Intermingling of Chromosome Territories in Interphase Suggests Role in Translocations and Transcription-Dependent Associations

After mitosis, mammalian chromosomes partially decondense to occupy distinct territories in the cell nucleus. Current models propose that territories are separated by an interchromatin domain, rich in soluble nuclear machinery, where only rare interchromosomal interactions can occur via extended chromatin loops. In contrast, recent evidence for chromatin mobility and high frequency of chromosome translocations are consistent with significant levels of chromosome intermingling, with important consequences for genome function and stability. Here we use a novel high-resolution in situ hybridization procedure that preserves chromatin nanostructure to show that chromosome territories intermingle significantly in the nucleus of human cells. The degree of intermingling between specific chromosome pairs in human lymphocytes correlates with the frequency of chromosome translocations in the same cell type, implying that double-strand breaks formed within areas of intermingling are more likely to participate in interchromosomal rearrangements. The presence of transcription factories in regions of intermingling and the effect of transcription impairment on the interactions between chromosomes shows that transcription-dependent interchromosomal associations shape chromosome organization in mammalian cells. These findings suggest that local chromatin conformation and gene transcription influence the extent with which chromosomes interact and affect their overall properties, with direct consequences for cell-type specific genome stability

The N-terminus of Stag1 is required to repress the 2C program by maintaining rRNA expression and nucleolar integrity

Our understanding of how STAG proteins contribute to cell identity and disease have largely been studied from the perspective of chromosome topology and protein-coding gene expression. Here, we show that STAG1 is the dominant paralog in mouse embryonic stem cells (mESCs) and is required for pluripotency. mESCs express a wide diversity of naturally occurring Stag1 isoforms, resulting in complex regulation of both the levels of STAG paralogs and the proportion of their unique terminal ends. Skewing the balance of these isoforms impacts cell identity. We define a novel role for STAG1, in particular its N-terminus, in regulating repeat expression, nucleolar integrity, and repression of the two-cell (2C) state to maintain mESC identity. Our results move beyond protein-coding gene regulation via chromatin loops to new roles for STAG1 in nucleolar structure and function, and offer fresh perspectives on how STAG proteins, known to be cancer targets, contribute to cell identity and disease

Extraction, selection and comparison of features for an effective automated computer-aided diagnosis of Parkinson's disease based on [123I]FP-CIT SPECT images

Purpose This work aimed to assess the potential of a set of features extracted from [I-123] FP-CIT SPECT brain images to be used in the computer-aided "in vivo" confirmation of dopaminergic degeneration and therefore to assist clinical decision to diagnose Parkinson's disease.Methods Seven features were computed from each brain hemisphere: five standard features related to uptake ratios on the striatum and two features related to the estimated volume and length of the striatal region with normal uptake. The features were tested on a dataset of 652 [I-123] FP-CIT SPECT brain images from the Parkinson's Progression Markers Initiative. The discrimination capacities of each feature individually and groups of features were assessed using three different machine learning techniques: support vector machines (SVM), k-nearest neighbors and logistic regression.Results Cross-validation results based on SVM have shown that, individually, the features that generated the highest accuracies were the length of the striatal region (96.5%), the putaminal binding potential (95.4%) and the striatal binding potential (93.9%) with no statistically significant differences among them. The highest classification accuracy was obtained using all features simultaneously (accuracy 97.9%, sensitivity 98% and specificity 97.6%). Generally, slightly better results were obtained using the SVM with no statistically significant difference to the other classifiers for most of the features.Conclusions The length of the striatal region uptake is clinically useful and highly valuable to confirm dopaminergic degeneration "in vivo" as an aid to the diagnosis of Parkinson's disease. It compares fairly well to the standard uptake ratio-based features, reaching, at least, similar accuracies and is easier to obtain automatically. Thus, we propose its day to day clinical use, jointly with the uptake ratio-based features, in the computer-aided diagnosis of dopaminergic degeneration in Parkinson's disease

Divergent wiring of repressive and active chromatin interactions between mouse embryonic and trophoblast lineages.

The establishment of the embryonic and trophoblast lineages is a developmental decision underpinned by dramatic differences in the epigenetic landscape of the two compartments. However, it remains unknown how epigenetic information and transcription factor networks map to the 3D arrangement of the genome, which in turn may mediate transcriptional divergence between the two cell lineages. Here, we perform promoter capture Hi-C experiments in mouse trophoblast (TSC) and embryonic (ESC) stem cells to understand how chromatin conformation relates to cell-specific transcriptional programmes. We find that key TSC genes that are kept repressed in ESCs exhibit interactions between H3K27me3-marked regions in ESCs that depend on Polycomb repressive complex 1. Interactions that are prominent in TSCs are enriched for enhancer-gene contacts involving key TSC transcription factors, as well as TET1, which helps to maintain the expression of TSC-relevant genes. Our work shows that the first developmental cell fate decision results in distinct chromatin conformation patterns establishing lineage-specific contexts involving both repressive and active interactions

A Novel Ecological Approach Reveals Early Executive Function Impairments in Huntington’s Disease

Introduction: Impairments in executive functions are common in neurogenetic disorders such as Huntington’s disease (HD) and are thought to significantly influence the patient’s functional status. Reliable tools with higher ecological validity that can assess and predict the impact of executive dysfunction in daily-life performance are needed. This study aimed to develop and validate a novel non-immersive virtual reality task (“EcoKitchen”) created with the purpose of capturing cognitive and functional changes shown by HD carriers without clinical manifestations of the disease (Premanifest HD), in a more realistic setting.Materials and Methods: We designed a virtual reality task with three blocks of increasing executive load. The performance of three groups (Controls, CTRL; Premanifest HD individuals, HP; Early Manifest HD patients, HD) was compared in four main components of the study protocol: the EcoKitchen; a subjective (self-report) measure – “The Adults and Older Adults Functional Assessment Inventory (IAFAI)”; the “Behavioural Assessment of Dysexecutive Syndrome battery (BADS)”; and a conventional neuropsychological test battery. We also examined statistical associations between EcoKitchen and the other executive, functional and clinical measures used.Results: The HD group showed deficits in all the assessment methods used. In contrast, the HP group was only found to be impaired in the EcoKitchen task, particularly in the most cognitively demanding blocks, where they showed a higher number of errors compared to the CTRL group. Statistically significant correlations were identified between the EcoKitchen, measures of the other assessment tools, and HD clinical features.Discussion: The EcoKitchen task, developed as an ecological executive function assessment tool, was found to be sensitive to early deficits in this domain. Critically, in premanifest HD individuals, it identifies dysfunction prior to symptom onset. Further it adds a potential tool for diagnosis and management of the patients’ real-life problems

Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.

BACKGROUND: Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases and bisulfite conversion protocols. Although some steps in the procedure, such as PCR amplification, are known to introduce biases, a systematic evaluation of biases in WGBS strategies is missing. RESULTS: We perform a comparative analysis of several commonly used pre- and post-bisulfite WGBS library preparation protocols for their performance and quality of sequencing outputs. Our results show that bisulfite conversion per se is the main trigger of pronounced sequencing biases, and PCR amplification builds on these underlying artefacts. The majority of standard library preparation methods yield a significantly biased sequence output and overestimate global methylation. Importantly, both absolute and relative methylation levels at specific genomic regions vary substantially between methods, with clear implications for DNA methylation studies. CONCLUSIONS: We show that amplification-free library preparation is the least biased approach for WGBS. In protocols with amplification, the choice of bisulfite conversion protocol or polymerase can significantly minimize artefacts. To aid with the quality assessment of existing WGBS datasets, we have integrated a bias diagnostic tool in the Bismark package and offer several approaches for consideration during the preparation and analysis of WGBS datasets

Let there be light...

“Let there be light...” is a project in the scope of the International Year of Light 2015 (IYL 2015) targeted at children of the first school grade. Basically, it comprises nine recreational - scientific workshops that last for approximately 90 minutes. Each workshop is dedicated to a different topic, namely: bioluminescence, mineral observation, the rainbow, light-shadow contrast, battery production, just to name a few, and is designed, in differ- ent approaches, by a distinct team of scientists familiar to the scientific area focused. The activity starts with the dramatized storytelling of a children’s story related to the scientific subject and performed by the team of the public library expert in this area. This moment takes place in an almost magical environment opening the door to the science topic light-related that would be focused later on. In the third part of the workshop, the children are invited to produce plastic works (e.g. drawings, constructions and models) inspired in what they have learned, and that are to be collected in a public exhibition held at the same institution at the end of the project. In the present work, besides the description of the experience, you can find the critical analysis of the activity and the evaluation of the action by all the actors involved (project team and children/teachers that attended the workshops).info:eu-repo/semantics/publishedVersio

TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells.

BACKGROUND: Ten-eleven translocation (TET) enzymes oxidise DNA methylation as part of an active demethylation pathway. Despite extensive research into the role of TETs in genome regulation, little is known about their effect on transposable elements (TEs), which make up nearly half of the mouse and human genomes. Epigenetic mechanisms controlling TEs have the potential to affect their mobility and to drive the co-adoption of TEs for the benefit of the host. RESULTS: We performed a detailed investigation of the role of TET enzymes in the regulation of TEs in mouse embryonic stem cells (ESCs). We find that TET1 and TET2 bind multiple TE classes that harbour a variety of epigenetic signatures indicative of different functional roles. TETs co-bind with pluripotency factors to enhancer-like TEs that interact with highly expressed genes in ESCs whose expression is partly maintained by TET2-mediated DNA demethylation. TETs and 5-hydroxymethylcytosine (5hmC) are also strongly enriched at the 5' UTR of full-length, evolutionarily young LINE-1 elements, a pattern that is conserved in human ESCs. TETs drive LINE-1 demethylation, but surprisingly, LINE-1s are kept repressed through additional TET-dependent activities. We find that the SIN3A co-repressive complex binds to LINE-1s, ensuring their repression in a TET1-dependent manner. CONCLUSIONS: Our data implicate TET enzymes in the evolutionary dynamics of TEs, both in the context of exaptation processes and of retrotransposition control. The dual role of TET action on LINE-1s may reflect the evolutionary battle between TEs and the host

Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation

Background Vitamin C (vitC) enhances the activity of 2-oxoglutarate-dependent dioxygenases, including TET enzymes, which catalyse DNA demethylation, and Jumonji-domain histone demethylases. The epigenetic remodelling promoted by vitC improves the efficiency of induced pluripotent stem cell derivation, and is required to attain a ground-state of pluripotency in embryonic stem cells (ESCs) that closely mimics the inner cell mass of the early blastocyst. However, genome-wide DNA and histone demethylation can lead to upregulation of transposable elements (TEs), and it is not known how vitC addition in culture media affects TE expression in pluripotent stem cells. Results Here we show that vitC increases the expression of several TE families, including evolutionarily young LINE-1 (L1) elements, in mouse ESCs. We find that TET activity is dispensable for L1 upregulation, and that instead it occurs largely as a result of H3K9me3 loss mediated by KDM4A/C histone demethylases. Despite increased L1 levels, we did not detect increased somatic insertion rates in vitC-treated cells. Notably, treatment of human ESCs with vitC also increases L1 protein levels, albeit through a distinct, post-transcriptional mechanism. Conclusion VitC directly modulates the expression of mouse L1s and other TEs through epigenetic mechanisms, with potential for downstream effects related to the multiple emerging roles of L1s in cellular function.This work was supported by grants from the Wellcome Trust/Royal Society (101225/Z/13/Z) and MRC (MR/X008487/1) to M.R.B.; and BBSRC (BB/T000031/1) to M.R.B. and J.M.F.Peer reviewe