Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding

Responses of cells to stimuli are increasingly discovered to involve the binding of sequence-specific transcription factors outside of known target genes. We wanted to determine to what extent the genome-wide binding and function of a transcription factor are shaped by the cell type versus the stimulus. To do so, we induced the Heat Shock Response pathway in two different cancer cell lines with two different stimuli and related the binding of its master regulator HSF1 to nascent RNA and chromatin accessibility. Here, we show that HSF1 binding patterns retain their identity between basal conditions and under different magnitudes of activation, so that common HSF1 binding is globally associated with distinct transcription outcomes. HSF1-induced increase in DNA accessibility was modest in scale, but occurred predominantly at remote genomic sites. Apart from regulating transcription at existing elements including promoters and enhancers, HSF1 binding amplified during responses to stimuli may engage inactive chromatin.

Targeting the Transcriptome Through Globally Acting Components

Transcription is a step in gene expression that defines the identity of cells and its dysregulation is associated with diseases. With advancing technologies revealing molecular underpinnings of the cell with ever-higher precision, our ability to view the transcriptomes may have surpassed our knowledge of the principles behind their organization. The human RNA polymerase II (Pol II) machinery comprises thousands of components that, in conjunction with epigenetic and other mechanisms, drive specialized programs of development, differentiation, and responses to the environment. Parts of these programs are repurposed in oncogenic transformation. Targeting of cancers is commonly done by inhibiting general or broadly acting components of the cellular machinery. The critical unanswered question is how globally acting or general factors exert cell type specific effects on transcription. One solution, which is discussed here, may be among the events that take place at genes during early Pol II transcription elongation. This essay turns the spotlight on the well-known phenomenon of promoter-proximal Pol II pausing as a step that separates signals that establish pausing genome-wide from those that release the paused Pol II into the gene. Concepts generated in this rapidly developing field will enhance our understanding of basic principles behind transcriptome organization and hopefully translate into better therapies at the bedside.

Analysis of English free association network reveals mechanisms of efficient solution of Remote Association Tests

We study correlations between the structure and properties of a free association network of the English language, and solutions of psycholinguistic Remote Association Tests (RATs). We show that average hardness of individual RATs is largely determined by relative positions of test words (stimuli and response) on the free association network. We argue that the solution of RATs can be interpreted as a first passage search problem on a network whose vertices are words and links are associations between words. We propose different heuristic search algorithms and demonstrate that in "easily-solving" RATs (those that are solved in 15 seconds by more than 64% subjects) the solution is governed by "strong" network links (i.e. strong associations) directly connecting stimuli and response, and thus the efficient strategy consist in activating such strong links. In turn, the most efficient mechanism of solving medium and hard RATs consists of preferentially following sequence of "moderately weak" associations.

Non-backtracking walks reveal compartments in sparse chromatin interaction networks

Chromatin communities stabilized by protein machinery play essential role in gene regulation and refine global polymeric folding of the chromatin fiber. However, treatment of these communities in the framework of the classical network theory (stochastic block model, SBM) does not take into account intrinsic linear connectivity of the chromatin loci. Here we propose the polymer block model, paving the way for community detection in polymer networks. On the basis of this new model we modify the non-backtracking flow operator and suggest the first protocol for annotation of compartmental domains in sparse single cell Hi-C matrices. In particular, we prove that our approach corresponds to the maximum entropy principle. The benchmark analyses demonstrates that the spectrum of the polymer non-backtracking operator resolves the true compartmental structure up to the theoretical detectability threshold, while all commonly used operators fail above it. We test various operators on real data and conclude that the sizes of the non-backtracking single cell domains are most close to the sizes of compartments from the population data. Moreover, the found domains clearly segregate in the gene density and correlate with the population compartmental mask, corroborating biological significance of our annotation of the chromatin compartmental domains in single cells Hi-C matrices.

Self-isolation or borders closing: What prevents the spread of the epidemic better?

Pandemic propagation of COVID-19 motivated us to discuss the impact of the human network clustering on epidemic spreading. Today, there are two clustering mechanisms which prevent of uncontrolled disease propagation in a connected network: an "internal" clustering, which mimics self-isolation (SI) in local naturally arranged communities, and an "external" clustering, which looks like a sharp frontiers closing (FC) between cities and countries, and which does not care about the natural connections of network agents. SI networks are "evolutionarily grown" under the condition of maximization of small cliques in the entire network, while FC networks are instantly created. Running the standard SIR model on clustered SI and FC networks, we demonstrate that the evolutionary grown clustered network prevents the spread of an epidemic better than the instantly clustered network with similar parameters. We find that SI networks have the scale-free property for the degree distribution P(k)∼k^{η}, with a small critical exponent -2<η<-1. We argue that the scale-free behavior emerges as a result of the randomness in the initial degree distributions.

Brownian flights over a circle

The stationary radial distribution, P(ρ), of a random walk with the diffusion coefficient D, which winds at the tangential velocity V around an impenetrable disk of radius R for R≫D/V converges to the distribution involving the Airy function. Typical trajectories are localized in the circular strip [R,R+δR^{1/3}], where δ is a constant which depends on the parameters D and V and is independent of R.

Field-driven tracer diffusion through curved bottlenecks: fine structure of first passage events

Using scaling arguments and extensive numerical simulations, we study the dynamics of a tracer particle in a corrugated channel represented by a periodic sequence of broad chambers and narrow funnel-like bottlenecks enclosed by a hard-wall boundary.

The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing

Transcriptional regulation in eukaryotes occurs at promoter-proximal regions wherein transcriptionally engaged RNA polymerase II (Pol II) pauses before proceeding toward productive elongation. The role of chromatin in pausing remains poorly understood. Here, we demonstrate that the histone deacetylase SIRT6 binds to Pol II and prevents the release of the negative elongation factor (NELF), thus stabilizing Pol II promoter-proximal pausing. Genetic depletion of SIRT6 or its chromatin deficiency upon glucose deprivation causes intragenic enrichment of acetylated histone H3 at lysines 9 (H3K9ac) and 56 (H3K56ac), activation of cyclin-dependent kinase 9 (CDK9)-that phosphorylates NELF and the carboxyl terminal domain of Pol II-and enrichment of the positive transcription elongation factors MYC, BRD4, PAF1, and the super elongation factors AFF4 and ELL2. These events lead to increased expression of genes involved in metabolism, protein synthesis, and embryonic development. Our results identified SIRT6 as a Pol II promoter-proximal pausing-dedicated histone deacetylase.

Spectral peculiarity and criticality of a human connectome

We have performed the comparative spectral analysis of structural connectomes for various organisms using open-access data. Our results indicate new peculiar features of connectomes of higher organisms. We found that the spectral density of adjacency matrices of human connectome has maximal deviation from the one of randomized network, compared to other organisms. Considering the network evolution induced by the preference of 3-cycles formation, we discovered that for macaque and human connectomes the evolution with the conservation of local clusterization is crucial, while for primitive organisms the conservation of averaged clusterization is sufficient. Investigating for the first time the level spacing distribution of the spectrum of human connectome Laplacian matrix, we explicitly demonstrate that the spectral statistics corresponds to the critical regime, which is hybrid of Wigner-Dyson and Poisson distributions. This observation provides strong support for debated statement of the brain criticality.

Genome-wide RNA pol II initiation and pausing in neural progenitors of the rat

Background

Global RNA sequencing technologies have revealed widespread RNA polymerase II (Pol II) transcription outside of gene promoters. Small 5′-capped RNA sequencing (Start-seq) originally developed for the detection of promoter-proximal Pol II pausing has helped improve annotation of Transcription Start Sites (TSSs) of genes as well as identification of non-genic regulatory elements. However, apart from the most well studied genomes of human and mouse, mammalian transcription has not been profiled with sufficiently high precision.

Results

We prepared and sequenced Start-seq libraries from rat (Rattus norgevicus) primary neural progenitor cells. Over 48 million uniquely mappable reads from two independent biological replicates allowed us to define the TSSs of 7365 known genes in the rn6 genome, reannotating 2503 TSSs by more than 5 base pairs, characterize promoter-associated antisense transcription, and profile Pol II pausing. By combining TSS data with polyA-selected RNA sequencing, we also identified thousands of potential new genes producing stable RNA as well as non-genic transcripts representing possible regulatory elements.

Conclusions

Our study has produced the first Start-seq dataset for the rat. Apart from profiling transcription initiation, our data reaffirm the prevalence of Pol II pausing across the rat genome and indicate conservation of pausing mechanisms across metazoan genomes. We suggest that pausing location, at least in mammals, is constrained by a distance from initiation of transcription, whether it occurs at or outside of a gene promoter. Abundant antisense transcription initiation around protein coding genes indicates that Pol II recruited to the vicinity of a promoter is distributed to available start sites of transcription at either DNA strand. Transcriptome profiling of neural progenitors presented here will facilitate further studies of other rat cell types as well as other organisms.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5829-4) contains supplementary material, which is available to authorized users.

Many-body contacts in fractal polymer chains and fractional Brownian trajectories

We calculate the probabilities that a trajectory of a fractional Brownian motion with arbitrary fractal dimension d_{f} visits the same spot n≥3 times, at given moments t_{1},...,t_{n}, and obtain a determinant expression for these probabilities in terms of a displacement-displacement covariance matrix. Except for the standard Brownian trajectories with d_{f}=2, the resulting many-body contact probabilities cannot be factorized into a product of single-loop contributions. Within a Gaussian network model of a self-interacting polymer chain, which we suggested recently [K. Polovnikov et al., Soft Matter 14, 6561 (2018)1744-683X10.1039/C8SM00785C], the probabilities we calculate here can be interpreted as probabilities of multibody contacts in a fractal polymer conformation with the same fractal dimension d_{f}. This Gaussian approach, which implies a mapping from fractional Brownian motion trajectories to polymer conformations, can be used as a semiquantitative model of polymer chains in topologically stabilized conformations, e.g., in melts of unconcatenated rings or in the chromatin fiber, which is the material medium containing genetic information. The model presented here can be used, therefore, as a benchmark for interpretation of the data of many-body contacts in genomes, which we expect to be available soon in, e.g., Hi-C experiments.

Anomalous one-dimensional fluctuations of a simple two-dimensional random walk in a large-deviation regime

The following question is the subject of our work: could a two-dimensional (2D) random path pushed by some constraints to an improbable "large-deviation regime" possess extreme statistics with one-dimensional (1D) Kardar-Parisi-Zhang (KPZ) fluctuations? The answer is positive, though nonuniversal, since the fluctuations depend on the underlying geometry. We consider in detail two examples of 2D systems for which imposed external constraints force the underlying stationary stochastic process to stay in an atypical regime with anomalous statistics. The first example deals with the fluctuations of a stretched 2D random walk above a semicircle or a triangle. In the second example we consider a 2D biased random walk along a channel with forbidden voids of circular and triangular shapes. In both cases we are interested in the dependence of a typical span 〈d(t)〉∼t^{γ} of the trajectory of t steps above the top of the semicircle or the triangle. We show that γ=1/3, i.e., 〈d(t)〉 shares the KPZ statistics for the semicircle, while γ=0 for the triangle. We propose heuristic derivations of scaling exponents γ for different geometries, justify them by explicit analytic computations, and compare with numeric simulations. For practical purposes, our results demonstrate that the geometry of voids in a channel might have a crucial impact on the width of the boundary layer and, thus, on the heat transfer in the channel.

PARP-1/2 Inhibitor Olaparib Prevents or Partially Reverts EMT Induced by TGF-β in NMuMG Cells

Poly- adenosine diphosphate (ADP)-ribose (PAR) is a polymer synthesized as a posttranslational modification by some poly (ADP-ribose) polymerases (PARPs), namely PARP-1, PARP-2, tankyrase-1, and tankyrase-2 (TNKS-1/2). PARP-1 is nuclear and has also been detected in extracellular vesicles. PARP-2 and TNKS-1/2 are distributed in nuclei and cytoplasm. PARP or PAR alterations have been described in tumors, and in particular by influencing the Epithelial- Mesenchymal Transition (EMT), which influences cell migration and drug resistance in cancer cells. Pro-EMT and anti-EMT effects of PARP-1 have been reported while whether PAR changes occur specifically during EMT is currently unknown. The PARP-1/2 inhibitor Olaparib (OLA) is approved by FDA to treat certain patients harboring cancers with impaired homologous recombination. Here, we studied PAR changes and OLA effects on EMT. Total and nuclear PAR increased in EMT while PAR belts were disassembled. OLA prevented EMT, according to: (i) molecular markers evaluated by immuno-cytofluorescence/image quantification, Western blots, and RNA quantitation, (ii) morphological changes expressed as anisotropy, and (iii) migration capacity in the scratch assay. OLA also partially reversed EMT. OLA might work through unconventional mechanisms of action (different from synthetic lethality), even in non-BRCA (breast cancer 1 gene) mutated cancers.

BIOLOGICAL MARKERS OF EXTERNAL AND INTERNAL EXPOSURE IN SHELTER CONSTRUCTION WORKERS: A 13-YEAR EXPERIENCE

OBJECTIVE

The aim of this study is to investigate the cellular, molecular, genetic and non-invasive functional biomarkers of occupational irradiation in workers exposed to a combination of external gamma-radiation and incorporation of transuranium elements.

RESULTS

A study was performed in 688 radiation workers of Shelter object conversion into a safe system with mean shift dose of external exposure of 26.06 mSv (range: 0.1-113.35) and risk of internal exposure with transuranium elements. Several biological parameters could serve as biomarkers of exposure at radiation doses below 100 mSv and even in 20-50 mSv interval. The parallel changes were shown in decline of brain electric activity, telomere length, differences in CCND1, CDKN1A, CDKN2A, VEGFA, TP53, DDB2 genes expression. An increase in counts of dicentrics, pair fragments and TCR-variant lymphocytes at doses over professional limits shows the need of biological dosimetry. The most sensitive markers include TCR-CD4+, γ-H2AX+ and CyclinD1+ cell counts. Implementation of flow cytometry approach for these markers enables quick obtaining of quantitative data. Confounding factors included respiratory function and smoking. The study of the radiation workers with the history of chronic exposure in radiation area during 3-5 years demonstrates changes of compensatory origin, i.e. absence of telomere shortening, increased number of NK-cells in combination with lower expression of intracellular γ-H2AX.

CONCLUSION

This study confirms the presence of radiation-induced changes in gene regulation of cell proliferation, telomere function and apoptosis in radiation workers exposed to external and internal exposure at doses above professional limits and increase of compensatory changes.

Effective Hamiltonian of topologically stabilized polymer states

Topologically stabilized polymer conformations in melts of nonconcatenated polymer rings and crumpled globules are considered to be a good candidate for the description of the spatial structure of mitotic chromosomes. Despite significant efforts, the microscopic Hamiltonian capable of describing such systems still remains unknown. We describe a polymer conformation by a Gaussian network - a system with a Hamiltonian quadratic in all coordinates - and show that by tuning interaction constants, one can obtain equilibrium conformations with any fractal dimension between 2 (an ideal polymer chain) and 3 (a crumpled globule). Monomer-to-monomer distances in topologically stabilized states, according to available numerical data, fit very well the Gaussian distribution, giving an additional argument in support of the quadratic Hamiltonian model. Mathematically, the polymer conformations are mapped onto the trajectories of a subdiffusive fractal Brownian particle. Moreover, we explicitly show that the quadratic Hamiltonian with a hierarchical set of coupling constants provides the microscopic background for the description of the path integral of the fractional Brownian motion with an algebraically decaying kernel.

Finite plateau in spectral gap of polychromatic constrained random networks

We consider critical behavior in the ensemble of polychromatic Erdős-Rényi networks and regular random graphs, where network vertices are painted in different colors. The links can be randomly removed and added to the network subject to the condition of the vertex degree conservation. In these constrained graphs we run the Metropolis procedure, which favors the connected unicolor triads of nodes. Changing the chemical potential, μ, of such triads, for some wide region of μ, we find the formation of a finite plateau in the number of intercolor links, which exactly matches the finite plateau in the network algebraic connectivity (the value of the first nonvanishing eigenvalue of the Laplacian matrix, λ_{2}). We claim that at the plateau the spontaneously broken Z_{2} symmetry is restored by the mechanism of modes collectivization in clusters of different colors. The phenomena of a finite plateau formation holds also for polychromatic networks with M≥2 colors. The behavior of polychromatic networks is analyzed via the spectral properties of their adjacency and Laplacian matrices.

From geometric optics to plants: the eikonal equation for buckling

Optimal buckling of a tissue, e.g. a plant leaf, growing by means of exponential division of its peripheral cells, is considered in the framework of a conformal approach. It is shown that the boundary profile of a tissue is described by the 2D eikonal equation, which provides the geometric optic approximation for the wavefront propagating in a medium with an inhomogeneous refraction coefficient. A variety of optimal surfaces embedded in 3D is controlled by spatial dependence of the refraction coefficient which, in turn, is dictated by the local growth protocol.

MicroRNA and mRNA Transcriptome Profiling in Primary Human Astrocytes Infected with Borrelia burgdorferi

Lyme disease is caused by infection with the bacterium Borrelia burgdorferi (Bb), which is transmitted to humans by deer ticks. The infection manifests usually as a rash and minor systemic symptoms; however, the bacteria can spread to other tissues, causing joint pain, carditis, and neurological symptoms. Lyme neuroborreliosis presents itself in several ways, such as Bell's palsy, meningitis, and encephalitis. The molecular basis for neuroborreliosis is poorly understood. Analysis of the changes in the expression levels of messenger RNAs and non-coding RNAs, including microRNAs, following Bb infection could therefore provide vital information on the pathogenesis and clinical symptoms of neuroborreliosis. To this end, we used cultured primary human astrocytes, key responders to CNS infection and important components of the blood-brain barrier, as a model system to study RNA and microRNA changes in the CNS caused by Bb. Using whole transcriptome RNA-seq, we found significant changes in 38 microRNAs and 275 mRNAs at 24 and 48 hours following Bb infection. Several of the RNA changes affect pathways involved in immune response, development, chromatin assembly (including histones) and cell adhesion. Further, several of the microRNA predicted target mRNAs were also differentially regulated. Overall, our results indicate that exposure to Bb causes significant changes to the transcriptome and microRNA profile of astrocytes, which has implications in the pathogenesis, and hence potential treatment strategies to combat this disease.

Eigenvalue tunneling and decay of quenched random network

We consider the canonical ensemble of N-vertex Erdős-Rényi (ER) random topological graphs with quenched vertex degree, and with fugacity μ for each closed triple of bonds. We claim complete defragmentation of large-N graphs into the collection of [p^{-1}] almost full subgraphs (cliques) above critical fugacity, μ_{c}, where p is the ER bond formation probability. Evolution of the spectral density, ρ(λ), of the adjacency matrix with increasing μ leads to the formation of a multizonal support for μ>μ_{c}. Eigenvalue tunneling from the central zone to the side one means formation of a new clique in the defragmentation process. The adjacency matrix of the network ground state has a block-diagonal form, where the number of vertices in blocks fluctuates around the mean value Np. The spectral density of the whole network in this regime has triangular shape. We interpret the phenomena from the viewpoint of the conventional random matrix model and speculate about possible physical applications.

Spontaneous symmetry breaking and phase coexistence in two-color networks

We consider an equilibrium ensemble of large Erdős-Renyi topological random networks with fixed vertex degree and two types of vertices, black and white, prepared randomly with the bond connection probability p. The network energy is a sum of all unicolor triples (either black or white), weighted with chemical potential of triples μ. Minimizing the system energy, we see for some positive μ the formation of two predominantly unicolor clusters, linked by a string of N_{bw} black-white bonds. We have demonstrated that the system exhibits critical behavior manifested in the emergence of a wide plateau on the N_{bw}(μ) curve, which is relevant to a spinodal decomposition in first-order phase transitions. In terms of a string theory, the plateau formation can be interpreted as an entanglement between baby universes in two-dimensional gravity. We conjecture that the observed classical phenomenon can be considered as a toy model for the chiral condensate formation in quantum chromodynamics.

RNA polymerase II pausing as a context-dependent reader of the genome

The RNA polymerase II (Pol II) transcribes all mRNA genes in eukaryotes and is among the most highly regulated enzymes in the cell. The classic model of mRNA gene regulation involves recruitment of the RNA polymerase to gene promoters in response to environmental signals. Higher eukaryotes have an additional ability to generate multiple cell types. This extra level of regulation enables each cell to interpret the same genome by committing to one of the many possible transcription programs and executing it in a precise and robust manner. Whereas multiple mechanisms are implicated in cell type-specific transcriptional regulation, how one genome can give rise to distinct transcriptional programs and what mechanisms activate and maintain the appropriate program in each cell remains unclear. This review focuses on the process of promoter-proximal Pol II pausing during early transcription elongation as a key step in context-dependent interpretation of the metazoan genome. We highlight aspects of promoter-proximal Pol II pausing, including its interplay with epigenetic mechanisms, that may enable cell type-specific regulation, and emphasize some of the pertinent questions that remain unanswered and open for investigation.

Searching the Human Genome for Snail and Slug With DNA@Home

DNA@Home is a volunteer computing project that aims to use Gibbs Sampling for the identification and location of DNA control signals on full genome-scale datasets. A fault tolerant and asynchronous implementation of Gibbs sampling using the Berkeley Open Infrastructure for Network Computing (BOINC) was used to identify the location of binding sites of the SNAI1 (Snail) and SNAI2 (Slug) transcription factors across the human genome. Genes regulated by Slug but not Snail, and genes regulated by Snail but not Slug provided two datasets with known motifs. These datasets contained up to 994 DNA sequences which to our knowledge is largest scale use of Gibbs sampling for discovery of binding sites. 1000 parallel sampling walks were used to search for the presence of 1, 2 or 3 possible motifs using small, medium, and full size sets of these sequences. These runs were performed over a period of two months using over 1500 volunteered computing hosts and generated over 2.2 Terabytes of sampling data. High performance computing resources were used for post processing. This paper presents intra and inter walk analyses used to determine walk convergence. The results were validated against current biological knowledge of the Snail and Slug promoter regions and present avenues for further biological study.

Epigenetic Modulation of Microglial Inflammatory Gene Loci in Helminth-Induced Immune Suppression: Implications for Immune Regulation in Neurocysticercosis

In neurocysticercosis, parasite-induced immune suppressive effects are thought to play an important role in enabling site-specific inhibition of inflammatory responses to infections. It is axiomatic that microglia-mediated (M1 proinflammatory) response causes central nervous system inflammation; however, the mechanisms by which helminth parasites modulate microglia activation remain poorly understood. Here, we show that microglia display a diminished expression of M1-inflammatory mediators such as tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and nitric oxide synthase 2 (NOS2) in murine neurocysticercosis. Microglia also exhibited a lack of myeloid cell maturation marker major histocompatibility complex (MHC)-II in these parasite-infected brains. Treatment of microglia with helminth soluble/secreted factors (HSFs) in vitro did not induce expression of M1-inflammatory signature molecule NOS2 as well as MHC-II in primary microglia. However, HSF treatment completely inhibited lipopolysaccharide-induced increase in expression of MHC-II, NOS2 and nitric oxide production in these cells. As epigenetic modulation of chromatin states that regulates recruitment of RNA polymerase II (Pol-II) is a key regulatory step in determining gene expression and functional outcome, we next evaluated whether HSF induced modulation of these phenomenon in microglia in vitro. Indeed, HSF downregulated Pol-II recruitment to the promoter region of TNF-α, IL-6, NOS2, MHC-II, and transcription factor CIITA (a regulator of MHC-II expression), by itself. Moreover, HSF suppressed the lipopolysaccharide-induced increase in Pol-II recruitment as well. In addition, HSF exposure reduced the positive histone marks H3K4Me3 and H3K9/14Ac at the promoter of TNF-α, IL-6, NOS2, MHC-II, and CIITA. These studies provide a novel mechanistic insight into helminth-mediated immune suppression in microglia via modulation of epigenetic processes.

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

Anti-sense transcription originating upstream of mammalian protein-coding genes is a well-documented phenomenon, but remarkably little is known about the regulation or function of anti-sense promoters and the non-coding RNAs they generate. Here we define at nucleotide resolution the divergent transcription start sites (TSSs) near mouse mRNA genes. We find that coupled sense and anti-sense TSSs precisely define the boundaries of a nucleosome-depleted region (NDR) that is highly enriched in transcription factor (TF) motifs. Notably, as the distance between sense and anti-sense TSSs increases, so does the size of the NDR, the level of signal-dependent TF binding, and gene activation. We further discover a group of anti-sense TSSs in macrophages with an enhancer-like chromatin signature. Interestingly, this signature identifies divergent promoters that are activated during immune challenge. We propose that anti-sense promoters serve as platforms for TF binding and establishment of active chromatin to further regulate or enhance sense-strand mRNA expression.

RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition

Promoter-proximal RNA polymerase II (Pol II) pausing is implicated in the regulation of gene transcription. However, the mechanisms of pausing including its dynamics during transcriptional responses remain to be fully understood. We performed global analysis of short capped RNAs and Pol II Chromatin Immunoprecipitation sequencing in MCF-7 breast cancer cells to map Pol II pausing across the genome, and used permanganate footprinting to specifically follow pausing during transcriptional activation of several genes involved in the epithelial to mesenchymal transition (EMT). We find that the gene for EMT master regulator Snail (SNAI1), but not Slug (SNAI2), shows evidence of Pol II pausing before activation. Transcriptional activation of the paused SNAI1 gene is accompanied by a further increase in Pol II pausing signal, whereas activation of non-paused SNAI2 gene results in the acquisition of a typical pausing signature. The increase in pausing signal reflects increased transcription initiation without changes in Pol II pausing. Activation of the heat shock HSP70 gene involves pausing release that speeds up Pol II turnover, but does not change pausing location. We suggest that Pol II pausing is retained during transcriptional activation and can further undergo regulated release in a signal-specific manner.

Ballistic deposition patterns beneath a growing Kardar-Parisi-Zhang interface

We consider a (1+1)-dimensional ballistic deposition process with next-nearest-neighbor interactions, which belongs to the Kardar-Parisi-Zhang (KPZ) universality class. The focus of our analysis is on the properties of structures appearing in the bulk of a growing aggregate: a forest of independent clusters separated by "crevices." Competition for growth (mutual screening) between different clusters results in "thinning" of this forest, i.e., the number density c(h) of clusters decreases with the height h of the pattern. For the discrete stochastic equation describing the process we introduce a variational formulation similar to that used for the randomly forced continuous Burgers equation. This allows us to identify the "clusters" and crevices with minimizers and shocks in the Burgers turbulence. Capitalizing on the ideas developed for the latter process, we find that c(h) ∼ h(-α) with α=2/3. We compute also scaling laws that characterize the ballistic deposition patterns in the bulk: the law of transversal fluctuations of cluster boundaries and the size distribution of clusters. It turns out that the intercluster interface is superdiffusive: the corresponding exponent is twice as large as the KPZ exponent for the surface of the aggregate. Finally we introduce a probabilistic concept of ballistic growth, dubbed the "hairy" Airy process in view of its distinctive geometric features. Its statistical properties are analyzed numerically.

Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation

Proper regulation of gene expression is essential for the differentiation, development and survival of all cells and organisms. Recent work demonstrates that transcription of many genes, including key developmental and stimulus-responsive genes, is regulated after the initiation step, by pausing of RNA polymerase II during elongation through the promoter-proximal region. Thus, there is great interest in better understanding the events that follow transcription initiation and the ways in which the efficiency of early elongation can be modulated to impact expression of these highly regulated genes. Here we describe our current understanding of the steps involved in the transition from an unstable initially transcribing complex into a highly stable and processive elongation complex. We also discuss the interplay between factors that affect early transcript elongation and the potential physiological consequences for genes that are regulated through transcriptional pausing.

The role of the T7 Gp2 inhibitor of host RNA polymerase in phage development

Bacteriophage T7 relies on its own RNA polymerase (RNAp) to transcribe its middle and late genes. Early genes, which include the viral RNAp gene, are transcribed by the host RNAp from three closely spaced strong promoters-A1, A2, and A3. One middle T7 gene product, gp2, is a strong inhibitor of the host RNAp. Gp2 is essential and is required late in infection, during phage DNA packaging. Here, we explore the role of gp2 in controlling host RNAp transcription during T7 infection. We demonstrate that in the absence of gp2, early viral transcripts continue to accumulate throughout the infection. Decreasing transcription from early promoter A3 is sufficient to make gp2 dispensable for phage infection. Gp2 also becomes dispensable when an antiterminating element boxA, located downstream of early promoters, is deleted. The results thus suggest that antiterminated transcription by host RNAp from the A3 promoter is interfering with phage development and that the only essential role for gp2 is to prevent this transcription.

Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila

Emerging evidence indicates that gene expression in higher organisms is regulated by RNA polymerase II stalling during early transcription elongation. To probe the mechanisms responsible for this regulation, we developed methods to isolate and characterize short RNAs derived from stalled RNA polymerase II in Drosophila cells. Significant levels of these short RNAs were generated from more than one-third of all genes, indicating that promoter-proximal stalling is a general feature of early polymerase elongation. Nucleotide composition of the initially transcribed sequence played an important role in promoting transcriptional stalling by rendering polymerase elongation complexes highly susceptible to backtracking and arrest. These results indicate that the intrinsic efficiency of early elongation can greatly affect gene expression.

NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly

The Negative Elongation Factor (NELF) is a transcription regulatory complex that induces stalling of RNA polymerase II (Pol II) during early transcription elongation and represses expression of several genes studied to date, including Drosophila Hsp70, mammalian proto-oncogene junB, and HIV RNA. To determine the full spectrum of NELF target genes in Drosophila, we performed a microarray analysis of S2 cells depleted of NELF and discovered that NELF RNAi affects many rapidly inducible genes involved in cellular responses to stimuli. Surprisingly, only one-third of NELF target genes were, like Hsp70, up-regulated by NELF-depletion, whereas the majority of target genes showed decreased expression levels upon NELF RNAi. Our data reveal that the presence of stalled Pol II at this latter group of genes enhances gene expression by maintaining a permissive chromatin architecture around the promoter-proximal region, and that loss of Pol II stalling at these promoters is accompanied by a significant increase in nucleosome occupancy and a decrease in histone H3 Lys 4 trimethylation. These findings identify a novel, positive role for stalled Pol II in regulating gene expression and suggest that there is a dynamic interplay between stalled Pol II and chromatin structure.

The elusive object of desire--interactions of bacteriophages and their hosts

Bacteria and their viruses (phages) are locked in an evolutionary contest, with each side producing constantly changing mechanisms of attack and defense that are aimed to increase the odds of survival. As a result, phages play central roles in a great variety of genetic processes and increase the rate of evolutionary change of the bacterial host, which could ultimately work to the benefit of the host in a long run.

Dissection of the bacteriophage T4 late promoter complex

Activated transcription of the bacteriophage T4 late genes is generated by a mechanism that stands apart from the common modalities of transcriptional regulation: the activator is gp45, the viral replisome's sliding clamp; two sliding-clamp-binding proteins, gp33 and gp55, replace the host RNA polymerase (RNAP) sigma subunit. We have mutagenized, reconfigured and selectively disrupted individual interactions of the sliding clamp with gp33 and gp55 and have monitored effects on transcription. The C-terminal sliding-clamp-binding epitopes of gp33 and gp55 are perfectly interchangeable, but the functions of these two RNAP-sliding clamp connections differ: only the gp33-gp45 linkage is essential for activation, while loss of the gp55-gp45 linkage impairs but does not abolish activation. Formation of transcription-ready promoter complexes by the sliding-clamp-activated wild-type T4 RNAP resists competition by high concentrations of the polyanion heparin. This avid formation of promoter complexes requires both linkages of the T4 late RNAP to the sliding clamp. Preopening the promoter compensates for loss of the gp55-gp45 but not the gp33-gp45 linkage. We interpret the relationship of these findings and our prior analysis to the common model of transcriptional initiation in bacteria in terms of two parallel pathways, with two RNAP holoenzymes and two DNA templates: (1) gp55-RNAP and the T4 late promoter execute basal transcription; (2) gp55-gp33-RNAP and the T4 late promoter with its mobile enhancer, the T4 sliding clamp, execute activated transcription. gp55 and gp33 perform sigma-like functions, gp55 in promoter recognition and gp33 (as well as gp55) in enhancer recognition. gp33 operates the switch between these two pathways by repressing basal transcription.

Promoter-proximal Pol II: when stalling speeds things up

Expression of genes was long thought to be regulated primarily at the level of RNA polymerase II (Pol II) recruitment to a gene promoter, and the dozen genes that did not fit this paradigm were regarded as exceptions. However, recent analyses of genome-wide Pol II distribution in Drosophila and mammalian systems have indicated that a large number of genes might be regulated at a step subsequent to Pol II recruitment, during early transcription elongation. At these genes, Pol II begins transcription but stalls after synthesizing a short RNA, and it is the release of this engaged Pol II from the promoter-proximal region that is rate limiting for transcription. Notably, promoter-proximal Pol II stalling is prevalent at genes involved in development and response to stimuli, suggesting that Pol II stalling during early elongation plays important roles in rapid and precise control of gene expression. Here we briefly summarize the current data on promoter-proximal Pol II stalling and discuss implications of this newly appreciated regulatory strategy.

Bethe Ansatz in the Bernoulli matching model of random sequence alignment

For the Bernoulli matching model of the sequence alignment problem we apply the Bethe Ansatz technique via an exact mapping to the five-vertex model on a square lattice. Considering the terracelike representation of the sequence alignment problem, we reproduce by the Bethe Ansatz the results for the averaged length of the longest common subsequence in the Bernoulli approximation. In addition, we compute the average number of nucleation centers of the terraces.

RNA polymerase is poised for activation across the genome

Regulation of gene expression is integral to the development and survival of all organisms. Transcription begins with the assembly of a pre-initiation complex at the gene promoter, followed by initiation of RNA synthesis and the transition to productive elongation. In many cases, recruitment of RNA polymerase II (Pol II) to a promoter is necessary and sufficient for activation of genes. However, there are a few notable exceptions to this paradigm, including heat shock genes and several proto-oncogenes, whose expression is attenuated by regulated stalling of polymerase elongation within the promoter-proximal region. To determine the importance of polymerase stalling for transcription regulation, we carried out a genome-wide search for Drosophila melanogaster genes with Pol II stalled within the promoter-proximal region. Our data show that stalling is widespread, occurring at hundreds of genes that respond to stimuli and developmental signals. This finding indicates a role for regulation of polymerase elongation in the transcriptional responses to dynamic environmental and developmental cues.

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

It is widely assumed that the key rate-limiting step in gene activation is the recruitment of RNA polymerase II (Pol II) to the core promoter. Although there are well-documented examples in which Pol II is recruited to a gene but stalls, a general role for Pol II stalling in development has not been established. We have carried out comprehensive Pol II chromatin immunoprecipitation microarray (ChIP-chip) assays in Drosophila embryos and identified three distinct Pol II binding behaviors: active (uniform binding across the entire transcription unit), no binding, and stalled (binding at the transcription start site). The notable feature of the approximately 10% genes that are stalled is that they are highly enriched for developmental control genes, which are either repressed or poised for activation during later stages of embryogenesis. We propose that Pol II stalling facilitates rapid temporal and spatial changes in gene activity during development.

Longest increasing subsequence as expectation of a simple nonlinear stochastic partial differential equation with a low noise intensity

We report some observations concerning the statistics of longest increasing subsequences (LIS). We argue that the expectation of LIS, its variance, and apparently the full distribution function appears in statistical analysis of some simple nonlinear stochastic partial differential equation in the limit of very low noise intensity.

Design and operation of the internal dosimetry program for the Chornobyl 'shelter implementation plan'

The paper discusses the system of individual monitoring for internal exposure, deployed by the Ukrainian Radiation Protection Institute as an integral component of the Shelter Implementation Plan (SIP) at the Chornobyl industrial site. SIP anticipates involving of up to 10,00 workers of numerous SIP contractors. A typical daily shift comprises several hundred workers. Most of them have a direct contact with the irradiated nuclear fuel, fuel-contained aerosols and other contaminated materials on the industrial site. The hierarchical SIP individual monitoring program has been designed with consideration of peculiarities of SIP exposure conditions and aims at the timely and reliable identification of intakes, assessment of doses and initiation of measures for prevention of further intakes.

How long does it take to pull an ideal polymer into a small hole?

We present scaling estimates for characteristic times taulin and taubr of pulling ideal linear and randomly branched polymers of N monomers into a small hole by a force f. We show that the absorbtion process develops as sequential straightening of folds of the initial polymer configuration. By estimating the typical size of the fold involved into the motion, we arrive at the following predictions, taulin(N) approximately N3/2/f and taubr(N)approximately N5/4/f, and we also confirm them by the molecular dynamics experiment.

The role of an upstream promoter interaction in initiation of bacterial transcription

The bacterial RNA polymerase (RNAP) recognizes promoters through sequence-specific contacts of its promoter-specificity components (sigma) with two DNA sequence motifs. Contacts with the upstream ('-35') promoter motif are made by sigma domain 4 attached to the flap domain of the RNAP beta subunit. Bacteriophage T4 late promoters consist solely of an extended downstream ('-10') motif specifically recognized by the T4 gene 55 protein (gp55). Low level basal transcription is sustained by gp55-RNAP holoenzyme. The late transcription coactivator gp33 binds to the beta flap and represses this basal transcription. Gp33 can also repress transcription by Escherichia coli sigma70-RNAP holoenzyme mutated to allow gp33 access to the beta flap. We propose that repression is due to gp33 blocking an upstream sequence-independent DNA-binding site on RNAP (as sigma70 domain 4 does) but, unlike sigma70 domain 4, providing no new DNA interaction. We show that this upstream interaction is essential only at an early step of transcription initiation, and discuss the role of this interaction in promoter recognition and transcriptional regulation.

Application of a two-length-scale field theory to the solvation of neutral and charged molecules

We develop a continuous self-consistent theory of solute-water interactions that allows determination of the hydrophobic layer around a solute molecule of any geometry, with an explicit account of solvent structure described by its correlation function. We compute the mean solvent density profile n(r) surrounding the solute molecule as well as its solvation free energy deltaG. We compare the two-length-scale field theory to the numerical data of Monte Carlo simulations found in the literature for spherical molecules and discuss the possibility of self-consistent adjustment of the free parameters of the theory. In the framework of this approach, we compute the solvation free energies of alkane molecules and the free energy of interaction of two spheres of radius R separated by the distance D. We describe the general setting of the self-consistent account of electrostatic interactions in the framework of our model where the water is considered not as a continuous medium but as a gas of dipoles. We analyze the limiting cases where the proposed theory coincides with the electrostatics of a continuous medium.

Exact asymptotic results for the Bernoulli matching model of sequence alignment

Finding analytically the statistics of the longest common subsequence (LCS) of a pair of random sequences drawn from c alphabets is a challenging problem in computational evolutionary biology. We present exact asymptotic results for the distribution of the LCS in a simpler, yet nontrivial, variant of the original model called the Bernoulli matching (BM) model. We show that in the BM model, for all c , the distribution of the asymptotic length of the LCS, suitably scaled, is identical to the Tracy-Widom distribution of the largest eigenvalue of a random matrix whose entries are drawn from a Gaussian unitary ensemble.

The bacteriophage T4 late-transcription coactivator gp33 binds the flap domain of Escherichia coli RNA polymerase

Transcription of bacteriophage T4 late genes requires concomitant DNA replication. T4 late promoters, which consist of a single 8-bp -10 motif, are recognized by a holoenzyme containing Escherichia coli RNA polymerase core and the T4-encoded promoter specificity subunit, gp55. Initiation of transcription at these promoters by gp55-holoenzyme is inefficient, but is greatly activated by the DNA-loaded DNA polymerase sliding clamp, gp45, and the coactivator, gp33. We report that gp33 attaches to the flap domain of the Escherichia coli RNA polymerase beta-subunit and that this interaction is essential for activation. The beta-flap also mediates recognition of -35 promoter motifs by binding to sigma(70) domain 4. The results suggest that gp33 is an analogue of sigma(70) domain 4 and that gp55 and gp33 together constitute two parts of the T4 late sigma. We propose a model for the role of the gp45 sliding clamp in activation of T4 late-gene transcription.