Wednesday, January 26, 2011

Hot off the presses! Feb 01 TRENDS GENET

The Feb 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(2):i (2011)
  • Disclosure of individual genetic data to research participants: the debate reconsidered
    - TRENDS GENET 27(2):41-47 (2011)
    Despite extensive debate, there is no consensus on whether individual genetic data should be disclosed to research participants. The emergence of whole-genome sequencing methods is increasingly generating unequalled amounts of genetic data, making the need for a clear feedback policy even more urgent. In this debate two positions can be broadly discerned: a restrictive disclosure policy ('no feedback except life-saving data') and an intermediate policy of qualified disclosure ('feedback if the results meet certain conditions'). We explain both positions and present the principal underlying arguments. We suggest that the debate should no longer address whether genetic research results should be returned, but instead how best to make an appropriate selection and how to strike a balance between the possible benefits of disclosure and the harms of unduly hindering biomedical research.
  • The cooperative amoeba: Dictyostelium as a model for social evolution
    - TRENDS GENET 27(2):48-54 (2011)
    Social interactions, including cooperation and altruism, are characteristic of numerous species, but many aspects of the evolution, ecology and genetics of social behavior remain unclear. The microbial soil amoeba Dictyostelium discoideum is a model system for the study of social evolution and provides insights into the nature of social cooperation and its genetic basis. This species exhibits altruism during both asexual and sexual cycles of its life history, and recent studies have uncovered several possible genetic mechanisms associated with kin discrimination and cheating behavior during asexual fruiting-body formation. By contrast, the molecular and evolutionary mechanisms that underlie sexual macrocyst formation remain largely enigmatic. D. discoideum, given its utility in molecular genetic studies, should continue to help us address these and other relevant questions in sociobiology, and thereby contribute to a coherent theoretical framework for the nature of soc! ial cooperation.
  • Understanding gene circuits at cell-fate branch points for rational cell reprogramming
    - TRENDS GENET 27(2):55-62 (2011)
    Cell-type reprogramming, the artificial induction of a switch of cell lineage and developmental stage, holds great promise for regenerative medicine. However, how does the metazoan body itself 'program' the various cell lineages in the first place? Knowledge of how multipotent cells make cell-fate decisions and commit to a particular lineage is crucial for a rational reprogramming strategy and to avoid trial-and-error approaches in choosing the appropriate set of transcription factors to use. In the past few years, a general principle has emerged in which small gene circuits of cross-inhibition and self-activation govern the decision at branch points of cell development. A formal theoretical treatment of such circuits that deal with their dynamics on the 'epigenetic landscape' could offer some guidance to find the optimal way of cell reprogramming.
  • Genome organization influences partner selection for chromosomal rearrangements
    - TRENDS GENET 27(2):63-71 (2011)
    Chromosomal rearrangements occur as a consequence of the erroneous repair of DNA double-stranded breaks, and often underlie disease. The recurrent detection of specific tumorigenic rearrangements suggests that there is a mechanism behind chromosomal partner selection involving the shape of the genome. With the advent of novel high-throughput approaches, detailed genome integrity and folding maps are becoming available. Integrating these data with knowledge of experimentally induced DNA recombination strongly suggests that partner choice in chromosomal rearrangement primarily follows the three-dimensional conformation of the genome. Local rearrangements are favored over distal and interchromosomal rearrangements. This is seen for neutral rearrangements, but not necessarily for rearrangements that drive oncogenesis. The recurrent detection of tumorigenic rearrangements probably reflects their exceptional capacity to confer growth advantage to the rare cells that contain ! them. The abundant presence of neutral rearrangements suggests that somatic genome variation is also common in healthy tissue.
  • The study of eQTL variations by RNA-seq: from SNPs to phenotypes
    - TRENDS GENET 27(2):72-79 (2011)
    Common DNA variants alter the expression levels and patterns of many human genes. Loci responsible for this genetic control are known as expression quantitative trait loci (eQTLs). The resulting variation of gene expression across individuals has been postulated to be a determinant of phenotypic variation and susceptibility to complex disease. In the past, the application of expression microarray and genetic variation data to study populations enabled the rapid identification of eQTLs in model organisms and humans. Now, a new technology promises to revolutionize the field. Massively parallel RNA sequencing (RNA-seq) provides unprecedented resolution, allowing us to accurately monitor not only the expression output of each genomic locus but also reconstruct and quantify alternatively spliced transcripts. RNA-seq also provides new insights into the regulatory mechanisms underlying eQTLs. Here, we discuss the major advances introduced by RNA-seq and summarize current prog! ress towards understanding the role of eQTLs in determining human phenotypic diversity.

No comments: