Jordanka Zlatanova

Single molecule force spectroscopy in biology using the atomic force microscope.

The importance of forces in biology has been recognized for quite a while but only in the past decade have we acquired instrumentation and methodology to directly measure interactive forces at the level of single biological macromolecules and/or their complexes. This review focuses on force measurements performed with the atomic force microscope. A general introduction to the principle of action is followed by review of the types of interactions being studied, describing the main results and discussing the biological implications.

Linker histone binding and displacement: versatile mechanism for transcriptional regulation

In recent years, the connection between chromatin structure and its transcriptional activity has attracted considerable experimental effort. The post‐translational modifications to both the core histones and the linker histones are finely tuned through interactions with transcriptional regulators and change chromatin structure in a way to allow transcription to occur. Here we review evidence for the involvement of linker histones in transcriptional regulation and suggest a scenario in which the reversible and controllable binding/displacement of proteins of this class to the nucleosome entry/exit point determine the accessibility of the nucleosomal DNA to the transcriptional machinery.—Zlatanova, J., Caiafa, P., van Holde, K. Linker histone binding and displacement: versatile mechanism for transcriptional regulation. FASEB J. 14, 1697–1704 (2000)

Histone H1 zero: a major player in cell differentiation?

Histone H1° was initially described as a member of the lysine‐rich histone class, typically present in nondividing mammalian cells. Since then it has been found in almost every animal or plant species studied. The protein accumulates in terminally differentiated cells that have stopped dividing. It has also been implicated in changes in chromatin structure and function accompanying malignant transformation. Despite its involvement in these fundamental cellular processes, its precise role remains elusive, as do the molecular mechanisms via which it acts. This review is an attempt to summarize and critically discuss the huge relevant literature, trying to highlight the problems that still await answers.—Zlatanova, J., Doenecke, D., Histone H1°: a major player in cell differentiation? FASEB J. 8, 1260‐1268 (1994)

Chromatin fiber structure: morphology, molecular determinants, structural transitions.

Despite 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.

Histone H1 and the regulation of transcription of eukaryotic genes

Histone H1 plays a role in the formation of chromatin structure, both at the level of the nucleosome particle itself and in the formation of the higher-order structures of the chromatin fibre. Histone H1 is regarded as a part of a general repressor mechanism that ensures a strong and stable repression of gene expression. In addition to serving as a general repressor for relatively large chromatin fragments, histone H1 might also be involved in controlling the transcriptional activity of individual genes.

The Linker Histones and Chromatin Structure: New Twists

Publisher Summary This chapter discusses the properties of linker histones and their interactions with other chromatin components. The way the fibers of chromatin are folded in the eukaryotic nucleus has interested biologists and biochemists for decades. It has long been recognized that histones play a major part in this folding. The lysine-rich histones are characterized by a high lysine-to-arginine ratio, after which they are named. In each cell, the lysine-rich histones are represented by several molecular types (subfractions or isohistones), which differ in molecular mass, aminoacid composition and sequence, and physicochemical and immunochemical properties. Several lines of evidence suggest that artificial Hl/DNA complexes can be used as appropriate model systems for studying the role of histone in chromatin. The early electron-microscope observations of the salt-dependent conformational transitions of soluble chromatin fragments pointed to the importance of linker histones in the formation and maintenance of the higher order structures of chromatin. Valuable information concerning the role played by linker histones in determining chromatin fiber structure can be obtained by studying ionic strengths below 10 mM. Under these conditions, the fiber is expanded and it becomes possible to resolve individual nucleosomes by microscopic techniques and to study their disposition along the fiber.

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

The 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.

Linker histones versus HMG1/2: a struggle for dominance?

The linker histones (H1, H1 zero, H5, etc.) and a group of abundant non-histone chromosomal proteins (HMG1/2) bind to linker DNA in chromatin and exhibit both generalized and specific effects on gene transcription. The two classes of proteins share many features of DNA binding behaviour, although they are structurally unrelated. While the linker histones and HMG1/2 exhibit direct competition in binding to such structures as four-way junction DNA, whether they compete for binding to the nucleosome has not been investigated. The possibility for either opposite or synergistic effects on gene regulation must be considered at this point.

The nucleosome core particle: does it have structural and physiologic relevance?

Although the nucleosomal core particle has been extensively studied as the basic building block of chromatin, the biological significance of a unit carrying exactly 146 bp of DNA remains unclear. Herein, we present data to show that the histone octamer can stably accommodate anywhere from about 100 to 170 bp of DNA. The unfolded structures containing less than 146 bp may well be of greater biological importance than the canonical core particle.

The Non-histone Chromatin Protein HMG1 Protects Linker DNA on the Side Opposite to That Protected by Linker Histones

Linker histones and HMG1/2 constitute the two major proteins that bind to linker DNA in chromatin. While the location of linker histones on the nucleosome has attracted considerable research effort, only a few studies have addressed the location of HMG1 in the particles. In this study, we use a procedure based on micrococcal nuclease digestion of reconstituted nucleosomal particles to which HMG1 has been bound, followed by analysis of the protected DNA by restriction nuclease digestion, to locate the HMG1 binding site. Nucleosomal particles were reconstituted on a 235-base pair DNA fragment, which is known to be a strong nucleosome positioning sequence. The results unequivocally show that HMG1 protects linker DNA on one side of the core particle. Importantly, and possibly of physiological relevance, the linker DNA site protected by HMG1 was located on the side opposite to that already shown to be protected by linker histone binding.