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A collection of 19 stories featuring princesses from Disney films.

During mouse embryonic development, pluripotent cells rapidly divide and diversify, yet the regulatory programs that define the cell repertoire for each organ remain ill-defined. To delineate comprehensive chromatin landscapes during early organogenesis, we mapped chromatin accessibility in 19,453 single nuclei from mouse embryos at 8.25 days post-fertilization. Identification of cell-type-specific regions of open chromatin pinpointed two TAL1-bound endothelial enhancers, which we validated using transgenic mouse assays. Integrated gene expression and transcription factor motif enrichment analyses highlighted cell-type-specific transcriptional regulators. Subsequent in vivo experiments in zebrafish revealed a role for the ETS factor FEV in endothelial identity downstream of ETV2 (Etsrp in zebrafish). Concerted in vivo validation experiments in mouse and zebrafish thus illustrate how single-cell open chromatin maps, representative of a mammalian embryo, provide access to the regulatory blueprint for mammalian organogenesis.Pijuan-Sala et al. present a comprehensive single-nucleus open chromatin map of early mouse embryogenesis and validate the role of ETS transcription factor FEV in endothelial identity in zebrafish.

Cellular decision-making is mediated by a complex interplay of external stimuli with the intracellular environment, in particular transcription factor regulatory networks. Here we have determined the expression of a network of 18 key haematopoietic transcription factors in 597 single primary blood stem and progenitor cells isolated from mouse bone marrow. We demonstrate that different stem/progenitor populations are characterized by distinctive transcription factor expression states, and through comprehensive bioinformatic analysis reveal positively and negatively correlated transcription factor pairings, including previously unrecognized relationships between Gata2 , Gfi1 and Gfi1b . Validation using transcriptional and transgenic assays confirmed direct regulatory interactions consistent with a regulatory triad in immature blood stem cells, where Gata2 may function to modulate cross-inhibition between Gfi1 and Gfi1b . Single-cell expression profiling therefore identifies network states and allows reconstruction of network hierarchies involved in controlling stem cell fate choices, and provides a blueprint for studying both normal development and human disease. Gottgens and colleagues have analysed the expression of 18 haematopoietic factors in single primary blood and progenitor cells from mouse bone marrow. They delineate distinct states of expression for these transcription factors and identify regulatory relationships between the key factors Gata2, Gfi1 and Gfi2.

Margaret Goodell and colleagues report genome-wide mapping of 5-methylcytosine and 5-hydroxymethylcytosine in purified mouse hematopoietic stem cells. They identify large regions of low methylation with borders marked by 5-hydroxymethylcytosine. These borders become eroded in the absence of DNA methyltransferase 3a. Gains and losses in DNA methylation are prominent features of mammalian cell types. To gain insight into the mechanisms that promote shifts in DNA methylation and contribute to changes in cell fate, including malignant transformation, we performed genome-wide mapping of 5-methylcytosine and 5-hydroxymethylcytosine in purified mouse hematopoietic stem cells. We discovered extended regions of low methylation (canyons) that span conserved domains frequently containing transcription factors and are distinct from CpG islands and shores. About half of the genes in these methylation canyons are coated with repressive histone marks, whereas the remainder are covered by activating histone marks and are highly expressed in hematopoietic stem cells (HSCs). Canyon borders are demarked by 5-hydroxymethylcytosine and become eroded in the absence of DNA methyltransferase 3a (Dnmt3a). Genes dysregulated in human leukemias are enriched for canyon-associated genes. The new epigenetic landscape we describe may provide a mechanism for the regulation of hematopoiesis and may contribute to leukemia development.

Cytoplasmic mislocalisation and nuclear depletion of TDP-43 are pathological hallmarks of amyotrophic lateral sclerosis (ALS), including mutations in the C9ORF72 gene that characterise the most common genetic form of ALS (C9ALS). Studies in human cells and animal models have associated cytoplasmic mislocalisation of TDP-43 with abnormalities in nuclear transport receptors, referred to as karyopherins, that mediate the nucleocytoplasmic shuttling of TDP-43. Yet the relationship between karyopherin abnormalities and TDP-43 pathology are unclear. Here we report karyopherin-α4 (KPNA4) pathology in the spinal cord of TDP-43-positive sporadic ALS and C9ALS patients. Structural analyses revealed the selective interaction between KPNA subtypes, especially KPNA4, with the nuclear localisation signal (NLS) of TDP-43. Targeted cytoplasmic mislocalisation and nuclear depletion of TDP-43 caused KPNA4 pathology in human cells. Similar phenotypes were observed in Drosophila whereby cytoplasmic accumulation of the TDP-43 homolog, TBPH, caused the nuclear decrease and cytosolic mislocalisation of the KPNA4 homolog, Importin-α3 (Impα3). In contrast, induced accumulation of Impα3 was not sufficient to cause TBPH mislocalisation. Instead, targeted gain of Impα3 in the presence of accumulating cytosolic TBPH, restored Impα3 localisation and partially rescued nuclear TBPH. These results demonstrate that cytoplasmic accumulation of TDP-43 causes karyopherin pathology that characterises ALS spinal cord. Together with earlier reports, our findings establish KPNA4 abnormalities as a molecular signature of TDP-43 proteinopathies and identify it as a potential therapeutic target to sustain nuclear TDP-43 essential for cellular homeostasis affected in ALS and frontotemporal dementia.

Transcription factor (TF) networks determine cell-type identity by establishing and maintaining lineage-specific expression profiles, yet reconstruction of mammalian regulatory network models has been hampered by a lack of comprehensive functional validation of regulatory interactions. Here, we report comprehensive ChIP-Seq, transgenic and reporter gene experimental data that have allowed us to construct an experimentally validated regulatory network model for haematopoietic stem/progenitor cells (HSPCs). Model simulation coupled with subsequent experimental validation using single cell expression profiling revealed potential mechanisms for cell state stabilisation, and also how a leukaemogenic TF fusion protein perturbs key HSPC regulators. The approach presented here should help to improve our understanding of both normal physiological and disease processes. Blood stem cells and blood progenitor cells replenish a person’s entire blood system throughout their life and are crucial for survival. The stem cells have the potential to become any type of blood cell – including white blood cells and red blood cells – while the progenitor cells are slightly more restricted in the types of blood cell they can become. It is important to understand how the balance of cell types is maintained because, in cancers of the blood (also known as leukaemias), this organisation is lost and some cells proliferate abnormally. Almost all of a person’s cells will contain the same genetic information, but different cell types arise when different genes are switched on or off. The genes encoding proteins called transcription factors are particularly important because the proteins can control – either by activating or repressing – many other genes. Importantly, some of these genes will encode other transcription factors, meaning that these proteins essentially work together in networks. Schütte et al. have now combined extensive biochemical experiments with computational modelling to study some of the transcription factors that define blood stem cells and blood progenitor cells in mice. Firstly, nine transcription factors, which were already known to be important in blood stem cells, were thoroughly studied in mouse cells that could be grown in the laboratory. These experiments provided an overall view of which other genes these transcription factors control. Additional targeted investigations of the nine transcription factors then revealed how these proteins act in combination to activate or repress their respective activities. With this information, Schütte et al. built a computational model, which accurately reproduced how real mouse blood stem and progenitor cells behave when, for example, a transcription factor is deleted. Furthermore, the model could also predict what happens in single cells if the amounts of the transcription factors change. Lastly, Schütte et al. studied a common type of leukaemia. The model showed that the mutations that occur in this cancer change the finely tuned balance of the nine transcription factors; this may explain why leukaemia cells behave abnormally. In future these models could be extended to more transcription factors and other cell types and cancers.

Purpose This paper aims to examine the need for outcome research in secure children’s homes, explaining the problems for young people and how we can remedy this. Design/methodology/approach This is a discussion paper raising issues of importance as to who these children are, what is provided and how well they work in providing what is a very expensive service. Findings There is a great need to investigate the efficacy of secure children’s homes by assessing outcomes. Originality/value As far as the authors are aware, this topic has not been previously discussed in academic journals.

Gene expression governs cell fate, and is regulated via a complex interplay of transcription factors and molecules that change chromatin structure. Advances in sequencing-based assays have enabled investigation of these processes genome-wide, leading to large datasets that combine information on the dynamics of gene expression, transcription factor binding and chromatin structure as cells differentiate. While numerous studies focus on the effects of these features on broader gene regulation, less work has been done on the mechanisms of gene-specific transcriptional control. In this study, we have focussed on the latter by integrating gene expression data for the in vitro differentiation of murine ES cells to macrophages and cardiomyocytes, with dynamic data on chromatin structure, epigenetics and transcription factor binding. Combining a novel strategy to identify communities of related control elements with a penalized regression approach, we developed individual models to identify the potential control elements predictive of the expression of each gene. Our models were compared to an existing method and evaluated using the existing literature and new experimental data from embryonic stem cell differentiation reporter assays. Our method is able to identify transcriptional control elements in a gene specific manner that reflect known regulatory relationships and to generate useful hypotheses for further testing.

Zebrafish (Danio rerio) larvae prefer the olfactory cues of kin to non-kin. We examined the potential benefits of kin preference by comparing growth rate, shoaling, and aggressive behavior in juvenile zebrafish housed in groups of either familiar kin or unfamiliar non-kin. Over an observation period of 5 days, the animals grew 33% more in kin groups; however, neither shoaling nor the frequency of aggressive interactions was different in groups of related versus unrelated individuals. Shoaling behavior increased with increasing observation time and increasing age, while aggressive behavior remained the same. We conclude that associating with kin probably creates a less stressful environment that allows for higher growth rates, which can lead to higher direct fitness based on increased survival and earlier reproduction. Kin recognition leading to kin-structured groups may therefore be under positive selection.