Drug-induced loss of imprinting revealed using bioluminescent reporters of Cdkn1c

Genomic imprinting is an epigenetically mediated mechanism that regulates allelic expression of genes based upon parent-of-origin and provides a paradigm for studying epigenetic silencing and release. Here, bioluminescent reporters for the maternally-expressed imprinted gene Cdkn1c are used to examine the capacity of chromatin-modifying drugs to reverse paternal Cdkn1c silencing. Exposure of reporter mouse embryonic stem cells (mESCs) to 5-Azacytidine, HDAC inhibitors, BET inhibitors or GSK-J4 (KDM6A/B inhibitor) relieved repression of paternal Cdkn1c, either selectively or by inducing biallelic effects. Treatment of reporter fibroblasts with HDAC inhibitors or GSK-J4 resulted in similar paternal Cdkn1c activation, whereas BET inhibitor-induced loss of imprinting was specific to mESCs. Changes in allelic expression were generally not sustained in dividing cultures upon drug removal, indicating that the underlying epigenetic memory of silencing was maintained. In contrast, Cdkn1c de-repression by GSK-J4 was retained in both mESCs and fibroblasts following inhibitor removal, although this impact may be linked to cellular stress and DNA damage. Taken together, these data introduce bioluminescent reporter cells as tools for studying epigenetic silencing and disruption, and demonstrate that Cdkn1c imprinting requires distinct and cell-type specific chromatin features and modifying enzymes to enact and propagate a memory of silencing

The methyl binding domain 3/nucleosome remodelling and deacetylase complex regulates neural cell fate determination and terminal differentiation in the cerebral cortex.

BACKGROUND: Chromatin-modifying complexes have key roles in regulating various aspects of neural stem cell biology, including self-renewal and neurogenesis. The methyl binding domain 3/nucleosome remodelling and deacetylation (MBD3/NuRD) co-repressor complex facilitates lineage commitment of pluripotent cells in early mouse embryos and is important for stem cell homeostasis in blood and skin, but its function in neurogenesis had not been described. Here, we show for the first time that MBD3/NuRD function is essential for normal neurogenesis in mice. RESULTS: Deletion of MBD3, a structural component of the NuRD complex, in the developing mouse central nervous system resulted in reduced cortical thickness, defects in the proper specification of cortical projection neuron subtypes and neonatal lethality. These phenotypes are due to alterations in PAX6+ apical progenitor cell outputs, as well as aberrant terminal neuronal differentiation programmes of cortical plate neurons. Normal numbers of PAX6+ apical neural progenitor cells were generated in the MBD3/NuRD-mutant cortex; however, the PAX6+ apical progenitor cells generate EOMES+ basal progenitor cells in reduced numbers. Cortical progenitor cells lacking MBD3/NuRD activity generate neurons that express both deep- and upper-layer markers. Using laser capture microdissection, gene expression profiling and chromatin immunoprecipitation, we provide evidence that MBD3/NuRD functions to control gene expression patterns during neural development. CONCLUSIONS: Our data suggest that although MBD3/NuRD is not required for neural stem cell lineage commitment, it is required to repress inappropriate transcription in both progenitor cells and neurons to facilitate appropriate cell lineage choice and differentiation programmes.We wish to thank Nicola Reynolds for the help with figures; Aoife O’Shaughnessy for the critical reading of the manuscript; Peter Humphreys, the SCI Biofacility staff and Margaret McLeish for technical assistance; Stephanie Hall and Gerard Evan for access to the Laser Capture Microscope and Nathalie Saurat and members of the BH lab for useful discussions. This work was supported by a Wellcome Trust Senior Fellowship in the Basic Biomedical Sciences awarded to BH and a bourse de formation from the Fonds de la Recherche en Santé Québec awarded to EK.This is the final published version of the article. It was originally published in Neural Development (Knock E, et al., Neural Development, 2015, 10:13, doi:10.1186/s13064-015-0040-z). The final version is available at http://dx.doi.org/10.1186/s13064-015-0040-

Sociological and Human Developmental Explanations of Crime: Conflict or Consensus

This paper examines multidisciplinary correlates of delinquency in an attempt to integrate sociological and environmental theories of crime with human developmental and biological explanations of crime. Structural equation models are applied to assess links among biological, psychological, and environmental variables collected prospectively from birth through age 17 on a sample of 800 black children at high risk for learning and behavioral disorders. Results show that for both males and females, aggression and disciplinary problems in school during adolescence are the strongest predictors of repeat offense behavior. Whereas school achievement and family income and stability are also significant predictors of delinquency for males, early physical development is the next strongest predictor for females. Results indicate that some effects on delinquency also vary during different ages. It is suggested that behavioral and learning disorders have both sociological and developmental correlates and that adequate educational resources are necessary to ensure channels of legitimate opportunities for high-risk youths

What binds biosociality? The collective effervescence of the parent-led conference

Questions of community are central to many research sites in the social sciences. Rabinow argued that, in the wake of the Human Genome Project, an increasingly important form of collectivity would be biosociality. Biosociality highlights the central role of biomedical knowledge in constructing genetic identities and producing and reproducing social relationships. Accordingly, it is often imagined as a new form of social interaction. We draw on observations of parent-led conferences organised around a particular genetic syndrome – 22q11 deletion syndrome – to empirically explore the mechanism through which biosociality is enacted. The conferences took place within the UK between 2007 and 2010 and were observed as part of a multi-sited ethnography. What binds individuals and creates a sense of community is a social process, and conferences are significant occasions where such biosociality ‘happens’. Furthermore, we suggest that the creation of bonds between members of a community is facilitated by the expression of a traditional theoretical social process - collective effervescence. This paper therefore demonstrates a commonality between established sociological understanding of collective effervescence and more recent theories of biosociality. We argue that in the case of the 22q11 deletion syndrome groups examined in this paper, parent conferences brings individuals together physically, and it is the shared emotional experience of the conference – the collective effervescence – that consolidates and renews the connection between members of the community

Harnessing bioluminescence for drug discovery and epigenetic research

The naturally occurring phenomenon of bioluminescence has intrigued on-lookers for decades and is now being developed as a powerful tool for medical research and preclinical imaging. Luciferase enzymes emit light upon substrate encounter, enabling their activity to be visualised and dynamically tracked. By inserting luciferase genes into specific sites in the genome, it is possible to engineer reporters to monitor gene expression in its native context, and to detect epigenetic change in vivo. Endogenous bioluminescent reporters provide a highly sensitive, quantitative read-out of gene expression that is both well suited to longitudinal studies and can be adapted for high-throughput drug screens. In this article we outline some of the applications and benefits of bioluminescent reporters for epigenetic research, with a particular focus on revealing new therapeutic options for treating genetic and epigenetic disorders

PBK/TOPK mediates Ikaros, Aiolos and CTCF displacement from mitotic chromosomes and alters chromatin accessibility at selected C2H2-zinc finger protein binding sites

PBK/TOPK is a mitotic kinase implicated in haematological and non-haematological cancers. Here we show that the key haemopoietic regulators Ikaros and Aiolos require PBK-mediated phosphorylation to dissociate from chromosomes in mitosis. Eviction of Ikaros is rapidly reversed by addition of the PBK-inhibitor OTS514, revealing dynamic regulation by kinase and phosphatase activities. To identify more PBK targets, we analysed loss of mitotic phosphorylation events in Pbk–/– preB cells and performed proteomic comparisons on isolated mitotic chromosomes. Among a large pool of C2H2-zinc finger targets, PBK is essential for evicting the CCCTC-binding protein CTCF and zinc finger proteins encoded by Ikzf1, Ikzf3, Znf131 and Zbtb11. PBK-deficient cells were able to divide but showed altered chromatin accessibility and nucleosome positioning consistent with CTCF retention. Our studies reveal that PBK controls the dissociation of selected factors from condensing mitotic chromosomes and contributes to their compaction

“I stretch them out as long as possible:” U.S. women’s experiences of menstrual product insecurity during the COVID-19 pandemic

Background: A growing body of evidence highlights how the COVID-19 pandemic has exacerbated gender inequalities in the US. This resulted in women being more vulnerable to economic insecurity and decreases in their overall well-being. One relevant issue that has been less explored is that of women’s menstrual health experiences, including how inconsistent access to menstrual products may negatively impact their daily lives. Methods: This qualitative study, conducted from March through May 2021, utilized in-depth interviews that were nested within a national prospective cohort study. The interviews (n = 25) were conducted with a sub-sample of cis-gender women living across the US who had reported challenges accessing products during the first year of the pandemic. The interviews sought to understand the barriers that contributed to experiencing menstrual product insecurity, and related coping mechanisms. Malterud’s ‘systematic text condensation’, an inductive thematic analysis method, was utilized to analyze the qualitative transcripts. Results: Respondents came from 17 different states across the U.S. Three key themes were identified: financial and physical barriers existed to consistent menstrual product access; a range of coping strategies in response to menstrual product insecurity, including dependence on makeshift and poorer quality materials; and heightened experiences of menstrual-related anxiety and shame, especially regarding the disclosure of their menstruating status to others as a result of inadequate menstrual leak protection. Conclusions: Addressing menstrual product insecurity is a critical step for ensuring that all people who menstruate can attain their most basic menstrual health needs. Key recommendations for mitigating the impact of menstrual product insecurity require national and state-level policy reform, such as the inclusion of menstrual products in existing safety net basic needs programs, and the reframing of menstrual products as essential items. Improved education and advocacy are needed to combat menstrual stigma

“I stretch them out as long as possible:” U.S. women’s experiences of menstrual product insecurity during the COVID-19 pandemic

Background A growing body of evidence highlights how the COVID-19 pandemic has exacerbated gender inequalities in the US. This resulted in women being more vulnerable to economic insecurity and decreases in their overall well-being. One relevant issue that has been less explored is that of women’s menstrual health experiences, including how inconsistent access to menstrual products may negatively impact their daily lives. Methods This qualitative study, conducted from March through May 2021, utilized in-depth interviews that were nested within a national prospective cohort study. The interviews (n = 25) were conducted with a sub-sample of cis-gender women living across the US who had reported challenges accessing products during the first year of the pandemic. The interviews sought to understand the barriers that contributed to experiencing menstrual product insecurity, and related coping mechanisms. Malterud’s ‘systematic text condensation’, an inductive thematic analysis method, was utilized to analyze the qualitative transcripts. Results Respondents came from 17 different states across the U.S. Three key themes were identified: financial and physical barriers existed to consistent menstrual product access; a range of coping strategies in response to menstrual product insecurity, including dependence on makeshift and poorer quality materials; and heightened experiences of menstrual-related anxiety and shame, especially regarding the disclosure of their menstruating status to others as a result of inadequate menstrual leak protection. Conclusions Addressing menstrual product insecurity is a critical step for ensuring that all people who menstruate can attain their most basic menstrual health needs. Key recommendations for mitigating the impact of menstrual product insecurity require national and state-level policy reform, such as the inclusion of menstrual products in existing safety net basic needs programs, and the reframing of menstrual products as essential items. Improved education and advocacy are needed to combat menstrual stigma

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

The mammalian genome harbors up to one million regulatory elements often located at great distances from their target genes. Long-range elements control genes through physical contact with promoters and can be recognized by the presence of specific histone modifications and transcription factor binding. Linking regulatory elements to specific promoters genome-wide is currently impeded by the limited resolution of high-throughput chromatin interaction assays. Here we apply a sequence capture approach to enrich Hi-C libraries for &gt;22,000 annotated mouse promoters to identify statistically significant, long-range interactions at restriction fragment resolution, assigning long-range interacting elements to their target genes genome-wide in embryonic stem cells and fetal liver cells. The distal sites contacting active genes are enriched in active histone modifications and transcription factor occupancy, whereas inactive genes contact distal sites with repressive histone marks, demonstrating the regulatory potential of the distal elements identified. Furthermore, we find that coregulated genes cluster nonrandomly in spatial interaction networks correlated with their biological function and expression level. Interestingly, we find the strongest gene clustering in ES cells between transcription factor genes that control key developmental processes in embryogenesis. The results provide the first genome-wide catalog linking gene promoters to their longrange interacting elements and highlight the complex spatial regulatory circuitry controlling mammalian gene expression.</p

Protein restriction during pregnancy alters Cdkn1c silencing, dopamine circuitry and offspring behaviour without changing expression of key neuronal marker genes

We tracked the consequences of in utero protein restriction in mice throughout their development and life course using a luciferase-based allelic reporter of imprinted Cdkn1c. Exposure to gestational low-protein diet (LPD) results in the inappropriate expression of paternally inherited Cdkn1c in the brains of embryonic and juvenile mice. These animals were characterised by a developmental delay in motor skills, and by behavioural alterations indicative of reduced anxiety. Exposure to LPD in utero resulted in significantly more tyrosine hydroxylase positive (dopaminergic) neurons in the midbrain of adult offspring as compared to age-matched, control-diet equivalents. Positron emission tomography (PET) imaging revealed an increase in striatal dopamine synthesis capacity in LPD-exposed offspring, where elevated levels of dopamine correlated with an enhanced sensitivity to cocaine. These data highlight a profound sensitivity of the developing epigenome to gestational protein restriction. Our data also suggest that loss of Cdkn1c imprinting and p57KIP2 upregulation alters the cellular composition of the developing midbrain, compromises dopamine circuitry, and thereby provokes behavioural abnormalities in early postnatal life. Molecular analyses showed that despite this phenotype, exposure to LPD solely during pregnancy did not significantly change the expression of key neuronal- or dopamine-associated marker genes in adult offspring