'; ?> geneimprint : Hot off the Press http://www.geneimprint.com/site/hot-off-the-press Daily listing of the most recent articles in epigenetics and imprinting, collected from the PubMed database. en-us Sun, 07 Feb 2016 03:29:14 PST Sun, 07 Feb 2016 03:29:14 PST jirtle@radonc.duke.edu james001@jirtle.com LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. Sheffield NC, Bock C
Bioinformatics (Feb 2016)

Genomic datasets are often interpreted in the context of large-scale reference databases. One approach is to identify significantly overlapping gene sets, which works well for gene-centric data. However, many types of high-throughput data are based on genomic regions. Locus Overlap Analysis (LOLA) provides easy and automatable enrichment analysis for genomic region sets, thus facilitating the interpretation of functional genomics and epigenomics data.]]>
Sat, 06 Feb 2016 00:00:00 PST
Telomere length in Parkinson's disease: A meta-analysis. Forero DA, González-Giraldo Y, López-Quintero C, Castro-Vega LJ, Barreto GE, Perry G
Exp Gerontol (Mar 2016)

Parkinson's disease (PD) is a common and severe movement disorder. Differences in telomere length (TL) have been reported as possible risk factors for several neuropsychiatric disorders, including PD. Results from published studies for TL in PD are inconsistent, highlighting the need for a meta-analysis. In the current work, a meta-analysis of published studies for TL in PD was carried out. PubMed, Web of Science and Google Scholar databases were used to identify relevant articles that reported TL in groups of PD patients and controls. A random-effects model was used for meta-analytical procedures. The meta-analysis included eight primary studies, derived from populations of European and Asian descent, and did not show a significant difference in TL between 956 PD patients and 1284 controls (p value: 0.246). Our results show that there is no consistent evidence of shorter telomeres in PD patients and suggest the importance of future studies on TL and PD that analyze other populations and also include assessment of TL from different brain regions.]]>
Sat, 06 Feb 2016 00:00:00 PST
Regulatory links between imprinted genes: evolutionary predictions and consequences. Patten MM, Cowley M, Oakey RJ, Feil R
Proc Biol Sci (Feb 2016)

Genomic imprinting is essential for development and growth and plays diverse roles in physiology and behaviour. Imprinted genes have traditionally been studied in isolation or in clusters with respect to cis-acting modes of gene regulation, both from a mechanistic and evolutionary point of view. Recent studies in mammals, however, reveal that imprinted genes are often co-regulated and are part of a gene network involved in the control of cellular proliferation and differentiation. Moreover, a subset of imprinted genes acts in trans on the expression of other imprinted genes. Numerous studies have modulated levels of imprinted gene expression to explore phenotypic and gene regulatory consequences. Increasingly, the applied genome-wide approaches highlight how perturbation of one imprinted gene may affect other maternally or paternally expressed genes. Here, we discuss these novel findings and consider evolutionary theories that offer a rationale for such intricate interactions among imprinted genes. An evolutionary view of these trans-regulatory effects provides a novel interpretation of the logic of gene networks within species and has implications for the origin of reproductive isolation between species.]]>
Thu, 04 Feb 2016 00:00:00 PST
Epigenomics: Parallel single-cell sequencing. Koch L
Nat Rev Genet (Jan 2016)

Tue, 02 Feb 2016 00:00:00 PST
Epigenomics in marine fishes. Metzger DC, Schulte PM
Mar Genomics (Jan 2016)

Epigenetic mechanisms are an underappreciated and often ignored component of an organism's response to environmental change and may underlie many types of phenotypic plasticity. Recent technological advances in methods for detecting epigenetic marks at a whole-genome scale have launched new opportunities for studying epigenomics in ecologically relevant non-model systems. The study of ecological epigenomics holds great promise to better understand the linkages between genotype, phenotype, and the environment and to explore mechanisms of phenotypic plasticity. The many attributes of marine fish species, including their high diversity, variable life histories, high fecundity, impressive plasticity, and economic value provide unique opportunities for studying epigenetic mechanisms in an environmental context. To provide a primer on epigenomic research for fish biologists, we start by describing fundamental aspects of epigenetics, focusing on the most widely studied and most well understood of the epigenetic marks: DNA methylation. We then describe the techniques that have been used to investigate DNA methylation in marine fishes to date and highlight some new techniques that hold great promise for future studies. Epigenomic research in marine fishes is in its early stages, so we first briefly discuss what has been learned about the establishment, maintenance, and function of DNA methylation in fishes from studies in zebrafish and then summarize the studies demonstrating the pervasive effects of the environment on the epigenomes of marine fishes. We conclude by highlighting the potential for ongoing research on the epigenomics of marine fishes to reveal critical aspects of the interaction between organisms and their environments.]]>
Tue, 02 Feb 2016 00:00:00 PST
Species-wide patterns of DNA methylation variation in Quercus lobata and its association with climate gradients. Gugger PF, Fitz-Gibbon S, Pellegrini M, Sork VL
Mol Ecol (Feb 2016)

DNA methylation in plants affects transposon silencing, transcriptional regulation, and thus phenotypic variation. One unanswered question is whether DNA methylation could be involved in local adaptation of plant populations to their environments. If methylation alters phenotypes to improve plant response to the environment, then methylation sites or the genes that affect them could be a target of natural selection. Using reduced-representation bisulfite sequencing (RRBS) data, we assessed whether climate is associated with variation in DNA methylation levels among 58 naturally occurring, species-wide samples of valley oak (Quercus lobata) collected across climate gradients. We identified the genomic context of these variants referencing a new draft valley oak genome sequence. Methylation data were obtained for 341,107 cytosines, of which we deemed 57,488 as single-methylation variants (SMVs), found in the CG, CHG, and CHH sequence contexts. Environmental association analyses revealed 43 specific SMVs that are significantly associated with any of four climate variables, the majority of which are associated with mean maximum temperature. The 43 climate-associated SMVs tend to occur in or near genes, several of which have known involvement in plant response to environment. Multivariate analyses show that climate and spatial variables explain more overall variance in CG-SMVs among individuals than in SNPs, CHG-SMVs, or CHH-SMVs. Together, these results from natural oak populations provide initial evidence for a role of CG methylation in locally adaptive evolution or plasticity in plant response. This article is protected by copyright. All rights reserved.]]>
Tue, 02 Feb 2016 00:00:00 PST
Tissue-specific patterns of allelically-skewed DNA methylation. Marzi SJ, Meaburn EL, Dempster EL, Lunnon K, Paya-Cano JL, Smith RG, Volta M, Troakes C, Schalkwyk LC, Mill J
Epigenetics (Jan 2016)

While DNA methylation is usually thought to be symmetrical across both alleles, there are some notable exceptions. Genomic imprinting and X chromosome inactivation are two well-studied sources of allele-specific methylation (ASM), but recent research has indicated a more complex pattern in which genotypic variation can be associated with allelically-skewed DNA methylation in cis. Given the known heterogeneity of DNA methylation across tissues and cell types we explored inter- and intra-individual variation in ASM across several regions of the human brain and whole blood from multiple individuals. Consistent with previous studies, we find widespread ASM with > 4% of the ∼220,000 loci interrogated showing evidence of allelically-skewed DNA methylation. We identify ASM flanking known imprinted regions, and show that ASM sites are enriched in DNase I hypersensitivity sites and often located in an extended genomic context of intermediate DNA methylation. We also detect examples of genotype-driven ASM, some of which are tissue-specific. These findings contribute to our understanding of the nature of differential DNA methylation across tissues and have important implications for genetic studies of complex disease. As a resource to the community, ASM patterns across each of the tissues studied are available in a searchable online database: http://epigenetics.essex.ac.uk/ASMBrainBlood .]]>
Mon, 01 Feb 2016 00:00:00 PST
Placental examination: prognosis after delivery of the growth-restricted fetus. Tachibana M, Nakayama M, Miyoshi Y
Curr Opin Obstet Gynecol (Jan 2016)

This article describes the role of placental examination in the prognostic evaluation of fetal growth restriction (FGR) infants.]]>
Sat, 30 Jan 2016 00:00:00 PST
Key Signaling Events for Committing Mouse Pluripotent Stem Cells to the Germline Fate. Wang JQ, Cao WG
Biol Reprod (Dec 2016)

The process of germline development carries genetic information and preparatory totipotency across generations. The last decade has witnessed remarkable successes in the generation of germline cells from mouse pluripotent stem cells, especially induced germline cells with the capacity for producing viable offspring, suggesting clinical applications of induced germline cells in humans. However, to date, the culture systems for germline induction with accurate sex-specific meiosis and epigenetic reprogramming have not been well-established. In this study, we primarily focus on the mouse model to discuss key signaling events for germline induction. We review mechanisms of competent regulators on primordial germ cell induction and discuss current achievements and difficulties in inducing sex-specific germline development. Furthermore, we review the developmental identities of mouse embryonic stem cells and epiblast stem cells under certain defined culture conditions as it relates to the differentiation process of becoming germline cells.]]>
Fri, 29 Jan 2016 00:00:00 PST
Endosperm-based postzygotic hybridization barriers: developmental mechanisms and evolutionary drivers. Lafon-Placette C, Köhler C
Mol Ecol (Jan 2016)

The endosperm is a nourishing tissue that serves to support embryo growth. Failure of endosperm development will ultimately cause embryo arrest and seed lethality, a phenomenon that is frequently observed upon hybridization of related plant species or species that differ in ploidy. Endosperm-based interspecies or interploidy hybridization barriers depend on the direction of the hybridization, causing non-reciprocal seed defects. This reveals that the parental genomes are not equivalent, implicating parent-of-origin specific genes generating this type of hybridization barrier. Recent work revealed that endosperm-based hybridization barriers are rapidly evolving. In this review we discuss the developmental mechanisms causing hybrid seed lethality in angiosperms as well as the evolutionary forces establishing endosperm-based postzygotic hybridization barriers. This article is protected by copyright. All rights reserved.]]>
Thu, 28 Jan 2016 00:00:00 PST
Advancing sports and exercise genomics: moving from hypothesis-driven single study approaches to large multi-omics collaborative science. Tanaka M, Wang G, Pitsiladis YP
Physiol Genomics (Jan 2016)

The primary use of the traditional candidate gene approach over the past decades in sports genetics has had limited success in identifying genes associated with elite athletic performance. Advances in high-throughput technologies now permit the application of "omics" (e.g. genomics, transcriptomics, metabolomics, proteomics and epigenomics) approaches to examine the global features of a cell, tissue or organism. "Omics" approaches are being applied with some success to a wide range of pertinent biomedical problems such as cancer diagnosis but also in sports science and sports medicine such as for the identification of biomarkers of trainability or blood doping. There is good evidence to suggest that a combined "omics" solution will greatly facilitate discovery of the genetic influences on sporting performance, training response, injury predisposition and other potential determinants of successful human performance. In this regard, large-scale, collaborative efforts involving well-phenotyped cohorts will be essential for major progress to be made. A recent consensus emerged among 15 research groups active in the field of sports genetics to unite their efforts under one new collaborative initiative named the Athlome Project Consortium. The primary aim of the Athlome Project is to combine resources from individual studies and consortia worldwide to collectively study the genotype and phenotype data available on elite athletes, the adaptation to exercise training (in both human and animal models) and the determinants of exercise-related musculoskeletal injuries. This editorial summarizes the challenges and opportunities facing the Athlome Project Consortium and the field of sports and exercise genomics in general.]]>
Wed, 27 Jan 2016 00:00:00 PST
Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells. Barnicle A, Seoighe C, Golden A, Greally JM, Egan LJ
Physiol Genomics (Jan 2016)

Region and cell-type specific differences in the molecular make up of colon epithelial cells have been reported. Those differences may underlie the region-specific characteristics of common colon epithelial diseases such as colorectal cancer and inflammatory bowel disease. DNA methylation is a cell-type specific epigenetic mark, essential for transcriptional regulation, silencing of repetitive DNA and genomic imprinting. Little is known about any region-specific variations in methylation patterns in human colon epithelial cells. Using purified epithelial cells and whole biopsies (n=19) from human subjects, epigenome-wide DNA methylation data (using the HELP-tagging assay) was generated, comparing the methylation signatures of the proximal and distal colon. A total of 125 differentially methylated sites (DMS) were identified, mapping to transcription start sites of protein-coding genes, most notably several members of the homeobox (HOX) family of genes. Patterns of differential methylation were also validated using MassArray EpiTYPER. DNA methylation was also examined in whole biopsies, applying a computational technique to deconvolve variation in methylation within cell types and variation in cell-type composition across biopsies. Including inferred epithelial proportions as a covariate in differential methylation analysis applied to the whole biopsies resulted in greater overlap with the results obtained from purified epithelial cells compared to when the covariate was not included. Results obtained using both approaches highlight region-specific methylation patterns of HOX genes in colonic epithelium. Regional variation in methylation patterns has implications for the study of diseases that exhibit regional expression patterns in the human colon, such as inflammatory bowel disease and colorectal cancer.]]>
Wed, 27 Jan 2016 00:00:00 PST
Ushering Hypertension Into a New Era of Precision Medicine. Kotchen TA, Cowley AW, Liang M
JAMA (Jan 2016)

Wed, 27 Jan 2016 00:00:00 PST
[The biobank of the German National Cohort as a resource for epidemiologic research]. Wichmann HE, Hörlein A, Ahrens W, Nauck M
Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz (Jan 2016)

The linkage of high-quality biosamples with detailed data from medical examinations, questionnaires and interviews offers great opportunities for research. This is particularly true for large-scale prospective epidemiological studies with long observation periods, like the German National Cohort (GNC).]]>
Tue, 26 Jan 2016 00:00:00 PST
Structure Prediction: New Insights into Decrypting Long Noncoding RNAs. Yan K, Arfat Y, Li D, Zhao F, Chen Z, Yin C, Sun Y, Hu L, Yang T, Qian A
Int J Mol Sci (2016)

Long noncoding RNAs (lncRNAs), which form a diverse class of RNAs, remain the least understood type of noncoding RNAs in terms of their nature and identification. Emerging evidence has revealed that a small number of newly discovered lncRNAs perform important and complex biological functions such as dosage compensation, chromatin regulation, genomic imprinting, and nuclear organization. However, understanding the wide range of functions of lncRNAs related to various processes of cellular networks remains a great experimental challenge. Structural versatility is critical for RNAs to perform various functions and provides new insights into probing the functions of lncRNAs. In recent years, the computational method of RNA structure prediction has been developed to analyze the structure of lncRNAs. This novel methodology has provided basic but indispensable information for the rapid, large-scale and in-depth research of lncRNAs. This review focuses on mainstream RNA structure prediction methods at the secondary and tertiary levels to offer an additional approach to investigating the functions of lncRNAs.]]>
Mon, 25 Jan 2016 00:00:00 PST
A role for chromatin topology in imprinted domain regulation. MacDonald WA, Sachani SS, White CR, Mann MR
Biochem Cell Biol (Feb 2016)

Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.]]>
Mon, 25 Jan 2016 00:00:00 PST
Living long and ageing well: is epigenomics the missing link between nature and nurture? Rea IM, Dellet M, Mills KI,  
Biogerontology (Feb 2016)

Human longevity is a complex trait and increasingly we understand that both genes and lifestyle interact in the longevity phenotype. Non-genetic factors, including diet, physical activity, health habits, and psychosocial factors contribute approximately 50 % of the variability in human lifespan with another 25 % explained by genetic differences. Family clusters of nonagenarian and centenarian siblings, who show both exceptional age-span and health-span, are likely to have inherited facilitatory gene groups, but also have nine decades of life experiences and behaviours which have interacted with their genetic profiles. Identification of their shared genes is just one small step in the link from genes to their physical and psychological profiles. Behavioural genomics is beginning to demonstrate links to biological mechanisms through regulation of gene expression, which directs the proteome and influences the personal phenotype. Epigenetics has been considered the missing link between nature and nurture. Although there is much that remains to be discovered, this article will discuss some of genetic and environmental factors which appear important in good quality longevity and link known epigenetic mechanisms to themes identified by nonagenarians themselves related to their longevity. Here we suggest that exceptional 90-year old siblings have adopted a range of behaviours and life-styles which have contributed to their ageing-well-phenotype and which link with important public health messages.]]>
Sat, 23 Jan 2016 00:00:00 PST
Transgenerational epigenetic inheritance of diabetes risk as a consequence of early nutritional imbalances. Jimenez-Chillaron JC, Ramon-Krauel M, Ribo S, Diaz R
Proc Nutr Soc (Feb 2016)

In today's world, there is an unprecedented rise in the prevalence of chronic metabolic diseases, including obesity, insulin resistance and type 2 diabetes (T2D). The pathogenesis of T2D includes both genetic and environmental factors, such as excessive energy intake and physical inactivity. It has recently been suggested that environmental factors experienced during early stages of development, including the intrauterine and neonatal periods, might play a major role in predisposing individuals to T2D. Furthermore, several studies have shown that such early environmental conditions might even contribute to disease risk in further generations. In this review, we summarise recent data describing how parental nutrition during development increases the risk of diabetes in the offspring. We also discuss the potential mechanisms underlying transgenerational inheritance of metabolic disease, with particular emphasis on epigenetic mechanisms.]]>
Wed, 20 Jan 2016 00:00:00 PST
Assisted Reproduction Causes Reduced Fetal Growth Associated with Downregulation of Paternally Expressed Imprinted Genes That Enhance Fetal Growth. Li B, Chen S, Tang N, Xiao X, Huang J, Jiang F, Huang X, Sun F, Wang X
Biol Reprod (Jan 2016)

Alteration of intrauterine growth trajectory is linked to metabolic diseases in adulthood. In mammalian and human, pregnancies through assisted reproductive technology (ART) are associated with changes in intrauterine growth trajectory. However, it is still unclear how ART alters intrauterine growth trajectory, especially reduced fetal growth in early to mid-gestation. In this study, using a mouse model, it was found that ART procedures reduce fetal and placental growth at Embryonic Day 10.5. Further, ART lead to decreased methylation levels at H19, KvDMR1, and SNRPN imprinting control regions in the placentae, instead of fetuses. Furthermore, in the placenta, ART downregulated a majority of parentally expressed imprinted genes which enhance fetal growth, whereas it upregulated a majority of maternally expressed genes which repress fetal growth. Additionally, the expression of genes that regulate placental development was also affected by ART. ART also downregulated a majority of placental nutrient transporters. Disruption of genomic imprinting and abnormal expression of developmentally and functionally relevant genes in placenta may influence the placental development and function, which affect fetal growth and reprogramming.]]>
Thu, 14 Jan 2016 00:00:00 PST
50 years of Arabidopsis research: highlights and future directions. Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P
New Phytol (Feb 2016)

922 I. 922 II. 922 III. 925 IV. 925 V. 926 VI. 927 VII. 928 VIII. 929 IX. 930 X. 931 XI. 932 XII. 933 XIII. Natural variation and genome-wide association studies 934 XIV. 934 XV. 935 XVI. 936 XVII. 937 937 References 937 SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.]]>
Wed, 13 Jan 2016 00:00:00 PST