Thursday, March 3, 2011

Hot off the presses! Mar 01 TRENDS GENET

The Mar 01 issue of the TRENDS GENET is now up on Pubget (About TRENDS GENET): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

  • Editorial Board
    - TRENDS GENET 27(3):i (2011)
  • Unisexual reproduction among vertebrates
    - TRENDS GENET 27(3):81-88 (2011)
    The past decade has seen a remarkable revision of perspectives on unisexual reproduction in vertebrates. One can no longer view it as a rare curiosity far outside the mainstream of evolution. More than 80 taxa of fish, amphibians, and reptiles are now known to reproduce by parthenogenesis (Greek for 'virgin birth') or its variants, and they persist in nature as all-female lineages. Other lower vertebrates that ordinarily rely on sexual reproduction can resort to facultative parthenogenesis under extenuating circumstances that isolate females from males. Molecular tools have now been applied to the study of unisexual organisms, and fascinating insights have emerged regarding the molecular mechanisms that preserve heterozygosity and increase genetic diversity in all-female populations. A deeper understanding of the underlying genetics increasingly calls into question the assumption that unisexuality in vertebrates is an evolutionary dead-end.
  • Understanding splicing regulation through RNA splicing maps
    - TRENDS GENET 27(3):89-97 (2011)
    Alternative splicing is a highly regulated process that greatly increases the proteome diversity and plays an important role in cellular differentiation and disease. Interactions between RNA-binding proteins (RBPs) and pre-mRNA are the principle regulator of splicing decisions. Findings from recent genome-wide studies of protein–RNA interactions have been combined with assays of the global effects of RBPs on splicing to create RNA splicing maps. These maps integrate information from all pre-mRNAs regulated by single RBPs to identify the global positioning principles guiding splicing regulation. Recent studies using this approach have identified a set of positional principles that are shared between diverse RBPs. Here, we discuss how insights from RNA splicing maps of different RBPs inform the mechanistic models of splicing regulation.
  • Population genetics of genomics-based crop improvement methods
    - TRENDS GENET 27(3):98-106 (2011)
    Many genome-wide association studies (GWAS) in humans are concluding that, even with very large sample sizes and high marker densities, most of the genetic basis of complex traits may remain unexplained. At the same time, recent research in plant GWAS is showing much greater success with fewer resources. Both GWAS and genomic selection (GS), a method for predicting phenotypes by the use of genome-wide marker data, are receiving considerable attention among plant breeders. In this review we explore how differences in population genetic histories, as well as past selection for traits of interest, have produced trait architectures and patterns of linkage disequilibrium (LD) that frequently differ dramatically between domesticated plants and humans, making detection of quantitative trait loci (QTL) effects in crops more rewarding and less costly than in humans.
  • Gene–environment interactions in human disease: nuisance or opportunity?
    - TRENDS GENET 27(3):107-115 (2011)
    Many environmental risk factors for common, complex human diseases have been revealed by epidemiologic studies, but how genotypes at specific loci modulate individual responses to environmental risk factors is largely unknown. Gene–environment interactions will be missed in genome-wide association studies and could account for some of the 'missing heritability' for these diseases. In this review, we focus on asthma as a model disease for studying gene–environment interactions because of relatively large numbers of candidate gene–environment interactions with asthma risk in the literature. Identifying these interactions using genome-wide approaches poses formidable methodological problems, and elucidating molecular mechanisms for these interactions has been challenging. We suggest that studying gene–environment interactions in animal models, although more tractable, might not be sufficient to shed light on the genetic architecture of human diseases. Lastly, ! we propose avenues for future studies to find gene–environment interactions.
  • A twin approach to unraveling epigenetics
    - TRENDS GENET 27(3):116-125 (2011)
    The regulation of gene expression plays a pivotal role in complex phenotypes, and epigenetic mechanisms such as DNA methylation are essential to this process. The availability of next-generation sequencing technologies allows us to study epigenetic variation at an unprecedented level of resolution. Even so, our understanding of the underlying sources of epigenetic variability remains limited. Twin studies have played an essential role in estimating phenotypic heritability, and these now offer an opportunity to study epigenetic variation as a dynamic quantitative trait. High monozygotic twin discordance rates for common diseases suggest that unexplained environmental or epigenetic factors could be involved. Recent genome-wide epigenetic studies in disease-discordant monozygotic twins emphasize the power of this design to successfully identify epigenetic changes associated with complex traits. We describe how large-scale epigenetic studies of twins can improve our unders! tanding of how genetic, environmental and stochastic factors impact upon epigenetics, and how such studies can provide a comprehensive understanding of how epigenetic variation affects complex traits.

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