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Eskeland R, Eberharter A, Imhof A. HP1 binding to chromatin methylated at H3K9 is enhanced by auxiliary factors. Mol Cell Biol 2006; 27:453-65. [PMID: 17101786 PMCID: PMC1800810 DOI: 10.1128/mcb.01576-06] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A large portion of the eukaryotic genome is packaged into transcriptionally silent heterochromatin. Several factors that play important roles during the establishment and maintenance of this condensed form have been identified. Methylation of lysine 9 within histone H3 and the subsequent binding of the chromodomain protein heterochromatin protein 1 (HP1) are thought to initiate heterochromatin formation in vivo and to propagate a heterochromatic state lasting through several cell divisions. For the present study we analyzed the binding of HP1 to methylated chromatin in a fully reconstituted system. In contrast to its strong binding to methylated peptides, HP1 binds only weakly to methylated chromatin. However, the addition of recombinant SU(VAR) protein, such as ACF1 or SU(VAR)3-9, facilitates HP1 binding to chromatin methylated at lysine 9 within the H3 N terminus (H3K9). We propose that HP1 has multiple target sites that contribute to its recognition of chromatin, only one of them being methylated at H3K9. These findings have implications for the mechanisms of recognition of specific chromatin modifications in vivo.
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Affiliation(s)
- Ragnhild Eskeland
- Histone Modifications Group, Adolf-Butenandt Institut, University of Munich, Schillerstrasse 44, 80336 Munich, Germany
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52
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Dang W, Kagalwala MN, Bartholomew B. Regulation of ISW2 by concerted action of histone H4 tail and extranucleosomal DNA. Mol Cell Biol 2006; 26:7388-96. [PMID: 17015471 PMCID: PMC1636884 DOI: 10.1128/mcb.01159-06] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The stable contact of ISW2 with nucleosomal DNA approximately 20 bp from the dyad was shown by DNA footprinting and photoaffinity labeling using recombinant histone octamers to require the histone H4 N-terminal tail. Efficient ISW2 remodeling also required the H4 N-terminal tail, although the lack of the H4 tail can be mostly compensated for by increasing the incubation time or concentration of ISW2. Similarly, the length of extranucleosomal DNA affected the stable contact of ISW2 with this same internal nucleosomal site, with the optimal length being 70 to 85 bp. These data indicate the histone H4 tail, in concert with a favorable length of extranucleosomal DNA, recruits and properly orients ISW2 onto the nucleosome for efficient nucleosome remodeling. One consequence of this property of ISW2 is likely its previously observed nucleosome spacing activity.
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Affiliation(s)
- Weiwei Dang
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, 1245 Lincoln Dr., Neckers Bldg., Room 229, Carbondale, IL 62901-4413, USA
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53
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Roopa T, Shivashankar GV. Direct measurement of local chromatin fluidity using optical trap modulation force spectroscopy. Biophys J 2006; 91:4632-7. [PMID: 17012315 PMCID: PMC1779931 DOI: 10.1529/biophysj.106.086827] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromatin assembly is condensed by histone tail-tail interactions and other nuclear proteins into a highly compact structure. Using an optical trap modulation force spectroscopy, we probe the effect of tail interactions on local chromatin fluidity. Chromatin fibers, purified from mammalian cells, are tethered between a microscope coverslip and a glass micropipette. Mechanical unzipping of tail interactions, using the micropipette, lead to the enhancement of local fluidity. This is measured using an intensity-modulated optically trapped bead positioned as a force sensor on the chromatin fiber. Enzymatic digestion of the histone tail interactions of tethered chromatin fiber also leads to a similar increase in fluidity. Our experiments show that an initial increase in the local fluidity precedes chromatin decompaction, suggesting possible mechanisms by which chromatin-remodeling machines access regulatory sites.
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Affiliation(s)
- T Roopa
- Raman Research Institute, Bangalore, India
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54
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Wang X, Hayes JJ. Physical methods used to study core histone tail structures and interactions in solutionThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process. Biochem Cell Biol 2006; 84:578-88. [PMID: 16936830 DOI: 10.1139/o06-076] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The core histone tail domains are key regulatory elements in chromatin. The tails are essential for folding oligonucleosomal arrays into both secondary and tertiary structures, and post-translational modifications within these domains can directly alter DNA accessibility. Unfortunately, there is little understanding of the structures and interactions of the core histone tail domains or how post-translational modifications within the tails may alter these interactions. Here we review NMR, thermal denaturation, cross-linking, and other selected solution methods used to define the general structures and binding behavior of the tail domains in various chromatin environments. All of these methods indicate that the tail domains bind primarily electrostatically to sites within chromatin. The data also indicate that the tails adopt specific structures when bound to DNA and that tail structures and interactions are plastic, depending on the specific chromatin environment. In addition, post-translational modifications, such as acetylation, can directly alter histone tail structures and interactions.
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Affiliation(s)
- Xiaodong Wang
- Department of Biochemistry and Biophysics, Box 712, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester NY, USA
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55
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Bancaud A, Conde e Silva N, Barbi M, Wagner G, Allemand JF, Mozziconacci J, Lavelle C, Croquette V, Victor JM, Prunell A, Viovy JL. Structural plasticity of single chromatin fibers revealed by torsional manipulation. Nat Struct Mol Biol 2006; 13:444-50. [PMID: 16622406 DOI: 10.1038/nsmb1087] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Accepted: 03/14/2006] [Indexed: 11/09/2022]
Abstract
Magnetic tweezers were used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large amount of supercoiling without much change in length. This behavior is quantitatively described by a molecular model of the chromatin three-dimensional architecture. In this model, we assume the existence of a dynamic equilibrium between three conformations of the nucleosome, corresponding to different crossing statuses of the entry/exit DNAs (positive, null or negative, respectively). Torsional strain displaces that equilibrium, leading to an extensive reorganization of the fiber's architecture. The model explains a number of long-standing topological questions regarding DNA in chromatin and may provide the basis to better understand the dynamic binding of chromatin-associated proteins.Note: In the supplementary information initially published online to accompany this article, Supplementary Figure 2 was mistakenly replaced by Supplementary Equation 2. The error has been corrected online.
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56
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Jagannathan I, Cole HA, Hayes JJ. Base excision repair in nucleosome substrates. Chromosome Res 2006; 14:27-37. [PMID: 16506094 DOI: 10.1007/s10577-005-1020-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 11/01/2005] [Indexed: 01/29/2023]
Abstract
Eukaryotic cells must repair DNA lesions within the context of chromatin. Much of our current understanding regarding the activity of enzymes involved in DNA repair processes comes from in-vitro studies utilizing naked DNA as a substrate. Here we review current literature investigating how enzymes involved in base excision repair (BER) contend with nucleosome substrates, and discuss the possibility that some of the activities involved in BER are compatible with the organization of DNA within nucleosomes. In addition, we examine evidence for the role of accessory factors, such as histone modification enzymes, and the role of the histone tail domains in moderating the activities of BER factors on nucleosomal substrates.
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Affiliation(s)
- Indu Jagannathan
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Box 712, NY 14642, USA
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57
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Abstract
Patterns of histone post-translational modifications correlate with distinct chromosomal states that regulate access to DNA, leading to the histone-code hypothesis. However, it is not clear how modification of flexible histone tails leads to changes in nucleosome dynamics and, thus, chromatin structure. The recent discovery that, like the flexible histone tails, the structured globular domain of the nucleosome core particle is also extensively modified adds a new and exciting dimension to the histone-code hypothesis, and calls for the re-examination of current models for the epigenetic regulation of chromatin structure. Here, we review these findings and other recent studies that suggest the structured globular domain of the nucleosome core particle plays a key role regulating chromatin dynamics.
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58
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Sun J, Zhang Q, Schlick T. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation. Proc Natl Acad Sci U S A 2005; 102:8180-5. [PMID: 15919827 PMCID: PMC1140479 DOI: 10.1073/pnas.0408867102] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agreement with hydrodynamic measurements and suggest that the array adopts highly irregular 3D zig-zag conformations at high (physiological) salt concentrations and transitions into the extended "beads-on-a-string" conformation at low salt. Energy analyses indicate that the repulsion among linker DNA leads to this extended form, whereas internucleosome attraction drives the folding at high salt. The balance between these two contributions determines the salt-dependent condensation. Importantly, the internucleosome and linker DNA-nucleosome attractions require histone tails; we find that the H3 tails, in particular, are crucial for stabilizing the moderately folded fiber at physiological monovalent salt.
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Affiliation(s)
- Jian Sun
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
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59
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Perico A, La Penna G, Arcesi L. Electrostatic interactions with histone tails may bend linker DNA in chromatin. Biopolymers 2005; 81:20-8. [PMID: 16167325 DOI: 10.1002/bip.20371] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Is linker DNA bent in the 30-nm chromatin fiber at physiological conditions? We show here that electrostatic interactions between linker DNA and histone tails including salt condensation and release may bend linker DNA, thus affecting the higher order organization of chromatin.
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Affiliation(s)
- Angelo Perico
- Istituto per lo Studio delle Macromolecole (ISMac), Section of Genova, Italy.
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60
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Brower-Toland B, Wacker DA, Fulbright RM, Lis JT, Kraus WL, Wang MD. Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes. J Mol Biol 2004; 346:135-46. [PMID: 15663933 DOI: 10.1016/j.jmb.2004.11.056] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Revised: 11/21/2004] [Accepted: 11/22/2004] [Indexed: 12/22/2022]
Abstract
The distinct contributions of histone tails and their acetylation to nucleosomal stability were examined by mechanical disruption of individual nucleosomes in a single chromatin fiber using an optical trap. Enzymatic removal of H2A/H2B tails primarily decreased the strength of histone-DNA interactions located approximately +/-36bp from the dyad axis of symmetry (off-dyad strong interactions), whereas removal of the H3/H4 tails played a greater role in regulating the total amount of DNA bound. Similarly, nucleosomes composed of histones acetylated to different degrees by the histone acetyltransferase p300 exhibited significant decreases in the off-dyad strong interactions and the total amount of DNA bound. Acetylation of H2A/H2B appears to play a particularly critical role in weakening the off-dyad strong interactions. Collectively, our results suggest that the destabilizing effects of tail acetylation may be due to elimination of specific key interactions in the nucleosome.
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Affiliation(s)
- Brent Brower-Toland
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
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61
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Angelov D, Beylot B, Spassky A. Origin of the heterogeneous distribution of the yield of guanyl radical in UV laser photolyzed DNA. Biophys J 2004; 88:2766-78. [PMID: 15613625 PMCID: PMC1305372 DOI: 10.1529/biophysj.104.049015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oxidative guanine lesions were analyzed, at the nucleotide level, within DNA exposed to nanosecond ultraviolet (266 nm) laser pulses of variable intensity (0.002-0.1 J/cm(2)). Experiments were carried out, at room temperature, in TE buffer (20 mM Tris-HCl, pH 7.5; 1 mM EDTA) containing 35 mM NaCl, on 5'-end radioactively labeled double-stranded and single-stranded oligomer DNA at a size of 33-37 nucleobases. Lesions were analyzed on polyacrylamide gel electrophoresis by taking advantage of the specific removal of 8-oxodG from DNA by the formamidopyrimidine DNA glycosylase (Fpg protein) and of the differential sensitivity of 8-oxodG and oxazolone to piperidine. The quantum yields of lesions at individual sites, determined from the normalized intensities of bands, were plotted against the irradiation energy levels. Simplified model fitting of the experimental data enabled to evaluate the spectroscopic parameters characterizing excitation and photoionization processes. Results show that the distribution of guanine residues, excited to the lowest triplet state or photoionized, is heterogeneous and depends on the primary and secondary DNA structure. These findings are generalized in terms of excitation energy and charge-migration mediated biphotonic ionization. On the basis of the changes in the yield of the guanyl radical resulting from local helical perturbations in the DNA pi-stack, it can be assessed that the distance range of migration is <6-8 bp.
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Affiliation(s)
- Dimitar Angelov
- UMR 8113 French National Center for Scientific Research, Institut Gustave Roussy, 94805 Villejuif, France
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62
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Nicholson JM, Wood CM, Reynolds CD, Brown A, Lambert SJ, Chantalat L, Baldwin JP. Histone Structures: Targets for Modifications by Molecular Assemblies. Ann N Y Acad Sci 2004; 1030:644-55. [PMID: 15659848 DOI: 10.1196/annals.1329.075] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The core histone proteins contain modification sites that are key elements in the regulation of the cell cycle, DNA replication and repair with histone assembly, control of gene expression, and transcriptional elongation. Much work has been done on the various molecular assemblies that remodel nucleosomes, methylate, ubiquitinate, and cause ADP-ribosylation of histones, and acetylate and phosphorylate core histone tails. The core histones are the final targets of the enzymes in the molecular assemblies. What structural changes in the histones are correlated with these modifications? This paper considers the high-resolution structure of the histone octamer and stresses the importance of histone docking sequences in the binding of the two (H2A-H2B) dimers to the (H3-H4)(2) tetramer. There is an extensive acid-base area of interaction between histone octamers in crystals at high salt, which may have implications for nucleosome remodeling. We show that there are regions of high alpha-helix probability in all core histone N-terminal tails in regions where lysine acetylation occurs. There are also consensus sequences spanning up to eight amino acid residues between some histone tail regions. Circular dichroism studies using synchrotron radiation at wavelengths as low as 130 nm are promising for the accurate measurement of changes of histone secondary structure related to function.
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Affiliation(s)
- James M Nicholson
- Biology and Medicine College, Council for the Central Laboratories of the Research Councils Daresbury Laboratory, Warrington, Cheshire WA4 4AD, U.K.
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63
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Abstract
We have carried out an investigation of the electrostatic forces involved in gradual removal of the DNA from the histone proteins in chromatin. Two simple models of DNA-histone core dissociation were considered. Calculations of the electrostatic free energy within the Poisson-Boltzmann theory gave similar results for the both models, which turned out to be in a qualitative agreement with recent optical tweezers stretching experiments measuring the force necessary to unwrap DNA from the histone core. Our analysis shows that the electrostatic interactions between the highly negatively charged polymeric DNA and the positively charged histones play a determining role in stabilizing the nucleosomes at physiological conditions.
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Affiliation(s)
- Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore.
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64
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Sivolob A, Prunell A. Nucleosome conformational flexibility and implications for chromatin dynamics. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2004; 362:1519-1547. [PMID: 15306464 DOI: 10.1098/rsta.2004.1387] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The active role of chromatin in the regulation of gene activity seems to imply a conformational flexibility of the basic chromatin structural unit, the nucleosome. This review is devoted to our recent results pertaining to this subject, using an original approach based on the topology of single particles reconstituted on DNA minicircles, combined with their theoretical simulation. Three types of chromatin particles have been studied so far: a subnucleosome, that is, the (H3-H4)(2) histone tetramer-containing particle, now known as the tetrasome; the nucleosome; and the linker histone H5/H1-bearing nucleosome (the chromatosome). All the particles were found to exist in two to three conformational states, which differ by their topological and mechanical properties. Our approach unveiled the molecular mechanisms of nucleosome conformational dynamics and will help to understand its functional relevance. A most surprising conclusion of the work was perhaps that DNA overall flexibility increases considerably upon particle formation, which might indeed be a requirement of genome function.
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Affiliation(s)
- Andrei Sivolob
- Department of General and Molecular Genetics, Taras Shevchenko National University, 64 Vladimirskaya Street, 01033 Kiev, Ukraine.
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65
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Gautier T, Abbott DW, Molla A, Verdel A, Ausio J, Dimitrov S. Histone variant H2ABbd confers lower stability to the nucleosome. EMBO Rep 2004; 5:715-20. [PMID: 15192699 PMCID: PMC1299093 DOI: 10.1038/sj.embor.7400182] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2003] [Revised: 05/07/2004] [Accepted: 05/10/2004] [Indexed: 11/10/2022] Open
Abstract
The histone H2ABbd is a novel histone variant of H2A with a totally unknown function. We have investigated the behaviour of the H2ABbd nucleosomes. Nucleosomes were reconstituted with recombinant histone H2ABbd and changes in their conformations at different salt concentrations were studied by analytical centrifugation. The data are in agreement with H2ABbd being less tightly bound compared with conventional H2A in the nucleosome. In addition, stable cell lines expressing either green fluorescent protein (GFP)-H2A or GFP-H2ABbd were established and the mobility of both fusions was measured by fluorescence recovery after photobleaching. We show that GFP-H2ABbd exchanges much more rapidly than GFP-H2A within the nucleosome. The reported data are compatible with a lower stability of the variant H2ABbd nucleosome compared with the conventional H2A particle.
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Affiliation(s)
- Thierry Gautier
- Institut Albert Bonniot, INSERM U309, 38706 La Tronche cedex, France
- These authors contributed equally to this work
| | - D Wade Abbott
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
- These authors contributed equally to this work
| | - Annie Molla
- Institut Albert Bonniot, INSERM U309, 38706 La Tronche cedex, France
| | - Andre Verdel
- Institut Albert Bonniot, INSERM U309, 38706 La Tronche cedex, France
| | - Juan Ausio
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
- Tel: +1 250 721 8863; Fax: +1 250 721 8855; E-mail:
| | - Stefan Dimitrov
- Institut Albert Bonniot, INSERM U309, 38706 La Tronche cedex, France
- Tel: +33 4 76 54 94 73; Fax: +33 4 76 54 95 95; E-mail:
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66
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Affiliation(s)
- Katherine L West
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA
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67
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Lu J, Pazin MJ, Ravid K. Properties of ets-1 binding to chromatin and its effect on platelet factor 4 gene expression. Mol Cell Biol 2004; 24:428-41. [PMID: 14673175 PMCID: PMC303331 DOI: 10.1128/mcb.24.1.428-441.2004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ets-1 is important for transcriptional regulation in several hematopoietic lineages, including megakaryocytes. Some transcription factors bind to naked DNA and chromatin with different affinities, while others do not. In the present study we used the megakaryocyte-specific promoters platelet factor 4 (PF4), and glycoprotein IIb (GPIIb) as model systems to explore the properties of Ets-1 binding to chromatin. Chromatin immunoprecipitation assays indicated that Ets-1 binds to proximal regions in the PF4 and GPIIb promoters in vivo. In vitro and in vivo experiments showed that Ets-1 binding to chromatin on lineage-specific promoters does not require lineage-specific factors. Moreover, this binding shows the same order of affinity as the binding to naked DNA and does not require ATP-dependent or Sarkosyl-sensitive factors. The effect of Ets-1 binding on promoter activity was examined using the PF4 promoter as a model. We identified a novel Ets-1 site (at -50), and a novel Sarkosyl-sensitive DNase I-hypersensitive site generated by Ets-1 binding to chromatin, which significantly affect PF4 promoter activity. Taken together, our results suggest a model by which Ets-1 binds to chromatin without the need for lineage-specific accessory factors, and Ets-1 binding induces changes in chromatin and affects transactivation, which are essential for PF4 promoter activation.
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Affiliation(s)
- Jun Lu
- Department of Biochemistry, Cancer Center, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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68
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The role of HMGN proteins in chromatin function. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-7306(03)39006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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69
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Meehan RR, Kao CF, Pennings S. HP1 binding to native chromatin in vitro is determined by the hinge region and not by the chromodomain. EMBO J 2003; 22:3164-74. [PMID: 12805230 PMCID: PMC162158 DOI: 10.1093/emboj/cdg306] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2002] [Revised: 04/29/2003] [Accepted: 04/29/2003] [Indexed: 11/13/2022] Open
Abstract
We have isolated the complete coding sequences for two Xenopus laevis isoforms of heterochromatin protein 1, corresponding to HP1alpha and HP1gamma. The sequence of xHP1alpha shows considerable divergence from its mammalian homologues, whereas xHP1gamma is highly conserved. Functionally, xHP1alpha behaves identically to human HP1alpha. We observe unexpected differences between the two HP1 variants in binding native soluble chromatin, which seem to correlate with their distinct nuclear distributions in vivo. A surprising finding is that the characteristic interaction of HP1 chromodomains with histone H3 at methylated lysine 9 is not detected in preformed chromatin due to its inaccessibility. Instead, we localize a strong chromatin-binding activity to the short hinge region between the chromodomain and the chromoshadow domain of xHP1alpha but not xHP1gamma. This novel chromatin-binding activity has a non-specific DNA-binding component in addition to a linker histone-dependent preference for an altered chromatin structure with a likely heterochromatin organization.
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Affiliation(s)
- Richard R Meehan
- Genes and Development Group, Department of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
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70
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Angelov D, Charra M, Müller CW, Cadet J, Dimitrov S. Solution study of the NF-kappaB p50-DNA complex by UV laser protein-DNA cross-linking. Photochem Photobiol 2003; 77:592-6. [PMID: 12870843 DOI: 10.1562/0031-8655(2003)077<0592:ssotnp>2.0.co;2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In this study, we describe a new approach for studying protein-DNA interactions in solution. The approach is based on mapping the UV laser-induced protein-DNA cross-links between the amino acids of the protein and the DNA bases that are in direct contact. The approach was applied for studying the solution structure of the human necrosis factor (NF)-kappaB p50 homodimer bound to a 37 base pair DNA. Several points of contact identical to those observed in the NF-kappaB-DNA crystal structure were found between the two biomolecules. Evidence is provided for the occurrence of two new contact points, one for each DNA strand. These new points of contact are located symmetrically a base apart from the extremity of the binding sequence.
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Affiliation(s)
- Dimitar Angelov
- Laboratoire de Biologie Moléculaire et Cellulaire de la Différenciation, INSERM Institut Albert Bonniot, Domaine de la Merci, La Tronche Cedex, France
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71
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Siino JS, Yau PM, Imai BS, Gatewood JM, Bradbury EM. Effect of DNA length and H4 acetylation on the thermal stability of reconstituted nucleosome particles. Biochem Biophys Res Commun 2003; 302:885-91. [PMID: 12646255 DOI: 10.1016/s0006-291x(03)00277-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To examine the factors involved with nucleosome stability, we reconstituted nonacetylated particles containing various lengths (192, 162, and 152 base pairs) of DNA onto the Lytechinus variegatus nucleosome positioning sequence in the absence of linker histone. We characterized the particles and examined their thermal stability. DNA of less than chromatosome length (168 base pairs) produces particles with altered denaturation profiles, possibly caused by histone rearrangement in those core-like particles. We also examined the effects of tetra-acetylation of histone H4 on the thermal stability of reconstituted nucleosome particles. Tetra-acetylation of H4 reduces the nucleosome thermal stability by 0.8 degrees C as compared with nonacetylated particles. This difference is close to values published comparing bulk nonacetylated nucleosomes and core particles to ones enriched for core histone acetylation, suggesting that H4 acetylation has a dominant effect on nucleosome particle energetics.
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Affiliation(s)
- Joseph S Siino
- Department of Microbiology, University of California, Davis, California 95616, USA.
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72
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Sivolob A, Lavelle C, Prunell A. Sequence-dependent nucleosome structural and dynamic polymorphism. Potential involvement of histone H2B N-terminal tail proximal domain. J Mol Biol 2003; 326:49-63. [PMID: 12547190 DOI: 10.1016/s0022-2836(02)01372-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Relaxation of nucleosomes on an homologous series (pBR) of ca 350-370 bp DNA minicircles originating from plasmid pBR322 was recently used as a tool to study their structure and dynamics. These nucleosomes thermally fluctuated between three distinct DNA conformations within a histone N-terminal tail-modulated equilibrium: one conformation was canonical, with 1.75 turn wrapping and negatively crossed entering and exiting DNAs; another was also "closed", but with these DNAs positively crossed; and the third was "open", with a lower than 1.5 turn wrapping and uncrossed DNAs. In this work, a new minicircle series (5S) of similar size was used, which contained the 5S nucleosome positioning sequence. Results showed that DNA in pBR nucleosomes was untwisted by approximately 0.2 turn relative to 5S nucleosomes, which DNase I footprinting confirmed in revealing a approximately 1 bp untwisting at each of the two dyad-distal sites where H2B N-terminal tails pass between the two gyres. In contrast, both nucleosomes showed untwistings at the dyad-proximal sites, i.e. on the other gyre, which were also observed in the high-resolution crystal structure. 5S nucleosomes also differ with respect to their dynamics: they hardly accessed the positively crossed conformation, but had an easier access to the negatively crossed conformation. Simulation showed that such reverse effects on the conformational free energies could be simply achieved by slightly altering the trajectories of entering and exiting DNAs. We propose that this is accomplished by H2B tail untwisting at the distal sites through action at a distance ( approximately 20 bp) on H3-tail interactions with the small groove at the nucleosome entry-exit. These results may help to gain a first glimpse into the two perhaps most intriguing features of the high-resolution structure: the alignment of the grooves on the two gyres and the passage of H2B and H3 N-terminal tails between them.
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Affiliation(s)
- Andrei Sivolob
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Denis Diderot Paris 7, et Université P. et M. Curie Paris 6, 2 place Jussieu, 75251 Cédex 05, Paris, France
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73
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Armstrong JA, Papoulas O, Daubresse G, Sperling AS, Lis JT, Scott MP, Tamkun JW. The Drosophila BRM complex facilitates global transcription by RNA polymerase II. EMBO J 2002; 21:5245-54. [PMID: 12356740 PMCID: PMC129039 DOI: 10.1093/emboj/cdf517] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Drosophila brahma (brm) encodes the ATPase subunit of a 2 MDa complex that is related to yeast SWI/SNF and other chromatin-remodeling complexes. BRM was identified as a transcriptional activator of Hox genes required for the specification of body segment identities. To clarify the role of the BRM complex in the transcription of other genes, we examined its distribution on larval salivary gland polytene chromosomes. The BRM complex is associated with nearly all transcriptionally active chromatin in a pattern that is generally non-overlapping with that of Polycomb, a repressor of Hox gene transcription. Reduction of BRM function dramatically reduces the association of RNA polymerase II with salivary gland chromosomes. A few genes, such as induced heat shock loci, are not associated with the BRM complex; transcription of these genes is not compromised by loss of BRM function. The distribution of the BRM complex thus correlates with a dependence on BRM for gene activity. These data suggest that the chromatin remodeling activity of the BRM complex plays a general role in facilitating transcription by RNA polymerase II.
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Affiliation(s)
| | | | - Gary Daubresse
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064,
Departments of Developmental Biology and Genetics, Howard Hughes Medical Institute, Beckman Center, Stanford University School of Medicine, Stanford, CA 94305 and Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA Corresponding author e-mail:
| | | | - John T. Lis
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064,
Departments of Developmental Biology and Genetics, Howard Hughes Medical Institute, Beckman Center, Stanford University School of Medicine, Stanford, CA 94305 and Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA Corresponding author e-mail:
| | - Matthew P. Scott
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064,
Departments of Developmental Biology and Genetics, Howard Hughes Medical Institute, Beckman Center, Stanford University School of Medicine, Stanford, CA 94305 and Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA Corresponding author e-mail:
| | - John W. Tamkun
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064,
Departments of Developmental Biology and Genetics, Howard Hughes Medical Institute, Beckman Center, Stanford University School of Medicine, Stanford, CA 94305 and Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA Corresponding author e-mail:
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74
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Shen CH, Leblanc BP, Neal C, Akhavan R, Clark DJ. Targeted histone acetylation at the yeast CUP1 promoter requires the transcriptional activator, the TATA boxes, and the putative histone acetylase encoded by SPT10. Mol Cell Biol 2002; 22:6406-16. [PMID: 12192040 PMCID: PMC135642 DOI: 10.1128/mcb.22.18.6406-6416.2002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The relationship between chromatin remodeling and histone acetylation at the yeast CUP1 gene was addressed. CUP1 encodes a metallothionein required for cell growth at high copper concentrations. Induction of CUP1 with copper resulted in targeted acetylation of both H3 and H4 at the CUP1 promoter. Nucleosomes containing upstream activating sequences and sequences farther upstream were the targets for H3 acetylation. Targeted acetylation of H3 and H4 required the transcriptional activator (Ace1p) and the TATA boxes, suggesting that targeted acetylation occurs when TATA-binding protein binds to the TATA box or at a later stage in initiation. We have shown previously that induction results in nucleosome repositioning over the entire CUP1 gene, which requires Ace1p but not the TATA boxes. Therefore, the movement of nucleosomes occurring on CUP1 induction is independent of targeted acetylation. Targeted acetylation of both H3 and H4 also required the product of the SPT10 gene, which encodes a putative histone acetylase implicated in regulation at core promoters. Disruption of SPT10 was lethal at high copper concentrations and correlated with slower induction and reduced maximum levels of CUP1 mRNA. These observations constitute evidence for a novel mechanism of chromatin activation at CUP1, with a major role for the TATA box.
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Affiliation(s)
- Chang-Hui Shen
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-8028, USA
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75
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Hansen JC. Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2002; 31:361-92. [PMID: 11988475 DOI: 10.1146/annurev.biophys.31.101101.140858] [Citation(s) in RCA: 384] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromatin fibers are dynamic macromolecular assemblages that are intimately involved in nuclear function. This review focuses on recent advances centered on the molecular mechanisms and determinants of chromatin fiber dynamics in solution. Major points of emphasis are the functions of the core histone tail domains, linker histones, and a new class of proteins that assemble supramolecular chromatin structures. The discussion of important structural issues is set against a background of possible functional significance.
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Affiliation(s)
- Jeffrey C Hansen
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, Mail Code 7760, San Antonio, TX 78229-3900, USA.
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76
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Nishioka K, Rice JC, Sarma K, Erdjument-Bromage H, Werner J, Wang Y, Chuikov S, Valenzuela P, Tempst P, Steward R, Lis JT, Allis CD, Reinberg D. PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol Cell 2002; 9:1201-13. [PMID: 12086618 DOI: 10.1016/s1097-2765(02)00548-8] [Citation(s) in RCA: 436] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have purified a human histone H4 lysine 20 methyltransferase and cloned the encoding gene, PR/SET07. A mutation in Drosophila pr-set7 is lethal: second instar larval death coincides with the loss of H4 lysine 20 methylation, indicating a fundamental role for PR-Set7 in development. Transcriptionally competent regions lack H4 lysine 20 methylation, but the modification coincided with condensed chromosomal regions on polytene chromosomes, including chromocenter and euchromatic arms. The Drosophila male X chromosome, which is hyperacetylated at H4 lysine 16, has significantly decreased levels of lysine 20 methylation compared to that of females. In vitro, methylation of lysine 20 and acetylation of lysine 16 on the H4 tail are competitive. Taken together, these results support the hypothesis that methylation of H4 lysine 20 maintains silent chromatin, in part, by precluding neighboring acetylation on the H4 tail.
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Affiliation(s)
- Kenichi Nishioka
- Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Department of Biochemistry, UMDNJ-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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77
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Nishioka K, Chuikov S, Sarma K, Erdjument-Bromage H, Allis CD, Tempst P, Reinberg D. Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation. Genes Dev 2002; 16:479-89. [PMID: 11850410 PMCID: PMC155346 DOI: 10.1101/gad.967202] [Citation(s) in RCA: 438] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A novel histone methyltransferase, termed Set9, was isolated from human cells. Set9 contains a SET domain, but lacks the pre- and post-SET domains. Set9 methylates specifically lysine 4 (K4) of histone H3 (H3-K4) and potentiates transcription activation. The histone H3 tail interacts specifically with the histone deacetylase NuRD complex. Methylation of histone H3-K4 by Set9 precludes the association of NuRD with the H3 tail. Moreover, methylation of H3-K4 impairs Suv39h1-mediated methylation at K9 of H3 (H3-K9). The interplay between the Set9 and Suv39h1 histone methyltransferases is specific, as the methylation of H3-K9 by the histone methyltransferase G9a was not affected by Set9 methylation of H3-K4. Our studies suggest that Set9-mediated methylation of H3-K4 functions in transcription activation by competing with histone deacetylases and by precluding H3-K9 methylation by Suv39h1. Our results suggest that the methylation of histone tails can have distinct effects on transcription, depending on its chromosomal location, the combination of posttranslational modifications, and the enzyme (or protein complex) involved in the particular modification.
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Affiliation(s)
- Kenichi Nishioka
- Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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78
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Malik HS, Vermaak D, Henikoff S. Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone. Proc Natl Acad Sci U S A 2002; 99:1449-54. [PMID: 11805302 PMCID: PMC122211 DOI: 10.1073/pnas.032664299] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2001] [Accepted: 12/12/2001] [Indexed: 11/18/2022] Open
Abstract
All eukaryotes contain centromere-specific histone H3 variants (CenH3s), which replace H3 in centromeric chromatin. We have previously documented the adaptive evolution of the Drosophila CenH3 (Cid) in comparisons of Drosophila melanogaster and Drosophila simulans, a divergence of approximately 2.5 million years. We have proposed that rapidly changing centromeric DNA may be driving CenH3's altered DNA-binding specificity. Here, we compare Cid sequences from a phylogenetically broader group of Drosophila species to suggest that Cid has been evolving adaptively for at least 25 million years. Our analysis also reveals conserved blocks not only in the histone-fold domain but also in the N-terminal tail. In several lineages, the N-terminal tail of Cid is characterized by subgroup-specific oligopeptide expansions. These expansions resemble minor groove DNA binding motifs found in various histone tails. Remarkably, similar oligopeptides are also found in N-terminal tails of human and mouse CenH3 (Cenp-A). The recurrent evolution of these motifs in CenH3 suggests a packaging function for the N-terminal tail, which results in a unique chromatin organization at the primary constriction, the cytological marker of centromeres.
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Affiliation(s)
- Harmit S Malik
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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79
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Hamiche A, Kang JG, Dennis C, Xiao H, Wu C. Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF. Proc Natl Acad Sci U S A 2001; 98:14316-21. [PMID: 11724935 PMCID: PMC64679 DOI: 10.1073/pnas.251421398] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nucleosome Remodeling Factor (NURF) is an ATP-dependent nucleosome remodeling complex that alters chromatin structure by catalyzing nucleosome sliding, thereby exposing DNA sequences previously associated with nucleosomes. We systematically studied how the unstructured N-terminal residues of core histones (the N-terminal histone tails) influence nucleosome sliding. We used bacterially expressed Drosophila histones to reconstitute hybrid nucleosomes lacking one or more histone N-terminal tails. Unexpectedly, we found that removal of the N-terminal tail of histone H2B promoted uncatalyzed nucleosome sliding during native gel electrophoresis. Uncatalyzed nucleosome mobility was enhanced by additional removal of other histone tails but was not affected by hyperacetylation of core histones by p300. In addition, we found that the N-terminal tail of the histone H4 is specifically required for ATP-dependent catalysis of nucleosome sliding by NURF. Alanine scanning mutagenesis demonstrated that H4 residues 16-KRHR-19 are critical for the induction of nucleosome mobility, revealing a histone tail motif that regulates NURF activity. An exchange of histone tails between H4 and H3 impaired NURF-induced sliding of the mutant nucleosome, indicating that the location of the KRHR motif in relation to global nucleosome structure is functionally important. Our results provide functions for the N-terminal histone tails in regulating the mobility of nucleosomes.
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Affiliation(s)
- A Hamiche
- Laboratory of Molecular Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA
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80
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Loyola A, LeRoy G, Wang YH, Reinberg D. Reconstitution of recombinant chromatin establishes a requirement for histone-tail modifications during chromatin assembly and transcription. Genes Dev 2001; 15:2837-51. [PMID: 11691835 PMCID: PMC312801 DOI: 10.1101/gad.937401] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The human ISWI-containing factor RSF (remodeling and spacing factor) was found to mediate nucleosome deposition and, in the presence of ATP, generate regularly spaced nucleosome arrays. Using this system, recombinant chromatin was reconstituted with bacterially produced histones. Acetylation of the histone tails was found to play an important role in establishing regularly spaced nucleosome arrays. Recombinant chromatin lacking histone acetylation was impaired in directing transcription. Histone-tail modifications were found to regulate transcription from the recombinant chromatin. Acetylation of the histone tails by p300 was found to increase transcription. Methylation of the histone H3 tail by Suv39H1 was found to repress transcription in an HP1-dependent manner. The effects of histone-tail modifications were observed in nuclear extracts. A highly reconstituted RNA polymerase II transcription system was refractory to the effect imposed by acetylation and methylation.
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Affiliation(s)
- A Loyola
- Howard Hughes Medical Institute, Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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