of chromatin that stabilizes the nucleosome and compacts the nucleofilament into higher-order structures. The biology of histone H1 remains, however, poorly understood. Here we show that Drosophila histone H1 (dH1) prevents genome instability as indicated by the increased γH2Av (H2AvS137P) content and the high incidence of DNA breaks and sister-chromatid exchanges observed in dH1-depleted cells. Increased γH2Av occurs preferentially at heterochromatic elements, which are upregulated upon dH1 depletion, and is due to the abnormal accumulation of DNA:RNA hybrids (R-loops). R-loops accumulation is readily detectable in G1-phase, whereas γH2Av increases mainly during DNA replication. These defects induce JNK-mediated apoptosis and are specific of dH1 depletion since they are not observed when heterochromatin silencing is relieved by HP1a depletion. Altogether, our results suggest that histone H1 prevents R-loops-induced DNA damage in heterochromatin and unveil its essential contribution to maintenance of genome stability.While structural importance of linker histone H1 in packaging eukaryotic genome into chromatin is well known, its biological function remains poorly understood. Here the authors reveal that Drosophila linker histone H1 prevents DNA:RNA hybrids accumulation and genome instability in heterochromatin.
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Affiliation(s)
- Aleix Bayona-Feliu
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028, Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
| | - Anna Casas-Lamesa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028, Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Jordi Bernués
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028, Barcelona, Spain.
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028, Barcelona, Spain.
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.
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19
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Merlo MA, Iziga R, Portela-Bens S, Cross I, Kosyakova N, Liehr T, Manchado M, Rebordinos L. Analysis of the histone cluster in Senegalese sole (Solea senegalensis): evidence for a divergent evolution of two canonical histone clusters. Genome 2016; 60:441-453. [PMID: 28177835 DOI: 10.1139/gen-2016-0143] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Senegalese sole (Solea senegalensis) is commercially very important and a priority species for aquaculture product diversification. The main histone cluster was identified within two BAC clones. However, two replacement histones (H1.0 and H3.3) were found in another BAC clone. Different types of canonical histones H2A and H2B were found within the same species for the first time. Phylogenetic analysis demonstrated that the different types of H1, H2A, and H2B histones were all more similar to each other than to canonical histones from other species. The canonical histone H3 of S. senegalensis differs from subtypes H3.1 and H3.2 in humans at the site of residue 96, where a serine is found instead of an alanine. This same polymorphism has been found only in Danio rerio. The karyotype of S. senegalensis comprises 21 pairs of chromosomes, distributed in 3 metacentric pairs, 2 submetacentric pairs, 4 subtelocentric pairs, and 12 acrocentric pairs. The two BAC clones that contain the clusters of canonical histones were both mapped on the largest metacentric pair, and mFISH analysis confirmed the co-location with the dmrt1 gene in that pair. Three chromosome markers have been identified which, in addition to those previously described, account for 18 chromosome pairs in S. senegalensis.
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Affiliation(s)
- Manuel Alejandro Merlo
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| | - Roger Iziga
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| | - Silvia Portela-Bens
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| | - Ismael Cross
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| | - Nadezda Kosyakova
- b Institut für Humangenetik, Universitätsklinikum Jena, 07743 Jena, Germany
| | - Thomas Liehr
- b Institut für Humangenetik, Universitätsklinikum Jena, 07743 Jena, Germany
| | - Manuel Manchado
- c Centro IFAPA "El Toruño", 11500 Puerto de Santa María, Cádiz, Spain
| | - Laureana Rebordinos
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
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20
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Abstract
The fidelity of mitosis is essential for life, and successful completion of this process relies on drastic changes in chromosome organization at the onset of nuclear division. The mechanisms that govern chromosome compaction at every cell division cycle are still far from full comprehension, yet recent studies provide novel insights into this problem, challenging classical views on mitotic chromosome assembly. Here, we briefly introduce various models for chromosome assembly and known factors involved in the condensation process (e.g. condensin complexes and topoisomerase II). We will then focus on a few selected studies that have recently brought novel insights into the mysterious way chromosomes are condensed during nuclear division.
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Affiliation(s)
- Ewa Piskadlo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras, 2780-156 , Portugal
| | - Raquel A Oliveira
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras, 2780-156 , Portugal
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21
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Abstract
Histone H1 variants, known as linker histones, are essential chromatin components in higher eukaryotes, yet compared to the core histones relatively little is known about their in vivo functions. The filamentous fungus Neurospora crassa encodes a single H1 protein that is not essential for viability. To investigate the role of N. crassa H1, we constructed a functional FLAG-tagged H1 fusion protein and performed genomic and molecular analyses. Cell fractionation experiments showed that H1-3XFLAG is a chromatin binding protein. Chromatin-immunoprecipitation combined with sequencing (ChIP-seq) revealed that H1-3XFLAG is globally enriched throughout the genome with a subtle preference for promoters of expressed genes. In mammals, the stoichiometry of H1 impacts nucleosome repeat length. To determine if H1 impacts nucleosome occupancy or nucleosome positioning in N. crassa, we performed micrococcal nuclease digestion in the wild-type and the ΔhH1 strain followed by sequencing (MNase-seq). Deletion of hH1 did not significantly impact nucleosome positioning or nucleosome occupancy. Analysis of DNA methylation by whole-genome bisulfite sequencing (MethylC-seq) revealed a modest but global increase in DNA methylation in the ΔhH1 mutant. Together, these data suggest that H1 acts as a nonspecific chromatin binding protein that can limit accessibility of the DNA methylation machinery in N. crassa.
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22
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Abstract
The primary function of the genome is to store, propagate, and express the genetic information that gives rise to a cell's architectural and functional machinery. However, the genome is also a major structural component of the cell. Besides its genetic roles, the genome affects cellular functions by nongenetic means through its physical and structural properties, particularly by exerting mechanical forces and by serving as a scaffold for binding of cellular components. Major cellular processes affected by nongenetic functions of the genome include establishment of nuclear structure, signal transduction, mechanoresponses, cell migration, and vision in nocturnal animals. We discuss the concept, mechanisms, and implications of nongenetic functions of the genome.
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Affiliation(s)
| | - Tom Misteli
- National Cancer Institute, Bethesda, MD 20892, USA
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23
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Staneva D, Georgieva M, Miloshev G. Kluyveromyces lactis genome harbours a functional linker histone encoding gene. FEMS Yeast Res 2016; 16:fow034. [PMID: 27189369 DOI: 10.1093/femsyr/fow034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2016] [Indexed: 11/14/2022] Open
Abstract
Linker histones are essential components of chromatin in eukaryotes. Through interactions with linker DNA and nucleosomes they facilitate folding and maintenance of higher-order chromatin structures and thus delicately modulate gene activity. The necessity of linker histones in lower eukaryotes appears controversial and dubious. Genomic data have shown that Schizosaccharomyces pombe does not possess genes encoding linker histones while Kluyveromyces lactis has been reported to have a pseudogene. Regarding this controversy, we have provided the first direct experimental evidence for the existence of a functional linker histone gene, KlLH1, in K. lactis genome. Sequencing of KlLH1 from both genomic DNA and copy DNA confirmed the presence of an intact open reading frame. Transcription and splicing of the KlLH1 sequence as well as translation of its mRNA have been studied. In silico analysis revealed homology of KlLH1p to the histone H1/H5 protein family with predicted three domain structure characteristic for the linker histones of higher eukaryotes. This strongly proves that the yeast K. lactis does indeed possess a functional linker histone gene thus entailing the evolutionary preservation and significance of linker histones. The nucleotide sequences of KlLH1 are deposited in the GenBank under accession numbers KT826576, KT826577 and KT826578.
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Affiliation(s)
- Dessislava Staneva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
| | - Milena Georgieva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
| | - George Miloshev
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
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24
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Abstract
Size and shape are important aspects of nuclear structure. While normal cells maintain nuclear size within a defined range, altered nuclear size and shape are associated with a variety of diseases. It is unknown if altered nuclear morphology contributes to pathology, and answering this question requires a better understanding of the mechanisms that control nuclear size and shape. In this review, we discuss recent advances in our understanding of the mechanisms that regulate nuclear morphology, focusing on nucleocytoplasmic transport, nuclear lamins, the endoplasmic reticulum, the cell cycle, and potential links between nuclear size and size regulation of other organelles. We then discuss the functional significance of nuclear morphology in the context of early embryonic development. Looking toward the future, we review new experimental approaches that promise to provide new insights into mechanisms of nuclear size control, in particular microfluidic-based technologies, and discuss how altered nuclear morphology might impact chromatin organization and physiology of diseased cells.
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Affiliation(s)
- Richik N Mukherjee
- a Department of Molecular Biology , University of Wyoming , Laramie , WY USA
| | - Pan Chen
- a Department of Molecular Biology , University of Wyoming , Laramie , WY USA
| | - Daniel L Levy
- a Department of Molecular Biology , University of Wyoming , Laramie , WY USA
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25
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Kalashnikova AA, Rogge RA, Hansen JC. Linker histone H1 and protein-protein interactions. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:455-61. [PMID: 26455956 PMCID: PMC4775371 DOI: 10.1016/j.bbagrm.2015.10.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 09/21/2015] [Accepted: 10/05/2015] [Indexed: 01/11/2023]
Abstract
Linker histones H1 are ubiquitous chromatin proteins that play important roles in chromatin compaction, transcription regulation, nucleosome spacing and chromosome spacing. H1 function in DNA and chromatin structure stabilization is well studied and established. The current paradigm of linker histone mode of function considers all other cellular roles of linker histones to be a consequence from H1 chromatin compaction and repression. Here we review the multiple processes regulated by linker histones and the emerging importance of protein interactions in H1 functioning. We propose a new paradigm which explains the multi functionality of linker histones through linker histones protein interactions as a way to directly regulate recruitment of proteins to chromatin.
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Affiliation(s)
- Anna A Kalashnikova
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Ryan A Rogge
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA.
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Vuković LD, Jevtić P, Edens LJ, Levy DL. New Insights into Mechanisms and Functions of Nuclear Size Regulation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 322:1-59. [PMID: 26940517 DOI: 10.1016/bs.ircmb.2015.11.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nuclear size is generally maintained within a defined range in a given cell type. Changes in cell size that occur during cell growth, development, and differentiation are accompanied by dynamic nuclear size adjustments in order to establish appropriate nuclear-to-cytoplasmic volume relationships. It has long been recognized that aberrations in nuclear size are associated with certain disease states, most notably cancer. Nuclear size and morphology must impact nuclear and cellular functions. Understanding these functional implications requires an understanding of the mechanisms that control nuclear size. In this review, we first provide a general overview of the diverse cellular structures and activities that contribute to nuclear size control, including structural components of the nucleus, effects of DNA amount and chromatin compaction, signaling, and transport pathways that impinge on the nucleus, extranuclear structures, and cell cycle state. We then detail some of the key mechanistic findings about nuclear size regulation that have been gleaned from a variety of model organisms. Lastly, we review studies that have implicated nuclear size in the regulation of cell and nuclear function and speculate on the potential functional significance of nuclear size in chromatin organization, gene expression, nuclear mechanics, and disease. With many fundamental cell biological questions remaining to be answered, the field of nuclear size regulation is still wide open.
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Affiliation(s)
- Lidija D Vuković
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America
| | - Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America
| | - Lisa J Edens
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America.
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Linhoff MW, Garg SK, Mandel G. A high-resolution imaging approach to investigate chromatin architecture in complex tissues. Cell 2015; 163:246-55. [PMID: 26406379 DOI: 10.1016/j.cell.2015.09.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 05/22/2015] [Accepted: 08/11/2015] [Indexed: 01/08/2023]
Abstract
We present ChromATin, a quantitative high-resolution imaging approach for investigating chromatin organization in complex tissues. This method combines analysis of epigenetic modifications by immunostaining, localization of specific DNA sequences by FISH, and high-resolution segregation of nuclear compartments using array tomography (AT) imaging. We then apply this approach to examine how the genome is organized in the mammalian brain using female Rett syndrome mice, which are a mosaic of normal and Mecp2-null cells. Side-by-side comparisons within the same field reveal distinct heterochromatin territories in wild-type neurons that are altered in Mecp2-null nuclei. Mutant neurons exhibit increased chromatin compaction and a striking redistribution of the H4K20me3 histone modification into pericentromeric heterochromatin, a territory occupied normally by MeCP2. These events are not observed in every neuronal cell type, highlighting ChromATin as a powerful in situ method for examining cell-type-specific differences in chromatin architecture in complex tissues.
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Affiliation(s)
- Michael W Linhoff
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Saurabh K Garg
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Gail Mandel
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
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Pan C, Fan Y. Role of H1 linker histones in mammalian development and stem cell differentiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:496-509. [PMID: 26689747 DOI: 10.1016/j.bbagrm.2015.12.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/09/2015] [Accepted: 12/09/2015] [Indexed: 12/19/2022]
Abstract
H1 linker histones are key chromatin architectural proteins facilitating the formation of higher order chromatin structures. The H1 family constitutes the most heterogeneous group of histone proteins, with eleven non-allelic H1 variants in mammals. H1 variants differ in their biochemical properties and exhibit significant sequence divergence from one another, yet most of them are highly conserved during evolution from mouse to human. H1 variants are differentially regulated during development and their cellular compositions undergo dramatic changes in embryogenesis, gametogenesis, tissue maturation and cellular differentiation. As a group, H1 histones are essential for mouse development and proper stem cell differentiation. Here we summarize our current knowledge on the expression and functions of H1 variants in mammalian development and stem cell differentiation. Their diversity, sequence conservation, complex expression and distinct functions suggest that H1s mediate chromatin reprogramming and contribute to the large variations and complexity of chromatin structure and gene expression in the mammalian genome.
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Affiliation(s)
- Chenyi Pan
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA; The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Yuhong Fan
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA; The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Liao R, Mizzen CA. Interphase H1 phosphorylation: Regulation and functions in chromatin. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:476-85. [PMID: 26657617 DOI: 10.1016/j.bbagrm.2015.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/25/2022]
Abstract
Many metazoan cell types differentially express multiple non-allelic amino acid sequence variants of histone H1. Although early work revealed that H1 variants, collectively, are phosphorylated during interphase and mitosis, differences between individual H1 variants in the sites they possess for mitotic and interphase phosphorylation have been elucidated only relatively recently. Here, we review current knowledge on the regulation and function of interphase H1 phosphorylation, with a particular emphasis on how differences in interphase phosphorylation among the H1 variants of mammalian cells may enable them to have differential effects on transcription and other chromatin processes.
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Affiliation(s)
- Ruiqi Liao
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, USA
| | - Craig A Mizzen
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, USA; Institute for Genomic Biology, University of Illinois at Urbana Champaign, USA.
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Bednar J, Hamiche A, Dimitrov S. H1-nucleosome interactions and their functional implications. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:436-43. [PMID: 26477489 DOI: 10.1016/j.bbagrm.2015.10.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 01/13/2023]
Abstract
Linker histones are three domain proteins and consist of a structured (globular) domain, flanked by two likely non-structured NH2- and COOH-termini. The binding of the linker histones to the nucleosome was characterized by different methods in solution. Apparently, the globular domain interacts with the linker DNA and the nucleosome dyad, while the binding of the large and rich in lysines COOH-terminus results in "closing" the linker DNA of the nucleosome and the formation of the "stem" structure. What is the mode of binding of the linker histones within the chromatin fiber remains still elusive. Nonetheless, it is clear that linker histones are essential for both the assembly and maintenance of the condensed chromatin fiber. Interestingly, linker histones are post-translationally modified and how this affects both their binding to chromatin and functions is now beginning to emerge. In addition, linker histones are highly mobile in vivo, but not in vitro. No explanation of this finding is reported for the moment. The higher mobility of the linker histones should, however, have strong impact on their function. Linker histones plays an important role in gene expression regulation and other chromatin related process and their function is predominantly regulated by their posttranslational modifications. However, the detailed mechanism how the linker histones do function remains still not well understood despite numerous efforts. Here we will summarize and analyze the data on the linker histone binding to the nucleosome and the chromatin fiber and will discuss its functional consequences.
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Affiliation(s)
- Jan Bednar
- Université de Grenoble Alpes/CNRS, Laboratoire Interdisciplinaire de Physique, UMR 5588, 140 rue de la Physique, B.P. 87, St. Martin d'Heres, F-38402, France.
| | - Ali Hamiche
- Equipe labellisée Ligue contre le Cancer, Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UDS, CNRS, INSERM, 1 rue Laurent Fries, B.P. 10142, 67404 Illkirch Cedex, France
| | - Stefan Dimitrov
- INSERM/UJF, Institut Albert Bonniot, U823, Site Santé-BP 170, 38042 Grenoble Cedex 9, France
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Brush GS. Evidence that histone H1 is dispensable for proper meiotic recombination in budding yeast. BMC Res Notes 2015; 8:275. [PMID: 26122007 PMCID: PMC4486124 DOI: 10.1186/s13104-015-1246-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/17/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone H1, referred to as the linker histone, associates with the nucleosome core particle. While there is indication that the budding yeast version of histone H1 (Hho1) contributes to regulation of chromatin structure and certain chromatin-related processes, such as DNA double-strand break repair, cells lacking Hho1 are healthy and display subtle phenotypes. A recent report has revealed that Hho1 is required for optimal sporulation. The studies described here were conducted to determine whether Hho1 influences meiotic recombination, an event that occurs during sporulation, involves generation and repair of DNA double-strand breaks, and is critical for spore viability. FINDINGS Through tetrad analysis, cells with or without Hho1 were compared for meiotic reciprocal recombination events within several chromosome XV intervals. Parameters investigated included crossover frequency (genetic map distance) and crossover interference. No significant differences were detected between the two cell types. In agreement with earlier studies, spore viability was not affected by Hho1 absence. CONCLUSION These data suggest that complete absence of Hho1 from chromatin does not affect reciprocal recombination between homologous chromosomes during meiosis. Therefore, the basal level of Hho1 that remains after its reported depletion early in meiosis is unlikely to be important for regulating recombination. Furthermore, the subsequent accumulation of Hho1 as the haploid products mature does not appear to be crucial for spore viability.
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Affiliation(s)
- George S Brush
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA. .,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA.
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Abstract
How eukaryotic genomes are packaged into compact cylindrical chromosomes in preparation for cell divisions has remained one of the major unsolved questions of cell biology. Novel approaches to study the topology of DNA helices inside the nuclei of intact cells, paired with computational modeling and precise biomechanical measurements of isolated chromosomes, have advanced our understanding of mitotic chromosome architecture. In this Review Essay, we discuss - in light of these recent insights - the role of chromatin architecture and the functions and possible mechanisms of SMC protein complexes and other molecular machines in the formation of mitotic chromosomes. Based on the information available, we propose a stepwise model of mitotic chromosome condensation that envisions the sequential generation of intra-chromosomal linkages by condensin complexes in the context of cohesin-mediated inter-chromosomal linkages, assisted by topoisomerase II. The described scenario results in rod-shaped metaphase chromosomes ready for their segregation to the cell poles.
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Affiliation(s)
- Marc Kschonsak
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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Analysis of DNA replication associated chromatin decondensation: in vivo assay for understanding chromatin remodeling mechanisms of selected proteins. Methods Mol Biol 2015; 1288:289-303. [PMID: 25827886 DOI: 10.1007/978-1-4939-2474-5_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Of critical importance to many of the events underlying transcriptional control of gene expression are modifications to core and linker histones that regulate the accessibility of trans-acting factors to the DNA substrate within the context of chromatin. Likewise, control over the initiation of DNA replication, as well as the ability of the replication machinery to proceed during elongation through the multiple levels of chromatin condensation that are likely to be encountered, is known to involve the creation of chromatin accessibility. In the latter case, chromatin access will likely need to be a transient event so as to prevent total genomic unraveling of the chromatin that would be deleterious to cells. While there are many molecular and biochemical approaches in use to study histone changes and their relationship to transcription and chromatin accessibility, few techniques exist that allow a molecular dissection of the events underlying DNA replication control as it pertains to chromatin changes and accessibility. Here, we outline a novel experimental strategy for addressing the ability of specific proteins to induce large-scale chromatin unfolding (decondensation) in vivo upon site-specific targeting to an engineered locus. Our laboratory has used this powerful system in novel ways to directly address the ability of DNA replication proteins to create chromatin accessibility, and have incorporated modifications to the basic approach that allow for a molecular genetic analysis of the mechanisms and associated factors involved in causing chromatin decondensation by a protein of interest. Alternative approaches involving co-expression of other proteins (competitors or stimulators), concurrent drug treatments, and analysis of co-localizing histone modifications are also addressed, all of which are illustrative of the utility of this experimental system for extending basic findings to physiologically relevant mechanisms. Although used by our group to analyze mechanisms underlying DNA replication associated chromatin accessibility, this unique and powerful experimental system has the propensity to be a valuable tool for understanding chromatin remodeling mechanisms orchestrated by other cellular processes such as DNA repair, recombination, mitotic chromosome condensation, or other chromosome dynamics involving chromatin alterations and accessibility.
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Liu J, Wang H, Ma F, Xu D, Chang Y, Zhang J, Wang J, Zhao M, Lin C, Huang C, Qian H, Zhan Q. MTA1 regulates higher-order chromatin structure and histone H1-chromatin interaction in-vivo. Mol Oncol 2015; 9:218-35. [PMID: 25205035 PMCID: PMC5528677 DOI: 10.1016/j.molonc.2014.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/04/2014] [Accepted: 08/18/2014] [Indexed: 11/27/2022] Open
Abstract
In the current study, for the first time, we found that metastasis-associated gene 1 (MTA1) was a higher-order chromatin structure organizer that decondenses the interphase chromatin and mitotic chromosomes. MTA1 interacts dynamically with nucleosomes during the cell cycle progression, prominently contributing to the mitotic chromatin/chromosome structure transitions at both prophase and telophase. We showed that the decondensation of interphase chromatin by MTA1 was independent of Mi-2 chromatin remodeling activity. H1 was reported to stabilize the compact higher-order chromatin structure through its interaction with DNA. Our data showed that MTA1 caused a reduced H1-chromatin interaction in-vivo. Moreover, the dynamic MTA1-chromatin interaction in the cell cycle contributed to the periodical H1-chromatin interaction, which in turn modulated chromatin/chromosome transitions. Although MTA1 drove a global decondensation of chromatin structure, it changed the expression of only a small proportion of genes. After MTA1 overexpression, the up-regulated genes were distributed in clusters along with down-regulated genes on chromosomes at parallel frequencies.
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Affiliation(s)
- Jian Liu
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China; Medical Research Center, Beijing ChaoYang Hospital, Capital Medical University, Beijing 100020, China
| | - Haijuan Wang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Fei Ma
- Department of Medical Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, State Key Laboratory of Molecular Oncology, Beijing 100021, China
| | - Dongkui Xu
- Department of Abdominal Surgery, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, State Key Laboratory of Molecular Oncology, Beijing 100021, China
| | - Yanan Chang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Jinlong Zhang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Jia Wang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Mei Zhao
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Chen Lin
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Changzhi Huang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China.
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China.
| | - Qimin Zhan
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China.
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Pena AC, Pimentel MR, Manso H, Vaz-Drago R, Pinto-Neves D, Aresta-Branco F, Rijo-Ferreira F, Guegan F, Pedro Coelho L, Carmo-Fonseca M, Barbosa-Morais NL, Figueiredo LM. Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo. Mol Microbiol 2014; 93:645-63. [PMID: 24946224 PMCID: PMC4285223 DOI: 10.1111/mmi.12677] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2014] [Indexed: 11/30/2022]
Abstract
Trypanosoma brucei is a unicellular parasite that causes sleeping sickness in humans. Most of its transcription is constitutive and driven by RNA polymerase II. RNA polymerase I (Pol I) transcribes not only ribosomal RNA genes, but also protein-encoding genes, including variant surface glycoproteins (VSGs) and procyclins. In T. brucei, histone H1 (H1) is required for VSG silencing and chromatin condensation. However, whether H1 has a genome-wide role in transcription is unknown. Here, using RNA sequencing we show that H1 depletion changes the expression of a specific cohort of genes. Interestingly, the predominant effect is partial loss of silencing of Pol I loci, such as VSG and procyclin genes. Labelling of nascent transcripts with 4-thiouridine showed that H1 depletion does not alter the level of labelled Pol II transcripts. In contrast, the levels of 4sU-labelled Pol I transcripts were increased by two- to sixfold, suggesting that H1 preferentially blocks transcription at Pol I loci. Finally, we observed that parasites depleted of H1 grow almost normally in culture but they have a reduced fitness in mice, suggesting that H1 is important for host-pathogen interactions.
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Affiliation(s)
- Ana C Pena
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisboa, Portugal
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Maree JP, Patterton HG. The epigenome of Trypanosoma brucei: a regulatory interface to an unconventional transcriptional machine. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:743-50. [PMID: 24942804 DOI: 10.1016/j.bbagrm.2014.05.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 05/09/2014] [Accepted: 05/28/2014] [Indexed: 12/15/2022]
Abstract
The epigenome represents a major regulatory interface to the eukaryotic genome. Nucleosome positions, histone variants, histone modifications and chromatin associated proteins all play a role in the epigenetic regulation of DNA function. Trypanosomes, an ancient branch of the eukaryotic evolutionary lineage, exhibit some highly unusual transcriptional features, including the arrangement of functionally unrelated genes in large, polymerase II transcribed polycistronic transcription units, often exceeding hundreds of kilobases in size. It is generally believed that transcription initiation plays a minor role in regulating the transcript level of genes in trypanosomes, which are mainly regulated post-transcriptionally. Recent advances have revealed that epigenetic mechanisms play an essential role in the transcriptional regulation of Trypanosoma brucei. This suggested that the modulation of gene activity, particularly that of pol I transcribed genes, is, indeed, an important control mechanism, and that the epigenome is critical in regulating gene expression programs that allow the successful migration of this parasite between hosts, as well as the continuous evasion of the immune system in mammalian hosts. A wide range of epigenetic signals, readers, writers and erasers have been identified in trypanosomes, some of which have been mapped to essential genetic functions. Some epigenetic mechanisms have also been observed to be unique to trypanosomes. We review recent advances in our understanding of epigenetic control mechanisms in T. brucei, the causative agent of African sleeping sickness, and highlight the utility of epigenetic targets in the possible development of new therapies for human African trypanosomiasis.
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Affiliation(s)
- Johannes P Maree
- Advanced Biomolecular Research Cluster, University of the Free State, PO Box 339, Bloemfontein 9332, South Africa
| | - Hugh-G Patterton
- Advanced Biomolecular Research Cluster, University of the Free State, PO Box 339, Bloemfontein 9332, South Africa.
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Core Histone Charge and Linker Histone H1 Effects on the Chromatin Structure ofSchizosaccharomyces pombe. Biosci Biotechnol Biochem 2014; 76:2261-6. [DOI: 10.1271/bbb.120548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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38
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Nalabothula N, McVicker G, Maiorano J, Martin R, Pritchard JK, Fondufe-Mittendorf YN. The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation. BMC Genomics 2014; 15:92. [PMID: 24484546 PMCID: PMC3928079 DOI: 10.1186/1471-2164-15-92] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 01/30/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. While these proteins are almost certainly important for gene regulation they have been studied far less than the core histone proteins. RESULTS Here we describe the genomic distributions and functional roles of two chromatin architectural proteins: histone H1 and the high mobility group protein HMGD1 in Drosophila S2 cells. Using ChIP-seq, biochemical and gene specific approaches, we find that HMGD1 binds to highly accessible regulatory chromatin and active promoters. In contrast, H1 is primarily associated with heterochromatic regions marked with repressive histone marks. We find that the ratio of HMGD1 to H1 binding is a better predictor of gene activity than either protein by itself, which suggests that reciprocal binding between these proteins is important for gene regulation. Using knockdown experiments, we show that HMGD1 and H1 affect the occupancy of the other protein, change nucleosome repeat length and modulate gene expression. CONCLUSION Collectively, our data suggest that dynamic and mutually exclusive binding of H1 and HMGD1 to nucleosomes and their linker sequences may control the fluid chromatin structure that is required for transcriptional regulation. This study provides a framework to further study the interplay between chromatin architectural proteins and epigenetics in gene regulation.
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Jevtić P, Levy DL. Mechanisms of nuclear size regulation in model systems and cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 773:537-69. [PMID: 24563365 DOI: 10.1007/978-1-4899-8032-8_25] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Changes in nuclear size have long been used by cytopathologists as an important parameter to diagnose, stage, and prognose many cancers. Mechanisms underlying these changes and functional links between nuclear size and malignancy are largely unknown. Understanding mechanisms of nuclear size regulation and the physiological significance of proper nuclear size control will inform the interplay between altered nuclear size and oncogenesis. In this chapter we review what is known about molecular mechanisms of nuclear size control based on research in model experimental systems including yeast, Xenopus, Tetrahymena, Drosophila, plants, mice, and mammalian cell culture. We discuss how nuclear size is influenced by DNA ploidy, nuclear structural components, cytoplasmic factors and nucleocytoplasmic transport, the cytoskeleton, and the extracellular matrix. Based on these mechanistic insights, we speculate about how nuclear size might impact cell physiology and whether altered nuclear size could contribute to cancer development and progression. We end with some outstanding questions about mechanisms and functions of nuclear size regulation.
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Affiliation(s)
- Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY, 82071, USA,
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40
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Takagi M, Imamoto N. Control of nuclear size by NPC proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 773:571-91. [PMID: 24563366 DOI: 10.1007/978-1-4899-8032-8_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The architecture of the cell nucleus in cancer cells is often altered in a manner associated with the tumor type and aggressiveness. Therefore, it has been the central criterion in the pathological diagnosis and prognosis of cancer. However, the molecular mechanism behind these observed changes in nuclear morphology, including size, remains completely unknown. Based on our current understanding of the physiology of the nuclear pore complex (NPC) and its constituents, which are collectively referred to as nucleoporins (Nups), we discuss how the structural and functional ablation of the NPC and Nups could directly or indirectly contribute to the changes in nuclear size observed in cancer cells.
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Affiliation(s)
- Masatoshi Takagi
- Cellular Dynamics Laboratory, RIKEN, WAKO, Saitama, 351-0198, Japan,
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Abstract
Research using ciliates revealed early examples of epigenetic phenomena and continues to provide novel findings. These protozoans maintain separate germline and somatic nuclei that carry transcriptionally silent and active genomes, respectively. Examining the differences in chromatin within distinct nuclei of Tetrahymena identified histone variants and established that transcriptional regulators act by modifying histones. Formation of somatic nuclei requires both transcriptional activation of silent chromatin and large-scale DNA elimination. This somatic genome remodeling is directed by homologous RNAs, acting with an RNA interference (RNAi)-related machinery. Furthermore, the content of the parental somatic genome provides a homologous template to guide this genome restructuring. The mechanisms regulating ciliate DNA rearrangements reveal the surprising power of homologous RNAs to remodel the genome and transmit information transgenerationally.
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Affiliation(s)
- Douglas L Chalker
- Department of Biology, Washington University, St. Louis, Missouri 63130
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Hox genes are involved in vascular wall-resident multipotent stem cell differentiation into smooth muscle cells. Sci Rep 2013; 3:2178. [PMID: 24145756 PMCID: PMC3804857 DOI: 10.1038/srep02178] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/02/2013] [Indexed: 01/10/2023] Open
Abstract
Human vascular wall-resident CD44+ multipotent stem cells (VW-MPSCs) within the vascular adventitia are capable to differentiate into pericytes and smooth muscle cells (SMC). This study demonstrates HOX-dependent differentiation of CD44(+) VW-MPSCs into SMC that involves epigenetic modification of transgelin as a down-stream regulated gene. First, HOXB7, HOXC6 and HOXC8 were identified to be differentially expressed in VW-MPSCs as compared to terminal differentiated human aortic SMC, endothelial cells and undifferentiated pluripotent embryonic stem cells. Silencing these HOX genes in VW-MPSCs significantly reduced their sprouting capacity and increased expression of the SMC markers transgelin and calponin and the histone gene histone H1. Furthermore, the methylation pattern of the TAGLN promoter was altered. In summary, our findings suggest a role for certain HOX genes in regulating differentiation of human VW-MPSC into SMCs that involves epigenetic mechanisms. This is critical for understanding VW-MPSC-dependent vascular disease processes such as neointima formation and tumor vascularization.
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Nolen LD, Boyle S, Ansari M, Pritchard E, Bickmore WA. Regional chromatin decompaction in Cornelia de Lange syndrome associated with NIPBL disruption can be uncoupled from cohesin and CTCF. Hum Mol Genet 2013; 22:4180-93. [PMID: 23760082 PMCID: PMC3781641 DOI: 10.1093/hmg/ddt265] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 06/03/2013] [Indexed: 01/09/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a developmental disorder caused by mutations in NIPBL, a protein which has functionally been associated with the cohesin complex. Mutations in core cohesin complex components have also been reported in individuals with CdLS-like phenotypes. In addition to its role in sister chromatid cohesion, cohesin is thought to play a role in regulating gene expression during development. The mechanism of this gene regulation remains unclear, but NIPBL and cohesin have been reported to affect long-range chromosomal interactions, both independently and through interactions with CTCF. We used fluorescence in situ hybridization to investigate whether the disruption of NIPBL affects chromosome architecture. We show that cells from CdLS patients exhibit visible chromatin decompaction, that is most pronounced across gene-rich regions of the genome. Cells carrying mutations predicted to have a more severe effect on NIPBL function show more extensive chromatin decompaction than those carrying milder mutations. This cellular phenotype was reproduced in normal cells depleted for NIPBL with siRNA, but was not seen following the knockdown of either the cohesin component SMC3, or CTCF. We conclude that NIPBL has a function in modulating chromatin architecture, particularly for gene-rich areas of the chromosome, that is not dependent on SMC3/cohesin or CTCF, raising the possibility that the aetiology of disorders associated with the mutation of core cohesin components is distinct from that associated with the disruption of NIPBL itself in classical CdLS.
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Affiliation(s)
| | | | | | | | - Wendy A. Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
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Machha VR, Waddle JR, Turner AL, Wellman S, Le VH, Lewis EA. Calorimetric studies of the interactions of linker histone H1(0) and its carboxyl (H1(0)-C) and globular (H1(0)-G) domains with calf-thymus DNA. Biophys Chem 2013; 184:22-8. [PMID: 24036047 DOI: 10.1016/j.bpc.2013.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 01/04/2023]
Abstract
Histone H1 is a chromatin protein found in most eukaryotes. ITC and CD have been used to study the binding of H1(0) and its C-terminal, H1(0)-C, and globular, H1(0)-G, domains to a highly polymerized DNA. ITC results indicate that H1(0) and H1(0)-C bind tightly to DNA (Ka≈1×10(7)), with an unfavorable ΔH (ΔH≈+22kcal/mol) and a favorable ΔS (-TΔS≈-30kcal/mol). Binding H1(0)-G to DNA at 25°C is calorimetrically silent. A multiple independent site model fits the ITC data, with the anomaly in the data near saturation attributed to rearrangement of bound H1, maximizing the number of binding sites. CD experiments indicate that H1(0)/DNA and H1(0)-C/DNA complexes form with little change in protein structure but with some DNA restructuring. Salt dependent ITC experiments indicate that the electrostatic contribution to binding H1(0) or H1(0)-C is small ranging from 6% to 17% of the total ΔG.
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Affiliation(s)
- V R Machha
- Department of Chemistry, Mississippi State University, Box 9573, Mississippi State, MS 39762, United States
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Harshman SW, Young NL, Parthun MR, Freitas MA. H1 histones: current perspectives and challenges. Nucleic Acids Res 2013; 41:9593-609. [PMID: 23945933 PMCID: PMC3834806 DOI: 10.1093/nar/gkt700] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
H1 and related linker histones are important both for maintenance of higher-order chromatin structure and for the regulation of gene expression. The biology of the linker histones is complex, as they are evolutionarily variable, exist in multiple isoforms and undergo a large variety of posttranslational modifications in their long, unstructured, NH2- and COOH-terminal tails. We review recent progress in understanding the structure, genetics and posttranslational modifications of linker histones, with an emphasis on the dynamic interactions of these proteins with DNA and transcriptional regulators. We also discuss various experimental challenges to the study of H1 and related proteins, including limitations of immunological reagents and practical difficulties in the analysis of posttranslational modifications by mass spectrometry.
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Affiliation(s)
- Sean W Harshman
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, USA, College of Medicine and Arthur G. James Comprehensive Cancer Center, Columbus, Ohio, USA, National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA and Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio, USA
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Yazdani M, Deogracias R, Guy J, Poot RA, Bird A, Barde YA. Disease modeling using embryonic stem cells: MeCP2 regulates nuclear size and RNA synthesis in neurons. Stem Cells 2013; 30:2128-39. [PMID: 22865604 DOI: 10.1002/stem.1180] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Mutations in the gene encoding the methyl-CpG-binding protein MECP2 are the major cause of Rett syndrome, an autism spectrum disorder mainly affecting young females. MeCP2 is an abundant chromatin-associated protein, but how and when its absence begins to alter brain function is still far from clear. Using a stem cell-based system allowing the synchronous differentiation of neuronal progenitors, we found that in the absence of MeCP2, the size of neuronal nuclei fails to increase at normal rates during differentiation. This is accompanied by a marked decrease in the rate of ribonucleotide incorporation, indicating an early role of MeCP2 in regulating total gene transcription, not restricted to selected mRNAs. We also found that the levels of brain-derived neurotrophic factor (BDNF) were decreased in mutant neurons, while those of the presynaptic protein synaptophysin increased at similar rates in wild-type and mutant neurons. By contrast, nuclear size, transcription rates, and BDNF levels remained unchanged in astrocytes lacking MeCP2. Re-expressing MeCP2 in mutant neurons rescued the nuclear size phenotype as well as BDNF levels. These results reveal a new role of MeCP2 in regulating overall RNA synthesis in neurons during the course of their maturation, in line with recent findings indicating a reduced nucleolar size in neurons of the developing brain of mice lacking Mecp2.
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Edens LJ, White KH, Jevtic P, Li X, Levy DL. Nuclear size regulation: from single cells to development and disease. Trends Cell Biol 2012; 23:151-9. [PMID: 23277088 DOI: 10.1016/j.tcb.2012.11.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 11/07/2012] [Accepted: 11/12/2012] [Indexed: 10/27/2022]
Abstract
Cell size varies greatly among different cell types and organisms, especially during early development when cell division is rapid with little overall growth. A fundamental question is how organelle size is regulated relative to cell size. The nucleus exhibits exquisite size scaling during development and between species, and nuclear size is often altered in cancer cells. Recent studies have elucidated mechanisms of nuclear size regulation in a variety of experimental systems, opening the door to future research on how nuclear size impacts upon cell and nuclear function and subnuclear organization. In this review we discuss studies that have clarified nuclear size control mechanisms and how these results have or will contribute to our understanding of the functional significance of nuclear size.
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Affiliation(s)
- Lisa J Edens
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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Povelones ML, Gluenz E, Dembek M, Gull K, Rudenko G. Histone H1 plays a role in heterochromatin formation and VSG expression site silencing in Trypanosoma brucei. PLoS Pathog 2012; 8:e1003010. [PMID: 23133390 PMCID: PMC3486875 DOI: 10.1371/journal.ppat.1003010] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 09/20/2012] [Indexed: 11/30/2022] Open
Abstract
The African sleeping sickness parasite Trypanosoma brucei evades the host immune system through antigenic variation of its variant surface glycoprotein (VSG) coat. Although the T. brucei genome contains ∼1500 VSGs, only one VSG is expressed at a time from one of about 15 subtelomeric VSG expression sites (ESs). For antigenic variation to work, not only must the vast VSG repertoire be kept silent in a genome that is mainly constitutively transcribed, but the frequency of VSG switching must be strictly controlled. Recently it has become clear that chromatin plays a key role in silencing inactive ESs, thereby ensuring monoallelic expression of VSG. We investigated the role of the linker histone H1 in chromatin organization and ES regulation in T. brucei. T. brucei histone H1 proteins have a different domain structure to H1 proteins in higher eukaryotes. However, we show that they play a key role in the maintenance of higher order chromatin structure in bloodstream form T. brucei as visualised by electron microscopy. In addition, depletion of histone H1 results in chromatin becoming generally more accessible to endonucleases in bloodstream but not in insect form T. brucei. The effect on chromatin following H1 knock-down in bloodstream form T. brucei is particularly evident at transcriptionally silent ES promoters, leading to 6–8 fold derepression of these promoters. T. brucei histone H1 therefore appears to be important for the maintenance of repressed chromatin in bloodstream form T. brucei. In particular H1 plays a role in downregulating silent ESs, arguing that H1-mediated chromatin functions in antigenic variation in T. brucei. Trypanosoma brucei causes African sleeping sickness, endemic to sub-Saharan Africa. Bloodstream form T. brucei is covered with a dense coat of variant surface glycoprotein (VSG). Only one VSG is expressed at a time out of a vast repertoire of ∼1500 VSGs. The active VSG is transcribed in a telomeric VSG expression site (ES), and VSG switching allows immune evasion. Exactly how monoallelic exclusion of VSG ESs operates, and how switching between ESs is mediated remains mysterious, although epigenetics and chromatin structure clearly play a major role. The linker histone H1 is thought to orchestrate higher order chromatin structure in eukaryotes, but its exact function is unclear. We investigated the role of histone H1 in the regulation of antigenic variation in T. brucei. We show that histone H1 is associated with chromatin and is required for higher order chromatin structure. Depletion of histone H1 results in derepression of silent VSG ES promoters, indicating that H1-mediated chromatin functions in antigenic variation in T. brucei.
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Affiliation(s)
- Megan L. Povelones
- Division of Cell and Molecular Biology, Imperial College London, South Kensington, London, United Kingdom
| | - Eva Gluenz
- The Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Marcin Dembek
- Division of Cell and Molecular Biology, Imperial College London, South Kensington, London, United Kingdom
| | - Keith Gull
- The Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Gloria Rudenko
- Division of Cell and Molecular Biology, Imperial College London, South Kensington, London, United Kingdom
- * E-mail:
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Kostova NN, Srebreva L, Markov DV, Sarg B, Lindner HH, Rundquist I. Histone H5-chromatin interactions in situ are strongly modulated by H5 C-terminal phosphorylation. Cytometry A 2012; 83:273-9. [DOI: 10.1002/cyto.a.22221] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 09/21/2012] [Accepted: 09/22/2012] [Indexed: 12/23/2022]
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Chaudhary N, Nakka KK, Maulik N, Chattopadhyay S. Epigenetic manifestation of metabolic syndrome and dietary management. Antioxid Redox Signal 2012; 17:254-81. [PMID: 22229755 DOI: 10.1089/ars.2011.4387] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE Metabolic syndrome constitutes a group of disorders such as insulin resistance, hypertension, and hypertriglyceridemia, predisposing an individual to risk factors such as cardiovascular disease, diabetes, obesity, and dyslipidemia. A majority of these diseases are influenced by the environmental factors, nutrient uptake, and genetic profile of an individual that together dysregulate gene function. These genetic and nongenetic factors are reported to introduce epigenetic cues that modulate the gene function which is inherited by the offspring. RECENT ADVANCES Considering the epigenetic modulation of the metabolic disorders, nutrigenomics has been distinctly categorized as a branch that deals with modulatory effect of nutrients on metabolic disorders and disease progression by supplementing the individuals with key nutrient-enriched diets which are derived from plant and animal sources. CRITICAL ISSUES Nutritional components of the diet regulate the metabolic health of an individual either by controlling the expression of some key genes related to metabolic pathways or by modulating the epigenetic events on such genes. The present article discusses various metabolic disorders in detail and the effect of nutrients on the specific genes causing those disorders. We also highlight the molecular mechanisms of some metabolic disorders through epigenetic modifications and possible therapeutic interventions. FUTURE DIRECTIONS With the advent of high-throughput technologies and epigenetic modulation of the metabolic disorders, an altered epigenetic code that is programmed due to improper nutrients can be reverted back by supplementing the diet with various plant-derived compounds. The implication of small molecular drugs is also of utmost significance for challenging the metabolic disorders.
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Affiliation(s)
- Nidhi Chaudhary
- Department of Chromatin and Disease, National Centre for Cell Science, Pune, India
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