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Current Opinion in Genetics & Development

Jeffrey L Bennetzen, Minkyu Park
Most annotations of large eukaryotic genomes initially find transposable elements (TEs) and other repeats, then mask them so that subsequent efforts can be concentrated on the annotation and study of non-TE genes. However, TEs often contribute to host biology, and their community biologies are of intrinsic interest. This review discusses the challenges, rationale and technologies for comprehensive TE annotation in the commonly giant genomes of animals and plants. Complete discovery of the TEs in a fully sequenced genome is laborious, but feasible, with current strategies in the hands of a careful researcher...
March 12, 2018: Current Opinion in Genetics & Development
Ruth Jf Loos
Genome-wide discovery efforts have identified more than 500 genetic loci associated with adiposity traits. The vast majority of these loci were found through large-scale meta-analyses for body mass index (BMI) and waist-to-hip ratio (WHR), and in European ancestry populations. However, alternative approaches, focusing on non-European ancestry populations, more refined adiposity measures, and low-frequency (minor allele frequency (MAF)<5%) coding variants, identified additional novel loci that had not been identified before...
March 9, 2018: Current Opinion in Genetics & Development
Aoi Hosaka, Tetsuji Kakutani
Although transposable elements (TEs) have been regarded as genomic parasites, accumulating evidence suggests that they can also have beneficial roles in evolution of diverse biological processes. In this review, we focus on epigenetic control of TEs as sources of selectable phenotypic variation, with an emphasis on their connections to defense responses.
March 8, 2018: Current Opinion in Genetics & Development
Zoé Joly-Lopez, Thomas E Bureau
Transposable elements (TEs) are mobile genetic elements that were once perceived as merely selfish, but are now recognized as potent agents of adaptation. One way TEs contribute to genome evolution is through TE exaptation, a process whereby TEs, which usually persist by replicating in the genome, transform into novel host genes, which thereafter persist by conferring phenotypic benefits. Exapted TEs are known to contribute diverse and vital functions, and may facilitate punctuated equilibrium, yet we have little understanding about the process of TE exaptation...
March 8, 2018: Current Opinion in Genetics & Development
Aaron Leong, Eleanor Wheeler
Glycated hemoglobin (HbA1c) measures the amount of glucose in the blood in the previous 2-3 months and is used to test whether an individual has diabetes (HbA1c≥6.5%), or how well they are managing their diabetes. Genome-wide association studies have successfully identified multiple genomic loci influencing HbA1c, through both glycemic (factors that affect the amount blood glucose levels) and erythrocytic (factors that affect the red blood cell) pathways. Inaccuracies in HbA1c, due to non-glycemic variants, could lead to suboptimal care or adverse health consequences...
March 6, 2018: Current Opinion in Genetics & Development
Mette Korre Andersen, Niels Grarup, Ida Moltke, Anders Albrechtsen, Torben Hansen
In this mini-review, we give an overview of what is known about the genetic architecture of obesity and related metabolic traits with a primary focus on recent insights from studies of historically small and isolated populations. We start by briefly explaining what genetic architecture is and why studies of isolated populations in general are valuable if we want a complete picture of the genetic architecture of diseases and other traits among humans. Then we contrast what is known about the genetic architecture of obesity and related metabolic traits among large outbred populations, like Europeans, with results from recent studies of isolated populations...
March 3, 2018: Current Opinion in Genetics & Development
Lu Wang, I King Jordan
A convergence of novel genome analysis technologies is enabling population genomic studies of human transposable elements (TEs). Population surveys of human genome sequences have uncovered thousands of individual TE insertions that segregate as common genetic variants, i.e. TE polymorphisms. These recent TE insertions provide an important source of naturally occurring human genetic variation. Investigators are beginning to leverage population genomic data sets to execute genome-scale association studies for assessing the phenotypic impact of human TE polymorphisms...
March 2, 2018: Current Opinion in Genetics & Development
Clément Gilbert, Cédric Feschotte
It is becoming clear that most eukaryotic transposable elements (TEs) owe their evolutionary success in part to horizontal transfer events, which enable them to invade new species. Recent large-scale studies are beginning to unravel the mechanisms and ecological factors underlying this mode of transmission. Viruses are increasingly recognized as vectors in the process but also as a direct source of genetic material horizontally acquired by eukaryotic organisms. Because TEs and endogenous viruses are major catalysts of variation and innovation in genomes, we argue that horizontal inheritance has had a more profound impact in eukaryotic evolution than is commonly appreciated...
March 2, 2018: Current Opinion in Genetics & Development
Ewan R Pearson
In diabetes, pharmacogenetics can be used both to identify patient subgroups who will have most benefit and/or least harm from a particularly treatment, and to gain insights into the molecular mechanisms of drug action and disease aetiology. There is increasing evidence that genetic variation alters response to diabetes treatments-both in terms of glycaemic response and side effects. This can be seen with dramatic impact on clinical care, in patients with genetic forms of diabetes such as Maturity Onset Diabetes of the Young caused by HNF1A mutations, and Neonatal diabetes due to activating mutations in ABCC8 or KCNJ11...
February 24, 2018: Current Opinion in Genetics & Development
A Melvin, S O'Rahilly, D B Savage
Insulin resistance underpins the link between obesity and most of its associated metabolic disorders including type 2 diabetes, fatty liver disease, dyslipidaemia and cardiovascular disease. Despite its importance and extensive scientific endeavour, its precise molecular pathogenesis remains unclear. Monogenic syndromes of extreme insulin resistance, whilst rare in themselves, can provide unique insights into the pathogenesis of human insulin resistance. Severe insulin resistance syndromes are broadly classified into three categories: lipodystrophies, primary insulin signalling defects or complex syndromes including severe insulin resistance...
February 22, 2018: Current Opinion in Genetics & Development
Andrew P Morris
Candidate gene, genome-wide association, exome array and sequencing studies have identified more than 140 loci associated with type 2 diabetes (T2D) susceptibility. In this review, progress in understanding the genetic architecture of T2D susceptibility across diverse populations and in localising potential causal variants for the disease through fine-mapping studies is discussed. The additional insights gained from these genetic studies into novel molecular mechanisms and pathophysiology underlying T2D susceptibility are described, and the prospects for future genomic investigations of the disease are considered...
February 21, 2018: Current Opinion in Genetics & Development
Tamara S Roman, Karen L Mohlke
Many genome-wide association studies (GWAS) have identified signals located in non-coding regions, and an increasing number of functional genomics annotations of regulatory elements and assays of regulatory activity have been used to investigate mechanisms. Genome-wide datasets that characterize chromatin structure help detect potential regulatory elements. Assays to experimentally assess candidate variants include transcriptional reporter assays, and recently, massively parallel reporter assays (MPRAs). Additionally, the effect of candidate regulatory elements and variants on gene expression and function can be evaluated using genomic editing with the CRISPR-Cas9 technology...
February 19, 2018: Current Opinion in Genetics & Development
Paul W Franks, Jordi Merino
Type 2 diabetes (T2D) is widespread, affecting the health of hundreds of millions worldwide. The disease results from the complex interplay of lifestyle factors acting on a backdrop of inherited DNA risk variants. Detecting and understanding biomarkers, whether genotypes or other downstream biological features that dictate a person's phenotypic response to different lifestyle exposures, may have tremendous utility in the prevention of T2D. Here, we explore (i) evidence of how human genetic adaptation to diverse local environments might interact with lifestyle factors in T2D, (ii) the key challenges facing the research area of gene×lifestyle interactions in T2D, and (iii) the solutions that might be pursued in future studies...
February 16, 2018: Current Opinion in Genetics & Development
Lisa R Letourneau, Siri Atma W Greeley
The majority of patients diagnosed with diabetes less than 6 months of age, and many cases diagnosed between 6 and 12 months of age, have a gene mutation that causes permanent or transient hyperglycemia. Recent research advances have allowed for the discovery of new causes of congenital diabetes, including genes involved in pancreatic development (GATA4, NKX2-2, MNX1) and monogenic causes of autoimmune dysregulation (STAT3, LRBA). Ongoing follow-up of patients with KCNJ11 and ABCC8 mutations has supported the safety and efficacy of sulfonylureas, as well as the use of insulin pumps and continuous glucose monitors in infants with insulin-requiring forms of monogenic diabetes...
February 14, 2018: Current Opinion in Genetics & Development
Catherine C Robertson, Stephen S Rich
Type 1 diabetes is the most common autoimmune disorder in childhood, characterized by the development of autoimmunity through unknown environmental insults in genetically susceptible individuals. There are now over 50 regions of the genome that harbor type 1 diabetes susceptibility genes, with much of the genetic risk now well-defined in youth of Northern European ancestry. The impact of these genetic variants on initiation and progression of the autoimmune process (islet autoimmunity) is now being understood; however, studies are only now being conducted to understand the function of the variants associated with type 1 diabetes risk...
February 13, 2018: Current Opinion in Genetics & Development
Niina Sandholm, Per-Henrik Groop
Diabetic kidney disease and other long-term complications are common in diabetes, and comprise the main cause of co-morbidity and premature mortality in individuals with diabetes. While familial clustering and heritability have been reported for all diabetic complications, the genetic background and the molecular mechanisms remain poorly understood. In recent years, genome-wide association studies have identified a few susceptibility loci for the renal complications as well as for diabetic retinopathy, diabetic cardiovascular disease and mortality...
February 13, 2018: Current Opinion in Genetics & Development
Sarah N Anderson, Nathan M Springer
Changes in gene expression can have profound effects on phenotype. Nature has provided many complex patterns of gene regulation such as imprinting. Imprinted genes exhibit differences in the expression of the maternal and paternal alleles, even though they reside in the same nucleus with access to the same trans-acting factors. Significant attention has been focused on the potential reasons that imprinted expression could be beneficial and stabilized by selection. However, less attention has focused on understanding how imprinted expression might arise or decay...
February 13, 2018: Current Opinion in Genetics & Development
Gina M Peloso, Pradeep Natarajan
Plasma lipid levels are heritable quantitative risk factors and therapeutic targets for cardiovascular disease. Plasma lipids have been a model for translating genetic observations across the allele frequency spectrum to unique biological and therapeutic insights. Most large studies to date predominately comprised of individuals of European ancestry. This review focuses on contemporary evidence from 2016 to 2017 looking at the effect of genetic variants on plasma lipid levels across the allele frequency spectrum with incrementally larger sample sizes and the contribution of non-European ancestry studies to the genetic etiology of plasma lipid levels...
February 12, 2018: Current Opinion in Genetics & Development
Jonathan F Wendel, Damon Lisch, Guanjing Hu, Annaliese S Mason
We consider the rapidly advancing discipline of plant evolutionary genomics, with a focus on the evolution of polyploid genomes. In many lineages, polyploidy is followed by 'biased fractionation', the unequal loss of genes from ancestral progenitor genomes. Mechanistically, it has been proposed that biased fractionation results from changes in the epigenetic landscape near genes, likely mediated by transposable elements. These epigenetic changes result in unequal gene expression between duplicates, establishing differential fitness that leads to biased gene loss with respect to ancestral genomes...
February 10, 2018: Current Opinion in Genetics & Development
Ivan Vannini, Francesca Fanini, Muller Fabbri
MicroRNAs (miRNAs) have emerged as important regulators of human carcinogenesis by affecting the expression of key oncogenes and tumor suppressor genes. MiRNAs elicit their function through post-transcriptional regulation of the mRNA translation into protein as well as functioning as ligands for proteic receptors called miRceptors. Our understanding of the role of miRNAs in cancer biology has enormously improved in the last few years, providing the rationale for new therapeutics. Here we discuss the most recent findings on the role of miRNAs in modulating cancer biology with a specific focus on their role as modulators of the biology of the tumor microenvironment both as cargo of extracellular vesicles and as extra-vesicular miRNAs...
February 8, 2018: Current Opinion in Genetics & Development
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