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Mediterranean coasts are prone to tsunamis due to high seismicity in some well-known areas near plate margins. However, tsunamis have a low frequency of occurrence despite having highly destructive potential. The low frequency of occurrence and historicity of the most destructive events lead to minimizing or neglecting this risk. Past research identified socio-demographic and spatial factors that may affect tsunami risk perception. This research is based on CATI survey (Computer Assisted Telephone Interview) to a sample of 5842 respondents designed to investigate whether and how risk perception and risk knowledge were affected by a major event such as the 1908 Reggio Calabria Messina tsunami, by making a comparison between areas hit by that event and unaffected areas, also providing some explanatory hypotheses. Despite differences between Calabria and Sicily, data show higher levels of tsunami risk perception in the area affected by the 1908 event, along with a major role of interpersonal sources, playing a relevant role in information gathering and understanding. Research also suggests the need to better integrate different sources of knowledge to improve people’s understanding so as to effectively cope with tsunami risk.

In the Mediterranean, the probability of tsunamis is lower than in other coastal areas such as the Pacific Ring, where tsunamis are more familiar and memory of past events and anticipatory signals and protective measures is preserved by local culture, along with media and scientific sources, therefore tsunami risk is more likely to be downplayed or neglected. Past research identified socio-demographic and spatial factors that may affect tsunami risk perception. This research is based on a sample of 5842 CATI interviews to investigate whether and how risk perception and risk knowledge were affected by a major event such as the 1908 Reggio Calabria Messina tsunami, by making a comparison between areas hit by that event and unaffected areas, also providing some explanatory hypotheses. Despite differences between Calabria and Sicily, data anyway show higher levels of tsunami risk perception in the area affected by the 1908 event, along with a major role of interpersonal sources, playing a relevant role in information gathering and understanding. Research also suggests the need to better integrate different sources of knowledge to improve people’s understanding as to effectively cope with tsunami risk.

Large-scale coastal urban sprawl, development of tourist accommodations and industrial maritime poles have highly increased the tsunami risk to people living and/or traveling along the coasts of our planet. The disastrous tsunamis in the Indian Ocean (2004) and in the Pacific Ocean (2011), as well as a suite of other damaging events worldwide, have encouraged International Institutions, first of all UNESCO Intergovernmental Oceanographic Commission, National Governments and Local Communities to implement Tsunami Warning Systems (TWS), to raise awareness on tsunami risk, and to create a multilevel risk governance. In this framework, research on tsunami risk perception plays a key role. The results of these studies should be taken into account in designing risk mitigation programs and tools (such as drills, activities with local communities, emergency plans, etc.). This paper presents a review of such studies, carried out in several countries worldwide through many thousands of interviews performed with different techniques. Most tsunami risk perception studies were carried out in the regions where the Indian Ocean Tsunami Warning System and the Pacific Ocean one (PTWS) operate. In the NEAMTWS (North-East Atlantic, Mediterranean and connected seas Tsunami Warning Systems) region, only few specific studies were conducted, mostly within the EU-funded ASTARTE project (2013–2017) and more recently in a few extensive surveys on tsunami risk perception conducted in Italy between 2019 and 2021. Although the twenty-three studies analyzed in our review show a strong heterogeneity of methodological approaches and population samples, they allow us to outline some general considerations on tsunami risk as perceived by people in the different regions of the world. With the help of a table, we schematically summarized the emerging strengths, weaknesses and lessons learned in the twenty-three papers, noting an increase in the number of such studies in the last 5 years. The surveys were mostly concentrated in high-risk areas and focused on local residents. Some differences emerged depending on the memory of past tsunamis, education level, and local cultures. This provides useful hints for sound citizen-based tsunami risk reduction actions, including improved risk communication aimed at increasing the resilience of tsunami-prone populations. The need for increasing the assessment of tourists’ tsunami risk perception, and for a more homogeneous survey strategy also emerge from our analysis.

The Tsunami Alert Centre of the National Institute of Geophysics and Volcanology (CAT-INGV) has been promoting, since 2018, the study of tsunami risk perception in Italy. Between 2018 and 2021 a semi-structured questionnaire on the perception of tsunami risk was administered to a sample of 5842 citizens residing in 450 Italian coastal municipalities, representative of more than 12 million people. The survey was conducted with the computer-assisted telephone interviewing (CATI) methodology, described in Cerase et al. (2019), who published the results of the first pilot survey (about 1000 interviews). The large sample and the socio-demographic stratification give an excellent representation of the resident population in the surveyed Italian coastal municipalities. Moreover, in 2021 an optimized version of the questionnaire was also administered via Telepanel (a tool for collecting proportional and representative opinions of citizens) that was representative of the Italian population and included 1500 people distributed throughout the country. In this work we present the main results of the three survey phases, with a comparison among the eight surveyed regions and between the coastal regions and some coastal metropolitan cities involved in the investigations (Rome, Naples, Bari, Reggio Calabria, and Catania). Data analysis reveals heterogeneous and generally low tsunami risk perception. Some seaside populations, in fact, show a good perception of tsunami risk, while others, such as in Apulia and Molise, reveal a lower perception, most likely due to the long time elapsed since the last event and lack of memory. We do not find relevant differences related to the socio-demographic characteristics (age, gender) of the sample, whereas the education degree appears to affect people's perception. The survey shows that the respondents' predominant source of information on tsunamis is the television and other media sources (such as newspapers, books, films, internet), while the official sources (e.g., civil protection, local authorities, universities and research institutes) do not contribute significantly. Also, we find an interesting difference in people's understanding of the words tsunami and maremoto, the local term commonly used in Italy until the 2004 Sumatra–Andaman event, which should be taken into account in scientific and risk communication. The Telepanel survey, based on a nationwide sample, highlights a lower level of tsunami risk perception in comparison to average risk perception levels found in the coastal-municipality sample. Our results are being used to drive our communication strategy aimed at reducing tsunami risk in Italy, to activate dissemination and educational programs (data driven), to fill the data gap on tsunami risk perception in the North-Eastern Atlantic, Mediterranean and connected seas (NEAM) area, and to implement multilevel civil protection actions (national and local, top-down and bottom-up). Not least, outputs can address a better development of the UNESCO Tsunami Ready program in Italy.

X chromosome inactivation (XCI) is the process of silencing one of the X chromosomes in cells of the female mammal which ensures dosage compensation between the sexes. Although theoretically random in somatic tissues, the choice of which X chromosome is chosen to be inactivated can be biased in mice by genetic element(s) associated with the so-called X-controlling element ( Xce ). Although the Xce was first described and genetically localized nearly 40 y ago, its mode of action remains elusive. In the approach presented here, we identify a single long noncoding RNA (lncRNA) within the Xce locus, Lppnx, which may be the driving factor in the choice of which X chromosome will be inactivated in the developing female mouse embryo. Comparing weak and strong Xce alleles we show that Lppnx modulates the expression of Xist lncRNA , one of the key factors in XCI, by controlling the occupancy of pluripotency factors at Intron1 of Xist . This effect is counteracted by enhanced binding of Rex1 in DxPas34 , another key element in XCI regulating the activity of Tsix lncRNA, the main antagonist of Xist, in the strong but not in the weak Xce allele. These results suggest that the different susceptibility for XCI observed in weak and strong Xce alleles results from differential transcription factor binding of Xist Intron 1 and DxPas34 , and that Lppnx represents a decisive factor in explaining the action of the Xce .

Supplementary data: The following is the Supplementary data to this article: Acrobat PDF file (2MB) available at: https://ars.els-cdn.com/content/image/1-s2.0-S2212420921007329-mmc1.pdf Copyright © 2022 The Authors. Very large tsunamis are associated with low probabilities of occurrence. In many parts of the world, these events have usually occurred in a distant time in the past. As a result, there is low risk perception and a lack of collective memories, making tsunami risk communication both challenging and complex. Furthermore, immense challenges lie ahead as population and risk exposure continue to increase in coastal areas. Through the last decades, tsunamis have caught coastal populations off-guard, providing evidence of lack of preparedness. Recent tsunamis, such as the Indian Ocean Tsunami in 2004, 2011 Tohoku and 2018 Palu, have shaped the way tsunami risk is perceived and acted upon. Based on lessons learned from a selection of past tsunami events, this paper aims to review the existing body of knowledge and the current challenges in tsunami risk communication, and to identify the gaps in the tsunami risk management methodologies. The important lessons provided by the past events call for strengthening community resilience and improvement in risk-informed actions and policy measures. This paper shows that research efforts related to tsunami risk communication remain fragmented. The analysis of tsunami risk together with a thorough understanding of risk communication gaps and challenges is indispensable towards developing and deploying comprehensive disaster risk reduction measures. Moving from a broad and interdisciplinary perspective, the paper suggests that probabilistic hazard and risk assessments could potentially contribute towards better science communication and improved planning and implementation of risk mitigation measures. COST (European Cooperation in Science and Technology); Royal Society, UK (grant number CHL\R1\180173); Severo Ochoa Centers of Excellence Program (CEX 2018-000797-S) funded by MCIN/ AEI /10.13039/501100011033; Lloyd's Tercentenary Research Foundation, the Lighthill Risk Network, and the Lloyd's Register Foundation-Data Centric Engineering Programme of the Alan Turing Institute.

The genomes of metazoans are organized at multiple spatial scales, ranging from the double helix of DNA to whole chromosomes. The intermediate genomic scale of kilobases to megabases, which corresponds to the 50–300 nm spatial scale, is particularly interesting, as the 3D arrangement of chromatin is implicated in multiple regulatory mechanisms. In this context, polycomb group (PcG) proteins stand as major epigenetic modulators of chromatin function, acting prevalently as repressors of gene transcription by combining chemical modifications of target histones with physical crosslinking of distal genomic regions and phase separation. The recent development of super-resolution microscopy (SRM) has strongly contributed to improving our comprehension of several aspects of nano-/mesoscale (10–200 nm) chromatin domains. Here, we review the current state-of-the-art SRM applied to PcG proteins, showing that the application of SRM to PcG activity and organization is still quite limited and mainly focused on the 3D assembly of PcG-controlled genomic loci. In this context, SRM approaches have mostly been applied to multilabel fluorescence in situ hybridization (FISH). However, SRM data have complemented the maps obtained from chromosome capture experiments and have opened a new window to observe how 3D chromatin topology is modulated by PcGs.

Genomic repeats have been intensely studied as regulatory elements controlling gene transcription, splicing and genome architecture. Our understanding of the role of the repetitive RNA such as the RNA coming from genomic repeats, or repetitive sequences embedded in mRNA/lncRNAs, in nuclear and cellular functions is instead still limited. In this review we discuss evidence supporting the multifaceted roles of repetitive RNA and RNA binding proteins in nuclear organization, gene regulation, and in the formation of dynamic membrane-less aggregates. We hope that our review will further stimulate research in the consolidating field of repetitive RNA biology.

Neurological and neuropsychiatric disorders affect men and women differently. Multiple sclerosis, Alzheimer's disease, anxiety disorders, depression, meningiomas and late-onset schizophrenia affect women more frequently than men. By contrast, Parkinson's disease, autism spectrum condition, attention-deficit hyperactivity disorder, Tourette's syndrome, amyotrophic lateral sclerosis and early-onset schizophrenia are more prevalent in men. Women have been historically under-recruited or excluded from clinical trials, and most basic research uses male rodent cells or animals as disease models, rarely studying both sexes and factoring sex as a potential source of variation, resulting in a poor understanding of the underlying biological reasons for sex and gender differences in the development of such diseases. Putative pathophysiological contributors include hormones and epigenetics regulators but additional biological and non-biological influences may be at play. We review here the evidence for the underpinning role of the sex chromosome complement, X chromosome inactivation, and environmental and epigenetic regulators in sex differences in the vulnerability to brain disease. We conclude that there is a pressing need for a better understanding of the genetic, epigenetic and environmental mechanisms sustaining sex differences in such diseases, which is critical for developing a precision medicine approach based on sex-tailored prevention and treatment.

The long non-coding RNA Xist induces heterochromatinization of the X chromosome by recruiting repressive protein complexes to chromatin. Here we gather evidence, from the literature and from computational analyses, showing that Xist assemblies are similar in size, shape and composition to phase-separated condensates, such as paraspeckles and stress granules. Given the progressive sequestration of Xist’s binding partners during X-chromosome inactivation, we formulate the hypothesis that Xist uses phase separation to perform its function.

Female mammals achieve dosage compensation by inactivating one of their two X chromosomes during development, a process entirely dependent on Xist, an X-linked long non-coding RNA (lncRNA). At the onset of X chromosome inactivation (XCI), Xist is up-regulated and spreads along the future inactive X chromosome. Contextually, it recruits repressive histone and DNA modifiers that transcriptionally silence the X chromosome. Xist regulation is tightly coupled to differentiation and its expression is under the control of both pluripotency and epigenetic factors. Recent evidence has suggested that chromatin remodelers accumulate at the X Inactivation Center (XIC) and here we demonstrate a new role for Chd8 in Xist regulation in differentiating ES cells, linked to its control and prevention of spurious transcription factor interactions occurring within Xist regulatory regions. Our findings have a broader relevance, in the context of complex, developmentally-regulated gene expression., Communications Biology, 4 (1), ISSN:2399-3642

Mutations in the gene encoding Lamin B receptor (LBR), a nuclear-membrane protein with sterol reductase activity, have been linked to rare human disorders. Phenotypes range from a benign blood disorder, such as Pelger-Huet anomaly (PHA), affecting the morphology and chromatin organization of white blood cells, to embryonic lethality as for Greenberg dysplasia (GRBGD). Existing PHA mouse models do not fully recapitulate the human phenotypes, hindering efforts to understand the molecular etiology of this disorder. Here we show, using CRISPR/Cas-9 gene editing technology, that a 236bp N-terminal deletion in the mouse Lbr gene, generating a protein missing the N-terminal domains of LBR, presents a superior model of human PHA. Further, we address recent reports of a link between Lbr and defects in X chromosome inactivation (XCI) and show that our mouse mutant displays minor X chromosome inactivation defects that do not lead to any overt phenotypes in vivo. We suggest that our N-terminal deletion model provides a valuable pre-clinical tool to the research community and will aid in further understanding the etiology of PHA and the diverse functions of LBR., Communications Biology, 4 (1), ISSN:2399-3642

The tsunami risk perception survey is promoted by the Tsunami Alert Centre of the National Institute of Geophysics and Volcanology, operating within the Italian System for Tsunami Alert (SiAM) with the Civil Protection Department and ISPRA, and acting as Tsunami Service Provider in the NEAMTWS.Conducting studies on tsunami risk perception is important in order to obtain data on population’s knowledge and awareness, and understanding people’s perception of tsunami risk. These data are going to be added to those from two previous surveys on tsunami risk perception being issued in 2018 and 2020, to integrate the available knowledge on these issues and will provide publics, experts and policy makers with relevant tools to implement risk mitigation policies. The third phase of the survey was completed in January 2021, administering a total of 4,207 questionnaires to the population living on the coastal areas of Sicily, Campania, Latium and Sardinia, in addition to the 1,635 interviewees considered in previous surveys.The survey used a semi-structured questionnaire consisting of 27 items, with closed alternative questions, and four sets of Likert scale questions. The questionnaire was optimized for CATI administration, taking into account the need for conciseness and comprehensibility of the questions.All the studied regions are located in the central Mediterranean basin (including central and southern Tyrrhenian Sea, Sardinian Sea, Sicily Channel), some of which are characterized by high tsunami hazard, and in some cases they have been affected by recorded tsunamis in a close or distant past. Some regions are located in areas where potential seismic tsunami sources are present, others surround waters where active volcanoes exist, both on islands (such as Stromboli, Vulcano) and below the sea (Marsili, Palinuro). In addition, the four studied regions have a high risk exposure due to the high density of population living on, or visiting the coastal areas for tourism. In the areas where the questionnaire was administered, five highly populated regional capitals are located, including Palermo, Messina, Naples, Rome and Cagliari, together with other important towns (such as Catania, Siracusa, Trapani, Salerno, Olbia etc.). Moreover, the coastal shores involved in the survey, live of a significant tourist affluence in the summer period (and not only), with many tourist facilities and large hotels located along the coasts.The survey's main aim is to analyze the perception of tsunami risk by the coastal population and to correlate levels of tsunami risk perception with scientific data from probabilistic tsunami hazard assessment (PTHA) for the considered coastal area. We will present some preliminary results of this last survey, with a comparison with the previous analyses on other regions in southern Italy.

The onset of random X inactivation in mouse requires the switch from a symmetric to an asymmetric state, where the identities of the future inactive and active X chromosomes are assigned. Here we show that RIF1 and KAP1 are two fundamental factors for the definition of the asymmetry. Our data show that at the onset of mESC differentiation, upregulation of the long non-coding RNA Tsix weakens the symmetric RIF1 association with the Xist promoter, and opens a window of opportunity for a more stable association of KAP1. KAP1 is required to sustain high levels of Tsix, thus reinforcing and propagating the asymmetry, and, as a result, marking the future active X chromosome. Furthermore, we show that RIF1 association with the future inactive X chromosome is essential for Xist upregulation. This double-bookmarking system, based on the mutually exclusive relationships of Tsix and RIF1, and RIF1 and KAP1, thus coordinates the identification of the inactive and active X chromosomes and initiates a self-sustaining loop that transforms an initially stochastic event into a stably inherited asymmetric X chromosome state.

We present the results of an ongoing research for assessing tsunami risk perception in southern Italy. The study is motivated by the need of addressing a sound communication strategy for tsunami risk reduction, related to the activities of the Tsunami Alert Centre (CAT) of INGV, operating within the framework of the Italian civil protection system. The area of the second step of this study includes five regions of Italy (Basilicata, Calabria, Molise, Puglia, Sicily), facing on Adriatic, Ionian and Tyrrhenian seas, located in one of the most hazardous areas of the Mediterranean. In all the area the memory of relevant tsunamis is loose, since the last destructive event dates back to 1908 (due to the Messina-Reggio Calabria M~7 earthquake). The main goal of this study is to verify how people’s perception of tsunami risk compares with the hazard assessed by scientific data, and which are the main factors controlling people’s knowledge and awareness. We analysed a sample of more than 1,600 interviewees representing about 4 million people living in the coastal municipalities of the five considered regions. Results show that risk perception appears to be generally low, with significant differences among different areas, likely due to the the time elapsed since the last events. The survey results for the first two investigated regions (Calabria and Puglia, see Cerase et al., NHESS, 2019) showed that people’s perception and understanding of tsunamis are affected by media accounts of the mega-tsunamis of Sumatra 2004 and Japan 2011. At the same time, the risk posed by small tsunamis is basically underrated or neglected, posing some critical questions for risk mitigation strategies, particularly in touristic areas. Furthermore, the survey’s results show that for lay people the word ‘tsunami’ has a different meaning with respect to the Italian traditional word ‘maremoto’, implying that the same physical phenomenon would be understood in two different ways by younger, educated people and elders with low education level. In addition, people have high expectations from authorities, CPAs, research institutions about warnings. Moreover, living in different coastal areas appears to have a significant influence on the way tsunami hazard is perceived: Interviewees of Tyrrhenian Calabria are more likely to associate tsunami risk to volcanoes with respect to those living in the Ionian coastal areas, coherently with the presence of Aeolian volcanic islands and feared submarine volcanoes in the Tyrrhenian. A somehow unexpected result is that TV emerges as the most relevant source of knowledge for 90% of the sample. Some categories declared to prefer getting early warnings through broadcast media and sirens rather than receiving by SMS or apps, suggesting the need for redundancy and modulation of EW messages. We will present an update of the survey which is presently ongoing, related to the five regions. These results could help in addressing risk communication and mitigation policies.

Background Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutations in the X-linked methyl-CpG binding protein 2 (MeCP2) gene. While MeCP2 mutations are lethal in most males, females survive birth but show severe neurological defects. Because X-chromosome inactivation (XCI) is a random process, approximately 50% of the cells silence the wild-type (WT) copy of the MeCP2 gene. Thus, reactivating the silent WT copy of MeCP2 could provide therapeutic intervention for RTT. Methods Toward this goal, we screened ~ 28,000 small-molecule compounds from several libraries using a MeCP2-luciferase reporter cell line and cortical neurons from a MeCP2-EGFP mouse model. We used gain/increase of luminescence or fluorescence as a readout of MeCP2 reactivation and tested the efficacy of these drugs under different drug regimens, conditions, and cellular contexts. Results We identified inhibitors of the JAK/STAT pathway as XCI-reactivating agents, both by in vitro and ex vivo assays. In particular, we show that AG-490, a Janus Kinase 2 (JAK2) kinase inhibitor, and Jaki, a pan JAK/STAT inhibitor, are capable of reactivating MeCP2 from the inactive X chromosome, in different cellular contexts. Conclusions Our results suggest that inhibition of the JAK/STAT pathway is a new potential pathway to reinstate MeCP2 gene expression as an efficient RTT treatment.

Polycomb steps to inactivate X XX females silence one of their X chromosomes. This involves a process whereby a noncoding RNA known as Xist coats one of the X chromosomes and recruits chromatin silencing factors. The Polycomb complexes PRC1 and PRC2 are also known to be involved in X chromosome inactivation. Almeida et al. elucidate a key role of a specific complex, PCGF3/5-PRC1, in initiating Polycomb recruitment by Xist RNA. They further demonstrate that Polycomb recruitment is critical for Xist-mediated chromosome silencing and female embryogenesis. Science , this issue p. 1081

Mice carrying single chromosome substitutions (consomic mice) provide a unique platform for investigating complex phenotypes. A proportion of such phenotypes fall into the category of transgressive phenotypes, i.e. heritable extreme phenotypes lying outside the range of either parent. We hypothesized that analysis of transgressive phenotype in consomic mice potentially reveals unique cellular and molecular signatures associated with extreme phenotypic variations. We used a system-biology approach to build a reference set of 571 transgressive phenotypes in consomic mice using phenome metadata and additional 13 B-cell specific transgressive phenotypes using experimental data. As a proof of concept, we investigated clinically-relevant hyper-IgM phenotype. A combination of flow-cytometry, RNA-Sequencing and in-vitro validation confirmed that the hyper-IgM is associated with defective B-cell lymphopoiesis at the cellular and the down-regulation of the CCR7 gene at the molecular level. Our approach provides a complete pipeline to discover and validate transgressive phenotypes relevant to health and disease conditions.

Development is a complex process regulated both by genetic and epigenetic and environmental clues. Recently, long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression in several tissues including the brain. Altered expression of lncRNAs has been linked to several neurodegenerative, neurodevelopmental and mental disorders. The identification and characterization of lncRNAs that are deregulated or mutated in neurodevelopmental and mental health diseases are fundamental to understanding the complex transcriptional processes in brain function. Crucially, lncRNAs can be exploited as a novel target for treating neurological disorders. In our review, we first summarize the recent advances in our understanding of lncRNA functions in the context of cell biology and then discussing their association with selected neuronal development and neurological disorders.

The rise of racism in Europe In recent years online racism has seen a quick and serious growth in many European and non-European countries, till to become a worrying global phenomenon. One of the most striking examples of such process is the rise of White Supremacist Movements online. Their strategy mainly consists in disguising their hidden political agenda and attempting to subvert and destroy civil rights by presenting their standpoints through an overturn of the rhetoric of the civil rights movement. Undoubtedly, the increasing racism which is rotten in hidden racist expressions, is exploiting “favorable” conditions as the financial crisis, the increase of social conflicts and the rise of populist issues in politics. In Italy, as an example, UNAR, the Italian national anti-discrimination Office, documented that complaints for online racism weighed for 30.9% of the overall cases involving the media (UNAR, 2013). Similar situations also occurred in other European countries such as Slovenia, Finland, Hungary and United Kingdom, as it emerged by part of the research carried out within the framework of the European project LIGHT ON. Nowadays, racist claims are often hidden under a subtle and sophisticated rethoric. In fact, a huge amount of disguised racist contents is currently published on the Internet in form of occasional bigotry or individuals’ outburst, whereas they are, as a matter of fact, intended to foster racist attitudes among people and to support the “normalization” of racism. Some scholars defined as “common sense racism” or “rational racism” talking against immigrants, refugees, minority members (as well as homosexuals and disabled) as undesirable and avoiding to be labeled as “racist”.

Xist long non-coding RNA induces heterochromatinization of the X-chromosome by accumulating in large ribonucleoprotein assemblies. We suggest that Xist regulates X chromosome inactivation by recruiting RNA-binding proteins via a mechanism of liquid-liquid phase separation. To support this hypothesis, we provide evidence that Xist forms ribonucleoprotein condensates that are similiar in size, shape and protein composition to paraspeackles and stress granules. We show that Xist interactome is particularly enriched in proteins that are intrinsically disordered and capable of phase separating. We suggest that Xist reinforces Xi heterochromatinization by sequestering repressive complexes, such as Polycomb proteins, in an indirect way through phase separation. This process is complementary to the canonical chromatin-mediated recruitment.

The word media hype is often used as rhetorical argument to dismiss waves of media attention as overblown, disproportional and exaggerated. But these explosive news waves, as well as - nowadays - the twitter storms, are object of scientific research, because they are an important phenomenon in the public area. Sometimes it is indeed 'much ado about nothing' but in many cases these media storms have play an important role in political issues, scandals and crises. Twitter storms sometimes ruin reputations within hours. Although different concepts are used, such as media hypes, news waves, media storms, information cascades or risk amplification, all the studies in this book refer to the same process in which key events trigger a chain of reactions and interactions, building up huge news waves in the media or rapidly spreading social epidemics in the social media. This book offers the first comprehensive overview of this important topic. It is not only interesting for scholars and students in media and journalism, but also for professionals in PR and communication, crisis communication and reputation management.

Recent experimental evidence indicates that lncRNAs can act as regulatory molecules in the context of development and disease. Xist, the master regulator of X chromosome inactivation, is a classic example of how lncRNAs can exert multi-layered and fine-tuned regulatory functions, by acting as a molecular scaffold for recruitment of distinct protein factors. In this review, we discuss the methodologies employed to define Xist RNA structures and the tight interplay between structural clues and functionality of lncRNAs. This model of modular function dictated by structure, can be also generalized to other lncRNAs, beyond the field of X chromosome inactivation, to explain common features of similarly folded RNAs.

Long noncoding RNAs (lncRNAs, which comprise 68% of the human transcriptome with average length of 1,000 nt) interact with various RNA-binding proteins (RBPs) to mediate cellular functions1. Identification of lncRNA interactions through experimental methods is challenging and can be complemented by the use of computational models to predict protein partners. Yet it is currently impractical to calculate RBP–lncRNA interactions for large transcripts2.We introduce Global Score as a means to predict protein interactions with large RNAs (http://service.tartaglialab.com/new_submission/globalscore).

Summary The Polycomb-repressive complexes PRC1 and PRC2 play a key role in chromosome silencing induced by the non-coding RNA Xist. Polycomb recruitment is initiated by the PCGF3/5-PRC1 complex, which catalyzes chromosome-wide H2A lysine 119 ubiquitylation, signaling recruitment of other PRC1 complexes, and PRC2. However, the molecular mechanism for PCGF3/5-PRC1 recruitment by Xist RNA is not understood. Here we define the Xist RNA Polycomb Interaction Domain (XR-PID), a 600 nt sequence encompassing the Xist B-repeat element. Deletion of XR-PID abolishes Xist-dependent Polycomb recruitment, in turn abrogating Xist-mediated gene silencing and reversing Xist-induced chromatin inaccessibility. We identify the RNA-binding protein hnRNPK as the principal XR-PID binding factor required to recruit PCGF3/5-PRC1. Accordingly, synthetically tethering hnRNPK to Xist RNA lacking XR-PID is sufficient for Xist-dependent Polycomb recruitment. Our findings define a key pathway for Polycomb recruitment by Xist RNA, providing important insights into mechanisms of chromatin modification by non-coding RNA., Graphical Abstract, Highlights • A 600 nt element in Xist RNA, XR-PID, is required for Polycomb recruitment • Deletion of XR-PID abrogates Xist-mediated chromosome silencing • hnRNPK binds XR-PID to recruit the Polycomb-initiating complex PCGF3/5-PRC1 • Tethering hnRNPK to Xist RNA bypasses the requirement for XR-PID, This study advances our understanding of the molecular mechanism of X chromosome inactivation in mammals, defining XR-PID, the critical element in Xist RNA that recruits Polycomb complexes to the inactive X chromosome, and further demonstrating that the RNA binding protein hnRNPK bridges XR-PID with the initiating Polycomb complex, PCGF3/5-PRC1.

The Xist long noncoding RNA orchestrates X chromosome inactivation, a process that entails chromosome-wide silencing and remodeling of the three-dimensional (3D) structure of the X chromosome. Yet, it remains unclear whether these changes in nuclear structure are mediated by Xist and whether they are required for silencing. Here, we show that Xist directly interacts with the Lamin B receptor, an integral component of the nuclear lamina, and that this interaction is required for Xist-mediated silencing by recruiting the inactive X to the nuclear lamina and by doing so enables Xist to spread to actively transcribed genes across the X. Our results demonstrate that lamina recruitment changes the 3D structure of DNA, enabling Xist and its silencing proteins to spread across the X to silence transcription.

The compensation of the different level of transcripts of X-linked genes in male and female mammals is achieved through X chromosome inactivation, a complex process that differentially regulates the sex chromosomes of female cells. This mechanism has been dissected at evolutionary, genetic and molecular levels: here, we discuss some of the latest examples that illustrate better these intricate connections, focusing particularly on the emerging role of spatial and three-dimensional chromatin arrangements in the building of this special chromosome, the inactive X chromosome.

In female m ammals, one of the two X chromosomes in each cell is transcriptionally silenced in order to achieve dosage compensation between the genders in a process called X chromosome inactivation. The master regulator of this process is the long non-coding RNA Xist. During X-inactivation, Xist accumulates in cis on the future inactive X chromosome, triggering a cascade of events that provoke the stable silencing of the entire chromosome, with relatively few genes remaining active. How Xist spreads, what are its binding sites, how it recruits silencing factors and how it induces a specific topological and nuclear organization of the chromatin all remain largely unanswered questions. Recent studies have improved our understanding of Xist localization and the proteins with which it interacts, allowing a reappraisal of ideas about Xist function. We discuss recent advances in our knowledge of Xist-mediated silencing, focusing on Xist spreading, the nuclear organization of the inactive X chromosome, recruitment of the polycomb complex and the role of the nuclear matrix in the process of X chromosome inactivation.

Maintenance of X-inactivation is achieved through a combination of different repressive mechanisms, thus perpetuating the silencing message through many cell generations. The second human X-Y pseudoautosomal region 2 (PAR2) is a useful model to explore the features and internal relationships of the epigenetic circuits involved in this phenomenon. Recently, we demonstrated that DNA methylation plays an essential role for the maintenance of X- and Y-inactivation of the PAR2 gene SYBL1; here we report that the silencing of the second repressed PAR2 gene, SPRY3, appears to be independent of DNA methylation. In contrast to SYBL1, the inactive X and Y alleles of SPRY3 are not reactivated in cells treated with a DNA methylation inhibitor and in cells from ICF (immunodeficiency, centromeric instability, facial anomalies) syndrome patients, which have mutations in the DNA methyltransferase gene DNMT3B. SPRY3 X- and Y-inactivation is associated with a differential enrichment of repressive histone modifications and the recruitment of Polycomb 2 group proteins compared to the active X allele. Another major factor in SPRY3 repression is late replication; the inactive X and Y alleles of SPRY3 have delayed replication relative to the active X allele, even in ICF syndrome cells where the closely linked SYBL1 gene is reactivated and advanced in replication. The relatively stable maintenance of SPRY3 silencing compared with SYBL1 suggests that genes without CpG islands may be less prone to reactivation than previously thought and that genes with CpG islands require promoter methylation as an additional layer of repression.

In female mammals, one of the two X chromosomes is transcriptionally silenced to equalize X-linked gene dosage relative to XY males, a process termed X chromosome inactivation. Mechanistically, this is thought to occur via directed recruitment of chromatin modifying factors by the master regulator, X-inactive specific transcript (Xist) RNA, which localizes in cis along the entire length of the chromosome. A well-studied example is the recruitment of polycomb repressive complex 2 (PRC2), for which there is evidence of a direct interaction involving the PRC2 proteins Enhancer of zeste 2 (Ezh2) and Supressor of zeste 12 (Suz12) and the A-repeat region located at the 5' end of Xist RNA. In this study, we have analyzed Xist-mediated recruitment of PRC2 using two approaches, microarray-based epigenomic mapping and superresolution 3D structured illumination microscopy. Making use of an ES cell line carrying an inducible Xist transgene located on mouse chromosome 17, we show that 24 h after synchronous induction of Xist expression, acquired PRC2 binding sites map predominantly to gene-rich regions, notably within gene bodies. Paradoxically, these new sites of PRC2 deposition do not correlate with Xist-mediated gene silencing. The 3D structured illumination microscopy was performed to assess the relative localization of PRC2 proteins and Xist RNA. Unexpectedly, we observed significant spatial separation and absence of colocalization both in the inducible Xist transgene ES cell line and in normal XX somatic cells. Our observations argue against direct interaction between Xist RNA and PRC2 proteins and, as such, prompt a reappraisal of the mechanism for PRC2 recruitment in X chromosome inactivation.

CpG islands (CGIs) are associated with most mammalian gene promoters. A subset of CGIs act as polycomb response elements (PREs) and are recognized by the polycomb silencing systems to regulate expression of genes involved in early development. How CGIs function mechanistically as nucleation sites for polycomb repressive complexes remains unknown. Here we discover that KDM2B (FBXL10) specifically recognizes non-methylated DNA in CGIs and recruits the polycomb repressive complex 1 (PRC1). This contributes to histone H2A lysine 119 ubiquitylation (H2AK119ub1) and gene repression. Unexpectedly, we also find that CGIs are occupied by low levels of PRC1 throughout the genome, suggesting that the KDM2B-PRC1 complex may sample CGI-associated genes for susceptibility to polycomb-mediated silencing. These observations demonstrate an unexpected and direct link between recognition of CGIs by KDM2B and targeting of the polycomb repressive system. This provides the basis for a new model describing the functionality of CGIs as mammalian PREs. DOI: http://dx.doi.org/10.7554/eLife.00205.001, eLife digest Gene expression in eukaryotic cells can be controlled in a number of different ways, including various epigenetic mechanisms that do not involve making changes to DNA sequences that define the genes themselves. A well-known epigenetic mechanism for silencing genes in vertebrates is DNA methylation—the addition of a methyl group (CH3) to cytosine, which is one of the four bases found in the DNA. Methylation is thought to silence genes by preventing transcription factors from binding to the DNA, and also by recruiting proteins that inhibit the transcription of DNA. DNA methylation occurs naturally throughout the genome, mostly at positions where cytosine is bonded to guanine to form a CpG dinucleotide. While the cytosine bases in most CpG dinucleotides are methylated, there are short stretches of DNA known as CpG islands that contain a high proportion of unmethylated CpG dinucleotides. These islands contain a large number of cytosine and guanine bases, and they are often found at or near transcription start sites. The lack of methylation at CpG islands has long been assumed to have a passive role in gene expression, leaving the DNA easily accessible and available for transcription factors to bind and initiate transcription. However, recent work suggests that CpG islands may have a more active role. In particular, it has been shown that specific proteins bind to CpG islands to create chromatin environments that are more favourable for the initiation of gene expression. Moreover, a subset of CpG islands can also bind polycomb-group proteins, including the polycomb repressive complex 1 (PRC1) that silence gene expression. These complexes have an important role in the regulation of genes during early development in animals, but the mechanism by which PRC1 recognizes CpG islands in mammals has remained enigmatic. Farcas et al. now reveal that a protein, KDM2B (FBXL10), can recognize CpG islands and recruit PRC1 to them. To achieve this, KDM2B encodes a DNA binding domain that specifically recognizes non-methylated CpG dinucleotides. By interacting biochemically with a variant PRC1 complex, KDM2B then nucleates PRC1 at CpG islands, and PRC1 activity silences certain polycomb target genes in embryonic stem cells. Surprisingly, Farcas et al. also find low but appreciable levels of PRC1 at most CpG islands genome-wide, in addition to the high levels of PRC1 at selected islands: this suggests that KDM2B may sample the whole genome to find CpG islands where PRC1 can establish silencing. An improved understanding of the polycomb repressive system, and the role of CpG islands within it, could lead to new insights into the role of epigenetic mechanisms in mammalian development. DOI: http://dx.doi.org/10.7554/eLife.00205.002

Polycomb group (PcG) proteins play an important role in the control of developmental gene expression in higher organisms. In mammalian systems, PcG proteins participate in the control of pluripotency, cell fate, cell cycle regulation, X chromosome inactivation and parental imprinting. In this study we have analysed the function of the mouse PcG protein polycomblike 2 (Pcl2), one of three homologues of the Drosophila Polycomblike (Pcl) protein. We show that Pcl2 is expressed at high levels during early embryogenesis and in embryonic stem (ES) cells. At the biochemical level, Pcl2 interacts with core components of the histone H3K27 methyltransferase complex Polycomb repressive complex 2 (PRC2), to form a distinct substoichiometric biochemical complex, Pcl2-PRC2. Functional analysis using RNAi knockdown demonstrates that Pcl2-PRC2 facilitates both PRC2 recruitment to the inactive X chromosome in differentiating XX ES cells and PRC2 recruitment to target genes in undifferentiated ES cells. The role of Pcl2 in PRC2 targeting in ES cells is critically dependent on a conserved PHD finger domain, suggesting that Pcl2 might function through the recognition of a specific chromatin configuration.

Background X chromosome inactivation, the mechanism used by mammals to equalise dosage of X-linked genes in XX females relative to XY males, is triggered by chromosome-wide localisation of a cis-acting non-coding RNA, Xist. The mechanism of Xist RNA spreading and Xist-dependent silencing is poorly understood. A large body of evidence indicates that silencing is more efficient on the X chromosome than on autosomes, leading to the idea that the X chromosome has acquired sequences that facilitate propagation of silencing. LINE-1 (L1) repeats are relatively enriched on the X chromosome and have been proposed as candidates for these sequences. To determine the requirements for efficient silencing we have analysed the relationship of chromosome features, including L1 repeats, and the extent of silencing in cell lines carrying inducible Xist transgenes located on one of three different autosomes. Results Our results show that the organisation of the chromosome into large gene-rich and L1-rich domains is a key determinant of silencing efficiency. Specifically genes located in large gene-rich domains with low L1 density are relatively resistant to Xist-mediated silencing whereas genes located in gene-poor domains with high L1 density are silenced more efficiently. These effects are observed shortly after induction of Xist RNA expression, suggesting that chromosomal domain organisation influences establishment rather than long-term maintenance of silencing. The X chromosome and some autosomes have only small gene-rich L1-depleted domains and we suggest that this could confer the capacity for relatively efficient chromosome-wide silencing. Conclusions This study provides insight into the requirements for efficient Xist mediated silencing and specifically identifies organisation of the chromosome into gene-rich L1-depleted and gene-poor L1-dense domains as a major influence on the ability of Xist-mediated silencing to be propagated in a continuous manner in cis.

The compensation of the different level of transcripts of X-linked genes in male and female mammals is achieved through X chromosome inactivation, a complex process that differentially regulates the sex chromosomes of female cells. This mechanism has been dissected at evolutionary, genetic and molecular levels: here, we discuss some of the latest examples that illustrate better these intricate connections, focusing particularly on the emerging role of spatial and three-dimensional chromatin arrangements in the building of this special chromosome, the inactive X chromosome.

Epigenetic regulation is involved in the maintenance of long-term silencing phenomena, such as X-inactivation and genomic imprinting in mammals. Gene repression is mediated by several mechanisms, such as histone modifications, DNA methylation, and recruitment of Polycomb proteins. To understand the mechanistic relationships between these mechanisms for stable gene silencing, we analyzed the mechanisms of X- and Y-inactivation of the PAR2 gene SYBL1, previously showed to be regulated by concerted epigenetic mechanisms. Maintenance of stable repression occurs via the recruitment of both MBDPs and PRC2 complexes to SYBL1 promoter. Their binding is equally sensitive to defective DNA methylation seen in cells derived from ICF syndrome patients. Multiple occupancy is a feature shared within long-term repressed genes, such as the X-inactivated PGK1 and the imprinted IGF2. MBD2, MBD3, and MeCP2 occupy SYBL1 promoter simultaneously, as revealed by sequential ChIP. We did not find this co-occurring binding when looked for members of PRC2 complex together with any of the methyl-binding proteins. Furthermore, in co-transfection assays, MECP2 can silence methylated SYBL1 promoter, whereas the mutated protein fails. However, RNA interference of endogenous MECP2 does not induce the expression of the inactive SYBL1 alleles, suggesting that its silencing activity can be replaced by the other methyl-binding proteins. Our data suggest that maintenance of long-term silencing involves multiple layers of epigenetic control functionally redundant. PRC2 and MBD proteins could collaborate to different phases of this process, the former possibly recruiting DNMTs to the silenced promoters, the latter dictating the lock of the transcription. J. Cell. Physiol. 210: 711-719, 2007. (c) 2006 Wiley-Liss, Inc

BACKGROUND Microsatellite instability (MSI) has been reported in endometrial carcinoma (EC) and in colorectal carcinoma (CRC), primarily as a result of defective DNA mismatch repair (MMR). The MMR gene hMLH1 commonly is inactivated in both EC and CRC. In the current study, epigenetic mechanisms involved in hMLH1 inactivation have been investigated to further elucidate the role of these mechanisms in the pathogenesis of EC and CRC. METHODS Polymerase chain reaction (PCR)-based microsatellite analysis performed on paraffin-embedded tissues was used to select 42 sporadic carcinomas (21 ECs and 21 CRCs) with MSI. Immunohistochemistry (IHC), using the anti-hMLH1 antibody, and mutation analysis, using denaturing high-performance liquid chromatography and automated sequencing, were performed on unstable carcinoma samples. Methylation analysis, using modified protocols for bisulfite treatment and methylation-specific PCR (MSP), was performed on DNA from archival tissue samples. RESULTS No MSI-positive tumor samples with normal hMLH1 immunostaining (n = 7) exhibited hMLH1 promoter methylation, whereas 8 of 35 unstable cases with loss of hMLH1 expression (23%) exhibited MSP amplification. Among analyzed cases, germ-line mutations of hMLH1 were found in 4 of 20 unmethylated samples (20%) and in 0 of 8 methylated samples. Bisulfite sequencing of amplification products from methylated samples demonstrated that almost all CpG dinucleotides within the hMLH1 promoter elements underwent methylation. CONCLUSIONS Although an MMR gene other than hMLH1 may be responsible for genetic instability in MSI-positive/IHC-positive tumors, the presence of MSP amplification and allelic deletions within the hMLH1 locus in subsets of MSI-positive/IHC-negative cases strongly suggests that hMLH1 promoter methylation may contribute to the inactivation of both hMLH1 alleles. Bisulfite analysis suggests that the mechanisms of hMLH1 silencing may depend on CpG density rather than site-specific methylation. Cancer 2003;98:1540–6. © 2003 American Cancer Society. DOI 10.1002/cncr.11651