Principles of meiotic chromosome assembly revealed in S. cerevisiae

During meiotic prophase, chromosomes organise into a series of chromatin loops emanating from a proteinaceous axis, but the mechanisms of assembly remain unclear. Here we use Saccharomyces cerevisiae to explore how this elaborate three-dimensional chromosome organisation is linked to genomic sequence. As cells enter meiosis, we observe that strong cohesin-dependent grid-like Hi-C interaction patterns emerge, reminiscent of mammalian interphase organisation, but with distinct regulation. Meiotic patterns agree with simulations of loop extrusion with growth limited by barriers, in which a heterogeneous population of expanding loops develop along the chromosome. Importantly, CTCF, the factor that imposes similar features in mammalian interphase, is absent in S. cerevisiae, suggesting alternative mechanisms of barrier formation. While grid-like interactions emerge independently of meiotic chromosome synapsis, synapsis itself generates additional compaction that matures differentially according to telomere proximity and chromosome size. Collectively, our results elucidate fundamental principles of chromosome assembly and demonstrate the essential role of cohesin within this evolutionarily conserved process

Temperature of embryo culture for assisted reproduction

BACKGROUND: 'Infertility' is defined as the failure to achieve pregnancy after 12 months or more of regular unprotected sexual intercourse. One in six couples experience a delay in becoming pregnant. In vitro fertilisation (IVF) is one of the assisted reproductive techniques used to enable couples to achieve a live birth. One of the processes involved in IVF is embryo culture in an incubator, where a stable environment is created and maintained. The incubators are set at approximately 37°C, which is based on the human core body temperature, although several studies have shown that this temperature may in fact be lower in the female reproductive tract and that this could be beneficial. In this review we have included randomised controlled trials which compared different temperatures of embryo culture. OBJECTIVES: To assess different temperatures of embryo culture for human assisted reproduction, which may lead to higher live birth rates. SEARCH METHODS: We searched the following databases and trial registers: the Cochrane Gynaecology and Fertility (CGF) Group Specialised Register of Controlled Trials, the Cochrane Central Register of Studies Online, MEDLINE, Embase, PsycINFO, CINAHL, clinicaltrials.gov, The World Health Organization International Trials Registry Platform search portal, DARE, Web of Knowledge, OpenGrey, LILACS database, PubMed and Google Scholar. Furthermore, we manually searched the references of relevant articles and contacted experts in the field to obtain additional data. We did not restrict the search by language or publication status. We performed the last search on 6 March 2019. SELECTION CRITERIA: Two review authors independently screened the titles and abstracts of articles retrieved by the search. Full texts of potentially eligible randomised controlled trials (RCTs) were obtained and screened. We included all RCTs which compared different temperatures of embryo culture in IVF or intracytoplasmic sperm injection (ICSI), with a minimum difference in temperature between the two incubators of ≥ 0.5°C. The search process is shown in the PRISMA flow chart. DATA COLLECTION AND ANALYSIS: Two review authors independently assessed trial eligibility and risk of bias and extracted data from the included studies; the third review author resolved any disagreements. We contacted trial authors to provide additional data. The primary review outcomes were live birth and miscarriage. Clinical pregnancy, ongoing pregnancy, multiple pregnancy and adverse events were secondary outcomes. All extracted data were dichotomous outcomes, and odds ratios (OR) were calculated with 95% confidence intervals (CIs) on an intention-to-treat basis. We assessed the overall quality of the evidence for the main comparisons using GRADE methods. MAIN RESULTS: We included three RCTs, with a total of 563 women, that compared incubation of embryos at 37.0°C or 37.1°C with a lower incubator temperature (37.0°C versus 36.6°C, 37.1°C versus 36.0°C, 37.0° versus 36.5°C). Live birth, miscarriage, clinical pregnancy, ongoing pregnancy and multiple pregnancy were reported. After additional information from the authors, we confirmed one study as having no adverse events; the other two studies did not report adverse events. We did not perform a meta-analysis as there were not enough studies included per outcome. Live birth was not graded since there were no data of interest available. The evidence for the primary outcome, miscarriage, was of very low quality. The evidence for the secondary outcomes, clinical pregnancy, ongoing pregnancy and multiple pregnancy was also of very low quality. We downgraded the evidence because of high risk of bias (for performance bias) and imprecision due to limited included studies and wide CIs.Only one study reported the primary outcome, live birth (n = 52). They performed randomisation at the level of oocytes and not per woman, and used a paired design whereby two embryos, one from 36.0°C and one from 37.0°C, were transferred. The data from this study were not interpretable in a meaningful way and therefore not presented. Only one study reported miscarriage. We are uncertain whether incubation at a lower temperature decreases the miscarriage (odds ratio (OR) 0.90, 95% CI 0.52 to 1.55; 1 study, N = 412; very low-quality evidence).Of the two studies that reported clinical pregnancy, only one of them performed randomisation per woman. We are uncertain whether a lower temperature improves clinical pregnancy compared to 37°C for embryo incubation (OR 1.08, 95% CI 0.73 to 1.60; 1 study, N = 412; very low-quality evidence). For the outcome, ongoing pregnancy, we are uncertain if a lower temperature is better than 37°C (OR 1.10, 95% CI 0.75 to 1.62; 1 study, N = 412; very low quality-evidence). Multiple pregnancy was reported by two studies, one of which used a paired design, which made it impossible to report the data per temperature. We are uncertain if a temperature lower than 37°C reduces multiple pregnancy (OR 0.80, 95% CI 0.31 to 2.07; 1 study, N = 412; very low-quality evidence). There was insufficient evidence to make a conclusion regarding adverse events, as no studies reported data suitable for analysis. AUTHORS' CONCLUSIONS: This review evaluated different temperatures for embryo culture during IVF. There is a lack of evidence for the majority of outcomes in this review. Based on very low-quality evidence, we are uncertain if incubating at a lower temperature than 37°C improves pregnancy outcomes. More RCTs are needed for comparing different temperatures of embryo culture which require reporting of clinical outcomes as live birth, miscarriage, clinical pregnancy and adverse events

Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C(chromosomeconformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r=0.9, P<2.2×1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016) and also have a significant positive correlation withsomeremote functional DNA elements like enhancers and promoters (Enhancer: hESC: r=0.997, P=2.3×10−4; IMR90: r=0.934, P=2×10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes

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

Differential epigenetic reprogramming in response to specific endocrine therapies promotes cholesterol biosynthesis and cellular invasion

Endocrine therapies target the activation of the oestrogen receptor alpha (ERα) via distinct mechanisms, but it is not clear whether breast cancer cells can adapt to treatment using drug-specific mechanisms. Here we demonstrate that resistance emerges via drug-specific epigenetic reprogramming. Resistant cells display a spectrum of phenotypical changes with invasive phenotypes evolving in lines resistant to the aromatase inhibitor (AI). Orthogonal genomics analysis of reprogrammed regulatory regions identifies individual drug-induced epigenetic states involving large topologically associating domains (TADs) and the activation of super-enhancers. AI-resistant cells activate endogenous cholesterol biosynthesis (CB) through stable epigenetic activation in vitro and in vivo. Mechanistically, CB sparks the constitutive activation of oestrogen receptors alpha (ERα) in AI-resistant cells, partly via the biosynthesis of 27-hydroxycholesterol. By targeting CB using statins, ERα binding is reduced and cell invasion is prevented. Epigenomic-led stratification can predict resistance to AI in a subset of ERα-positive patients

Rnf12—A Jack of All Trades in X Inactivation?

International audiencePlacental mammals compensate the dosage imbalance of X-linked genes between males (XY) and females (XX) by silencing one randomly chosen X chromosome in females. This process is initiated during early embryonic development and can be recapitulated during differentiation of murine embryonic stem cells (mESCs). X chromosome inactivation (XCI) is initiated by up-regulation of a non-coding RNA on the future inactive X chromosome, named Xist, which lies within a large complex locus, called the X inactivation center (Xic). Subsequently, Xist RNA induces silencing of the entire chromosome in cis. Although central to the XCI process, the molecular mechanisms underlying Xist's regulation still remain to be deciphered. In particular, it is unclear (1) how the up-regulation of Xist is triggered at the onset of differentiation, (2) why this is restricted to female cells, and (3) why one allele and not the other is affected? Although each aspect could in principle be controlled by distinct factors and sequence elements, one protein has recently been proposed to regulate Xist at all three levels: the E3 ubiquitin ligase Rnf12/Rlim. The X-linked Rnf12 gene acts as a dose-dependent activator of Xist, which is expressed at elevated levels in female relative to male cells and is up-regulated during differentiation. Two recent studies shed further light on the precise role of Rnf12 in XCI

Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots in the germline

Abstract Background Chromatin loops form a basic unit of interphase nuclear organization, with chromatin loop anchor points providing contacts between regulatory regions and promoters. However, the mutational landscape at these anchor points remains under-studied. Here, we describe the unusual patterns of somatic mutations and germline variation associated with loop anchor points and explore the underlying features influencing these patterns. Results Analyses of whole genome sequencing datasets reveal that anchor points are strongly depleted for single nucleotide variants (SNVs) in tumours. Despite low SNV rates in their genomic neighbourhood, anchor points emerge as sites of evolutionary innovation, showing enrichment for structural variant (SV) breakpoints and a peak of SNVs at focal CTCF sites within the anchor points. Both CTCF-bound and non-CTCF anchor points harbour an excess of SV breakpoints in multiple tumour types and are prone to double-strand breaks in cell lines. Common fragile sites, which are hotspots for genome instability, also show elevated numbers of intersecting loop anchor points. Recurrently disrupted anchor points are enriched for genes with functions in cell cycle transitions and regions associated with predisposition to cancer. We also discover a novel class of CTCF-bound anchor points which overlap meiotic recombination hotspots and are enriched for the core PRDM9 binding motif, suggesting that the anchor points have been foci for diversity generated during recent human evolution. Conclusions We suggest that the unusual chromatin environment at loop anchor points underlies the elevated rates of variation observed, marking them as sites of regulatory importance but also genomic fragility

Spectral Analysis of Solar Radio Type III Bursts from 20 kHz to 410 MHz

We present the statistical analysis of the spectral response of solar radio type III bursts over the wide frequency range between 20 kHz and 410 MHz. For this purpose, we have used observations that were carried out using both spaced-based (Wind/Waves) and ground-based (Nançay Decameter Array and Nançay Radioheliograph) facilities. In order to compare the flux densities observed by the different instruments, we have carefully calibrated the data and displayed them in solar flux units. The main result of our study is that type III bursts, in the metric to hectometric wavelength range, statistically exhibit a clear maximum of their median radio flux density around 2 MHz. Although this result was already reported by inspecting the spectral profiles of type III bursts in the frequency range 20 kHz–20 MHz, our study extends such analysis for the first time to metric radio frequencies (i.e., from 20 kHz to 410 MHz) and confirms the maximum spectral response around 2 MHz. In addition, using a simple empirical model we show that the median radio flux S of the studied data set obeys the polynomial form Y = 0.04X3 − 1.63X2 + 16.30X − 41.24, with $X=\mathrm{ln}({F}_{\mathrm{MHz}})$ and with $Y=\mathrm{ln}({S}_{\mathrm{SFU}})$. Using the Sittler and Guhathakurtha model for coronal streamers, we have found that the maximum of radio power therefore falls in the range 4 to 10 R⊙, depending on whether the type III emissions are assumed to be at the fundamental or the harmonic

Protein/DNA interactions in complex DNA topologies: expect the unexpected

DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, “open” chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes