Critical aspects in dissolution testing of nanomaterials in the oro-gastrointestinal tract: the relevance of juice composition for hazard identification and grouping.

The dissolution of a nanomaterial (NM) in an in vitro simulant of the oro-gastrointestinal (OGI) tract is an important predictor of its biodurability in vivo. The cascade addition of simulated digestive juices (saliva, stomach and intestine), including inorganic/organic biomacromolecules and digestive enzymes (complete composition, referred to as "Type 1 formulation"), strives for realistic representation of chemical composition of the OGI tract. However, the data robustness requires consideration of analytical feasibility, such as the use of simplified media. Here we present a systematic analysis of the effects exerted by different digestive juice formulations on the dissolution% (or half-life values) of benchmark NMs (e.g., zinc oxide, titanium dioxide, barium sulfate, and silicon dioxide). The digestive juices were progressively simplified by removal of components such as organic molecules, enzymes, and inorganic molecules (Type 2, 3 and 4). The results indicate that the "Type 1 formulation" augments the dissolution via sequestration of ions by measurable factors compared to formulations without enzymes (i.e., Type 3 and 4). Type 1 formulation is thus regarded as a preferable option for predicting NM biodurability for hazard assessment. However, for grouping purposes, the relative similarity among diverse nanoforms (NFs) of a NM is decisive. Two similarity algorithms were applied, and additional case studies comprising NFs and non NFs of the same substance were included. The results support the grouping decision by simplified formulation (Type 3) as a robust method for screening and grouping purposes.

Grouping of orally ingested silica nanomaterials via use of an integrated approach to testing and assessment to streamline risk assessment.

BACKGROUND: Nanomaterials can exist in different nanoforms (NFs). Their grouping may be supported by the formulation of hypotheses which can be interrogated via integrated approaches to testing and assessment (IATA). IATAs are decision trees that guide the user through tiered testing strategies (TTS) to collect the required evidence needed to accept or reject a grouping hypothesis. In the present paper, we investigated the applicability of IATAs for ingested NFs using a case study that includes different silicon dioxide, SiO2 NFs. Two oral grouping hypotheses addressing local and systemic toxicity were identified relevant for the grouping of these NFs and verified through the application of oral IATAs. Following different Tier 1 and/or Tier 2 in vitro methods of the TTS (i.e., in vitro dissolution, barrier integrity and inflammation assays), we generated the NF datasets. Furthermore, similarity algorithms (e.g., Bayesian method and Cluster analysis) were utilized to identify similarities among the NFs and establish a provisional group(s). The grouping based on Tier 1 and/or Tier 2 testing was analyzed in relation to available Tier 3 in vivo data in order to verify if the read-across was possible and therefore support a grouping decision. RESULTS: The measurement of the dissolution rate of the silica NFs in the oro-gastrointestinal tract and in the lysosome identified them as gradually dissolving and biopersistent NFs. For the local toxicity to intestinal epithelium (e.g. cytotoxicity, membrane integrity and inflammation), the biological results of the gastrointestinal tract models indicate that all of the silica NFs were similar with respect to the lack of local toxicity and, therefore, belong to the same group; in vivo data (although limited) confirmed the lack of local toxicity of NFs. For systemic toxicity, Tier 1 data did not identify similarity across the NFs, with results across different decision nodes being inconsistent in providing homogeneous group(s). Moreover, the available Tier 3 in vivo data were also insufficient to support decisions based upon the obtained in vitro results and relating to the toxicity of the tested NFs. CONCLUSIONS: The information generated by the tested oral IATAs can be effectively used for similarity assessment to support a grouping decision upon the application of a hypothesis related to toxicity in the gastrointestinal tract. The IATAs facilitated a structured data analysis and, by means of the expert's interpretation, supported read-across with the available in vivo data. The IATAs also supported the users in decision making, for example, reducing the testing when the grouping was well supported by the evidence and/or moving forward to advanced testing (e.g., the use of more suitable cellular models or chronic exposure) to improve the confidence level of the data and obtain more focused information.

How can we justify grouping of nanoforms for hazard assessment? Concepts and tools to quantify similarity.

The risk of each nanoform (NF) of the same substance cannot be assumed to be the same, as they may vary in their physicochemical characteristics, exposure and hazard. However, neither can we justify a need for more animal testing and resources to test every NF individually. To reduce the need to test all NFs, (regulatory) information requirements may be fulfilled by grouping approaches. For such grouping to be acceptable, it is important to demonstrate similarities in physicochemical properties, toxicokinetic behaviour, and (eco)toxicological behaviour. The GRACIOUS Framework supports the grouping of NFs, by identifying suitable grouping hypotheses that describe the key similarities between different NFs. The Framework then supports the user to gather the evidence required to test these hypotheses and to subsequently assess the similarity of the NFs within the proposed group. The evidence needed to support a hypothesis is gathered by an Integrated Approach to Testing and Assessment (IATA), designed as decision trees constructed of decision nodes. Each decision node asks the questions and provides the methods needed to obtain the most relevant information. This White paper outlines existing and novel methods to assess similarity of the data generated for each decision node, either via a pairwise analysis conducted property-by-property, or by assessing multiple decision nodes simultaneously via a multidimensional analysis. For the pairwise comparison conducted property-by-property we included in this White paper: The x-fold, Bayesian and Arsinh-OWA distance algorithms performed comparably in the scoring of similarity between NF pairs. The Euclidean distance was also useful, but only with proper data transformation. The x-fold method does not standardize data, and thus produces skewed histograms, but has the advantage that it can be implemented without programming knowhow. A range of multidimensional evaluations, using for example dendrogram clustering approaches, were also investigated. Multidimensional distance metrics were demonstrated to be difficult to use in a regulatory context, but from a scientific perspective were found to offer unexpected insights into the overall similarity of very different materials. In conclusion, for regulatory purposes, a property-by-property evaluation of the data matrix is recommended to substantiate grouping, while the multidimensional approaches are considered to be tools of discovery rather than regulatory methods.

Ordered weighted average based grouping of nanomaterials with Arsinh and dose response similarity models.

In the context of the EU GRACIOUS project, we propose a novel procedure for similarity assessment and grouping of nanomaterials. This methodology is based on the (1) Arsinh transformation function for scalar properties, (2) full curve shape comparison by application of a modified Kolmogorov-Smirnov metric for bivariate properties, (3) Ordered Weighted Average (OWA) aggregation-based grouping distance, and (4) hierarchical clustering. The approach allows for grouping of nanomaterials that is not affected by the dataset, so that group membership will not change when new candidates are included in the set of assessed materials. To facilitate the application of the proposed methodology, a software script was developed by using the R programming language which is currently under migration to a web tool. The presented approach was tested against a dataset, derived from literature review, related to immobilization of Daphnia magna and reporting information on several nanomaterials and properties.

Bayesian based similarity assessment of nanomaterials to inform grouping.

Nanoforms can be manufactured in plenty of variants by differing their physicochemical properties and toxicokinetic behaviour which can affect their hazard potential. To avoid testing of each single nanomaterial and nanoform variation and subsequently save resources, grouping and read-across strategies are used to estimate groups of substances, based on carefully selected evidence, that could potentially have similar human health and environmental hazard impact. A novel computational similarity method is presented aiming to compare dose-response curves and identify sets of similar nanoforms. The suggested method estimates the statistical model that best fits the data by leveraging pairwise Bayes Factor analysis to compare pairs of curves and evaluate whether each of the nanoforms is sufficiently similar to all other nanoforms. Pairwise comparisons to benchmark materials are used to define threshold similarity values and set the criteria for identifying groups of nanoforms with comparatively similar toxicity. Applications to use case data are shown to demonstrate that the method can support grouping hypotheses linked to a certain hazard endpoint and route of exposure.

Determining nanoform similarity via assessment of surface reactivity by abiotic and in vitro assays.

Grouping of substances is a method used to streamline hazard and risk assessment. Assessment of similarity provides the scientific evidence needed for formation of groups. This work reports on justification of grouping of nanoforms (NFs) via similarity of their surface reactivity. Four reactivity assays were used for concentration dependent detection of reactive oxygen species (ROS) generated by NFs: abiotic assays FRAS, EPR and DCFH2-DA, as well as the in vitro assay of NRF2/ARE responsive luciferase reporter activation in the HEK293 cell line. Representative materials (CuO, Mn2O3, BaSO4, CeO2 and ZnO) and three case studies of each several NFs of iron oxides, Diketopyrrolopyrroles (DPP)-based organic pigments and silicas were assessed. A novel similarity assessment algorithm was applied to quantify similarities between pairs of NFs, in a four-step workflow on concentration-response curves, individual concentration and response ranges, and finally the representative materials. We found this algorithm to be applicable to all abiotic and in vitro assays that were tested. Justification of grouping must include the increased potency of smaller particles via the scaling of effects with specific surface, and hence quantitative similarity analysis was performed on concentration-response in mass-metrics. CuO and BaSO4 were the most and least reactive representative materials respectively, and all assays found BaSO4/CuO not similar, as confirmed by their different NOAECs of in vivo studies. However, similarity outcomes from different reactivity assays were not always in agreement, highlighting the need to generate data by one assay for the representative materials and the candidate group of NFs. Despite low similarity scores in vitro some pairs of case study NFs can be accepted as sufficiently similar because the in vivo NOAECs are similar, highlighting the conservative assessment by the abiotic assays.

A Weight of Evidence approach to classify nanomaterials according to the EU Classification, Labelling and Packaging Regulation criteria.

In the context of the European Union (EU) Horizon 2020 GRACIOUS project (Grouping, Read-Across, Characterisation and classification framework for regulatory risk assessment of manufactured nanomaterials and Safer design of nano-enabled products), we proposed a quantitative Weight of Evidence (WoE) approach for hazard classification of nanomaterials (NMs). This approach is based on the requirements of the European Regulation on Classification, Labelling and Packaging of Substances and Mixtures (the CLP regulation), which implements the United Nations' Globally Harmonized System of Classification and Labelling of Chemicals (UN GHS) in the European Union. The goal of this WoE methodology is to facilitate classification of NMs according to CLP criteria, following the decision trees defined in ECHA's CLP regulatory guidance. In the WoE, results from heterogeneous studies are weighted according to data quality and completeness criteria, integrated, and then evaluated by expert judgment to obtain a hazard classification, resulting in a coherent and justifiable methodology. Moreover, the probabilistic nature of the proposed approach enables highlighting the uncertainty in the analysis. The proposed methodology involves the following stages: (1) collection of data for different NMs related to the endpoint of interest: each study related to each NM is referred as a Line of Evidence (LoE); (2) computation of weighted scores for each LoE: each LoE is weighted by a score calculated based on data quality and completeness criteria defined in the GRACIOUS project; (3) comparison and integration of the weighed LoEs for each NM: A Monte Carlo resampling approach is adopted to quantitatively and probabilistically integrate the weighted evidence; and (4) assignment of each NM to a hazard class: according to the results, each NM is assigned to one of the classes defined by the CLP regulation. Furthermore, to facilitate the integration and the classification of the weighted LoEs, an online R tool was developed. Finally, the approach was tested against an endpoint relevant to CLP (Aquatic Toxicity) using data retrieved from the eNanoMapper database, results obtained were consistent to results in REACH registration dossiers and in recent literature.

MCDCalc: Markov Chain Molecular Descriptors Calculator for Medicinal Chemistry.

AIMS: Cheminformatics models are able to predict different outputs (activity, property, chemical reactivity) in single molecules or complex molecular systems (catalyzed organic synthesis, metabolic reactions, nanoparticles, etc.). BACKGROUND: Cheminformatics models are able to predict different outputs (activity, property, chemical reactivity) in single molecules or complex molecular systems (catalyzed organic synthesis, metabolic reactions, nanoparticles, etc.). OBJECTIVE: Cheminformatics prediction of complex catalytic enantioselective reactions is a major goal in organic synthesis research and chemical industry. Markov Chain Molecular Descriptors (MCDs) have been largely used to solve Cheminformatics problems. There are different types of Markov chain descriptors such as Markov-Shannon entropies (Shk), Markov Means (Mk), Markov Moments (πk), etc. However, there are other possible MCDs that have not been used before. In addition, the calculation of MCDs is done very often using specific software not always available for general users and there is not an R library public available for the calculation of MCDs. This fact, limits the availability of MCMDbased Cheminformatics procedures. METHODS: We studied the enantiomeric excess ee(%)[Rcat] for 324 α-amidoalkylation reactions. These reactions have a complex mechanism depending on various factors. The model includes MCDs of the substrate, solvent, chiral catalyst, product along with values of time of reaction, temperature, load of catalyst, etc. We tested several Machine Learning regression algorithms. The Random Forest regression model has R2 > 0.90 in training and test. Secondly, the biological activity of 5644 compounds against colorectal cancer was studied. RESULTS: We developed very interesting model able to predict with Specificity and Sensitivity 70-82% the cases of preclinical assays in both training and validation series. CONCLUSION: The work shows the potential of the new tool for computational studies in organic and medicinal chemistry.

Population pharmacokinetic reanalysis of a Diazepam PBPK model: a comparison of Stan and GNU MCSim.

The aim of this study is to benchmark two Bayesian software tools, namely Stan and GNU MCSim, that use different Markov chain Monte Carlo (MCMC) methods for the estimation of physiologically based pharmacokinetic (PBPK) model parameters. The software tools were applied and compared on the problem of updating the parameters of a Diazepam PBPK model, using time-concentration human data. Both tools produced very good fits at the individual and population levels, despite the fact that GNU MCSim is not able to consider multivariate distributions. Stan outperformed GNU MCSim in sampling efficiency, due to its almost uncorrelated sampling. However, GNU MCSim exhibited much faster convergence and performed better in terms of effective samples produced per unit of time.

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations.

Many groups within the broad field of nanoinformatics are already developing data repositories and analytical tools driven by their individual organizational goals. Integrating these data resources across disciplines and with non-nanotechnology resources can support multiple objectives by enabling the reuse of the same information. Integration can also serve as the impetus for novel scientific discoveries by providing the framework to support deeper data analyses. This article discusses current data integration practices in nanoinformatics and in comparable mature fields, and nanotechnology-specific challenges impacting data integration. Based on results from a nanoinformatics-community-wide survey, recommendations for achieving integration of existing operational nanotechnology resources are presented. Nanotechnology-specific data integration challenges, if effectively resolved, can foster the application and validation of nanotechnology within and across disciplines. This paper is one of a series of articles by the Nanomaterial Data Curation Initiative that address data issues such as data curation workflows, data completeness and quality, curator responsibilities, and metadata.

A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions.

Increasing amounts of systems toxicology data, including omics results, are becoming publically available and accessible in databases. Data-driven and informatics-tool supported pipeline schemas for fitting such data into Adverse Outcome Pathway (AOP) descriptions could potentially aid the development of nonanimal-based hazard and risk assessment methods. We devised a 6-step workflow that integrated diverse types of toxicology data into a novel AOP scheme for pulmonary fibrosis. Mining of literature references and diverse data sources covering previous pathway descriptions and molecular results were coupled in a stepwise manner with informatics tools applications that enabled gene linkage and pathway identification in molecular interaction maps. Ultimately, a network of functional elements coupled 64 pulmonary fibrosis-associated genes into a novel, open-source AOP-linked molecular pathway, now available for commenting and improvements in WikiPathways (WP3624). Applying in silico-based knowledge extraction and modeling, the pipeline enabled screening and fusion of many different complex data types, including the integration of omics results. Overall, the taken, stepwise approach should be generally useful to construct novel AOP descriptions as well as to enrich developing AOP descriptions in progress.

toxFlow: A Web-Based Application for Read-Across Toxicity Prediction Using Omics and Physicochemical Data.

We present toxFlow, a web application developed for enrichment analysis of omics data coupled with read-across toxicity prediction. A sequential analysis workflow is suggested where users can filter omics data using enrichment scores and incorporate their findings into a correlation-based read-across technique for predicting the toxicity of a substance based on its analogs. Either embedded or in-house gene signature libraries can be used for enrichment analysis. The suggested approach can be used for toxicity prediction of diverse chemical entities; however, this article focuses on the multiperspective characterization of nanoparticles and selects their neighbors based on both physicochemical and biological similarity criteria. In addition, visualization options are offered to interactively explore correlation patterns in the data, whereas results can be exported for further analysis. toxFlow is accessible at http://147.102.86.129:3838/toxflow .

Jaqpot Quattro: A Novel Computational Web Platform for Modeling and Analysis in Nanoinformatics.

Engineered nanomaterials (ENMs) are increasingly infiltrating our lives as a result of their applications across multiple fields. However, ENM formulations may result in the modulation of pathways and mechanisms of toxic action that endanger human health and the environment. Alternative testing methods such as in silico approaches are becoming increasingly popular for assessing the safety of ENMs, as they are cost- and time-effective. Additionally, computational approaches support the industrial safer-by-design challenge and the REACH legislation objective of reducing animal testing. Because of the novelty of the field, there is also an evident need for harmonization in terms of databases, ontology, and modeling infrastructures. To this end, we present Jaqpot Quattro, a comprehensive open-source web application for ENM modeling with emphasis on predicting adverse effects of ENMs. We describe the system architecture and outline the functionalities, which include nanoQSAR modeling, validation services, read-across predictions, optimal experimental design, and interlaboratory testing.

Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces.

BACKGROUND: The term 'molecular cartography' encompasses a family of computational methods for two-dimensional transformation of protein structures and analysis of their physicochemical properties. The underlying algorithms comprise multiple manual steps, whereas the few existing implementations typically restrict the user to a very limited set of molecular descriptors. RESULTS: We present Structuprint, a free standalone software that fully automates the rendering of protein surface maps, given - at the very least - a directory with a PDB file and an amino acid property. The tool comes with a default database of 328 descriptors, which can be extended or substituted by user-provided ones. The core algorithm comprises the generation of a mould of the protein surface, which is subsequently converted to a sphere and mapped to two dimensions, using the Miller cylindrical projection. Structuprint is partly optimized for multicore computers, making the rendering of animations of entire molecular dynamics simulations feasible. CONCLUSIONS: Structuprint is an efficient application, implementing a molecular cartography algorithm for protein surfaces. According to the results of a benchmark, its memory requirements and execution time are reasonable, allowing it to run even on low-end personal computers. We believe that it will be of use - primarily but not exclusively - to structural biologists and computational biochemists.

The eNanoMapper database for nanomaterial safety information.

BACKGROUND: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. RESULTS: The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. CONCLUSION: We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the "representational state transfer" (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure-activity relationships for nanomaterials (NanoQSAR).

RRegrs: an R package for computer-aided model selection with multiple regression models.

BACKGROUND: Predictive regression models can be created with many different modelling approaches. Choices need to be made for data set splitting, cross-validation methods, specific regression parameters and best model criteria, as they all affect the accuracy and efficiency of the produced predictive models, and therefore, raising model reproducibility and comparison issues. Cheminformatics and bioinformatics are extensively using predictive modelling and exhibit a need for standardization of these methodologies in order to assist model selection and speed up the process of predictive model development. A tool accessible to all users, irrespectively of their statistical knowledge, would be valuable if it tests several simple and complex regression models and validation schemes, produce unified reports, and offer the option to be integrated into more extensive studies. Additionally, such methodology should be implemented as a free programming package, in order to be continuously adapted and redistributed by others. RESULTS: We propose an integrated framework for creating multiple regression models, called RRegrs. The tool offers the option of ten simple and complex regression methods combined with repeated 10-fold and leave-one-out cross-validation. Methods include Multiple Linear regression, Generalized Linear Model with Stepwise Feature Selection, Partial Least Squares regression, Lasso regression, and Support Vector Machines Recursive Feature Elimination. The new framework is an automated fully validated procedure which produces standardized reports to quickly oversee the impact of choices in modelling algorithms and assess the model and cross-validation results. The methodology was implemented as an open source R package, available at https://www.github.com/enanomapper/RRegrs, by reusing and extending on the caret package. CONCLUSION: The universality of the new methodology is demonstrated using five standard data sets from different scientific fields. Its efficiency in cheminformatics and QSAR modelling is shown with three use cases: proteomics data for surface-modified gold nanoparticles, nano-metal oxides descriptor data, and molecular descriptors for acute aquatic toxicity data. The results show that for all data sets RRegrs reports models with equal or better performance for both training and test sets than those reported in the original publications. Its good performance as well as its adaptability in terms of parameter optimization could make RRegrs a popular framework to assist the initial exploration of predictive models, and with that, the design of more comprehensive in silico screening applications.Graphical abstractRRegrs is a computer-aided model selection framework for R multiple regression models; this is a fully validated procedure with application to QSAR modelling.

eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.

Engineered nanomaterials (ENMs) are being developed to meet specific application needs in diverse domains across the engineering and biomedical sciences (e.g. drug delivery). However, accompanying the exciting proliferation of novel nanomaterials is a challenging race to understand and predict their possibly detrimental effects on human health and the environment. The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. Here, we describe the development of the eNanoMapper ontology based on adopting and extending existing ontologies of relevance for the nanosafety domain. The resulting eNanoMapper ontology is available at http://purl.enanomapper.net/onto/enanomapper.owl. We aim to make the re-use of external ontology content seamless and thus we have developed a library to automate the extraction of subsets of ontology content and the assembly of the subsets into an integrated whole. The library is available (open source) at http://github.com/enanomapper/slimmer/. Finally, we give a comprehensive survey of the domain content and identify gap areas. ENM safety is at the boundary between engineering and the life sciences, and at the boundary between molecular granularity and bulk granularity. This creates challenges for the definition of key entities in the domain, which we also discuss.

Collaborative mining and interpretation of large-scale data for biomedical research insights.

Biomedical research becomes increasingly interdisciplinary and collaborative in nature. Researchers need to efficiently and effectively collaborate and make decisions by meaningfully assembling, mining and analyzing available large-scale volumes of complex multi-faceted data residing in different sources. In line with related research directives revealing that, in spite of the recent advances in data mining and computational analysis, humans can easily detect patterns which computer algorithms may have difficulty in finding, this paper reports on the practical use of an innovative web-based collaboration support platform in a biomedical research context. Arguing that dealing with data-intensive and cognitively complex settings is not a technical problem alone, the proposed platform adopts a hybrid approach that builds on the synergy between machine and human intelligence to facilitate the underlying sense-making and decision making processes. User experience shows that the platform enables more informed and quicker decisions, by displaying the aggregated information according to their needs, while also exploiting the associated human intelligence.

Rad9 interacts with Aft1 to facilitate genome surveillance in fragile genomic sites under non-DNA damage-inducing conditions in S. cerevisiae.

DNA damage response and repair proteins are centrally involved in genome maintenance pathways. Yet, little is known about their functional role under non-DNA damage-inducing conditions. Here we show that Rad9 checkpoint protein, known to mediate the damage signal from upstream to downstream essential kinases, interacts with Aft1 transcription factor in the budding yeast. Aft1 regulates iron homeostasis and is also involved in genome integrity having additional iron-independent functions. Using genome-wide expression and chromatin immunoprecipitation approaches, we found Rad9 to be recruited to 16% of the yeast genes, often related to cellular growth and metabolism, while affecting the transcription of ∼2% of the coding genome in the absence of exogenously induced DNA damage. Importantly, Rad9 is recruited to fragile genomic regions (transcriptionally active, GC rich, centromeres, meiotic recombination hotspots and retrotransposons) non-randomly and in an Aft1-dependent manner. Further analyses revealed substantial genome-wide parallels between Rad9 binding patterns to the genome and major activating histone marks, such as H3K36me, H3K79me and H3K4me. Thus, our findings suggest that Rad9 functions together with Aft1 on DNA damage-prone chromatin to facilitate genome surveillance, thereby ensuring rapid and effective response to possible DNA damage events.