Enhanced frequency of transcription pre-initiation complexes assembly after exposure to UV irradiation results in increased repair activity and reduced probabilities for mutagenesis.

In addition to being essential for gene expression, transcription is crucial for the maintenance of genome integrity. Here, we undertook a systematic approach, to monitor the assembly kinetics of the pre-initiating RNA Polymerase (Pol) II at promoters at steady state and different stages during recovery from UV irradiation-stress, when pre-initiation and initiation steps have been suggested to be transiently shut down. Taking advantage of the reversible dissociation of pre-initiating Pol II after high salt treatment, we found that de novo recruitment of the available Pol II molecules at active promoters not only persists upon UV at all times tested but occurs significantly faster in the early phase of recovery (2 h) than in unexposed human fibroblasts at the majority of active genes. Our method unveiled groups of genes with significantly different pre-initiation complex (PIC) assembly dynamics after UV that present distinct rates of UV-related mutational signatures in melanoma tumours, providing functional relevance to the importance of keeping transcription initiation active during UV recovery. Our findings uncover novel mechanistic insights further detailing the multilayered transcriptional response to genotoxic stress and link PIC assembly dynamics after exposure to genotoxins with cancer mutational landscapes.

Prox1 inhibits neurite outgrowth during central nervous system development.

During central nervous system (CNS) development, proper and timely induction of neurite elongation is critical for generating functional, mature neurons, and neuronal networks. Despite the wealth of information on the action of extracellular cues, little is known about the intrinsic gene regulatory factors that control this developmental decision. Here, we report the identification of Prox1, a homeobox transcription factor, as a key player in inhibiting neurite elongation. Although Prox1 promotes acquisition of early neuronal identity and is expressed in nascent post-mitotic neurons, it is heavily down-regulated in the majority of terminally differentiated neurons, indicating a regulatory role in delaying neurite outgrowth in newly formed neurons. Consistently, we show that Prox1 is sufficient to inhibit neurite extension in mouse and human neuroblastoma cell lines. More importantly, Prox1 overexpression suppresses neurite elongation in primary neuronal cultures as well as in the developing mouse brain, while Prox1 knock-down promotes neurite outgrowth. Mechanistically, RNA-Seq analysis reveals that Prox1 affects critical pathways for neuronal maturation and neurite extension. Interestingly, Prox1 strongly inhibits many components of Ca2+ signaling pathway, an important mediator of neurite extension and neuronal maturation. In accordance, Prox1 represses Ca2+ entry upon KCl-mediated depolarization and reduces CREB phosphorylation. These observations suggest that Prox1 acts as a potent suppressor of neurite outgrowth by inhibiting Ca2+ signaling pathway. This action may provide the appropriate time window for nascent neurons to find the correct position in the CNS prior to initiation of neurites and axon elongation.

Insights into the local interaction mechanisms between fermenting broken maize and various binder materials for anaerobic digester structures.

Concrete structures of anaerobic digestion plants face chemically aggressive conditions due to the contact with the complex liquid fraction of the fermenting biowaste. This paper aims to determine the biogeochemical dynamic interaction phenomena at play between the biowaste and cementitious matrices at the local scale, and to identify durable binders in such environments. Binder materials likely to show increased durability - slag and calcium aluminate cement, and a metakaolin-based alkali-activated geopolymer - and a reference Portland cement were inserted into sealed bioeactors during 5 cycles (245 days) of broken maize anaerobic digestion. Cementitious pastes suffered chemical and mineralogical alteration related mainly to carbonation and leaching. However, they had no negative impact on the bioprocess in terms of pH, metabolic evolution of volatile fatty acids and NH4+, planktonic microbial community composition or CH4 production. In all reactors, the microbial community was able to perform the anaerobic digestion successfully. The MKAA was only slightly altered in its outermost layer. Its presence in the biowaste induced lower NH4+ concentrations, a slightly higher pH and a marked shift in the microbial community, but CH4 total production was not affected. Substantial enrichment of acid forming bacteria, especially members of the genus Clostridium, was observed in the biofilm formed on all materials.

Influence of Dissolved-Aluminum Concentration on Sulfur-Oxidizing Bacterial Activity in the Biodeterioration of Concrete.

Several studies undertaken on the biodeterioration of concrete sewer infrastructures have highlighted the better durability of aluminate-based materials. The bacteriostatic effect of aluminum has been suggested to explain the increase in durability of these materials. However, no clear demonstration of the negative effect of aluminum on cell growth has been yet provided in the literature. In the present study, we sought to investigate the inhibitory potential of dissolved aluminum on nonsterile microbial cultures containing sulfur-oxidizing microorganisms. Both kinetic (maximum specific growth rate) and stoichiometric (oxygen consumption yield) parameters describing cells activity were accurately determined by using respirometry measurements coupled with modeled data obtained from fed-batch cultures run for several days at pH below 4 and with increasing total aluminum (Altot) concentrations from 0 to 100 mM. Short-term inhibition was observed for cells poorly acclimated to high salinity. However, inhibition was significantly attenuated for cells grown on mortar substrate. Moreover, after a rapid adaptation, and for an Altot concentration up to 100 mM, both kinetic and stoichiometric growth parameters remained similar to those obtained in control culture conditions where no aluminum was added. This argued in favor of the impact of ionic strength change on the growth of sulfur-oxidizing microorganism rather than an inhibitory effect of dissolved aluminum. Other assumptions must therefore be put forward in order to explain the better durability of cement containing aluminate-based materials in sewer networks. Among these assumptions, the influence of physical or chemical properties of the material (phase reactivity, porosity, etc.) might be proposed.IMPORTANCE Biodeterioration of cement infrastructures represents 5 to 20% of observed deteriorations within the sewer network. Such biodeterioration events are mainly due to microbial sulfur-oxidizing activity which produces sulfuric acid able to dissolve cementitious material. Calcium aluminate cement materials are more resistant to biodeterioration compared to the commonly used Portland cement. Several theories have been suggested to describe this resistance, and the bacteriostatic effect of aluminum seems to be the most plausible explanation. However, results reported by the several studies on this exact topic are highly controversial. This present study provides a comprehensive analysis of the influence of dissolved aluminum on growth parameters of long-term cultures of sulfur-oxidizing bacterial consortia sampled from different origins. Kinetic and stoichiometric parameters estimated by respirometry measurements and modeling showed that total dissolved-aluminum concentrations up to 100 mM were not inhibitory, but it is more likely that a sudden increase in the ionic strength affects cell growth. Therefore, it appears that the bacteriostatic effect of aluminum on microbial growth cannot explain the better durability of aluminate based cementitious materials.

The dual role of LSD1 and HDAC3 in STAT5-dependent transcription is determined by protein interactions, binding affinities, motifs and genomic positions.

STAT5 interacts with other factors to control transcription, and the mechanism of regulation is of interest as constitutive active STAT5 has been reported in malignancies. Here, LSD1 and HDAC3 were identified as novel STAT5a interacting partners in pro-B cells. Characterization of STAT5a, LSD1 and HDAC3 target genes by ChIP-seq and RNA-seq revealed gene subsets regulated by independent or combined action of the factors and LSD1/HDAC3 to play dual role in their activation or repression. Genes bound by STAT5a alone or in combination with weakly associated LSD1 or HDAC3 were enriched for the canonical STAT5a GAS motif, and such binding induced activation or repression. Strong STAT5 binding was seen more frequently in intergenic regions, which might function as distal enhancer elements. Groups of genes bound weaker by STAT5a and stronger by LSD1/HDAC3 showed an absence of the GAS motif, and were differentially regulated based on their genomic binding localization and binding affinities. These genes exhibited increased binding frequency in promoters, and in conjunction with the absence of GAS sites, the data indicate a requirement for stabilization by additional factors, which might recruit LSD1/HDAC3. Our study describes an interaction network of STAT5a/LSD1/HDAC3 and a dual function of LSD1/HDAC3 on STAT5-dependent transcription, defined by protein-protein interactions, genomic binding localization/affinity and motifs.

Nucleotide Excision Repair: From Neurodegeneration to Cancer.

DNA damage poses a constant threat to genome integrity taking a variety of shapes and arising by normal cellular metabolism or environmental insults. Human syndromes, characterized by increased cancer pre-disposition or early onset of age-related pathology and developmental abnormalities, often result from defective DNA damage responses and compromised genome integrity. Over the last decades intensive research worldwide has made important contributions to our understanding of the molecular mechanisms underlying genomic instability and has substantiated the importance of DNA repair in cancer prevention in the general population. In this chapter, we discuss Nucleotide Excision Repair pathway, the causative role of its components in disease-related pathology and recent technological achievements that decipher mutational landscapes and may facilitate pathological classification and personalized therapy.

Comprehensive characterization of the neurogenic and neuroprotective action of a novel TrkB agonist using mouse and human stem cell models of Alzheimer's disease.

BACKGROUND: Neural stem cell (NSC) proliferation and differentiation in the mammalian brain decreases to minimal levels postnatally. Nevertheless, neurogenic niches persist in the adult cortex and hippocampus in rodents, primates and humans, with adult NSC differentiation sharing key regulatory mechanisms with development. Adult neurogenesis impairments have been linked to Alzheimer's disease (AD) pathology. Addressing these impairments by using neurotrophic factors is a promising new avenue for therapeutic intervention based on neurogenesis. However, this possibility has been hindered by technical difficulties of using in-vivo models to conduct screens, including working with scarce NSCs in the adult brain and differences between human and mouse models or ethical limitations. METHODS: Here, we use a combination of mouse and human stem cell models for comprehensive in-vitro characterization of a novel neurogenic compound, focusing on the brain-derived neurotrophic factor (BDNF) pathway. The ability of ENT-A011, a steroidal dehydroepiandrosterone derivative, to activate the tyrosine receptor kinase B (TrkB) receptor was tested through western blotting in NIH-3T3 cells and its neurogenic and neuroprotective action were assessed through proliferation, cell death and Amyloid-ß (Aß) toxicity assays in mouse primary adult hippocampal NSCs, mouse embryonic cortical NSCs and neural progenitor cells (NPCs) differentiated from three human induced pluripotent stem cell lines from healthy and AD donors. RNA-seq profiling was used to assess if the compound acts through the same gene network as BDNF in human NPCs. RESULTS: ENT-A011 was able to increase proliferation of mouse primary adult hippocampal NSCs and embryonic cortical NSCs, in the absence of EGF/FGF, while reducing Aß-induced cell death, acting selectively through TrkB activation. The compound was able to increase astrocytic gene markers involved in NSC maintenance, protect hippocampal neurons from Αß toxicity and prevent synapse loss after Aß treatment. ENT-A011 successfully induces proliferation and prevents cell death after Aß toxicity in human NPCs, acting through a core gene network shared with BDNF as shown through RNA-seq. CONCLUSIONS: Our work characterizes a novel BDNF mimetic with preferable pharmacological properties and neurogenic and neuroprotective actions in Alzheimer's disease via stem cell-based screening, demonstrating the promise of stem cell systems for short-listing competitive candidates for further testing.

Histone H2Bub dynamics in the 5' region of active genes are tightly linked to the UV-induced transcriptional response.

The timing and location of writing and erasing of histone modifications determine gene expression programs and are tightly controlled processes. One such modification is the monoubiquitination of histone H2B (H2Bub), whose precise level during transcription elongation is dynamically regulated by the synergistic action of RNF20/40 ubiquitin-ligase and the de-ubiquitinase (DUB) of the ATXN7L3-containing DUB modules. Here, we characterize the dynamics of H2Bub in transcription and explore its role in perspective with the recently updated model of UV damage-induced transcription reorganization. Employing integrative analysis of genome-wide high-throughput approaches, transcription inhibitors and ATXN7L3-DUB knockdown cells, we find that H2Bub levels and patterns depend on intron-exon architecture both in steady state and upon UV. Importantly, our analysis reveals a widespread redistribution of this histone mark, rather than a uniform loss as previously suggested, which closely mirrors the post-UV dynamics of elongating RNA Polymerase II (RNAPII) at transcribed loci. The observed effects are due to a direct inter-dependence on RNAPII local concentration and speed, and we show that deficient ATXN7L3-mediated DUB activity leads to increased elongation rates in both non-irradiated and irradiated conditions. Our data and the implementation of a high-resolution computational framework reveal that the H2Bub pattern follows that of RNAPII, both in the ATXNL3 knockdown and in response to UV guaranteeing faithful elongation speed, especially in the context of the transcription-driven DNA damage response.

PSTVd infection in Nicotiana benthamiana plants has a minor yet detectable effect on CG methylation.

Viroids are small circular RNAs infecting a wide range of plants. They do not code for any protein or peptide and therefore rely on their structure for their biological cycle. Observed phenotypes of viroid infected plants are thought to occur through changes at the transcriptional/translational level of the host. A mechanism involved in such changes is RNA-directed DNA methylation (RdDM). Till today, there are contradictory works about viroids interference of RdDM. In this study, we investigated the epigenetic effect of viroid infection in Nicotiana benthamiana plants. Using potato spindle tuber viroid (PSTVd) as the triggering pathogen and via bioinformatic analyses, we identified endogenous gene promoters and transposable elements targeted by 24 nt host siRNAs that differentially accumulated in PSTVd-infected and healthy plants. The methylation status of these targets was evaluated following digestion with methylation-sensitive restriction enzymes coupled with PCR amplification, and bisulfite sequencing. In addition, we used Methylation Sensitive Amplification Polymorphism (MSAP) followed by sequencing (MSAP-seq) to study genomic DNA methylation of 5-methylcytosine (5mC) in CG sites upon viroid infection. In this study we identified a limited number of target loci differentially methylated upon PSTVd infection. These results enhance our understanding of the epigenetic host changes as a result of pospiviroid infection.

Genomic analysis reveals a novel nuclear factor-κB (NF-κB)-binding site in Alu-repetitive elements.

The transcription factor NF-κB is a critical regulator of immune responses. To determine how NF-κB builds transcriptional control networks, we need to obtain a topographic map of the factor bound to the genome and correlate it with global gene expression. We used a ChIP cloning technique and identified novel NF-κB target genes in response to virus infection. We discovered that most of the NF-κB-bound genomic sites deviate from the consensus and are located away from conventional promoter regions. Remarkably, we identified a novel abundant NF-κB-binding site residing in specialized Alu-repetitive elements having the potential for long range transcription regulation, thus suggesting that in addition to its known role, NF-κB has a primate-specific function and a role in human evolution. By combining these data with global gene expression profiling of virus-infected cells, we found that most of the sites bound by NF-κB in the human genome do not correlate with changes in gene expression of the nearby genes and they do not appear to function in the context of synthetic promoters. These results demonstrate that repetitive elements interspersed in the human genome function as common target sites for transcription factors and may play an important role in expanding the repertoire of binding sites to engage new genes into regulatory networks.

Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis.

BACKGROUND: Synovial fibroblasts (SFs) are specialized cells of the synovium that provide nutrients and lubricants for the proper function of diarthrodial joints. Recent evidence appreciates the contribution of SF heterogeneity in arthritic pathologies. However, the normal SF profiles and the molecular networks that govern the transition from homeostatic to arthritic SF heterogeneity remain poorly defined. METHODS: We applied a combined analysis of single-cell (sc) transcriptomes and epigenomes (scRNA-seq and scATAC-seq) to SFs derived from naïve and hTNFtg mice (mice that overexpress human TNF, a murine model for rheumatoid arthritis), by employing the Seurat and ArchR packages. To identify the cellular differentiation lineages, we conducted velocity and trajectory analysis by combining state-of-the-art algorithms including scVelo, Slingshot, and PAGA. We integrated the transcriptomic and epigenomic data to infer gene regulatory networks using ArchR and custom-implemented algorithms. We performed a canonical correlation analysis-based integration of murine data with publicly available datasets from SFs of rheumatoid arthritis patients and sought to identify conserved gene regulatory networks by utilizing the SCENIC algorithm in the human arthritic scRNA-seq atlas. RESULTS: By comparing SFs from healthy and hTNFtg mice, we revealed seven homeostatic and two disease-specific subsets of SFs. In healthy synovium, SFs function towards chondro- and osteogenesis, tissue repair, and immune surveillance. The development of arthritis leads to shrinkage of homeostatic SFs and favors the emergence of SF profiles marked by Dkk3 and Lrrc15 expression, functioning towards enhanced inflammatory responses and matrix catabolic processes. Lineage inference analysis indicated that specific Thy1+ SFs at the root of trajectories lead to the intermediate Thy1+/Dkk3+/Lrrc15+ SF states and culminate in a destructive and inflammatory Thy1- SF identity. We further uncovered epigenetically primed gene programs driving the expansion of these arthritic SFs, regulated by NFkB and new candidates, such as Runx1. Cross-species analysis of human/mouse arthritic SF data determined conserved regulatory and transcriptional networks. CONCLUSIONS: We revealed a dynamic SF landscape from health to arthritis providing a functional genomic blueprint to understand the joint pathophysiology and highlight the fibroblast-oriented therapeutic targets for combating chronic inflammatory and destructive arthritic disease.

The fate of tetrathionate during the development of a biofilm in biogenic sulfuric acid attack on different cementitious materials.

The biodeterioration of cement-based materials in sewer environments occurs because of the production of sulfuric acid from the biochemical oxidation of H2S by sulfur-oxidizing bacteria (SOB). In the perspective of determining the possible reaction pathways for the sulfur cycle in such conditions, hydrated cementitious binders were exposed to an accelerated laboratory test (BAC test) to reproduce a biochemical attack similar to the one occurring in the sewer networks. Tetrathionate was used as a reduced sulfur source to naturally develop sulfur-oxidizing activities on the surfaces of materials. The transformation of tetrathionate was investigated on materials made from different binders: Portland cement, calcium aluminate cement, calcium sulfoaluminate cement and alkali-activated slag. The pH and the concentration of the different sulfur species were monitored in the leached solutions during 3 months of exposure. The results showed that the formation of different polythionates was independent of the nature of the material. The main parameter controlling the phenomena was the evolution of the pH of the leached solutions. Moreover, tetrathionate disproportionation was detected with the formation of more reduced forms of sulfur compounds (pentathionate, hexathionate and elemental sulfur) along with thiosulfate and sulfate. The experimental findings allowed numerical models to be developed to estimate the amount of sulfur compounds as a function of the pH evolution. In addition, biomass samples were collected from the exposed surface and from the deteriorated layers to identify the microbial populations. No clear influence of the cementitious materials on the selected populations was detected, confirming the previous results concerning the impact of the materials on the selected reaction pathways for tetrathionate transformation.

Blast-furnace slag cement and metakaolin based geopolymer as construction materials for liquid anaerobic digestion structures: Interactions and biodeterioration mechanisms.

In order to promote the development of the biogas industry, solutions are needed to improve concrete structures durability in this environment. This multiphysics study aims to analyse the multiphases interactions between the liquid phase of an anaerobic digestion system and cementitious matrices, focusing on (i) the impacts of the binder nature on the anaerobic digestion process at local scale, and (ii) the deterioration mechanisms of the materials. Cementitious pastes made of slag cement (CEM III), innovative metakaolin-based alkali-activated material (MKAA), with compositions presumed to resist chemically aggressive media, and a reference binder, ordinary Portland cement (CEM I), were tested by immersion in inoculated cattle manure in bioreactors for a long period of five digestion cycles. For the first time it was shown that the digestion process was disturbed in the short term by the presence of the materials that increased the pH of the liquid phase and slowed the acids consumption, with much more impact of the MKAA. However, the final total production of biogas was similar in all bioreactors. Material analyses showed that, in this moderately aggressive medium, the biodeterioration of the CEM I and CEM III pastes mainly led to cement matrix leaching (decalcification) and carbonation. MKAA showed a good behaviour with very low degraded depths. In addition, the material was found to have interesting ammonium adsorption properties in the chemical conditions (notably the pH range) of anaerobic digestion.

Laboratory Test to Evaluate the Resistance of Cementitious Materials to Biodeterioration in Sewer Network Conditions.

The biodeterioration of cementitious materials in sewer networks has become a major economic, ecological, and public health issue. Establishing a suitable standardized test is essential if sustainable construction materials are to be developed and qualified for sewerage environments. Since purely chemical tests are proven to not be representative of the actual deterioration phenomena in real sewer conditions, a biological test-named the Biogenic Acid Concrete (BAC) test-was developed at the University of Toulouse to reproduce the biological reactions involved in the process of concrete biodeterioration in sewers. The test consists in trickling a solution containing a safe reduced sulfur source onto the surface of cementitious substrates previously covered with a high diversity microbial consortium. In these conditions, a sulfur-oxidizing metabolism naturally develops in the biofilm and leads to the production of biogenic sulfuric acid on the surface of the material. The representativeness of the test in terms of deterioration mechanisms has been validated in previous studies. A wide range of cementitious materials have been exposed to the biodeterioration test during half a decade. On the basis of this large database and the expertise gained, the purpose of this paper is (i) to propose a simple and robust performance criterion for the test (standardized leached calcium as a function of sulfate produced by the biofilm), and (ii) to demonstrate the repeatability, reproducibility, and discriminability of the test method. In only a 3-month period, the test was able to highlight the differences in the performances of common cement-based materials (CEM I, CEM III, and CEM V) and special calcium aluminate cement (CAC) binders with different nature of aggregates (natural silica and synthetic calcium aluminate). The proposed performance indicator (relative standardized leached calcium) allowed the materials to be classified according to their resistance to biogenic acid attack in sewer conditions. The repeatability of the test was confirmed using three different specimens of the same material within the same experiment and the reproducibility of the results was demonstrated by standardizing the results using a reference material from 5 different test campaigns. Furthermore, developing post-testing processing and calculation methods constituted a first step toward a standardized test protocol.

Continuous transcription initiation guarantees robust repair of all transcribed genes and regulatory regions.

Inhibition of transcription caused by DNA damage-impaired RNA polymerase II (Pol II) elongation conceals a local increase in de novo transcription, slowly progressing from Transcription Start Sites (TSSs) to gene ends. Although associated with accelerated repair of Pol II-encountered lesions and limited mutagenesis, it is still unclear how this mechanism is maintained during genotoxic stress-recovery. Here we uncover a widespread gain in chromatin accessibility and preservation of the active H3K27ac mark after UV-irradiation. The concomitant increase in Pol II escape from promoter-proximal pause (PPP) sites of most active genes, PROMPTs and enhancer RNAs favors unrestrained initiation, as evidenced by the synthesis of nascent RNAs including start RNAs. Accordingly, drug-inhibition of PPP-release replenishes levels of pre-initiating Pol II at TSSs after UV. Our data show that such continuous engagement of Pol II molecules ensures maximal transcription-driven repair throughout expressed genes and regulatory loci. Importantly, revealing this unanticipated regulatory layer of UV-response provides physiological relevant traction to the emerging concept that Pol II initiation rate is determined by pause-release dynamics.

Nuclear-targeted chimeric vector enhancing nonviral gene transfer into skeletal muscle of Fabry mice in vivo.

Poor nuclear entry, especially into nondividing cells, is a limiting factor in nonviral gene delivery. We have engineered a novel chimeric vector relying on the controlled assembly of a TAT-tagged multisubunit DNA binding protein (EcoR124I) with expression plasmids containing the EcoR124I recognition site. Molecular interactions of this molecular assembly were studied by electrophoretic mobility shift assay and atomic force microscopy. Maintenance of nanocomplexes in an appropriate stoichiometric ratio was both necessary and sufficient to produce a significant (>8-fold) increase in the activity of the therapeutic alpha-galactosidase A enzyme after intramuscular administration in the mouse model of Fabry disease. To our knowledge, this is the first molecular targeting system significantly enhancing plasmid-based expression in skeletal muscle. Coinjection with pluronic SP1017 produced further enhancement of gene expression, demonstrating cumulative effects of the increased nuclear delivery by TAT chimeras and transcription activation by the pluronic. Cell penetration peptides (CPP), such as TAT, have been shown to improve delivery of macromolecules, when linked directly. However, in our system TAT-enhanced targeting took place even though it was linked to the plasmid DNA molecule indirectly via two noncovalent bonds. Therefore, this proof-of principle result indicates that TAT (and potentially other CPP) can be used for targeting modular chimeric vectors and therapeutic nanodevices.

Global unleashing of transcription elongation waves in response to genotoxic stress restricts somatic mutation rate.

Complex molecular responses preserve gene expression accuracy and genome integrity in the face of environmental perturbations. Here we report that, in response to UV irradiation, RNA polymerase II (RNAPII) molecules are dynamically and synchronously released from promoter-proximal regions into elongation to promote uniform and accelerated surveillance of the whole transcribed genome. The maximised influx of de novo released RNAPII correlates with increased damage-sensing, as confirmed by RNAPII progressive accumulation at dipyrimidine sites and by the average slow-down of elongation rates in gene bodies. In turn, this transcription elongation 'safe' mode guarantees efficient DNA repair regardless of damage location, gene size and transcription level. Accordingly, we detect low and homogenous rates of mutational signatures associated with UV exposure or cigarette smoke across all active genes. Our study reveals a novel advantage for transcription regulation at the promoter-proximal level and provides unanticipated insights into how active transcription shapes the mutagenic landscape of cancer genomes.

Emerging vectors and targeting methods for nonviral gene therapy.

Until recently, nonviral vectors were outside the mainstream of gene transfer technology. Recent problems in clinical trials using viral vectors renewed interest in these methods. The clinical usefulness of nonviral methods is still hindered by their relatively low gene delivery/transgene expression efficiencies. Vectors must navigate a series of obstacles before the therapeutic gene can be expressed. This review considers these barriers and the properties of components of nonviral vectors that are essential for nucleic acid transfer. Although developments of new physical methods (hydrodynamic delivery, ultrasound, electroporation) have made a significant impact on gene transfer efficiency, various chemical carriers (lipids and polymers) have been shown to achieve high-level gene delivery and functional expression. Success of nonviral gene targeting will depend not only on the efficacy, but also safety of this methodology, and this aspect is also discussed. Understanding problems associated with nonviral targeting can also help in designing better viral vectors. In fact, interplay between viral and nonviral technologies should lead to a continued refinement of both methodologies.

Thermoresponsive polymers as gene delivery vectors: cell viability, DNA transport and transfection studies.

A range of gene delivery vectors containing the thermoresponsive polymer, poly(N-isopropylacrylamide) (PNIPAm) was evaluated for effects on cell viability, intracellular trafficking and transgene expression in C2C12 mouse muscle cells. Polymers were complexed with plasmid DNA at pH 7.4 and the ability of the resulting particles to transfect cells was assessed via confocal microscopy and protein expression studies in tissue culture. Cell viability assays indicated that these polymers were toxic at high concentrations when not complexed to DNA or at certain polymer:DNA ratios. Poly(ethyleneimine) co-polymers with side-chain grafted PNIPAm were shown to be less toxic than poly(ethyleneimine) alone or PNIPAm-co-(N,N'-dimethylaminoethylmethacrylate) linear co-polymers and the effects were concentration dependent. Confocal micrographs of labeled polymers and DNA indicated rapid cellular entry for all the complexes but expression of Green Fluorescent Protein was achieved only when the branched PEI-PNIPAm co-polymers were used as vectors. The results indicate that design of appropriate co-polymer components and overall polymer architecture can be used to mediate, and perhaps ultimately control, DNA transport and transgene expression.

Composite macroH2A/NRF-1 Nucleosomes Suppress Noise and Generate Robustness in Gene Expression.

The histone variant macroH2A (mH2A) has been implicated in transcriptional repression, but the molecular mechanisms that contribute to global mH2A-dependent genome regulation remain elusive. Using chromatin immunoprecipitation sequencing (ChIP-seq) coupled with transcriptional profiling in mH2A knockdown cells, we demonstrate that singular mH2A nucleosomes occupy transcription start sites of subsets of both expressed and repressed genes, with opposing regulatory consequences. Specifically, mH2A nucleosomes mask repressor binding sites in expressed genes but activator binding sites in repressed genes, thus generating distinct chromatin landscapes that limit genetic or extracellular inductive signals. We show that composite nucleosomes containing mH2A and NRF-1 are stably positioned on gene regulatory regions and can buffer transcriptional noise associated with antiviral responses. In contrast, mH2A nucleosomes without NRF-1 bind promoters weakly and mark genes with noisier gene expression patterns. Thus, the strategic position and stabilization of mH2A nucleosomes in human promoters defines robust gene expression patterns.