diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data

Abstract Summary The 3D architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in DNA looping structure are associated with variation in gene expression and cell state. To systematically assess changes in DNA looping architecture between samples, we introduce diffloop, an R/Bioconductor package that provides a suite of functions for the quality control, statistical testing, annotation, and visualization of DNA loops. We demonstrate this functionality by detecting differences between ENCODE ChIA-PET samples and relate looping to variability in epigenetic state. Availability and implementation Diffloop is implemented as an R/Bioconductor package available at https://bioconductor.org/packages/release/bioc/html/diffloop.html Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online

Unequal childhoods: A case study application of Lareau’s ‘accomplishment of natural growth’ in British working-class and poor families

International authors have argued that social class inequalities can influence parental engagement in education (Bourdieu, 1974). Lareau argued that middle-class families possess the resources to actively cultivate their children to succeed academically, whereas working-class and poor families feel they lack such resources and allow their children to develop limited and passive relations with school. This paper applies a core element of Lareau’s typology of child rearing to examine disadvantaged British mothers’ experience of engaging with schools. A study involving 77 parents and caregivers of secondary school children, considered disadvantaged, sought to understand the experiences of parental engagement in primary and secondary education. Selective case studies have been chosen from this larger study, using a thematic analysis, to understand how these mothers interpreted their experiences of engaging with secondary education, their feelings of frustration, powerlessness and distance from secondary school. The stories presented illustrate that the ‘accomplishment of natural growth’ provides a contemporary class analysis framework to interpret the experiences of some disadvantaged British parents. Recommendations are made advising how Lareau’s typology of child rearing can inform policy and practice in the British education system and recommendations for future research are made with the purpose of promoting equal access to educational engagement and opportunitie

Preschool Verbal and Nonverbal Ability Mediate the Association Between Socioeconomic Status and School Performance

We compared the extent to which the long-term influence of family socioeconomic status (SES) on children's school performance from age 7 through 16 years was mediated by their preschool verbal and nonverbal ability. In 661 British children, who completed 17 researcher-administered ability tests at age 4.5 years, SES correlated more strongly with verbal than nonverbal ability (.39 vs.26). Verbal ability mediated about half of the association between SES and school performance at age 7, while nonverbal ability accounted for a third of the link. Only SES, but not verbal or nonverbal ability, was associated with changes in school performance from age 7 to 16. We found that SES-related differences in school performance are only partly transmitted through children's preschool verbal abilities

Childcare, choice and social class: Caring for young children in the UK

This paper draws on the results of two qualitative research projects examining parental engagements with the childcare market in the UK. Both projects are located in the same two London localities. One project focuses on professional middle class parents, and the other on working class families, and we discuss the key importance of social class in shaping parents' differential engagement with the childcare market, and their understandings of the role childcare plays in their children's lives. We identify and discuss the different "circuits" of care (Ball et al 1995) available to and used by families living physically close to each other, but in social class terms living in different worlds. We also consider parents' relationships with carers, and their social networks. We conclude that in order to fully understand childcare policies and practices and families' experiences of care, an analysis which encompasses social class and the workings of the childcare market is needed

Transcript-indexed ATAC-seq for precision immune profiling.

T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy

Heritability of fetal hemoglobin, white cell count, and other clinical traits from a sickle cell disease family cohort

Sickle cell disease (SCD) is the most common monogenic disorder in the world. Notably, there is extensive clinical heterogeneity in SCD that cannot be fully accounted for by known factors, and in particular, the extent to which the phenotypic diversity of SCD can be explained by genetic variation has not been reliably quantified. Here, in a family-based cohort of 449 patients with SCD and 755 relatives, we first show that 5 known modifiers affect 11 adverse outcomes in SCD to varying degrees. We then utilize a restricted maximum likelihood procedure to estimate the heritability of 20 hematologic traits, including fetal hemoglobin (HbF) and white blood cell count (WBC), in the clinically relevant context of inheritance from healthy carriers to SCD patients. We report novel estimations of heritability for HbF at 31.6% (±5.4%) and WBC at 41.2% (±6.8%) in our cohort. Finally, we demonstrate shared genetic bases between HbF, WBC, and other hematologic traits, but surprisingly little overlap between HbF and WBC themselves. In total, our analyses show that HbF and WBC have significant heritable components among individuals with SCD and their relatives, demonstrating the value of using family-based studies to better understand modifiers of SCD

Raising children with high self-esteem (but not narcissism)

With the rise of individualism since the 1960s, Western parents have become increasingly concerned with raising children’s self-esteem. This is understandable, given the benefits of self-esteem for children’s psychological health. However, parents’ well-intentioned attempts to raise self-esteem, such as inflated praise, may inadvertently breed narcissism. How, then, can parents raise self-esteem without breeding narcissism? Here, we propose a tripartite model of self-regard, which holds that the development of self-esteem without narcissism can be cultivated through realistic feedback (rather than inflated praise), focus on growth (rather than on outperforming others), and unconditional regard (rather than regard that is conditional). We review evidence in support of these practices and outline promising research directions. The tripartite model integrates existing research, stimulates theory development, and identifies leverage points for intervention concurrently to raise self-esteem and curtail narcissism from a young age

Single Cell Transcriptomics Implicate Novel Monocyte and T Cell Immune Dysregulation in Sarcoidosis

Sarcoidosis is a systemic inflammatory disease characterized by infiltration of immune cells into granulomas. Previous gene expression studies using heterogeneous cell mixtures lack insight into cell-type-specific immune dysregulation. We performed the first single-cell RNA-sequencing study of sarcoidosis in peripheral immune cells in 48 patients and controls. Following unbiased clustering, differentially expressed genes were identified for 18 cell types and bioinformatically assessed for function and pathway enrichment. Our results reveal persistent activation of circulating classical monocytes with subsequent upregulation of trafficking molecules. Specifically, classical monocytes upregulated distinct markers of activation including adhesion molecules, pattern recognition receptors, and chemokine receptors, as well as enrichment of immunoregulatory pathways HMGB1, mTOR, and ephrin receptor signaling. Predictive modeling implicated TGFβ and mTOR signaling as drivers of persistent monocyte activation. Additionally, sarcoidosis T cell subsets displayed patterns of dysregulation. CD4 naïve T cells were enriched for markers of apoptosis and Th17/T(reg) differentiation, while effector T cells showed enrichment of anergy-related pathways. Differentially expressed genes in regulatory T cells suggested dysfunctional p53, cell death, and TNFR2 signaling. Using more sensitive technology and more precise units of measure, we identify cell-type specific, novel inflammatory and regulatory pathways. Based on our findings, we suggest a novel model involving four convergent arms of dysregulation: persistent hyperactivation of innate and adaptive immunity via classical monocytes and CD4 naïve T cells, regulatory T cell dysfunction, and effector T cell anergy. We further our understanding of the immunopathology of sarcoidosis and point to novel therapeutic targets