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Current Opinion in Genetics & Development

Jennifer J Wernegreen
Phylogenetically independent bacterial lineages have undergone a profound lifestyle shift: from a free-living to obligately host-associated existence. Among these lineages, intracellular bacterial mutualists of insects are among the most intimate, constrained symbioses known. These obligate endosymbionts exhibit severe gene loss and apparent genome deterioration. Evolutionary theory provides a basis to link their unusual genomic features with shifts in fundamental mechanisms - selection, genetic drift, mutation, and recombination...
September 18, 2017: Current Opinion in Genetics & Development
Edward C Schrom, Andrea L Graham
Over recent years, extensive phenotypic variability and plasticity have been revealed among the T-helper cells of the mammalian adaptive immune system, even within clonal lineages of identical antigen specificity. This challenges the conventional view that T-helper cells assort into functionally distinct subsets following differential instruction by the innate immune system. We argue that the adaptive value of coping with uncertainty can reconcile the 'instructed subset' framework with T-helper variability and plasticity...
September 16, 2017: Current Opinion in Genetics & Development
Simon H Martin, Chris D Jiggins
Introgression, the transfer of genetic material between species through hybridisation, occurs in many taxa and has important consequences. Genomic studies allow us to characterise the landscape of introgression across the genome, shedding light on both its adaptive benefits and the incompatibilities that help to maintain species barriers. Studies taking a genome-wide view suggest that adaptive introgression may be common, but that introgressed variation between many species is selected against throughout much of the genome...
September 15, 2017: Current Opinion in Genetics & Development
Jenny Tung, Luis B Barreiro
Genome-wide data on genetic variation are now available for multiple primate species and populations, facilitating analyses of evolutionary history within and across taxa. One emerging theme from these studies involves the central role of admixture. Genomic data sets indicate that both ancient gene flow following initial taxonomic divergence and ongoing gene flow at current species boundaries are common. These findings are of particular interest given evidence for a complex history of admixture in our own lineage, including examples of ecologically driven adaptive introgression...
September 15, 2017: Current Opinion in Genetics & Development
June B Nasrallah
Flowering plants have evolved diverse mechanisms that promote outcrossing. The most widespread of these outbreeding devices are self-incompatibility systems, the highly selective prefertilization mating barriers that prevent self-fertilization by disrupting pollen-pistil interactions. Despite the advantages of outcrossing, loss of self-incompatibility has occurred repeatedly in many plant families. In the mustard family, the highly polymorphic receptors and ligands that mediate the recognition and inhibition of self-pollen in self-incompatibility have been characterized and the 3D structure of the receptor-ligand complex has been solved...
September 12, 2017: Current Opinion in Genetics & Development
Téo Fournier, Joseph Schacherer
Dissecting the genetic basis of natural phenotypic variation is a major goal in biology. We know that most traits are strongly heritable. However, their genetic architecture is a long-standing question, which is unfortunately confounded by the lack of complete knowledge of the genetic components as well as their phenotypic effect in a specific genetic background. Many genetic variants are known to affect phenotypes but the same functional variant can have a different effect on the phenotype in different individuals of the same species...
September 12, 2017: Current Opinion in Genetics & Development
Stefan Zdraljevic, Erik C Andersen
Organismal fitness depends on adaptation to complex niches where chemical compounds and pathogens are omnipresent. These stresses can lead to the fixation of alleles in both xenobiotic responses and proliferative signaling pathways that promote survival in these niches. However, both xenobiotic responses and proliferative pathways vary within and among species. For example, genetic differences can accumulate within populations because xenobiotic exposures are not constant and selection is variable. Additionally, neutral genetic variation can accumulate in conserved proliferative pathway genes because these systems are robust to genetic perturbations given their essential roles in normal cell-fate specification...
September 8, 2017: Current Opinion in Genetics & Development
James P Scott-Browne, Chan-Wang J Lio, Anjana Rao
The ten-eleven-translocation (TET) proteins oxidize 5-methylcytosine in DNA. Alterations in TET protein function have been linked to cancer, but TETs have also been observed to influence many cell differentiation processes. Here we review recent work assessing the contribution of TET proteins to natural and induced differentiation. Altogether these analyses have helped characterize how TETs and their enzymatic products influence DNA methylation patterns, regulatory element activity, DNA binding protein specificity and gene expression...
September 6, 2017: Current Opinion in Genetics & Development
Taylor N Medwig, David Q Matus
Cell invasion is a specialized cell behavior that likely co-evolved with the emergence of basement membranes in metazoans as a mechanism to break down the barriers that separate tissues. A variety of conserved and lineage-specific biological processes that occur during development and homeostasis rely on cell invasive behavior. Recent innovations in genome editing and live-cell imaging have shed some light on the programs that mediate acquisition of an invasive phenotype; however, comparative approaches among species are necessary to understand how this cell behavior evolved...
September 4, 2017: Current Opinion in Genetics & Development
Pradeep Gautam, Tao Yu, Yuin-Han Loh
Recent advances in our understanding of endogenous retroviruses (ERVs) regulation and its functional aspects have provided us with vast power to unravel its role in the host's genome. Co-evolutionary model of ERVs and Kruppel associated box-Zinc Finger Proteins (KRAB-ZFPs) provides a deeper knowledge of how the genome is shaped during the course of evolution. However, the role of ERVs in normal cellular function still remains an enigma. Here we review studies in recent years with a focus on the role of ERVs in maintaining stemness and cell fate reprogramming, along with the recent discoveries of novel regulatory factors which have been shown to mediate ERV expression in both canonical and non-canonical pathways...
August 31, 2017: Current Opinion in Genetics & Development
Arun Rajendra Chavan, Oliver William Griffith, Günter Paul Wagner
A widely discussed physiological puzzle of mammalian pregnancy is the immunological paradox, which asks: why is the semi-allogenic fetus not attacked by the mother's adaptive immune system? Here, we argue that an additional, and perhaps more fundamental paradox is the question: why is embryo implantation so similar to inflammation while inflammation is also the greatest threat to the continuation of pregnancy? Equally puzzling is the question of how this arose during evolution. We call this the inflammation paradox...
August 26, 2017: Current Opinion in Genetics & Development
Maria Aurelia Ricci, Maria Pia Cosma, Melike Lakadamyali
Chromatin fiber organization is essential for gene function in all cell types. Moreover it helps to determine cell fate in embryonic/adult stem cells and in somatic cells undergoing reprogramming to pluripotency. Until now the diffraction limit of light has limited the inspection of the chromatin fiber organization to a level sufficient to understand how it impacts gene function. The development of advanced microscopy methods, such as single molecule localization microscopy, has largely opened a new field of research providing us with the tools to visualize and quantitatively analyze chromatin fiber organization and thus gene activity at nanoscale resolution in single cells...
August 24, 2017: Current Opinion in Genetics & Development
Daniel Ortmann, Ludovic Vallier
Human pluripotent stem cells derived from embryos (human Embryonic Stem Cells or hESCs) or generated by direct reprogramming of somatic cells (human Induced Pluripotent Stem Cells or hiPSCs) can proliferate almost indefinitely in vitro while maintaining the capacity to differentiate into a broad diversity of cell types. These two properties (self-renewal and pluripotency) confers human pluripotent stem cells a unique interest for clinical applications since they could allow the production of infinite quantities of cells for disease modelling, drug screening and cell based therapy...
August 24, 2017: Current Opinion in Genetics & Development
Pixi Yan, Sai Luo, J Yuyang Lu, Xiaohua Shen
Pervasive transcription in mammalian genomes produces thousands of long noncoding RNA (lncRNA) transcripts. Although they have been implicated in diverse biological processes, the functional relevance of most lncRNAs remains unknown. Recent studies reveal the prevalence of lncRNA-mediated cis regulation on nearby transcription. In this review, we summarize cis- and trans-acting lncRNAs involved in stem cell pluripotency and reprogramming, highlighting the role of regulatory lncRNAs in providing an additional layer of complexity to the regulation of genes that govern cell fate during development...
August 19, 2017: Current Opinion in Genetics & Development
Anne-Marie Dion-Côté, Daniel A Barbash
Genome stability ensures individual fitness and reliable transmission of genetic information. Hybridization between diverging lineages can trigger genome instability, highlighting its potential role in post-zygotic reproductive isolation. We argue that genome instability is not merely one of several types of hybrid incompatibility, but rather that genome stability is one of the very first and most fundamental traits that can break down when two diverged genomes are combined. Future work will reveal how frequent and predictable genome instability is in hybrids, how it affects hybrid fitness, and whether it is a direct cause or consequence of speciation...
August 19, 2017: Current Opinion in Genetics & Development
Kaixuan Lin, Andrew Z Xiao
The advance of iPS technology holds great promise for regenerative medicine. Despite their global similarity to ES cells, fully reprogrammed iPS cells generated by current procedures still display clone-to-clone variations in molecular properties and developmental potentials, which calls for the development of reliable quality control assays. The differences in developmental potentials in iPS cells may be caused by epigenetic variations, such as histone variant H2A.X deposition. In this review, we discuss the current understanding of molecular variations of iPS cells and their implication on quality assessments...
August 17, 2017: Current Opinion in Genetics & Development
Yixuan Wang, Yan Bi, Shaorong Gao
Pluripotent stem cells, having self-renewal capacities and multi-lineage differentiation abilities, offer great potential in disease modeling and therapeutic applications. The successful generation of induced pluripotent stem cells (iPSCs) by the Yamanaka group in 2006 is a milestone event in both reprogramming and stem cell research fields, which makes in vitro somatic cell reprogramming and personalized stem cell therapy feasible. During the past 10 years, several important progresses have been made in uncovering the molecular mechanisms involved in the reprogramming process, which shed light on improving the reprogramming efficiency and iPSC quality...
August 17, 2017: Current Opinion in Genetics & Development
Christen K Mirth, Matthew Dw Piper
The rise in obesity in human populations has reinvigorated research focused on how nutrition impacts life history traits, including body size, lifespan, reproductive success, stress resistance and propensity for disease. Studies have ranged in their approach from identifying the molecular machinery responding to changes in nutrient levels, to understanding the hormonal changes that occur in response to diet, to mapping the response of differing life history traits over complex dietary landscapes. Connecting insights across these approaches presents significant challenges primarily because we lack information about how signalling pathways respond to dietary complexity...
August 17, 2017: Current Opinion in Genetics & Development
Joana Projecto-Garcia, Joseph F Biddle, Erik J Ragsdale
Developmental polyphenism affords a single genotype multiple solutions to match an organism to its environment. Because polyphenism is the extreme example of how development deviates from a linear genetic blueprint, it demands a genetic explanation for how environmental cues shunt development to hypothetically alternative modules. We highlight several recent advances that have begun to illuminate genetic mechanisms for polyphenism and how this recurring developmental novelty may arise. An emerging genetic knowledge of polyphenism is providing precise targets for testing hypotheses of how switch mechanisms are built-out of olfactory, nutrient-sensing, hormone-reception, and developmental and genetic buffering systems-to accommodate plasticity...
August 12, 2017: Current Opinion in Genetics & Development
Nade Abazova, Jeroen Krijgsveld
Stem cells are at the basis of organismal development, characterized by their potential to differentiate towards specific lineages upon receiving proper signals. To understand the molecular principles underlying gain and loss of pluripotency, proteomics plays an increasingly important role owing to technical developments in mass spectrometry and implementation of innovative biochemical approaches. Here we review how quantitative proteomics has been used to investigate protein expression, localization, interaction and modification in stem cells both in vitro and in vivo, thereby complementing other omics approaches to study fundamental properties of stem cell plasticity...
August 11, 2017: Current Opinion in Genetics & Development
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