Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo

SummaryThe realization that nuclear distribution of DNA, RNA, and proteins differs between cell types and developmental stages suggests that nuclear organization serves regulatory functions. Understanding the logic of nuclear architecture and how it contributes to differentiation and cell fate commitment remains challenging. Here, we use soft X-ray tomography (SXT) to image chromatin organization, distribution, and biophysical properties during neurogenesis in vivo. Our analyses reveal that chromatin with similar biophysical properties forms an elaborate connected network throughout the entire nucleus. Although this interconnectivity is present in every developmental stage, differentiation proceeds with concomitant increase in chromatin compaction and re-distribution of condensed chromatin toward the nuclear core. HP1β, but not nucleosome spacing or phasing, regulates chromatin rearrangements because it governs both the compaction of chromatin and its interactions with the nuclear envelope. Our experiments introduce SXT as a powerful imaging technology for nuclear architecture

Suv4-20h Histone Methyltransferases Promote Neuroectodermal Differentiation by Silencing the Pluripotency-Associated Oct-25 Gene

Post-translational modifications (PTMs) of histones exert fundamental roles in regulating gene expression. During development, groups of PTMs are constrained by unknown mechanisms into combinatorial patterns, which facilitate transitions from uncommitted embryonic cells into differentiated somatic cell lineages. Repressive histone modifications such as H3K9me3 or H3K27me3 have been investigated in detail, but the role of H4K20me3 in development is currently unknown. Here we show that Xenopus laevis Suv4-20h1 and h2 histone methyltransferases (HMTases) are essential for induction and differentiation of the neuroectoderm. Morpholino-mediated knockdown of the two HMTases leads to a selective and specific downregulation of genes controlling neural induction, thereby effectively blocking differentiation of the neuroectoderm. Global transcriptome analysis supports the notion that these effects arise from the transcriptional deregulation of specific genes rather than widespread, pleiotropic effects. Interestingly, morphant embryos fail to repress the Oct4-related Xenopus gene Oct-25. We validate Oct-25 as a direct target of xSu4-20h enzyme mediated gene repression, showing by chromatin immunoprecipitaton that it is decorated with the H4K20me3 mark downstream of the promoter in normal, but not in double-morphant, embryos. Since knockdown of Oct-25 protein significantly rescues the neural differentiation defect in xSuv4-20h double-morphant embryos, we conclude that the epistatic relationship between Suv4-20h enzymes and Oct-25 controls the transit from pluripotent to differentiation-competent neural cells. Consistent with these results in Xenopus, murine Suv4-20h1/h2 double-knockout embryonic stem (DKO ES) cells exhibit increased Oct4 protein levels before and during EB formation, and reveal a compromised and biased capacity for in vitro differentiation, when compared to normal ES cells. Together, these results suggest a regulatory mechanism, conserved between amphibians and mammals, in which H4K20me3-dependent restriction of specific POU-V genes directs cell fate decisions, when embryonic cells exit the pluripotent state

Expression of the normal epithelial cell-specific 1 (NES1; KLK10) candidate tumour suppressor gene in normal and malignant testicular tissue

The normal epithelial cell-specific 1 (NES1) gene (official name kallikrein gene 10; KLK10) is a new member of the expanding human kallikrein gene family and encodes for a secreted serine protease. Experimental evidence suggests that NES1 controls normal cell growth and may function as a tumour suppressor. NES1 is down-regulated during breast cancer progression. The NES1 gene is highly expressed in testicular as well as in other tissues. In this study, we investigated the expression level of the NES1 gene in cancerous and normal testicular tissues with reverse transcriptase-polymerase chain reaction (RT-PCR) and immunohistochemistry. In all 14 primary testicular germ-cell tumours examined, the NES1 gene expression was markedly reduced compared to adjacent (paired) normal tissues. We further examined 6 randomly selected primary germ-cell tumours and 8 normal tissues (obtained from different individuals). We confirmed the differential expression of the NES1 gene in germ-cell tumours (GCT) and pre-malignant carcinoma in situ (CIS). Our findings suggest that NES1 may act as a tumour suppressor and may play a role in the pathogenesis and progression of this malignancy. © 2001 Cancer Research Campaign http://www.bjcancer.co

Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

Several recent studies have examined different aspects of mammalian higher order chromatin structure - replication timing, lamina association and Hi-C inter-locus interactions - and have suggested that most of these features of genome organisation are conserved over evolution. However, the extent of evolutionary divergence in higher order structure has not been rigorously measured across the mammalian genome, and until now little has been known about the characteristics of any divergent loci present. Here, we generate a dataset combining multiple measurements of chromatin structure and organisation over many embryonic cell types for both human and mouse that, for the first time, allows a comprehensive assessment of the extent of structural divergence between mammalian genomes. Comparison of orthologous regions confirms that all measurable facets of higher order structure are conserved between human and mouse, across the vast majority of the detectably orthologous genome. This broad similarity is observed in spite of many loci possessing cell type specific structures. However, we also identify hundreds of regions (from 100 Kb to 2.7 Mb in size) showing consistent evidence of divergence between these species, constituting at least 10% of the orthologous mammalian genome and encompassing many hundreds of human and mouse genes. These regions show unusual shifts in human GC content, are unevenly distributed across both genomes, and are enriched in human subtelomeric regions. Divergent regions are also relatively enriched for genes showing divergent expression patterns between human and mouse ES cells, implying these regions cause divergent regulation. Particular divergent loci are strikingly enriched in genes implicated in vertebrate development, suggesting important roles for structural divergence in the evolution of mammalian developmental programmes. These data suggest that, though relatively rare in the mammalian genome, divergence in higher order chromatin structure has played important roles during evolution

The progestational and androgenic properties of medroxyprogesterone acetate: gene regulatory overlap with dihydrotestosterone in breast cancer cells

INTRODUCTION: Medroxyprogesterone acetate (MPA), the major progestin used for oral contraception and hormone replacement therapy, has been implicated in increased breast cancer risk. Is this risk due to its progestational or androgenic properties? To address this, we assessed the transcriptional effects of MPA as compared with those of progesterone and dihydrotestosterone (DHT) in human breast cancer cells. METHOD: A new progesterone receptor-negative, androgen receptor-positive human breast cancer cell line, designated Y-AR, was engineered and characterized. Transcription assays using a synthetic promoter/reporter construct, as well as endogenous gene expression profiling comparing progesterone, MPA and DHT, were performed in cells either lacking or containing progesterone receptor and/or androgen receptor. RESULTS: In progesterone receptor-positive cells, MPA was found to be an effective progestin through both progesterone receptor isoforms in transient transcription assays. Interestingly, DHT signaled through progesterone receptor type B. Expression profiling of endogenous progesterone receptor-regulated genes comparing progesterone and MPA suggested that although MPA may be a somewhat more potent progestin than progesterone, it is qualitatively similar to progesterone. To address effects of MPA through androgen receptor, expression profiling was performed comparing progesterone, MPA and DHT using Y-AR cells. These studies showed extensive gene regulatory overlap between DHT and MPA through androgen receptor and none with progesterone. Interestingly, there was no difference between pharmacological MPA and physiological MPA, suggesting that high-dose therapeutic MPA may be superfluous. CONCLUSION: Our comparison of the gene regulatory profiles of MPA and progesterone suggests that, for physiologic hormone replacement therapy, the actions of MPA do not mimic those of endogenous progesterone alone. Clinically, the complex pharmacology of MPA not only influences its side-effect profile; but it is also possible that the increased breast cancer risk and/or the therapeutic efficacy of MPA in cancer treatment is in part mediated by androgen receptor

Bullying behaviour in schools, socioeconomic position and psychiatric morbidity: a cross-sectional study in late adolescents in Greece

<p>Abstract</p> <p>Background</p> <p>Bullying is quite prevalent in the school setting and has been associated with the socioeconomic position and psychiatric morbidity of the pupils. The aim of the study was to investigate the association between bullying and socioeconomic status in a sample of Greek adolescents and to examine whether this is confounded by the presence of psychiatric morbidity, including sub-threshold forms of illness.</p> <p>Methods</p> <p>5,614 adolescents aged 16-18 years old and attending 25 senior high schools were screened and a stratified random sample of 2,427 were selected for a detailed interview. Psychiatric morbidity was assessed with a fully structured psychiatric interview, the revised Clinical Interview Schedule (CIS-R), while bullying was assessed with the revised Olweus bully/victim questionnaire. The following socio-economic variables were assessed: parental educational level and employment status, financial difficulties of the family and adolescents' school performance. The associations were investigated using multinomial logit models.</p> <p>Results</p> <p>26.4% of the pupils were involved in bullying-related behaviours at least once monthly either as victims, perpetrators or both, while more frequent involvement (at least once weekly) was reported by 4.1%. Psychiatric morbidity was associated with all types of bullying-related behaviours. No socioeconomic associations were reported for victimization. A lower school performance and unemployment of the father were significantly more likely among perpetrators, while economic inactivity of the mother was more likely in pupils who were both victims and perpetrators. These results were largely confirmed when we focused on high frequency behaviours only. In addition, being overweight increased the risk of frequent victimization.</p> <p>Conclusions</p> <p>The prevalence of bullying among Greek pupils is substantial. Perpetration was associated with some dimensions of adolescents' socioeconomic status, while victimization showed no socioeconomic associations. Our findings may add to the understanding of possible risk factors for bullying behaviours in adolescence.</p

Chromatin States Accurately Classify Cell Differentiation Stages

Gene expression is controlled by the concerted interactions between transcription factors and chromatin regulators. While recent studies have identified global chromatin state changes across cell-types, it remains unclear to what extent these changes are co-regulated during cell-differentiation. Here we present a comprehensive computational analysis by assembling a large dataset containing genome-wide occupancy information of 5 histone modifications in 27 human cell lines (including 24 normal and 3 cancer cell lines) obtained from the public domain, followed by independent analysis at three different representations. We classified the differentiation stage of a cell-type based on its genome-wide pattern of chromatin states, and found that our method was able to identify normal cell lines with nearly 100% accuracy. We then applied our model to classify the cancer cell lines and found that each can be unequivocally classified as differentiated cells. The differences can be in part explained by the differential activities of three regulatory modules associated with embryonic stem cells. We also found that the “hotspot” genes, whose chromatin states change dynamically in accordance to the differentiation stage, are not randomly distributed across the genome but tend to be embedded in multi-gene chromatin domains, and that specialized gene clusters tend to be embedded in stably occupied domains

Alcohol and cannabis use among adolescents in Flemish secondary school in Brussels: effects of type of education

<p>Abstract</p> <p>Background</p> <p>Research regarding socio-economic differences in alcohol and drug use in adolescence yields mixed results. This study hypothesizes that (1) when using education type as a proxy of one's social status, clear differences will exist between students from different types of education, regardless of students' familial socio-economic background; (2) and that the effects of education type differ according to their cultural background.</p> <p>Methods</p> <p>Data from the Brussels youth monitor were used, a school survey administered among 1,488 adolescents from the 3rd to 6th year of Flemish secondary education. Data were analyzed using multilevel logistic regression models.</p> <p>Results</p> <p>Controlling for their familial background, the results show that native students in lower educational tracks use alcohol and cannabis more often than students in upper educational tracks. Such a relationship was not found for students from another ethnic background.</p> <p>Conclusion</p> <p>Results from this study indicate that research into health risks should take into account both adolescents' familial background and individual social position as different components of youngsters' socio-economic background.</p

Association of the interferon-β gene with pericentromeric heterochromatin is dynamically regulated during virus infection through a YY1-dependent mechanism

Nuclear architecture as well as gene nuclear positioning can modulate gene expression. In this work, we have analyzed the nuclear position of the interferon-β (IFN-β) locus, responsible for the establishment of the innate antiviral response, with respect to pericentromeric heterochromatin (PCH) in correlation with virus-induced IFN-β gene expression. Experiments were carried out in two different cell types either non-infected (NI) or during the time course of three different viral infections. In NI cells, we showed a monoallelic IFN-β promoter association with PCH that strongly decreased after viral infection. Dissociation of the IFN-β locus away from these repressive regions preceded strong promoter transcriptional activation and was reversible within 12 h after infection. No dissociation was observed after infection with a virus that abnormally maintained the IFN-β gene in a repressed state. Dissociation induced after virus infection specifically targeted the IFN-β locus without affecting the general structure and nuclear distribution of PCH clusters. Using cell lines stably transfected with wild-type or mutated IFN-β promoters, we identified the proximal region of the IFN-β promoter containing YY1 DNA-binding sites as the region regulating IFN-β promoter association with PCH before as well as during virus infection