Electron microscopy analysis of ATP-independent nucleosome unfolding by FACT

FACT is a histone chaperone that participates in nucleosome removal and reassembly during transcription and replication. We used electron microscopy to study FACT, FACT:Nhp6 and FACT:Nhp6:nucleosome complexes, and found that all complexes adopt broad ranges of configurations, indicating high flexibility. We found unexpectedly that the DNA binding protein Nhp6 also binds to the C-terminal tails of FACT subunits, inducing more open geometries of FACT even in the absence of nucleosomes. Nhp6 therefore supports nucleosome unfolding by altering both the structure of FACT and the properties of nucleosomes. Complexes formed with FACT, Nhp6, and nucleosomes also produced a broad range of structures, revealing a large number of potential intermediates along a proposed unfolding pathway. The data suggest that Nhp6 has multiple roles before and during nucleosome unfolding by FACT, and that the process proceeds through a series of energetically similar intermediate structures, ultimately leading to an extensively unfolded form

Polymer reptation and nucleosome repositioning

We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem arises in the case of globular aggregates of proteins (histones) that are wound by DNA in the chromosomes of plants and animals; these beads (nucleosomes) are multiply wrapped and yet are able to reposition themselves over long distances, while remaining bound by the DNA chain.Comment: 9 pages, including 2 figures, to be published in Phys. Rev. Let

Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators

Long-distance regulatory interactions between enhancers and their target genes are commonplace in higher eukaryotes. Interposed boundaries or insulators are able to block these long distance regulatory interactions. The mechanistic basis for insulator activity and how it relates to enhancer action-at-a-distance remains unclear. Here we explore the idea that topological loops could simultaneously account for regulatory interactions of distal enhancers and the insulating activity of boundary elements. We show that while loop formation is not in itself sufficient to explain action at a distance, incorporating transient non-specific and moderate attractive interactions between the chromatin fibers strongly enhances long-distance regulatory interactions and is sufficient to generate a euchromatin-like state. Under these same conditions, the subdivision of the loop into two topologically independent loops by insulators inhibits inter-domain interactions. The underlying cause of this effect is a suppression of crossings in the contact map at intermediate distances. Thus our model simultaneously accounts for regulatory interactions at a distance and the insulator activity of boundary elements. This unified model of the regulatory roles of chromatin loops makes several testable predictions that could be confronted with \emph{in vitro} experiments, as well as genomic chromatin conformation capture and fluorescent microscopic approaches.Comment: 10 pages, originally submitted to an (undisclosed) journal in May 201

Механизмы действия растительных полифенолов на инициацию канцерогенеза

Genetic apparatus of human cells is constantly affected by a broad spectrum of mutagenic factors, both exogenous and endogenous. Genetic and epigenetic disorders, which emerge as a result of this influence, become the main cause of the majority of malignant neoplasias. Several different approaches were proposed to prevent these disorders, including the suppression of the activity of mutagenic factors by treatment with certain chemical compounds. Plant polyphenols are promising candidates for the development of chemopreventive drugs, as they exert the ability to regulate the metabolic activation of procarcinogens and modulate the cellular oxidative stress. In the present review, classification of plant phenolic compounds and their interactions  with biological macromolecules are described, along with the molecular mechanisms of their influence on the enzymes and regulatory pathways of phase I xenobiotic metabolism, and the prevention of oxidative stress. Interactions between natural polyphenols and patient’s microbiota is also described.Генетический аппарат клеток человеческого организма находится под постоянным воздействием большого спектра генотоксичных и негенотоксичных агентов, как экзогенных, так и эндогенных. возникающие в результате таких воздействий генетические и эпигенетические нарушения являются звеньями молекулярного патогенеза злокачественных новообразований. для профилактики развития таких нарушений предложены несколько различных подходов, включая подавление генотоксичного воздействия с помощью химических соединений. Благодаря способности оказывать влияние на активацию проканцерогенов и регуляцию окислительного стресса, растительные полифенольные соединения являются одними из перспективных кандидатов на роль химиопрофилактических антиканцерогенных препаратов. в обзоре рассмотрены структура и классификация полифенольных соединений и механизмы их взаимодействия с биологическими макромолекулами, а также молекулярные механизмы их влияния на ферменты, участвующие в 1-й фазе активации ксенобиотиков и регуляции окислительного стресса. Также проведен анализ эффектов природных полифенолов на микрофлору человека

Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast

Tracking of ancestral histone proteins over multiple generations of genome replication in yeast reveals that old histones move along genes from 3′ toward 5′ over time, and that maternal histones move up to around 400 bp during genomic replication

A polar barrier to transcription can be circumvented by remodeler-induced nucleosome translocation

Many eukaryotic genes are regulated at the level of transcript elongation. Nucleosomes are likely targets for this regulation. Previously, we have shown that nucleosomes formed on very strong positioning sequences (601 and 603), present a high, orientation-dependent barrier to transcription by RNA polymerase II in vitro. The existence of this polar barrier correlates with the interaction of a 16-bp polar barrier signal (PBS) with the promoter-distal histone H3–H4 dimer. Here, we show that the polar barrier is relieved by ISW2, an ATP-dependent chromatin remodeler, which translocates the nucleosome over a short distance, such that the PBS no longer interacts with the distal H3–H4 dimer, although it remains within the nucleosome. In vivo, insertion of the 603 positioning sequence into the yeast CUP1 gene results in a modest reduction in transcription, but this reduction is orientation-independent, indicating that the polar barrier can be circumvented. However, the 603-nucleosome is present at the expected position in only a small fraction of cells. Thus, the polar barrier is probably non-functional in vivo because the nucleosome is not positioned appropriately, presumably due to nucleosome sliding activities. We suggest that interactions between PBSs and chromatin remodelers might have significant regulatory potential

Contractile and histochemical properties of regenerating cross-transplanted fast and slow muscles in the rat

The soleus (SOL) or extensor digitorum longus (EDL) muscles of month-old rats were denervated for 14 days and then cross-transplanted so that the fast muscle was placed into the bed of the slow muscle and vice versa. At 17, 30, 60, and 90 days the transplants were tested for certain contractile and histochemical properties. By 90 days the cross-transplanted SOL showed complete conversion of the full contraction time and nearly complete conversion of the half relaxation time to those of the normal EDL. In contrast, the contraction and relaxation times of the cross-transplanted EDL became considerably slowed, but did not attain the values of the normal SOL. Histochemical staining for ATPase and SDH activity demonstrated similar transformations of fiber types. The degree of transformation of twitch and histochemical characteristics in cross-transplanted muscles was greater than the values reported after cross-innervation of the same muscles. The cross-transplantation model has certain advantages over nerve cross-union experiments because the cross-transplanted muscle is placed in the normal functional environment of the other muscle.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47444/1/424_2004_Article_BF00584286.pd

Effects of DNA supercoiling on chromatin architecture

Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales. This supercoiling changes the properties of the DNA helix in a manner that substantially alters the binding specificity of DNA binding proteins and complexes, including nucleosomes, polymerases, topoisomerases and transcription factors. For example, transient over-wound DNA destabilises nucleosome core particles ahead of a transcribing polymerase, whereas under-wound DNA facilitates pre-initiation complex formation, transcription factor binding and nucleosome core particle association behind the transcribing polymerase. Importantly, DNA supercoiling can also dissipate through DNA, even in a chromatinised context, to influence both local elements and large chromatin domains. We propose a model in which changes in unconstrained DNA supercoiling influences higher levels of chromatin organisation through the additive effects of DNA supercoiling on both DNA-protein and DNA-nucleosome interactions. This model links small-scale changes in DNA and chromatin to the higher-order fibre and large-scale chromatin structures, providing a mechanism relating gene regulation to chromatin architecture in vivo

PARP-1-Associated Pathological Processes: Inhibition by Natural Polyphenols

Poly (ADP-ribose) polymerase-1 (PARP-1) is a nuclear enzyme involved in processes of cell cycle regulation, DNA repair, transcription, and replication. Hyperactivity of PARP-1 induced by changes in cell homeostasis promotes development of chronic pathological processes leading to cell death during various metabolic disorders, cardiovascular and neurodegenerative diseases. In contrast, tumor growth is accompanied by a moderate activation of PARP-1 that supports survival of tumor cells due to enhancement of DNA lesion repair and resistance to therapy by DNA damaging agents. That is why PARP inhibitors (PARPi) are promising agents for the therapy of tumor and metabolic diseases. A PARPi family is rapidly growing partly due to natural polyphenols discovered among plant secondary metabolites. This review describes mechanisms of PARP-1 participation in the development of various pathologies, analyzes multiple PARP-dependent pathways of cell degeneration and death, and discusses representative plant polyphenols, which can inhibit PARP-1 directly or suppress unwanted PARP-dependent cellular processes