MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain

Mutations in the gene encoding the methyl-CG binding protein MeCP2 cause several neurological disorders including Rett syndrome. The di-nucleotide methyl-CG (mCG) is the classical MeCP2 DNA recognition sequence, but additional methylated sequence targets have been reported. Here we show by in vitro and in vivo analyses that MeCP2 binding to non-CG methylated sites in brain is largely confined to the tri-nucleotide sequence mCAC. MeCP2 binding to chromosomal DNA in mouse brain is proportional to mCAC + mCG density and unexpectedly defines large genomic domains within which transcription is sensitive to MeCP2 occupancy. Our results suggest that MeCP2 integrates patterns of mCAC and mCG in the brain to restrain transcription of genes critical for neuronal function

Neuronal non-CG methylation is an essential target for MeCP2 function

DNA methylation is implicated in neuronal biology via the protein MeCP2, the mutation of which causes Rett syndrome. MeCP2 recruits the NCOR1/2 co-repressor complexes to methylated cytosine in the CG dinucleotide, but also to sites of non-CG methylation, which are abundant in neurons. To test the biological significance of the dual-binding specificity of MeCP2, we replaced its DNA binding domain with an orthologous domain from MBD2, which can only bind mCG motifs. Knockin mice expressing the domain-swap protein displayed severe Rett-syndrome-like phenotypes, indicating that normal brain function requires the interaction of MeCP2 with sites of non-CG methylation, specifically mCAC. The results support the notion that the delayed onset of Rett syndrome is due to the simultaneous post-natal accumulation of mCAC and its reader MeCP2. Intriguingly, genes dysregulated in both Mecp2 null and domain-swap mice are implicated in other neurological disorders, potentially highlighting targets of relevance to the Rett syndrome phenotype

Molecular basis of R133C Rett syndrome

Rett syndrome is a debilitating autistic spectrum disorder affecting one in ten thousand girls. Patients develop normally for up to eighteen months before a period of regression involving stagnation in head growth, loss of speech, hand use and mobility. It is almost exclusively caused by mutation in Methyl CpG binding Protein 2 (MeCP2). MeCP2 has traditionally been thought of as a transcriptional repressor, although its exact function remains unknown and it has recently been shown that the protein can also bind to hydroxymethylation and non-CpG methylation, which occurs predominantly at CAC sites in the mature nervous system. Genotype-phenotype studies of the most common Rett-causing mutations in affected patients revealed that a missense mutation, R133C results in a milder form of Rett syndrome. The reasons for this are unclear, as the mutation lies right in the heart of the methylated DNA binding domain. Previous in vitro studies of R133C showed a severe deficit in binding to methylated cytosine. A subsequent study found that R133C binding to hydroxymethylated cytosine was specifically impaired, whereas binding to methylated cytosine was indistinguishable from wildtype. Defining the DNA binding impairment of MeCP2R133C would yield important insights into Rett disease pathophysiology and provide an explanation for the phenotypic spectrum seen in patients. To shed light on these matters, a novel mouse model of the R133C mutation was created. The R133C mouse had a phenotype that was less severe than other missense mutant mice, in terms of survival, growth, Rett-like phenotypic score and some behavioural paradigms thus recapitulating the patient data. At the molecular level in adult mouse brain, MeCP2R133C protein abundance was reduced. Immunohistochemistry showed that MeCP2R133C had an abnormal pattern of localisation in the nucleus of neurons. In vitro electrophoretic mobility shift assays suggested that MeCP2R133C binding to (hydroxy)methyl-CAC may be reduced to a greater extent than binding to mCpG. Chromatin immunoprecipitation experiments confirmed the deficit in binding to methylated sites and supported a disproportionate reduction in binding to methylation in a CAC sequence context. Analysis of adult mouse cerebellar gene expression revealed a subtle upregulation of long genes and downregulation of short genes. Based on these data, it is proposed that Rett syndrome caused by the R133C mutation results from a combination of protein instability and defective binding to methylated DNA. Methyl-CAC binding is potentially abolished. The downstream biological consequence of this is a length-dependent deregulation of gene expression in the brain

MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain

Mutations in the gene encoding the methyl-CG binding protein MeCP2 cause several neurological disorders including Rett syndrome. The di-nucleotide methyl-CG (mCG) is the classical MeCP2 DNA recognition sequence, but additional methylated sequence targets have been reported. Here we show by in vitro and in vivo analyses that MeCP2 binding to non-CG methylated sites in brain is largely confined to the tri-nucleotide sequence mCAC. MeCP2 binding to chromosomal DNA in mouse brain is proportional to mCAC + mCG density and unexpectedly defines large genomic domains within which transcription is sensitive to MeCP2 occupancy. Our results suggest that MeCP2 integrates patterns of mCAC and mCG in the brain to restrain transcription of genes critical for neuronal function.</p

Accounting for Ecosystem Alteration Doubles Estimates of Conservation Risk in the Conterminous United States

Previous national and global conservation assessments have relied on habitat conversion data to quantify conservation risk. However, in addition to habitat conversion to crop production or urban uses, ecosystem alteration (e.g., from logging, conversion to plantations, biological invasion, or fire suppression) is a large source of conservation risk. We add data quantifying ecosystem alteration on unconverted lands to arrive at a more accurate depiction of conservation risk for the conterminous United States. We quantify ecosystem alteration using a recent national assessment based on remote sensing of current vegetation compared with modeled reference natural vegetation conditions. Highly altered (but not converted) ecosystems comprise 23% of the conterminous United States, such that the number of critically endangered ecoregions in the United States is 156% higher than when calculated using habitat conversion data alone. Increased attention to natural resource management will be essential to address widespread ecosystem alteration and reduce conservation risk

Contesting longstanding conceptualisations of urban green space

Ever since the Victorian era saw the creation of “parks for the people,” health and wellbeing benefits have been considered a primary benefit of urban parks and green spaces. Today, public health remains a policy priority, with illnesses and conditions such as diabetes, obesity and depression a mounting concern, notably in increasingly urbanised environments. Urban green space often is portrayed as a nature-based solution for addressing such health concerns. In this chapter, Meredith Whitten investigates how the health and wellbeing benefits these spaces provide are limited by a narrow perspective of urban green space. Whitten explores how our understandings of urban green space remain rooted in Victorian ideals and calls into question how fit for purpose they are in twenty-first-century cities. Calling on empirical evidence collected in three boroughs in London with changing and increasing demographic populations, she challenges the long-held cultural underpinnings that lead to urban green space being portrayed “as a panacea to urban problems, yet treating it as a ‘cosmetic afterthought’” (Whitten, M, Reconceptualising green space: planning for urban green space in the contemporary city. Doctoral thesis, London School of Economics and Political Science, London, U.K. http://etheses.lse.ac.uk/. Accessed 12 Jun 2019, 2019b, p 18)

Signatures of degraded body tissues and environmental conditions in grave soils from a Roman and an Anglo-Scandinavian age burial from Hungate, York

Despite the importance of human burials in archaeological investigations of past peoples and their lives, the soil matrix that accommodates the remains is rarely considered, attention being focused mainly on visible features. The decomposition of a buried corpse and associated organic matter influences both the organic composition and, directly or indirectly, the microstructure of the burial matrix, producing signatures that could be preserved over archaeological timescales. If preserved, such signatures have potential to reveal aspects of the individual’s lifestyle and cultural practices as well as providing insights into taphonomic processes. Using organic chemical analysis and soil micromorphology we have identified organic signatures and physical characteristics relating to the presence of the body, and its decomposition in grave soils associated with two human skeletons (one Roman age and one Anglo-Scandinavian age) from Hungate, York, UK. The organic signatures, including contributions from body tissues, gut contents, bone degradation and input from microbiota, exhibit spatial variations with respect to anatomical location and features of the immediate burial environment. In the Roman grave broad changes in redox conditions associated with the decomposition of the corpse and disturbance from the excavation and use of an Anglo-Scandinavian age cess pit that partially cuts the grave were evident. Leachate from the cess pit was shown to exacerbate the degradation of the skeletal remains in the regions closest to it, also degrading and depleting spherulites in the soil, through decalcification of the bone and liberation of bone-derived cholesterol into the soil matrix. The findings from this work have implications for future archaeo- and contemporary forensic investigations of buried human remains

Search for strong gravity in multijet final states produced in pp collisions at √s=13 TeV using the ATLAS detector at the LHC

A search is conducted for new physics in multijet final states using 3.6 inverse femtobarns of data from proton-proton collisions at √s = 13TeV taken at the CERN Large Hadron Collider with the ATLAS detector. Events are selected containing at least three jets with scalar sum of jet transverse momenta (HT) greater than 1TeV. No excess is seen at large HT and limits are presented on new physics: models which produce final states containing at least three jets and having cross sections larger than 1.6 fb with HT > 5.8 TeV are excluded. Limits are also given in terms of new physics models of strong gravity that hypothesize additional space-time dimensions

Measurement of the correlation between flow harmonics of different order in lead-lead collisions at √sNN = 2.76 TeV with the ATLAS detector

Correlations between the elliptic or triangular flow coefficients vm (m=2 or 3) and other flow harmonics vn (n=2 to 5) are measured using √sNN=2.76 TeV Pb+Pb collision data collected in 2010 by the ATLAS experiment at the LHC, corresponding to an integrated luminosity of 7 μb−1. The vm−vn correlations are measured in midrapidity as a function of centrality, and, for events within the same centrality interval, as a function of event ellipticity or triangularity defined in a forward rapidity region. For events within the same centrality interval, v3 is found to be anticorrelated with v2 and this anticorrelation is consistent with similar anticorrelations between the corresponding eccentricities, ε2 and ε3. However, it is observed that v4 increases strongly with v2, and v5 increases strongly with both v2 and v3. The trend and strength of the vm−vn correlations for n=4 and 5 are found to disagree with εm−εn correlations predicted by initial-geometry models. Instead, these correlations are found to be consistent with the combined effects of a linear contribution to vn and a nonlinear term that is a function of v22 or of v2v3, as predicted by hydrodynamic models. A simple two-component fit is used to separate these two contributions. The extracted linear and nonlinear contributions to v4 and v5 are found to be consistent with previously measured event-plane correlations