In the past Jordanka Zlatanova has collaborated on articles with Ljuba Srebreva and Lubomir Stoilov. One of their most recent publications is Occurrence of histone H10-related fraction in differentiated maize roots. Which was published in journal Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression.

More information about Jordanka Zlatanova research including statistics on their citations can be found on their Copernicus Academic profile page.

Jordanka Zlatanova's Articles: (15)

Occurrence of histone H10-related fraction in differentiated maize roots

AbstractThe lysine-rich histones of maize roots extracted with 5% perchloric acid were studied in order to determine the presence of a protein similar to mammalian histone H10. The biochemical methods used involved sodium dodecyl-sulphate and acid-urea gel electrophoresis and gel filtration on Bio-Gel P-100. Specific rabbit antibodies elicited against chromatographically purified mouse liver H10 were applied for further characterization of the presumptive H10 fraction. The combined evidence from our electrophoretic, chromatographic and immunochemical studies shows that an H10-related protein is present in plants.

Genetic and molecular biologyDNA and histone synthesis are uncoupled during germination of maize embryos

AbstractThe rate of synthesis of DNA and histones was studied in germinating maize embryos as a function of the length of the germination period. To that end excised embryos from seeds germinated for different periods of time were pulse labelled either with [14C]protein hydrolysate or with [3H]TdR. Specific activities were determined for the total cellular proteins and the total histone fraction obtained by acid-extraction of the cellular homogenate and BioRex70 ion exchange chromatography. The results show that the early germination period is characterized by a lack of coupling between the histone synthesis and that of the nuclear DNA. The early histone synthesis peak might be necessitated by the reprogramming of the embryo genome that takes place during germination.

Transcriptional activity and DNA supercoiling during early germination in maize

AbstractThe possible link between the ability of DNA to be transcribed and its three-dimensional organization in the eukaryotic nucleus has been studied during germination of the plant embryo. In this model system there is a gradual increase in the transcriptional activity of chromatin and no nuclear DNA replication takes place for at least the first 20–24 h following water imbibition. Maize embryo nucleoids derived by nonionic detergent and high salt treatment from nuclei isolated at different time points of germination were analysed by sedimentation in a series of sucrose gradients containing increasing amounts of the intercalating agent ethidium bromide. The sedimentation of the dry embryo nucleoids shows no dependence on the concentration of ethidium bromide while the 16-h germinated embryo possesses the titration curve characteristic of the active plant genomes. On the other hand, DNA isolated from both the dry and the germinated material behaved upon EthBr intercalation as expected on theoretical grounds, i.e. its sedimentation rate decreased with increase of the EthBr concentration. The lack of a biphasic response to EthBr titration we interpret as an indication of a lack of supercoiled DNA loops in the dry embryo nuclei.

ArticleNucleosome Assembly Depends on the Torsion in the DNA Molecule: A Magnetic Tweezers Study

AbstractWe have used magnetic tweezers to study nucleosome assembly on topologically constrained DNA molecules. Assembly was achieved using chicken erythrocyte core histones and histone chaperone protein Nap1 under constant low force. We have observed only partial assembly when the DNA was topologically constrained and much more complete assembly on unconstrained (nicked) DNA tethers. To verify our hypothesis that the lack of full nucleosome assembly on topologically constrained tethers was due to compensatory accumulation of positive supercoiling in the rest of the template, we carried out experiments in which we mechanically relieved the positive supercoiling by rotating the external magnetic field at certain time points of the assembly process. Indeed, such rotation did lead to the same nucleosome saturation level as in the case of nicked tethers. We conclude that levels of positive supercoiling in the range of 0.025–0.051 (most probably in the form of twist) stall the nucleosome assembly process.

Chromatin Fiber Structure: Morphology, Molecular Determinants, Structural Transitions

AbstractDespite more than 20 years of research, the structure of the chromatin fiber and its molecular determinants remain enigmatic. Recent developments in high-resolution microscopic techniques, as well as the application of mathematical modeling to chromatin fiber structure, have allowed the acquisition of some new insights into the structure and its determinants. Here we present some of the newest data on the structure of the chromatin fiber in both its extended and compacted states, and bring together this new knowledge with older data in an attempt to provide a unified view of how chromatin components interact with each other to form its various conformations. The structural transitions that are believed to take place during transcriptional activation and its cessation are also discussed. It becomes obvious that despite some progress in our understanding of the fiber structure and its dynamics, huge gaps continue to exist. Bridging these gaps will require further improvements in already available techniques and the introduction of completely new approaches.

Contributions of Linker Histones and Histone H3 to Chromatin Structure: Scanning Force Microscopy Studies on Trypsinized Fibers

AbstractLittle is known about the mechanisms that organize linear arrays of nucleosomes into the three-dimensional structures of extended and condensed chromatin fibers. We have earlier defined, from scanning force microscopy (SFM) and mathematical modeling, a set of simple structural determinants of extended fiber morphology, the critical parameters being the entry-exit angle between consecutive linkers and linker length. Here we study the contributions of the structural domains of the linker histones (LHs) and of the N-terminus of histone H3 to extended fiber morphology by SFM imaging of progressively trypsinized chromatin fibers. We find that cleavage of LH tails is associated with a lengthening of the internucleosomal center-to-center distance, and that the somewhat later cleavage of the N-terminus of histone H3 is associated with a flattening of the fiber. The persistence of the “zigzag” fiber morphology, even at the latest stages of trypsin digestion, can be attributed to the retention of the globular domain of LH in the fiber.

Linker Histone Tails and N-Tails of Histone H3 Are Redundant: Scanning Force Microscopy Studies of Reconstituted Fibers

AbstractThe mechanisms responsible for organizing linear arrays of nucleosomes into the three-dimensional structure of chromatin are still largely unknown. In a companion paper (Leuba, S. H., et al. 1998. Biophys. J. 74:2823–2829), we study the contributions of linker histone domains and the N-terminal tail of core histone H3 to extended chromatin fiber structure by scanning force microscopy imaging of mildly trypsinized fibers. Here we complement and extend these studies by scanning force microscopy imaging of selectively reconstituted chromatin fibers, which differ in subtle but distinctive ways in their histone composition. We demonstrate an absolute requirement for the globular domain of the linker histones and a structural redundancy of the tails of linker histones and of histone H3 in determining conformational stability.

Research ArticlecAMP signaling induces rapid loss of histone H3 phosphorylation in mammary adenocarcinoma-derived cell lines

AbstractThe phosphorylation of histone H3 is known to play a role in regulation of transcription as well as preparation of chromosomes for mitosis. Various signaling cascades induce H3 phosphorylation, particularly at genes activated by these pathways. In this study, we show that signaling can also have the opposite effect. Activators of cAMP signaling induce a rapid and potent loss of H3 phosphorylation. This effect is not mediated through a cAMP metabolite since a membrane-permeable form of AMP had no effect on H3 phosphorylation and a phosphodiesterase-resistant cAMP analog efficiently reduced it. cAMP is also the likely regulator of H3 phosphorylation under physiological conditions since only supra-pharmacological doses of cGMP induce the loss of H3 phosphorylation. The loss of phosphorylation is specific for histone H3 since we do not observe drastic losses in total phosphorylation of other histones. In addition, other H3 modifications are unaffected with the exception of lysine 9 methylation, which is elevated. Analysis of cell growth and cell cycle shows that cAMP signaling inhibits cell growth and arrests cells at both G1 and G2/M. Similar effects of cAMP signaling on H3 phosphorylation are observed in a variety of mammary adenocarcinoma-derived cell lines. In syngeneic human breast-derived cell lines, one diploid and non-transformed, the other derived from a ductal carcinoma, the loss of H3 phosphorylation is significantly more sensitive to cAMP concentration in the transformed cell line.

Regular ArticleOn the Location of Histones H1 and H5 in the Chromatin Fiber: Studies with Immobilized Trypsin and Chymotrypsin

AbstractThe location of linker histones H1 and H5 in chicken erythrocyte chromatin was studied as a function of the fiber structure by the use of proteolytic enzymes immobilized onto Immmobilon membranes. The immobilization of trypsin and chymotrypsin creates proteolytic probes, specific respectively to the terminal portions of the molecules or to the phenylalanine in the globular domain, that are incapable of penetrating into the interior of the condensed fiber. The chromatin fiber was studied in three different conformations: open zig-zag (in Tris buffer), closed zig-zag (upon addition of 10 mM-NaC), or 30 nm fiber (upon addition of 0·35 mM-MgCl2). The results from digestion experiments performed on linker histones either in chicken erythrocyte chromatin, or free in solution or bound in mononucleosomes revealed several features relevant to linker histone location: (1) histone H5 is more protected than histone H1 in the fiber; (2) the N and C-terminal portions of histone H1 do not change their accessibility, and hence their location, upon compaction of the fiber; this behavior of H1 is in contrast to that of histone H5, whose tails become significantly internalized in the 30 nm fiber; (3) phenylalanine in the globular domain of both H1 and H5 is inaccessible (buried) both in the fiber and in the mononucleosomal particle. Sedimentation velocity measurements performed during the course of trypsin digestion demonstrate that the conformation of the fiber is highly sensitive to even a few cuts in some of the linker histone molecules; hence, the linker histones are an important factor in the organization of the fiber in all its different condensation states.

Regular ArticleOn the Location of Linker DNA in the Chromatin Fiber: Studies with Immobilized and Soluble Micrococcal Nuclease

AbstractThe structure of chicken erythrocyte chromatin fibers has been probed using micrococcal nuclease, both membrane-immobilized and free in solution. Under the extremely mild digestion conditions used, the linker DNA is almost completely protected against digestion with either immobilized or free enzyme in the 30 nm fibers, whereas it is readily accessible in the more extended structures. Control experiments with glutaraldehyde-fixed chromatin fibers gave essentially the same results. Experiments with fibers of intermediate degree of condensation revealed a direct relationship between the degree of compaction and the resistance of linker DNA to digestion. Our results favor models in which access to the linkers is limited by local steric hindrance due to the high compaction, rather than by internalization in the center of the fibers.

Single-Molecule Analysis of Chromatin

Publisher SummaryThis chapter describes the technical details of three single-molecule techniques that are utilized for the study of single chromatin fibers including the atomic force microscope (AFM), optical tweezers (OT), and magnetic tweezers (MT). The AFM produces digital topographical images of samples deposited on flat surfaces by raster-scanning the surface with a sharp tip mounted on the back of a flexible cantilever. Atoms on the tip interact with atoms on the surface, causing the cantilever to deflect upwards or downwards, depending on whether the tip-sample interaction is repulsive or attractive. The deflections of the cantilever are registered by a laser beam reflected off the back of the cantilever to produce a topographical image of the sample. OT technique uses for manipulating single molecules based on the interaction of light with matter. Light can exert forces on small beads of certain optical properties in such a way that the bead is kept suspended at a point close to the waist of a laser beam that is focused with an objective. In the MT, the macromolecule is attached between a surface and a magnetic bead. Manipulation of an external magnetic field can be used to apply stretching force to the tethered molecule, and/or to induce precisely known levels of supercoiling: stretching is achieved by changing the distance between the external magnet(s) and the cuvette, while supercoiling is introduced by rotating the external magnetic field either clockwise or counterclockwise.

The site of binding of linker histone to the nucleosome does not depend upon the amino termini of core histones

AbstractUsing nucleosomes reconstituted on a defined sequence of DNA, we have investigated the question as to whether the N-terminal tails of core histones play a role in determining the site of binding of a linker histone. Reconstitutes used histone cores of three types: intact, lacking the N-terminal H3 tails, or lacking all tails. In each case the same, single defined position for the histone core was observed, using high-resolution mapping. The affinity for binding of linker histone H1o was highest for the intact cores, lowest for the tailless cores. However, the location of the linker histone, as judged by micrococcal nuclease protection, was exactly the same in each case, an asymmetric site of about 17 bp to one side of the core particle DNA.

Histone H1o in developing rat brain cells

AbstractHistone H1o was found both in neuronal and oligodendrocyte rat-brain nuclei fractionated by sucrose-gradient isopycnic centrifugation. This histone was absent during the early stages of development when the brain cells were still proliferating, but it appeared in significant amounts in the terminally differentiated cells.

OpinionThe linker-protein network: control of nucleosomal DNA accessibility

Numerous studies have recently addressed the accessibility of nucleosomal DNA to protein factors. Two popular concepts – the histone code and chromatin remodeling – consider the nucleosome as a passive entity that ‘waits’ to be marked by histone modifications and is ‘mobilized’ by ATP-dependent remodelers. Here, we propose a holistic view of the nucleosome as an active, dynamic entity, the accessibility of which is controlled by binding of different linker proteins to the DNA entry/exit site. The linker proteins might directly compete for this binding site; alternatively, protein chaperones and/or chromatin remodelers might exchange one linker protein for another. Finally, according to our proposed model, the exchange factors are themselves controlled by post-translational modifications or binding of protein partners, to respond to the ever-changing intra- and extra-cellular environment.

ReviewChromatin fiber structure: Where is the problem now?

AbstractThe structure of the “30 nm chromatin fiber”, as observed in vitro, has been a matter of controversy for 30 years. Recent studies with new and more powerful techniques give some promise for resolution. However, this will not necessarily inform us as to the in vivo structure, which may be both heteromorphic and dynamic. In this chapter, we briefly review the older conjectures and some more recent studies of special interest. We attempt to point out the remaining contradictions and hopeful lines of future research.

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