Time-dependent genetic effects on gene expression implicate aging processes

Gene expression is dependent on genetic and environmental factors. In the last decade, a large body of research has significantly improved our understanding of the genetic architecture of gene expression. However, it remains unclear whether genetic effects on gene expression remain stable over time. Here, we show, using longitudinal whole-blood gene expression data from a twin cohort, that the genetic architecture of a subset of genes is unstable over time. In addition, we identified 2213 genes differentially expressed across time points that we linked with aging within and across studies. Interestingly, we discovered that most differentially expressed genes were affected by a subset of 77 putative causal genes. Finally, we observed that putative causal genes and down-regulated genes were affected by a loss of genetic control between time points. Taken together, our data suggest that instability in the genetic architecture of a subset of genes could lead to widespread effects on the transcriptome with an aging signature

The study of the mercury cycle in polar regions: An international study in Ny-Alesund, Svalbard

Mercury (Hg) is a toxic pollutant and it can be strongly accumulated in the food chain, especially in Polar Regions. This paper presents a part of the work that has been on-going for 3-4 years in Ny-Alesund, Svalbard within the frame of an international collaboration. In Ny-Alesund in spring 2003, the atmospheric chemistry of mercury has been studied so as to better understand the formation of oxidized mercury species in the atmosphere that could be deposited onto snow surfaces. The role of snow as a potential source of mercury to the atmosphere or as a sink has also been approached to better understand the behavior of this metal. Chemical and biological processes seem to play a major role in Hg storage in snow. When melting, snow could be a major source of Hg into the various ecosystems and this toxin could therefore be accumulated into the food chain

Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population

Abstract Background Expression quantitative trait loci (eQTL) studies provide insights into regulatory mechanisms underlying disease risk. Expanding studies of gene regulation to underexplored populations and to medically relevant tissues offers potential to reveal yet unknown regulatory variants and to better understand disease mechanisms. Here, we performed eQTL mapping in subcutaneous (S) and visceral (V) adipose tissue from 106 Greek individuals (Greek Metabolic study, GM) and compared our findings to those from the Genotype-Tissue Expression (GTEx) resource. Results We identified 1,930 and 1,515 eGenes in S and V respectively, over 13% of which are not observed in GTEx adipose tissue, and that do not arise due to different ancestry. We report additional context-specific regulatory effects in genes of clinical interest (e.g. oncogene ST7) and in genes regulating responses to environmental stimuli (e.g. MIR21, SNX33). We suggest that a fraction of the reported differences across populations is due to environmental effects on gene expression, driving context-specific eQTLs, and suggest that environmental effects can determine the penetrance of disease variants thus shaping disease risk. We report that over half of GM eQTLs colocalize with GWAS SNPs and of these colocalizations 41% are not detected in GTEx. We also highlight the clinical relevance of S adipose tissue by revealing that inflammatory processes are upregulated in individuals with obesity, not only in V, but also in S tissue. Conclusions By focusing on an understudied population, our results provide further candidate genes for investigation regarding their role in adipose tissue biology and their contribution to disease risk and pathogenesis

Snow-to-air exchanges of mercury in an Arctic seasonal snow pack in Ny-Ålesund, Svalbard

International audienceThe study of mercury (Hg) cycle in Arctic regions is a major subject of concern due to the dramatic increases of Hg concentrations in ecosystem in the last few decades. The causes of such increases are still in debate, and an important way to improve our knowledge on the subject is to study the exchanges of Hg between atmosphere and snow during springtime. We organized an international study from 10 April to 10 May 2003 in Ny-Ålesund, Svalbard, in order to assess these fluxes through measurements and derived calculations. Snow-to-air emission fluxes of Hg were measured using the flux chamber technique between 0 and 50 ng m−2 h−1. A peak in Gaseous Elemental Mercury (GEM) emission flux from the snow to the atmosphere has been measured just few hours after an Atmospheric Mercury Depletion Event (AMDE) recorded on 22 April 2004. Surprisingly, this peak in GEM emitted after this AMDE did not correspond to any increase in Hg concentration in snow surface. A peak in GEM flux after an AMDE was observed only for this single event but not for the four other AMDEs recorded during this spring period. In the snow pack which is seasonal and about 40 cm depth above permafrost, Hg is involved in both production and incorporation processes. The incorporation was evaluated to 5-40 pg m2 h. Outside of AMDE periods, Hg flux from the snow surface to the atmosphere was the consequence of GEM production in the air of snow and was about 15-50 ng m−2 h−1, with a contribution of deeper snow layers evaluated to 0.3-6.5 ng m−2 h−1. The major part of GEM production is then mainly a surface phenomenon. The internal production of GEM was largely increasing when snow temperatures were close to melting, indicating a chemical process occurring in the quasi-liquid layer at the surface of snow grains

Study of the origin of atmospheric mercury depletion events recorded in Ny-Ålesund, Svalbard, spring 2003

International audienceAn international campaign involving six teams was organized in Ny-Ålesund, Svalbard, in order to understand better the origin of atmospheric mercury depletion events (AMDEs). Special emphasis was given to determining the source region of the observed events and the physical and chemical processes leading to AMDEs. Five AMDEs were recorded during a one-month field experiment (10 April-10 May, 2003). The different events presented various characteristics, especially in terms of mercury species formation, atmospheric particle variations and meteorological conditions. After careful examination of each event, we postulate that two were probably due to advection of already depleted air masses and three were a product of local or regional chemistry. The roles of different surfaces (frost flowers, snow, ice aerosol in clouds) involved in heterogeneous reactions leading to AMDEs are also discussed. We speculate that ice clouds may explain the particle variations observed during the three more local events

Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing

Understanding how genetic variation affects distinct cellular phenotypes, such as gene expression levels, alternative splicing and DNA methylation levels, is essential for better understanding of complex diseases and traits. Furthermore, how inter-individual variation of DNA methylation is associated to gene expression is just starting to be studied. In this study, we use the GenCord cohort of 204 newborn Europeans' lymphoblastoid cell lines, T-cells and fibroblasts derived from umbilical cords. The samples were previously genotyped for 2.5 million SNPs, mRNA-sequenced, and assayed for methylation levels in 482,421 CpG sites. We observe that methylation sites associated to expression levels are enriched in enhancers, gene bodies and CpG island shores. We show that while the correlation between DNA methylation and gene expression can be positive or negative, it is very consistent across cell-types. However, this epigenetic association to gene expression appears more tissue-specific than the genetic effects on gene expression or DNA methylation (observed in both sharing estimations based on P-values and effect size correlations between cell-types). This predominance of genetic effects can also be reflected by the observation that allele specific expression differences between individuals dominate over tissue-specific effects. Additionally, we discover genetic effects on alternative splicing and interestingly, a large amount of DNA methylation correlating to alternative splicing, both in a tissue-specific manner. The locations of the SNPs and methylation sites involved in these associations highlight the participation of promoter proximal and distant regulatory regions on alternative splicing. Overall, our results provide high-resolution analyses showing how genome sequence variation has a broad effect on cellular phenotypes across cell-types, whereas epigenetic factors provide a secondary layer of variation that is more tissue-specific. Furthermore, the details of how this tissue-specificity may vary across inter-relations of molecular traits, and where these are occurring, can yield further insights into gene regulation and cellular biology as a whole

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

DNA methylation is an essential epigenetic mark whose role in gene regulation and its dependency on genomic sequence and environment are not fully understood. In this study we provide novel insights into the mechanistic relationships between genetic variation, DNA methylation and transcriptome sequencing data in three different cell-types of the GenCord human population cohort. We find that the association between DNA methylation and gene expression variation among individuals are likely due to different mechanisms from those establishing methylation-expression patterns during differentiation. Furthermore, cell-type differential DNA methylation may delineate a platform in which local inter-individual changes may respond to or act in gene regulation. We show that unlike genetic regulatory variation, DNA methylation alone does not significantly drive allele specific expression. Finally, inferred mechanistic relationships using genetic variation as well as correlations with TF abundance reveal both a passive and active role of DNA methylation to regulatory interactions influencing gene expression. DOI:http://dx.doi.org/10.7554/eLife.00523.001

An autocrine ActivinB mechanism drives TGF β/Activin signaling in Group 3 medulloblastoma

International audienceMedulloblastoma (MB) is a pediatric tumor of the cerebellum divided into four groups. Group 3 is of bad prognosis and remains poorly characterized. While the current treatment involving surgery, radiotherapy, and chemotherapy often fails, no alternative therapy is yet available. Few recurrent genomic alterations that can be therapeutically targeted have been identified. Amplifications of receptors of the TGFb/Activin pathway occur at very low frequency in Group 3 MB. However, neither their functional relevance nor activation of the downstream signaling pathway has been studied. We showed that this pathway is activated in Group 3 MB with some samples showing a very strong activation. Beside genetic alterations, we demonstrated that an ActivinB autocrine stimulation is responsible for pathway activation in a subset of Group 3 MB characterized by high PMEPA1 levels. Importantly, Galunisertib, a kinase inhibitor of the cognate receptors currently tested in clinical trials for Glioblastoma patients, showed efficacy on orthotopically grafted MB-PDX. Our data demonstrate that the TGFb/Activin pathway is active in a subset of Group 3 MB and can be therapeutically targeted

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

Chromatin state variation at gene regulatory elements is abundant across individuals, yet we understand little about the genetic basis of this variability. Here, we profiled several histone modifications, the transcription factor (TF) PU.1, RNA polymerase II, and gene expression in lymphoblastoid cell lines from 47 whole-genome sequenced individuals. We observed that distinct cis-regulatory elements exhibit coordinated chromatin variation across individuals in the form of variable chromatin modules (VCMs) at sub-Mb scale. VCMs were associated with thousands of genes and preferentially cluster within chromosomal contact domains. We mapped strong proximal and weak, yet more ubiquitous, distal-acting chromatin quantitative trait loci (cQTL) that frequently explain this variation. cQTLs were associated with molecular activity at clusters of cis-regulatory elements and mapped preferentially within TF-bound regions. We propose that local, sequence-independent chromatin variation emerges as a result of genetic perturbations in cooperative interactions between cis-regulatory elements that are located within the same genomic domain