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The genomic loci bound by the glucocorticoid receptor (GR), a hormone-activated transcription factor, show little overlap between cell types. To study the role of chromatin and sequence in specifying where GR binds, we used Bayesian modeling within the universe of accessible chromatin. Taken together, our results uncovered that although GR preferentially binds accessible chromatin, its binding is biased against accessible chromatin located at promoter regions. This bias can only be explained partially by the presence of fewer GR recognition sequences, arguing for the existence of additional mechanisms that interfere with GR binding at promoters. Therefore, we tested the role of H3K9ac, the chromatin feature with the strongest negative association with GR binding, but found that this correlation does not reflect a causative link. Finally, we find a higher percentage of promoter-proximal GR binding for genes regulated by GR across cell types than for cell type-specific target genes. Given that GR almost exclusively binds accessible chromatin, we propose that cell type-specific regulation by GR preferentially occurs via distal enhancers, whose chromatin accessibility is typically cell type-specific, whereas ubiquitous target gene regulation is more likely to result from binding to promoter regions, which are often accessible regardless of cell type examined.

Precise genome-editing relies on the repair of sequence-specific nuclease-induced DNA nicking or double-strand breaks (DSBs) by homology-directed repair (HDR). However, nonhomologous end-joining (NHEJ), an error-prone repair, acts concurrently, reducing the rate of high-fidelity edits. The identification of genome-editing conditions that favor HDR over NHEJ has been hindered by the lack of a simple method to measure HDR and NHEJ directly and simultaneously at endogenous loci. To overcome this challenge, we developed a novel, rapid, digital PCR-based assay that can simultaneously detect one HDR or NHEJ event out of 1,000 copies of the genome. Using this assay, we systematically monitored genome-editing outcomes of CRISPR-associated protein 9 (Cas9), Cas9 nickases, catalytically dead Cas9 fused to FokI, and transcription activator-like effector nuclease at three disease-associated endogenous gene loci in HEK293T cells, HeLa cells, and human induced pluripotent stem cells. Although it is widely thought that NHEJ generally occurs more often than HDR, we found that more HDR than NHEJ was induced under multiple conditions. Surprisingly, the HDR/NHEJ ratios were highly dependent on gene locus, nuclease platform, and cell type. The new assay system, and our findings based on it, will enable mechanistic studies of genome-editing and help improve genome-editing technology.

Purpose: Children with dyslexia often have related writing difficulties. In the simple view of writing model, high-quality writing depends on good transcription skills, working memory, and executive function--all of which can be difficult for children with dyslexia and result in poor spelling and low overall writing quality. In this article, we describe the challenges of children with dyslexia in terms of the simple view of writing and instructional strategies to increase spelling and overall writing quality in children with dyslexia. Method: For spelling strategies, we conducted systematic searches across 2 databases for studies examining the effectiveness of spelling interventions for students with dyslexia as well as including studies from 2 meta-analyses. To locate other instructional practices to increase writing quality (e.g., handwriting and executive function), we examined recent meta-analyses of writing and supplemented that by conducting forward searches. Results: Through the search, we found evidence of effective remedial and compensatory intervention strategies in spelling, transcription, executive function, and working memory. Some strategies included spelling using sound-spellings and morphemes and overall quality using text structure, sentence combining, and self-regulated strategy development. Conclusions: Many students with dyslexia experience writing difficulty in multiple areas. However, their writing (and even reading) skills can improve with the instructional strategies identified in this article. We describe instructional procedures and provide links to resources throughout the article.

In addition to guiding proteins to defined genomic loci, DNA can act as an allosteric ligand that influences protein structure and activity. Here we compared genome-wide binding, transcriptional regulation, and, using NMR, the conformation of two glucocorticoid receptor (GR) isoforms that differ by a single amino acid insertion in the lever arm, a domain that adopts DNA sequence-specific conformations. We show that these isoforms differentially regulate gene expression levels through two mechanisms: differential DNA binding and altered communication between GR domains. Our studies suggest a versatile role for DNA in both modulating GR activity and also in directing the use of GR isoforms. We propose that the lever arm is a "fulcrum" for bidirectional allosteric signaling, conferring conformational changes in the DNA reading head that influence DNA sequence selectivity, as well as conferring changes in the dimerization domain that connect functionally with remote regulatory surfaces, thereby influencing which genes are regulated and the magnitude of their regulation.

The ordered migration of thymocytes from the cortex to the medulla is critical for the appropriate selection of the mature T cell repertoire. Most studies of thymocyte migration rely on mouse models, but we know relatively little about how human thymocytes find their appropriate anatomical niches within the thymus. Moreover, the signals that retain CD4+CD8+ double-positive (DP) thymocytes in the cortex and prevent them from entering the medulla prior to positive selection have not been identified in mice or humans. Here, we examined the intrathymic migration of human thymocytes in both mouse and human thymic stroma and found that human thymocyte subsets localized appropriately to the cortex on mouse thymic stroma and that MHC-dependent interactions between human thymocytes and mouse stroma could maintain the activation and motility of DP cells. We also showed that CXCR4 was required to retain human DP thymocytes in the cortex, whereas CCR7 promoted migration of mature human thymocytes to the medulla. Thus, 2 opposing chemokine gradients control the migration of thymocytes from the cortex to the medulla. These findings point to significant interspecies conservation in thymocyte-stroma interactions and provide the first evidence that chemokines not only attract mature thymocytes to the medulla, but also play an active role in retaining DP thymocytes in the cortex prior to positive selection.

The complexity and specificity of metazoan transcription are determined by combinatorial control of the composition and activity of regulatory complexes. To investigate the basis of this specificity, we focused on the glucocorticoid receptor (GR), a single regulatory factor that integrates multiple signals to give rise to many distinct patterns of expression. We measured the expression of a set of genes, each directly GR-regulated, but by different mechanisms in two cell lines. We varied ligand (dose, chemistry, and duration of treatment), GR (expression level and functionality), and a non-GR regulatory factor that commonly interacts with GR. Our study revealed distinct expression patterns within this set of genes, but all could be modeled by an incoherent feed-forward regulatory logic. Cellular signals, operating on GR and other factors within regulatory complexes, may define and modulate the kinetics and strength of the activating or inhibitory paths of the regulatory logic. Thus, characterizing systems behavior by perturbing single or multiple signals can reveal general principles of regulation, providing an approach to the dissection and deconvolution of combinatorial control.

RNA viruses exist as dynamic and diverse populations shaped by constant mutation and selection. Yet little is known about how the mutant spectrum contributes to virus evolvability and pathogenesis. Because several codon choices are available for a given amino acid, a central question concerns whether viral sequences have evolved to optimize not only the protein coding consensus, but also the DNA/RNA sequences accessible through mutation. Here we directly test this hypothesis by comparing wild-type poliovirus to synthetic viruses carrying re-engineered capsid sequences with hundreds of synonymous mutations. Strikingly, such rewiring of the population's mutant network reduced its robustness and attenuated the virus in an animal model of infection. We conclude that the position of a virus in sequence space defines its mutant spectrum, evolutionary trajectory, and pathogenicity. This organizing principle for RNA virus populations confers tolerance to mutations and facilitates replication and spread within the dynamic host environment.

In eukaryotes, RNA polymerase II (Pol(II)) dependent gene expression requires accessory factors termed transcriptional coregulators. One coregulator that universally contributes to Pol(II)-dependent transcription is the Mediator, a multisubunit complex that is targeted by many transcriptional regulatory factors. For example, the Caenorhabditis elegans Mediator subunit MDT-15 confers the regulatory actions of the sterol response element binding protein SBP-1 and the nuclear hormone receptor NHR-49 on fatty acid metabolism. Here, we demonstrate that MDT-15 displays a broader spectrum of activities, and that it integrates metabolic responses to materials ingested by C. elegans. Depletion of MDT-15 protein or mutation of the mdt-15 gene abrogated induction of specific detoxification genes in response to certain xenobiotics or heavy metals, rendering these animals hypersensitive to toxin exposure. Intriguingly, MDT-15 appeared to selectively affect stress responses related to ingestion, as MDT-15 functional defects did not abrogate other stress responses, e.g., thermotolerance. Together with our previous finding that MDT-15:NHR-49 regulatory complexes coordinate a sector of the fasting response, we propose a model whereby MDT-15 integrates several transcriptional regulatory pathways to monitor both the availability and quality of ingested materials, including nutrients and xenobiotic compounds.

Introduction: Telepractice has the potential to align with the directive to reduce inequalities by United Nations Sustainable Development Goal 10. Telepractice additionally addresses a national digital health strategic plan for accessible digitally enabled models of care. To plan improvements, it is essential to understand the experience of telepractice for people with disability, which may be achieved through an approach such as journey mapping. The current article provides both a disability‐specific case study and a methodological guide for the inclusion of customers and clinicians in the meaningful redevelopment of services. The Perth, Australia‐based case study aimed to gain insights into the experience of telepractice for people with disability. The methodological aim describes using co‐design to produce a journey map in collaboration with customers and clinicians, for potential replication in a wide range of health and social care contexts. Method: Interview transcripts gathered from a cohort of customer participants (n = 17) were used to inform the journey map. A group of customers (n = 5) and clinicians plus one manager (n = 5) distributed the findings onto a customer experience journey map during a co‐design workshop. The journey map describes the emotional experience and actions taken, along five phases of a timeline through telepractice service interactions: (1) before, (2) selecting telepractice, (3) telepractice preparation, (4) during telepractice sessions and (5) after. Results: A journey map visualisation of customer experiences was produced that identified strengths of telepractice service delivery (flexibility) while noting challenges (with technology) as opportunities for improvement. The consensus of participants was the desire to have access to telepractice currently and in the future, in addition to in‐person delivery. Conclusion: These findings are valuable in the context of advocating for the incorporation of customers and clinicians through co‐design workshops in the content analysis and creation of a journey map that is representative of the lived experience of accessing telepractice services. Patient or Public Contribution: The paper forms part of a larger co‐design process that included customer participants throughout the design and planning of the project, inclusion of a peer researcher and the co‐designers in the workshops, journey map and this article production. [ABSTRACT FROM AUTHOR]

The article focuses on the performance of Gilbert and Sullivan's The Mikado by American Jewish communities between 1885 and 1939, examining its cultural implications and use as a tool for identity formation. Topics include the racial appropriation inherent in the performances, their role in fostering a sense of belonging and acculturation within American society, and the interplay of Jewish identity with broader racial and cultural hierarchies of the time.