Integrating transposable elements in the 3D genome

Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, in this commentary we discuss its potential applicability to aspects of TE biology. Based on recent works on the relationship between genome organisation and TE integration, we argue that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns. We suggest that these models may offer orthogonal and generic insights into the integration profiles (or "topography") of TEs across organisms. In addition, we provide simple polymer physics arguments and preliminary molecular dynamics simulations of TEs inserting into heterogeneously flexible polymers. By considering this simple model, we show how polymer folding and local flexibility may generically affect TE integration patterns. The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome

Lamin B1 regulates somatic mutations and progression of B-cell malignancies

Somatic hypermutation (SHM) is a pivotal process in adaptive immunity that occurs in the germinal centre and allows B cells to change their primary DNA sequence and diversify their antigen receptors. Here, we report that genome binding of Lamin B1, a component of the nuclear envelope involved in epigenetic chromatin regulation, is reduced during B-cell activation and formation of lymphoid germinal centres. Chromatin immunoprecipitation-Seq analysis showed that kappa and heavy variable immunoglobulin domains were released from the Lamin B1 suppressive environment when SHM was induced in B cells. RNA interference-mediated reduction of Lamin B1 resulted in spontaneous SHM as well as kappa-light chain aberrant surface expression. Finally, Lamin B1 expression level correlated with progression-free and overall survival in chronic lymphocytic leukaemia, and was strongly involved in the transformation of follicular lymphoma. In summary, here we report that Lamin B1 is a negative epigenetic regulator of SHM in normal B-cells and a 'mutational gatekeeper', suppressing the aberrant mutations that drive lymphoid malignancy

Patient-rated health status predicts prognosis following percutaneous coronary intervention with drug-eluting stenting

Purpose: In patients treated with percutaneous coronary intervention (PCI) with the paclitaxel-eluting stent, we examined whether patient-rated health status predicts adverse clinical events. Methods: Consecutive PCI patients treated with drug-eluting stenting (N = 870; 72.2% men; mean age = 62.6 ± 11.5) completed the EQ-5D post-PCI. The EQ-5D levels were dichotomized into 'no problems' (level 1) versus 'problems' (levels 2, 3); the visual analogue scale (VAS) was dichotomized using the 25th percentile (cut-off ≤60) indicating poor health status. Patients were followed up for 1-year clinical events (death or non-fatal myocardial infarction (MI)). Results: There were 53 deaths/MIs at follow-up. The EQ-5D health status dimensions mobility (HR:2.23; 95% CI:1.25-3.97), self-care (HR:3.09; 95% CI:1.54-6.20), and self-reported health status as measured with the EQ-VAS (HR:2.94; 95% CI:1.65-5.25) were independent predictors of death/MI and added to the predictive value of a model comprised of demographic and clinical characteristics. The EQ-5D dimensions usual activities, pain/discomfort, and anxiety/depression were not associated with adverse clinical events in adjusted analysis. Conclusions: Patient-rated health status predicted adverse clinical events at 1-year follow-up in PCI patients treated with drug-eluting stenting, with the risk being more than 2-fold indepe

Short-term health-related quality of life consequences in a lung cancer CT screening trial (NELSON)

Item does not contain fulltextBACKGROUND: In lung cancer CT screening, participants often have an indeterminate screening result at baseline requiring a follow-up CT. In subjects with either an indeterminate or a negative result after screening, we investigated whether health-related quality of life (HRQoL) changed over time and differed between groups in the short term. METHODS: A total of 733 participants in the NELSON trial received four questionnaires: T0, before randomisation; T1, 1 week before the baseline screening; T2, 1 day after the screening; and T3, 2 months after the screening results but before the 3-month follow-up CT. HRQoL was measured as generic HRQoL (the 12-item Short Form, SF-12; the EuroQol questionnaire, EQ-5D), anxiety (the Spielberger State-Trait Anxiety Inventory, STAI-6), and lung-cancer-specific distress (the Impact of Event Scale, IES). For analyses, repeated-measures analysis of variance was used, adjusted for covariates. RESULTS: Response to each questionnaire was 88% or higher. Scores on SF-12, EQ-5D, and STAI-6 showed no clinically relevant changes over time. At T3, IES scores that were clinically relevant increased after an indeterminate result, whereas these scores showed a significant decrease after a negative result. At T3, differences in IES scores between the two baseline result groups were both significant and clinically relevant (P<0.01). CONCLUSION: This longitudinal study among participants of a lung cancer screening programme showed that in the short term recipients of an indeterminate result experienced increased lung-cancer-specific distress, whereas the HRQoL changes after a negative baseline screening result may be interpreted as a relief

Altered Chromosomal Positioning, Compaction, and Gene Expression with a Lamin A/C Gene Mutation

Lamins A and C, encoded by the LMNA gene, are filamentous proteins that form the core scaffold of the nuclear lamina. Dominant LMNA gene mutations cause multiple human diseases including cardiac and skeletal myopathies. The nuclear lamina is thought to regulate gene expression by its direct interaction with chromatin. LMNA gene mutations may mediate disease by disrupting normal gene expression.To investigate the hypothesis that mutant lamin A/C changes the lamina's ability to interact with chromatin, we studied gene misexpression resulting from the cardiomyopathic LMNA E161K mutation and correlated this with changes in chromosome positioning. We identified clusters of misexpressed genes and examined the nuclear positioning of two such genomic clusters, each harboring genes relevant to striated muscle disease including LMO7 and MBNL2. Both gene clusters were found to be more centrally positioned in LMNA-mutant nuclei. Additionally, these loci were less compacted. In LMNA mutant heart and fibroblasts, we found that chromosome 13 had a disproportionately high fraction of misexpressed genes. Using three-dimensional fluorescence in situ hybridization we found that the entire territory of chromosome 13 was displaced towards the center of the nucleus in LMNA mutant fibroblasts. Additional cardiomyopathic LMNA gene mutations were also shown to have abnormal positioning of chromosome 13, although in the opposite direction.These data support a model in which LMNA mutations perturb the intranuclear positioning and compaction of chromosomal domains and provide a mechanism by which gene expression may be altered

Disparities exist between National food group recommendations and the dietary intakes of women

<p>Abstract</p> <p>Background</p> <p>Preconception and pregnancy dietary intakes can influence the health of future generations. In this study we compared the food intakes of reproductive-aged women by pregnancy status, to current Australian recommendations.</p> <p>Methods</p> <p>Data are from the Australian Longitudinal Study on Women's Health, younger cohort aged 25-30 years in 2003, with self-reported status as pregnant (n = 606), trying to conceive (n = 454), given birth in the last 12 months (n = 829) or other (n = 5597). Diet was assessed using a validated 74-item food frequency questionnaire. Food group servings and nutrient intakes were compared to the Australian Guide to Healthy Eating (AGHE) and Australian Nutrient Reference Values (NRVs).</p> <p>Results</p> <p>No women met all AGHE food group recommendations. Highest adherence rates [mean (95% CI) servings/day] were for meat [85%, 1.9(1.8-1.9)], fruit [44%, 2.1(2.1-2.2)] and dairy [35%, 1.8(1.8-1.9)], with < 14% meeting remaining recommendations. Women who achieved NRVs (folate, iron, calcium, zinc, fibre) for pregnancy, breastfeeding and adult life stages were 1.5%, 3.3% and 13.7%, respectively. Compared to AGHE, women consumed more servings of fruit (4.9 vs 4.0;<it>P </it>= 0.034) and dairy (3.4 vs 2.0;<it>P </it>= 0.006) to achieve pregnancy NRVs; more dairy (2.9 vs 2.0;<it>P </it>= 0.001), less fruit (3.9 vs 5.0;<it>P </it>< .001) and vegetables (3.4 vs 7.0;<it>P </it>< .001) to achieve breastfeeding NRVs; more fruit (3.6 vs 3.0;<it>P </it>< .001), dairy (2.5 vs 2.0;<it>P </it>< .001), meat (1.8 vs 1.5;<it>P </it>= 0.015), less vegetables (3.6 vs 5.0;<it>P </it>< .001) to achieve adult NRVs.</p> <p>Conclusions</p> <p>The AGHE does not align with contemporary diets of Australian women or enable them to meet all NRVs. Current tools to guide food consumption by women during pregnancy require revision.</p

Characteristics and management of HIV-1-infected pregnant women enrolled in a randomised trial: differences between Europe and the USA

<p>Abstract</p> <p>Background</p> <p>Rates of mother-to-child transmission of HIV-1 (MTCT) have historically been lower in European than in American cohort studies, possibly due to differences in population characteristics. The Pediatric AIDS Clinical Trials Group Protocol (PACTG) 316 trial evaluated the effectiveness of the addition of intrapartum/neonatal nevirapine in reducing MTCT in women already receiving antiretroviral prophylaxis. Participation of large numbers of pregnant HIV-infected women from the US and Western Europe enrolling in the same clinical trial provided the opportunity to identify and explore differences in their characteristics and in the use of non-study interventions to reduce MTCT.</p> <p>Methods</p> <p>In this secondary analysis, 1350 women were categorized according to enrollment in centres in the USA (n = 978) or in Europe (n = 372). Factors associated with receipt of highly active antiretroviral therapy and with elective caesarean delivery were identified with logistic regression.</p> <p>Results</p> <p>In Europe, women enrolled were more likely to be white and those of black race were mainly born in Sub-Saharan Africa. Women in the US were younger and more likely to have previous pregnancies and miscarriages and a history of sexually transmitted infections.</p> <p>More than 90% of women did not report symptoms of their HIV infection; however, more women from the US had symptoms (8%), compared to women from Europe (4%). Women in the US were less likely to have HIV RNA levels <400 copies/ml at delivery than women enrolling in Europe, and more likely to receive highly active antiretroviral therapy, and to start therapy earlier in pregnancy. The elective caesarean delivery rate in Europe was 61%, significantly higher than that in the US (22%). Overall, 1.48% of infants were infected and there was no significant difference in the rate of transmission between Europe and the US despite the different approaches to treatment and delivery.</p> <p>Conclusion</p> <p>These findings confirm that there are important historical differences between the HIV-infected pregnant populations in Western Europe and the USA, both in terms of the characteristics of the women and their obstetric and therapeutic management. Although highly active antiretroviral therapy predominates in pregnancy in both settings now, population differences are likely to remain.</p> <p>Trial registration</p> <p>NCT00000869</p

The NSL Complex Regulates Housekeeping Genes in Drosophila

MOF is the major histone H4 lysine 16-specific (H4K16) acetyltransferase in mammals and Drosophila. In flies, it is involved in the regulation of X-chromosomal and autosomal genes as part of the MSL and the NSL complexes, respectively. While the function of the MSL complex as a dosage compensation regulator is fairly well understood, the role of the NSL complex in gene regulation is still poorly characterized. Here we report a comprehensive ChIP–seq analysis of four NSL complex members (NSL1, NSL3, MBD-R2, and MCRS2) throughout the Drosophila melanogaster genome. Strikingly, the majority (85.5%) of NSL-bound genes are constitutively expressed across different cell types. We find that an increased abundance of the histone modifications H4K16ac, H3K4me2, H3K4me3, and H3K9ac in gene promoter regions is characteristic of NSL-targeted genes. Furthermore, we show that these genes have a well-defined nucleosome free region and broad transcription initiation patterns. Finally, by performing ChIP–seq analyses of RNA polymerase II (Pol II) in NSL1- and NSL3-depleted cells, we demonstrate that both NSL proteins are required for efficient recruitment of Pol II to NSL target gene promoters. The observed Pol II reduction coincides with compromised binding of TBP and TFIIB to target promoters, indicating that the NSL complex is required for optimal recruitment of the pre-initiation complex on target genes. Moreover, genes that undergo the most dramatic loss of Pol II upon NSL knockdowns tend to be enriched in DNA Replication–related Element (DRE). Taken together, our findings show that the MOF-containing NSL complex acts as a major regulator of housekeeping genes in flies by modulating initiation of Pol II transcription