A Non-Coding RNA Within the Rasgrf1 Locus in Mouse Is Imprinted and Regulated by Its Homologous Chromosome in Trans

BACKGROUND: Rasgrf1 is imprinted in mouse, displaying paternal allele specific expression in neonatal brain. Paternal expression is accompanied by paternal-specific DNA methylation at a differentially methylated domain (DMD) within the locus. The cis-acting elements necessary for Rasgrf1 imprinting are known. A series of tandem DNA repeats control methylation of the adjacent DMD, which is a methylation sensitive enhancer-blocking element. These two sequences constitute a binary switch that controls imprinting and represents the Imprinting Control Region (ICR). One paternally transmitted mutation, which helped define the ICR, induced paramutation, in trans, on the maternal allele. Like many imprinted genes, Rasgrf1 lies within an imprinted cluster. One of four noncoding transcripts in the cluster, AK015891, is known to be imprinted. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that an additional noncoding RNA, AK029869, is imprinted and paternally expressed in brain throughout development. Intriguingly, any of several maternally inherited ICR mutations affected expression of the paternal AK029869 transcript in trans. Furthermore, we found that the ICR mutations exert different trans effects on AK029869 at different developmental times. CONCLUSIONS/SIGNIFICANCE: Few trans effects have been defined in mammals and, those that exist, do not show the great variation seen at the Rasgrf1 imprinted domain, either in terms of the large number of mutations that produce the effects or the range of phenotypes that emerge when they are seen. These results suggest that trans regulation of gene expression may be more common than originally appreciated and that where trans regulation occurs it can change dynamically during development

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Drug discovery in advanced prostate cancer: translating biology into therapy.

Castration-resistant prostate cancer (CRPC) is associated with a poor prognosis and poses considerable therapeutic challenges. Recent genetic and technological advances have provided insights into prostate cancer biology and have enabled the identification of novel drug targets and potent molecularly targeted therapeutics for this disease. In this article, we review recent advances in prostate cancer target identification for drug discovery and discuss their promise and associated challenges. We review the evolving therapeutic landscape of CRPC and discuss issues associated with precision medicine as well as challenges encountered with immunotherapy for this disease. Finally, we envision the future management of CRPC, highlighting the use of circulating biomarkers and modern clinical trial designs

Advertising-versus-marketing mix carryover effects: An empirical evaluation

During the field campaign POPCORN (Photo oxidant formation by plant emitted compounds and OH radicals in North-eastern Germany) in Pennewitt (Mecklenburg-Vorpommern, Germany) in August 1994, carbon monoxide and nonmethane hydrocarbons were measured over a large maize field by in-situ gas chromatography. Throughout the campaign CO and NMHC showed, even for a remote rural area, unexpectedly low mixing ratios. Except a few episodes, CO mixing ratios were around 120 ppb. Ethane was the only hydrocarbon showing mixing ratios exceeding 1 ppb. The mixing ratios of all other NMHC ranged between several hundred ppt and the lower limit of detection which was between 20 and 5 ppt depending on the compound. During three frontal passages CO and NMHC mixing ratios increased significantly, while between August 13 and 16, 1994, polar air masses were encountered with CO and NMHC mixing ratios dropping to values which are typical for North Atlantic background air. During this period average CO mixing ratios were 85 ppb and ethane as the most abundant hydrocarbon decreased to 650 ppt. The large-scale meteorological situation is reflected in an unusual frequency distribution of CO. The distribution shows three maxima which can be assigned to the periods of the frontal passages, to the observation of polar air masses and the rest of the campaign. Two-day backward trajectories were calculated in order to obtain information about the origin of the air masses transported to the site. The observed NMHC and CO data can be attributed to the origin of the air masses and the air mass trajectories. NMHC and CO mixing ratios were well correlated indicating that these compounds originated from similar mostly anthropogenic sources. An exception was isoprene which showed no correlation with CO. With values below 100 ppt the mixing ratio of isoprene, which is emitted by terrestrial vegetation, was also unexpectedly low during the first half of the campaign although the maximum temperatures were around 35°C

Isobar separation at FRS-ESR - a development towards pure isomeric stored beams

One important goal of the ILIMA project at FAIR is the study of masses and decay properties of relativistic isomeric beams stored and cooled in the planned storage-ring complex. A new scheme is described, where a storage-cooler ring is used for high-resolution mass separation. Experimental results on the separation of the isobaric pair 140Pr-140Ce are presented