DOCSLIB.ORG

Review What Determines the Folding of the Chromatin Fiber?

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Review What Determines the Folding of the Chromatin Fiber? Proc. Natl. Acad. Sci. USA Vol. 93, pp. 10548-10555, October 1996 Review What determines the folding of the chromatin fiber? Kensal van Holde*t and Jordanka Zlatanova4 *Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305; and PInstitute of Genetics, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria ABSTRACT In this review, we attempt to summarize, in a DOES THE LINKER DNA BEND? critical manner, what is currently known about the processes of condensation and decondensation of chromatin fibers. We The solenoid model appeared to gain substantial support from begin with a critical analysis of the possible mechanisms for the studies of Yao et al. (6), which provided evidence that the condensation, considering both old and new evidence as to linker DNA in dinucleosomes did in fact contract or fold in whether the linker DNA between nucleosomes bends or re- some fashion as the salt concentration was raised from 0 to 20 mains straight in the condensed structure. Concluding that mM. The picture (and in particular, the putative role of linker the preponderance of evidence is for straight linkers, we ask histones) was complicated by a subsequent study (7), which what other fundamental process might allow condensation, showed that the same changes could be observed with dinu- and argue that there is evidence for linker histone-induced cleosomes from which linker histones had been removed. Yao contraction of the internucleosome angle, as salt concentra- et al. (6, 7) used two techniques to provide evidence for linker tion is raised toward physiological levels. We also ask how contraction: (i) direct visualization of fixed dinucleosomes by certain specific regions of chromatin can become decon- transmission electron microscopy (EM) and (ii) measurement densed, even at physiological salt concentration, to allow of the translational diffusion coefficient of dinucleosomes by transcription. We consider linker histone depletion and acet- dynamic light scattering. The latter measurements showed an ylation of the core histone tails, as possible mechanisms. On increase in the translational diffusion coefficient (D) with the basis ofrecent evidence, we suggest a unified model linking increasing salt concentration (Fig. IA, dashed line). This is targeted acetylation of specific genomic regions to linker most easily explained by a compaction of the particle, for such histone depletion, with unfolding of the condensed fiber as a compaction should produce a decrease in the frictional coef- ficient, f, and hence an increase in D, since D is inversely consequence. proportional tof. The results from hydrodynamic experiments were supported by EM studies, in which dinucleosomes in 20 The belated discovery by molecular biologists that chromatin mM Na+ or 2 mM Mg2+ were observed to be more compact structure might be of major importance in regulating DNA than those in 2 mM Na+. However, in a recent publication, transcription and replication has sparked a renewed interest in Bednar et al. (9) have repeated both experiments with quite some old questions: How does a chain of nucleosomes fold to different results. As Fig. 1A shows, they observe the diffusion produce the condensed fibers observed in the eukaryotic coefficient to be independent of salt concentration over the nucleus? What makes it unfold to allow transcription or same range. In addition, Bednar et al. (9) find by cryo-EM that replication? The latter question has been especially perplexing. the center-to-center distance between nucleosomes in dimers The earliest electron microscopy studies of isolated chromatin does not decrease as salt concentration is raised. Interestingly, fibers showed that at low salt concentrations an extended string they do, like Yao et al. (6, 7), find a contraction at higher salt of nucleosomes could be observed, whereas raising the ionic when the dinucleosome is studied by conventional transmis- strength to levels close to physiological led to the formation of sion EM. This indicates that either transmission EM or an irregular, highly condensed fiber about 30 nm in diameter. cryo-EM is giving an artifactual result. Speculations concerning the mechanisms of such folding and Thus, we have, at the focus of an important issue, a clear the structure of the "30 nm fiber" were rife in the early contradiction: Does the linker DNA contract with increasing postnucleosome years (for review, see refs. 1 and 2, and salt or does it not? On the resolution of this question depends references therein). Although many models for the condensed how we may visualize the condensed chromatin fiber, and what fiber structure were proposed, and hotly debated, the "sole- role the linker histones may play in that condensation. To noid" model of Finch and Klug (3) or variants thereof (4, 5) approach this issue, we have first asked: Are there other data gained acceptance by most researchers. In such structures, in the literature that might support one view or the other? nucleosomes adjacent on the DNA strand are packed cheek- In fact, there exists a wealth of relevant evidence, both in the by-jowl into a regular helix. earlier literature and from more contemporary work. Con- A corollary of the solenoid model is that the linker DNA sider, for example, the measurement of diffusion coefficients between adjacent nucleosomes must, at least at physiological of dinucleosomes by dynamic light scattering. In an earlier salt concentration, be bent or curled in some fashion to allow study, Marion et al. (8) find no change in D in up to 80 mM salt; adjacent nucleosomes to contact one another. This salt- their data are in almost exact quantitative agreement with dependent bending or coiling was postulated to be facilitated those of Bednar et al. (9) (Fig. 1A) and are inconsistent with by the interaction of linker DNA with "linker histones" (Hi, those of Yao et al. (6). H5, and the like), for these proteins have been demonstrated There is, in addition, extensive evidence from sedimentation to be essential for proper chromatin fiber condensation (see studies of dinucleosomes. If a dinucleosome contracts with below). In this review, we will try to critically evaluate the data increasing salt concentration, the sedimentation coefficient s on (i) linker DNA bending, (ii) nucleosome-nucleosome in- should increase, for like D, s is inversely proportional to the teractions, (iii) the role of linker histones, and (iv) the role of the core histone tails and their acetylation in the folding of the Abbreviations: EM, electron microscope/microscopy; SFM, scanning chromatin fiber. In addition, we present some speculations force microscope. concerning the unfolding of the fiber in transcription-related tTo whom reprint requests should be addressed. e-mail: vanholdk@ processes. bcc.orst.edu. 10548 Downloaded by guest on October 1, 2021 Review: van Holde and Zlatanova Proc. Natl. Acad. Sci. USA 93 (1996) 10549 A. A. I*- 21.1 nm- 2.4 center-to-conte (.t..::: distance ( \ --------- 2.3 i : t j < t -- J ^ 5.5 nm _1- linker DNA 2.2 - .1.. , U-' 2.1 [ U1 center-to-center o- X distance linker blNAj. .. 2.0 [ : -- :. 5.5 nm 23.6 nm \ J}. 1.9 F 1.8I'L.j B. 0 10 20 80 NaCl concentration (mM) B. 25 Predicted for compact dimers 20 _ _ _ _ _ __ _ 0 ...: . 4.4 15 omMom ,,.9j 11 1*Predicted for extended dimers .. 10 V)d) FIG. 2. Models of dinucleosomes and trinucleosomes. (A) Dinu- cleosome. The relationship between center-to-center distance and 5 linker length depends slightly on relative orientation of nucleosomes. Two extremes are shown for chicken erythrocyte dinucleosomes. (B) . Trinucleosome. The distance R13 depends on the angle between DNA duplexes entering and exiting nucleosome 2. 0 20 40 60 80 100 NaCl concentration (mM) each other) leads to a prediction of s2 = 19S (Fig. 1B, broken line). The difference is clearly far greater than can be ac- FIG. 1. Hydrodynamic studies of dinucleosomes as a function of counted for by experimental error. salt concentration. (A) Diffusion coefficient measurements from As a test for the credibility of the experimentally measured quasi-elastic light scattering: l, data of Marion et al. (8); *, data of values for D and s, we may ask if the combination of the best Yao et al. *, data of Bednar et al. Sedimentation (6); (9). (B) estimates forD (2.25 x 10-7 cm2/sec) and s (15.4 x 10-13 sec) coefficient measurements: *, data of Wittig and Wittig (10); *, data a molecular for an average dinucleo- of Stratling (11); O, data of Butler and Thomas (12). gives reasonable weight some. It is realized of course, that individual dinucleosomes frictional coefficient. Published results from a number of may vary in linker length, degree of external DNA trimming, laboratories are shown in Fig. 1B; all lead to the same and content of linker histones. Calculation of the molecular conclusion: there is no significant change in the sedimentation weight of a typical dinucleosome, based on reasonable struc- coefficient of dinucleosomes over the entire salt concentration tural parameters (total DNA length plus two histone octamers range from 0 to 100 mM. All data points lie close to an average plus two linker histones) gives a value ofM = 5.13 x 105 g/mol. value of 15.4S. We can make a rough estimate of the change This is in almost exact agreement with that calculated from s D in s to be expected from contraction of the linker by using the and from the Svedberg equation Kirkwood (13) formalism as adopted by Bloomfield et al. (14). RTS This expresses s, the sedimentation coefficient for an n-mer, M = 5.10 g/mol [2] in terms of si, the sedimentation coefficient of the monomer, =D(l1-p) the Stokes' radius of the monomer (r), and the set of distances when we have used the value given by Wittig and Wittig (10) (Rij) between units i and j in the n-mer, for the partial specific volume, P.
Load more

Recommended publications
  • H2A Ubiquitylated Mononucleosomes Next-Generation Substrates for Deubiquitylation Enzyme (DUB) Assays
    H2A Ubiquitylated Mononucleosomes Next-Generation Substrates for Deubiquitylation Enzyme (DUB) Assays Next-Generation DUB Assay Substrates are here. Get results that matter. • Enabling access to DUB targets that require nucleosome substrates in vitro • Proper substrates for DUB inhibitor development • Unmatched quality control for results you can trust Histone monoubiquitylation (ub1) acts as a critical signaling center that regulates cascades of downstream epigenetic enzymes to modify gene transcription. The physiological substrate for chromatin-targeting DUBs is the nucleosome (Nuc), the basic repeating unit of chromatin (comprised of histone proteins wrapped by DNA). Current high-throughput screening (HTS) DUB assays use unnatural modified or diubiquitin conjugates as substrates, which poorly mimic endogenous targets in vivo. In collaboration with Boston Biochem, EpiCypher is delivering ubiquitylated nucleosome substrates for drug screening and chromatin biology research. FIGURE 1 Ub Ub Schematic representation of mononucleosoms assembled from recombinant human histones Ub expressed in E. coli (two each of histones H2A, H2B, H3 and H4). H2A H2A Approximately 50% of the nucleosomes are monoubiquitylated on histone H2A lysine 118, while the other 50% are monoubiquitylated on both histone H2A lysine 118 and histone H2A lysine 119 (multi-mono- ubiquitylated). Next Generation Deubiquitylation Enzyme (DUB) Assay Substrates EpiCypher has developed recombinant mononucleosomes carrying monoubiquitylation on H2A. These ubiquitylated nucleosomes are generated enzymatically using the RING1B/BMI1 ubiquitin ligase complex. The resulting product is highly pure (>95% of nucleosomes are ubiquitylated) and consists of nucleosomes monoubiquitylated at H2A lysine 118/119 (Figure 1; the physiological target of RING1B/BMI1 in vivo). FIGURE 2 Deubiquitylation Assay Data: Mononucleosomes H2A Ubiquityl, Recombinant Human, Biotinylated (1 μg) were employed in a deubiquitylation (DUB) assay using no enzyme (Lane 1), USP5 (Lane 2) or USP16 (Lane 3) and run on an SDS PAGE gel.
    [Show full text]
  • The Nature of Genomes Viral Genomes Prokaryotic Genome
    The nature of genomes • Genomics: study of structure and function of genomes • Genome size – variable, by orders of magnitude – number of genes roughly proportional to genome size • Plasmids – symbiotic DNA molecules, not essential – mostly circular in prokaryotes • Organellar DNA – chloroplast, mitochondrion – derived by endosymbiosis from bacterial ancestors Chapter 2: Genes and genomes © 2002 by W. H. Freeman and Company Chapter 2: Genes and genomes © 2002 by W. H. Freeman and Company Viral genomes • Nonliving particle In prokaryotes, viruses are – nucleic acid sometimes referred to as – protein bacteriophages. • DNA or RNA – single-stranded or double-stranded – linear or circular • Compact genomes with little spacer DNA Chapter 2: Genes and genomes © 2002 by W. H. Freeman and Company Chapter 2: Genes and genomes © 2002 by W. H. Freeman and Company Prokaryotic genome • Usually circular double helix – occupies nucleoid region of cell – attached to plasma membrane • Genes are close together with little intergenic spacer • Operon – tandem cluster of coordinately regulated genes – transcribed as single mRNA • Introns very rare Chapter 2: Genes and genomes © 2002 by W. H. Freeman and Company Chapter 2: Genes and genomes © 2002 by W. H. Freeman and Company 1 Eukaryotic nuclear genomes • Each species has characteristic chromosome number • Genes are segments of nuclear chromosomes • Ploidy refers to number of complete sets of chromosomes –haploid (1n): one complete set of genes – diploid (2n) – polyploid (≥3n) • In diploids, chromosomes come in homologous pairs (homologs) In humans, somatic cells have – structurally similar 2n = 46 chromosomes. – same sequence of genes – may contain different alleles Chapter 2: Genes and genomes © 2002 by W. H.
    [Show full text]
  • Visualization of Chromatin Folding Patterns in Chicken Erythrocytes by Atomic Force Microscopy (AFM)
    Cell Research (1997), 7, 143-150 Visualization of chromatin folding patterns in chicken erythrocytes by atomic force microscopy (AFM) 1 QIAN RUO LAN ZHENG XIA LIU, MEI YUN ZHOU, HEN YUE XIE, CHU JIANG, ZHI JIANG YAN Shanghai Institute of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China LI MIN QIAN, YI ZHANG, JUN HU Shanghai Institute of Nuclear Research, Chinese Academy of Sciences, Shanghai 201800, China ABSTRACT The organization of the higher order structure of chro- matin in chicken erythrocytes has been examined with tapping-mode scanning force microscopy under conditions close to their native environment. Reproducible high- resolution AFM images of chromatin compaction at seve- ral levels can be demonstrated. An extended beads-on-a- string (width of ～ 15-20nm, height of ～ 2-3nm for each individual nucleosome) can be consistently observed. Fur- thermore, superbeads (width of ～ 40nm, height of ～ 7nm) are demonstrated. Visualization of the solenoid conforma- tion at the level of 30nm chromatin fiber is attained either by using AFM or by using electron microscopy. In addi- tion, tightly coiled chromatin fibers (～ 50-60nm and ～ 90- ll0nm) can be revealed. Our data suggest that the chro- matin in the interphase nucleus of chicken erythrocyte rep- resents a high-order conformation and AFM provides use- ful high-resolution structural information concerning the folding pattern of interphase chromatin fibers. Key words: The chromatin folding pattern, chicken erythrocyte, atomic force microscopy. 1. To whom correspondence should be addressed: Shanghai Institute of Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China. 143 The chromatin folding patterns in chicken erythrocytes by AFM INTRODUCTION Owing to the tremendous packing density and folding complexity in mitotic chro- mosomes, analysis of chromosome architecture has recently focused on interphase chromatin structure.
    [Show full text]
  • FACT Is Recruited to the +1 Nucleosome of Transcribed Genes and Spreads in a Chd1-Dependent Manner
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.20.259960; this version posted August 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner Célia Jeronimo1, Andrew Angel2, Christian Poitras1, Pierre Collin1, Jane Mellor2 and François Robert1,3,4* 1 Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada. 2Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK. 3 Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard- Montpetit, Montréal, QC H3T 1J4, Canada. 4 Lead Contact *Correspondence: [email protected] The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models for how FACT finds its way to transcriptionally active chromatin include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails and binding partially disassembled nucleosomes. Here, we systematically tested these and other scenarios in Saccharomyces cerevisiae and found that FACT binds transcribed chromatin, not RNAPII. Through a combination of experimental and mathematical modeling evidence, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1.
    [Show full text]
  • Watanabe S, Resch M, Lilyestrom W, Clark N
    NIH Public Access Author Manuscript Biochim Biophys Acta. Author manuscript; available in PMC 2010 November 1. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Biochim Biophys Acta. 2010 ; 1799(5-6): 480±486. doi:10.1016/j.bbagrm.2010.01.009. Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Shinya Watanabe1,*, Michael Resch2,*, Wayne Lilyestrom2, Nicholas Clark2, Jeffrey C. Hansen2, Craig Peterson1, and Karolin Luger2,3 1 Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St.; Worcester, Massachusetts 01605 2 Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870 3 Howard Hughes Medical Institute Abstract The posttranslational modification of histones is a key mechanism for the modulation of DNA accessibility. Acetylated lysine 56 in histone H3 is associated with nucleosome assembly during replication and DNA repair, and is thus likely to predominate in regions of chromatin containing nucleosome free regions. Here we show by x-ray crystallography that mutation of H3 lysine 56 to glutamine (to mimic acetylation) or glutamate (to cause a charge reversal) has no detectable effects on the structure of the nucleosome. At the level of higher order chromatin structure, the K to Q substitution has no effect on the folding of model nucleosomal arrays in cis, regardless of the degree of nucleosome density. In contrast, defects in array-array interactions in trans (‘oligomerization’) are selectively observed for mutant H3 lysine 56 arrays that contain nucleosome free regions. Our data suggests that H3K56 acetylation is one of the molecular mechanisms employed to keep chromatin with nucleosome free regions accessible to the DNA replication and repair machinery.
    [Show full text]
  • DNA Condensation and Packaging
    DNA condensation and packaging October 13, 2009 Professor Wilma K. Olson Viral DNA - chain molecules in confined spaces Viruses come in all shapes and sizes Clockwise: Human immuno deficiency virus (HIV); Aeromonas virus 31, Influenza virus, Orf virus, Herpes simplex virus (HSV), Small pox virus Image from U Wisconsin Microbial World website: http://bioinfo.bact.wisc.edu DNA packaging pathway of T3 and T7 bacteriophages • In vivo pathway - solid arrows Fang et al. (2008) “Visualization of bacteriophage T3 capsids with DNA incompletely packaged in vivo.” J. Mol. Biol. 384, 1384-1399 Cryo EM images of T3 capsids with 10.6 kbp packaged DNA • Labels mark particles representative of different types of capsids • Arrows point to tails on capsids Fang et al. (2008) “Visualization of bacteriophage T3 capsids with DNA incompletely packaged in vivo.”” J. Mol. Biol. 384, 1384-1399 Cryo EM images of representative particles • (b) 10.6 kbp DNA • (c) 22 kbp DNA • (d) bacteriophage T3 Fang et al. (2008) “Visualization of bacteriophage T3 capsids with DNA incompletely packaged in vivo.” J. Mol. Biol. 384, 1384-1399 3D icosohedral reconstructions of cryo-EM-imaged particles Threefold surface views and central cross sections • (b) 10.6 kbp DNA • (c) 22 kbp DNA • (d) bacteriophage T3 Fang et al. (2008) “Visualization of bacteriophage T3 capsids with DNA incompletely packaged in vivo.” J. Mol. Biol. 384, 1384-1399 Top-down views of λ phage DNA toroids captured in cryo-EM micrographs Note the circumferential winding of DNA found in collapsed toroidal particles produced in the presence of multi-valent cations. Hud & Vilfan (2005) “Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size.” Ann.
    [Show full text]
  • The Origin of the Eukaryotic Cell Based on Conservation of Existing
    The Origin of the Eukaryotic Albert D. G. de Roos The Beagle Armada Cell Based on Conservation Bioinformatics Division of Existing Interfaces Einsteinstraat 67 3316GG Dordrecht, The Netherlands [email protected] Abstract Current theories about the origin of the eukaryotic Keywords cell all assume that during evolution a prokaryotic cell acquired a Evolution, nucleus, eukaryotes, self-assembly, cellular membranes nucleus. Here, it is shown that a scenario in which the nucleus acquired a plasma membrane is inherently less complex because existing interfaces remain intact during evolution. Using this scenario, the evolution to the first eukaryotic cell can be modeled in three steps, based on the self-assembly of cellular membranes by lipid-protein interactions. First, the inclusion of chromosomes in a nuclear membrane is mediated by interactions between laminar proteins and lipid vesicles. Second, the formation of a primitive endoplasmic reticulum, or exomembrane, is induced by the expression of intrinsic membrane proteins. Third, a plasma membrane is formed by fusion of exomembrane vesicles on the cytoskeletal protein scaffold. All three self-assembly processes occur both in vivo and in vitro. This new model provides a gradual Darwinistic evolutionary model of the origins of the eukaryotic cell and suggests an inherent ability of an ancestral, primitive genome to induce its own inclusion in a membrane. 1 Introduction The origin of eukaryotes is one of the major challenges in evolutionary cell biology. No inter- mediates between prokaryotes and eukaryotes have been found, and the steps leading to eukaryotic endomembranes and endoskeleton are poorly understood. There are basically two competing classes of hypotheses: the endosymbiotic and the autogenic.
    [Show full text]
  • Investigating the Epigenetic Mechanisms of Trophoblast Giant Cells
    Biology ︱ Assistant Professor Koji Hayakawa NUCLEOSOME STRUCTURE OF TROPHOBLAST GIANT CELL (TGC) Diploid TSC Polyploid TGC H2A H2B H2AX/ Investigating the H2AZ epigenetic mechanisms Entry into DNA Endocycle H3 H4 H3.3 of trophoblast giant cells TGCs possess a loose chromatin structure owing to alterations in the histone composition of the nucleosomes, which involves the replacement of canonical histones with histone variants such as H2AX, H2AZ, and H3.3 during differentiation. Trophoblast giant cells (TGCs) ucleosome is a large molecule in the placenta of rodents, are a unique days, and that certain histone variants Many polyploid cells identified in plants are found in the placental in the cell which is primarily cell type that replicate their DNA until were associated with differentiated walls of rodents and play a Nmade up of DNA and proteins. the cell contains thousands of copies, cells. Overall, there was much less and animals appear to have a secretory role in maintaining pregnancy. The major protein in nucleosome is unlike most cells which normally contain variation in TGCs compared to the In contrast to most cell types called a histone, around which DNA two sets of chromosomes (diploid cells). undifferentiated, diploid cells. They or nutritive function. which contain two copies of wraps. These proteins are classified into The reasons for this condition are not found the histone profile to be very from undifferentiated cells showed distinct concentrations of salt buffer to disrupt each chromosome (diploid), canonical histones and non-canonical clear. However, it has been suggested similar in differentiated TSCs at day six bands when digested, demonstrating that DNA-protein bonds.
    [Show full text]
  • The Physics of Chromatin
    The physics of chromatin Helmut Schiessel Max-Planck-Institut f¨ur Polymerforschung, Theory Group, P.O.Box 3148, D-55021 Mainz, Germany Abstract. Recent progress has been made in the understanding of the physical properties of chromatin – the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of the hierarchy of DNA folding into the chromatin complex: (i) the nucleosome, the chromatin repeating unit consisting of a globular aggregate of eight histone proteins with the DNA wrapped around: its overcharging, the DNA unwrapping transition, the ”sliding” of the octamer along the DNA. (ii) The 30nm chromatin fiber, the necklace- like structure of nucleosomes connected via linker DNA: its geometry, its mechanical properties under stretching and its response to changing ionic conditions. I will stress that chromatin combines two seemingly contradictory features: (1) high compaction of DNA within the nuclear envelope and at the same time (2) accessibility to genes, promoter regions and gene regulatory sequences. Contents 1 Introduction 3 2 Single nucleosome 8 2.1 Experimentalfactsonthecoreparticle . 8 2.2 Polyelectrolyte–charged sphere complexes as model systems for the nucleosome 11 2.2.1 Single-sphere complex (highly charged case) . 12 2.2.2 Multi-sphere complex (highly charged case) . 14 2.2.3 Weaklychargedcase ......................... 16 2.2.4 Physiological conditions . 20 arXiv:cond-mat/0303455v1 [cond-mat.soft] 21 Mar 2003 2.3 Unwrappingtransition............................ 23 2.3.1 Instabilities of the nucleosome core particle at low and at high ionic strength 23 2.3.2 The rosette state at high ionic strength .
    [Show full text]
  • Archaea and the Origin of Eukaryotes
    REVIEWS Archaea and the origin of eukaryotes Laura Eme, Anja Spang, Jonathan Lombard, Courtney W. Stairs and Thijs J. G. Ettema Abstract | Woese and Fox’s 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor. Sister groups Two descendants that split The pioneering work by Carl Woese and colleagues In this Review, we discuss how culture- independent from the same node; the revealed that all cellular life could be divided into three genomics has transformed our understanding of descendants are each other’s major evolutionary lines (also called domains): the archaeal diversity and how this has influenced our closest relative.
    [Show full text]
  • Transcription Regulation in Eukaryotes HFSP Workshop Reports
    Transcription Regulation in Eukaryotes HFSP Workshop Reports Senior editor: Jennifer Altman Assistant editor: Chris Coath I. Coincidence Detection in the Nervous System, eds A. Konnerth, R. Y. Tsien, K. Mikoshiba and J. Altman (1996) II. Vision and Movement Mechanisms in the Cerebral Cortex, eds R. Caminiti, K.-P. Hoffmann, F. Laquaniti and J. Altman (1996) III. Genetic Control of Heart Development, eds R. P. Harvey, E. N. Olson, R. A. Schulz and J. S. Altman (1997) IV. Central Synapses: Quantal Mechanisms and Plasticity, eds D. S. Faber, H. Korn, S. J. Redman, S. M. Thompson and J. S. Altman (1998) V. Brain and Mind: Evolutionary Perspectives, eds M. S. Gazzaniga and J. S. Altman (1998) VI. Cell Surface Proteoglycans in Signalling and Development, eds A. Lander, H. Nakato, S. B. Selleck, J. E. Turnbull and C. Coath (1999) VII. Transcription Regulation in Eukaryotes, eds P. Chambon, T. Fukasawa, R. Kornberg and C. Coath (1999) Forthcoming VIII. Replicon Theory and Cell Division, eds M. Kohiyama, W. Fangman, T. Kishimoto and C. Coath IX. The Regulation of Sleep, eds A. A. Borbély, O. Hayaishi, T. Sejnowski and J. S. Altman X. Axis Formation in the Vertebrate Embryo, eds S. Ang, R. Behringer, H. Sasaki, J. S. Altman and C. Coath XI. Neuroenergetics: Relevance for Functional Brain Imaging, eds P. J. Magistretti, R. G. Shulman, R. S. J. Frackowiak and J. S. Altman WORKSHOP VII Transcription Regulation in Eukaryotes Copyright © 1999 by the Human Frontier Science Program Please use the following format for citations: “Transcription Regulation in Eukaryotes” Eds P. Chambon, T. Fukasawa, R.
    [Show full text]
  • Condensed DNA: Condensing the Concepts
    Progress in Biophysics and Molecular Biology 105 (2011) 208e222 Contents lists available at ScienceDirect Progress in Biophysics and Molecular Biology journal homepage: www.elsevier.com/locate/pbiomolbio Review Condensed DNA: Condensing the concepts Vladimir B. Teif a,b,*, Klemen Bohinc c,d a BioQuant and German Cancer Research Center, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany b Institute of Bioorganic Chemistry, Belarus National Academy of Sciences, Kuprevich 5/2, 220141, Minsk, Belarus c Faculty of Health Sciences, Zdravstvena pot 5, 1000 Ljubljana, Slovenia d Faculty of Electrical Engineering, University of Ljubljana, Trzaska 25, 1000 Ljubljana, Slovenia article info abstract Article history: DNA is stored in vivo in a highly compact, so-called condensed phase, where gene regulatory processes Available online 16 July 2010 are governed by the intricate interplay between different states of DNA compaction. These systems often have surprising properties, which one would not predict from classical concepts of dilute solutions. The Keywords: mechanistic details of DNA packing are essential for its functioning, as revealed by the recent devel- DNA condensation opments coming from biochemistry, electrostatics, statistical mechanics, and molecular and cell biology. Ligand binding Different aspects of condensed DNA behavior are linked to each other, but the links are often hidden in Counterion correlations the bulk of experimental and theoretical details. Here we try to condense some of these concepts and Macromolecular crowding fi Chromatin provide interconnections between the different elds. After a brief description of main experimental Gene regulation features of DNA condensation inside viruses, bacteria, eukaryotes and the test tube, main theoretical approaches for the description of these systems are presented.
    [Show full text]