Hot off the presses! Sep 01 Nat Rev Genet

The Sep 01 issue of the Nat Rev Genet is now up on Pubget (About Nat Rev 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:

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  - Nat Rev Genet 12(9):583 (2011)
  
• Human genetics: Recombination diversified
  - Nat Rev Genet 12(9):585 (2011)
  Studies of genome-wide patterns of human recombination have so far been limited to a small number of populations. Two new studies — one in African Americans and the other in African Americans and African Caribbeans — highlight recombination differences between human populations and hint at their molecular genetic basis.
• Systems biology: Plant networks
  - Nat Rev Genet 12(9):586 (2011)
  A network of ~6,000 binary protein–protein interactions in Arabidopsis thaliana has been generated by testing all pairwise combinations of ~8,000 plant proteins using yeast two-hybrid methodology. This map should aid characterization of some of the many genes with unknown function in this model plant and should provide insights into network evolution.
• Technology: Getting Moore from DNA sequencing
  - Nat Rev Genet 12(9):586 (2011)
  The rapid drop in cost and increase in scale of DNA sequencing is often compared to the trend seen in the semiconductor industry in the second half of the twentieth century, which was described by Moore's law. Aptly, the aim to continue this progress in DNA sequencing is likely to be advanced by a technology based on semiconductors.
• Evo-devo: Hidden rewiring comes to light
  - Nat Rev Genet 12(9):586 (2011)
  'Developmental systems drift' is the theory that, despite the strong conservation of developmental processes across species at the tissue level, the underlying molecular mechanisms may be diverse. New work in two nematode worm species reveals that the molecular rewiring that has taken place to give the same phenotype by different means has occurred at a surprisingly fine level: through the evolution of novel protein-binding motifs.
• Development | Translational genetics | Epigenetics | Comparative genomics
  - Nat Rev Genet 12(9):587 (2011)
  DMRT1 prevents female reprogramming in the postnatal mammalian testis Matson, C. K.et al. Nature 476, 101–104 (2011)
• Human disease: A short story of breast cancer risk
  - Nat Rev Genet 12(9):588 (2011)
  A study of blood cells shows that patients with familial breast cancer have shorter telomeres than those found in the general population, and that progressive telomere shortening across generations might explain the genetic anticipation that is seen in families with hereditary breast cancer.
• Technology | Epigenetics | Gene regulation | Stem cells
  - Nat Rev Genet 12(9):588 (2011)
  Tracking genome engineering outcome at individual DNA breakpoints Certo, M. T.et al. Nature Methods 8, 671–676 (2011)
• Ethics watch: The G.I. genome: ethical implications of genome sequencing in the military
  - Nat Rev Genet 12(9):589 (2011)
  The JASON Defense Advisory Panel (JASON), an independent group of scientific advisers to the US Department of Defense (DoD), recently published a report that highlighted the increased sophistication and cost-effectiveness of genome-sequencing technologies and recommended the creation of the necessary infrastructure to perform genetic research on military personnel1. This report is the latest evidence of the DoD's increased interest in the use of genome-sequencing technologies to improve the health and effectiveness of the armed forces; in addition to collecting DNA samples for the identification of remains, the military performs genetic testing for sickle cell anaemia and glucose 6-phosphate dehydrogenase (G6PD) in order to protect at-risk individuals from specific environments or occupations that may trigger adverse effects2.
• Systems-biology approaches for predicting genomic evolution
  - Nat Rev Genet 12(9):591 (2011)
  Is evolution predictable at the molecular level? The ambitious goal to answer this question requires an understanding of the mutational effects that govern the complex relationship between genotype and phenotype. In practice, it involves integrating systems-biology modelling, microbial laboratory evolution experiments and large-scale mutational analyses — a feat that is made possible by the recent availability of the necessary computational tools and experimental techniques. This Review investigates recent progresses in mapping evolutionary trajectories and discusses the degree to which these predictions are realistic.
• Learning about human population history from ancient and modern genomes
  - Nat Rev Genet 12(9):603 (2011)
  Genome-wide data, both from SNP arrays and from complete genome sequencing, are becoming increasingly abundant and are now even available from extinct hominins. These data are providing new insights into population history; in particular, when combined with model-based analytical approaches, genome-wide data allow direct testing of hypotheses about population history. For example, genome-wide data from both contemporary populations and extinct hominins strongly support a single dispersal of modern humans from Africa, followed by two archaic admixture events: one with Neanderthals somewhere outside Africa and a second with Denisovans that (so far) has only been detected in New Guinea. These new developments promise to reveal new stories about human population history, without having to resort to storytelling.
• Dynamic interactions between transposable elements and their hosts
  - Nat Rev Genet 12(9):615 (2011)
  Transposable elements (TEs) have a unique ability to mobilize to new genomic locations, and the major advance of second-generation DNA sequencing has provided insights into the dynamic relationship between TEs and their hosts. It now is clear that TEs have adopted diverse strategies — such as specific integration sites or patterns of activity — to thrive in host environments that are replete with mechanisms, such as small RNAs or epigenetic marks, that combat TE amplification. Emerging evidence suggests that TE mobilization might sometimes benefit host genomes by enhancing genetic diversity, although TEs are also implicated in diseases such as cancer. Here, we discuss recent findings about how, where and when TEs insert in diverse organisms.
• Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data
  - Nat Rev Genet 12(9):628 (2011)
  Genome and exome sequencing yield extensive catalogues of human genetic variation. However, pinpointing the few phenotypically causal variants among the many variants present in human genomes remains a major challenge, particularly for rare and complex traits wherein genetic information alone is often insufficient. Here, we review approaches to estimate the deleteriousness of single nucleotide variants (SNVs), which can be used to prioritize disease-causal variants. We describe recent advances in comparative and functional genomics that enable systematic annotation of both coding and non-coding variants. Application and optimization of these methods will be essential to find the genetic answers that sequencing promises to hide in plain sight.
• Understanding the transcriptome through RNA structure
  - Nat Rev Genet 12(9):641 (2011)
  RNA structure is crucial for gene regulation and function. In the past, transcriptomes have largely been parsed by primary sequences and expression levels, but it is now becoming feasible to annotate and compare transcriptomes based on RNA structure. In addition to computational prediction methods, the recent advent of experimental techniques to probe RNA structure by high-throughput sequencing has enabled genome-wide measurements of RNA structure and has provided the first picture of the structural organization of a eukaryotic transcriptome — the 'RNA structurome'. With additional advances in method refinement and interpretation, structural views of the transcriptome should help to identify and validate regulatory RNA motifs that are involved in diverse cellular processes and thereby increase understanding of RNA function.
• Advances in prenatal screening: the ethical dimension
  - Nat Rev Genet 12(9):657 (2011)
  Prenatal screening strategies are undergoing rapid changes owing to the introduction of new testing techniques. The overall tendency is towards broadening the scope of prenatal testing through increasingly sensitive ultrasound scans and genome-wide molecular tests. In addition, non-invasive prenatal diagnosis is likely to be introduced in the near future. These developments raise important ethical questions concerning meaningful reproductive choice, the autonomy rights of future children, equity of access and the proportionality of testing.
• Correspondence: Adaptation due to symbionts and conflicts between heritable agents of biological information
  - Nat Rev Genet 12(9):663 (2011)
  Calls for an extended evolutionary synthesis are flourishing in the scientific literature (as highlighted by a recent Review article in this journal (Beyond DNA: integrating exclusive inheritance into an extended theory of evolution. Nature Reviews Genetics 12, 475–486 (2011)1) and Refs 2, 3), so the identification of the necessary 'extensions' has become a crucial goal to many evolutionary biologists.
• Genomic imprinting: the emergence of an epigenetic paradigm
  - Nat Rev Genet 12(9):663 (2011)
  In figure 1Aa of the above article, the imprinting control region (ICR) on the paternal allele of the Airn gene was incorrectly shown as methylated (indicated by a dark grey octagon). This ICR should be shown as unmethylated (indicated by a white octagon). The corrected article is available at: http://www.nature.com/nrg/journal/v12/n8/full/nrg3032.html. The editors apologize for this error.