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:

• From the editors
  - Nat Rev Genet 10(9):587 (2009)
  
• Evolution: Partial penetrance keeps the options open
  - Nat Rev Genet 10(9):589 (2009)
  
• Stem cells: The highs and lows of pluripotency
  - Nat Rev Genet 10(9):590 (2009)
  
• Genome engineering: Breakneck evolution
  - Nat Rev Genet 10(9):590 (2009)
  
• Development: Polymerase stalling gets genes in sync
  - Nat Rev Genet 10(9):590 (2009)
  
• Disease therapy: A disruptive treatment
  - Nat Rev Genet 10(9):591 (2009)
  
• Genome stability: Pathways to integrity
  - Nat Rev Genet 10(9):592 (2009)
  
• Plant genetics: Exploring the maize of genetic variation
  - Nat Rev Genet 10(9):592 (2009)
  
• In brief: Model organisms, Complex disease, Mobile elements, Evolution
  - Nat Rev Genet 10(9):593 (2009)
  
• Technology: ADAM and evolution
  - Nat Rev Genet 10(9):594 (2009)
  
• In brief: Transcription, Evolution, Genome organization, Gene regulation
  - Nat Rev Genet 10(9):594 (2009)
  
• Genetics of human gene expression: mapping DNA variants that influence gene expression
  Cheung VG Spielman RS - Nat Rev Genet 10(9):595-604 (2009)
  There is extensive natural variation in human gene expression. As quantitative phenotypes, expression levels of genes are heritable. Genetic linkage and association mapping have identified cis- and trans-acting DNA variants that influence expression levels of human genes. New insights into human gene regulation are emerging from genetic analyses of gene expression in cells at rest and following exposure to stimuli. The integration of these genetic mapping results with data from co-expression networks is leading to a better understanding of how expression levels of individual genes are regulated and how genes interact with each other. These findings are important for basic understanding of gene regulation and of diseases that result from disruption of normal gene regulation.
• Insights from genomic profiling of transcription factors
  - Nat Rev Genet 10(9):605-616 (2009)
  A crucial question in the field of gene regulation is whether the location at which a transcription factor binds influences its effectiveness or the mechanism by which it regulates transcription. Comprehensive transcription factor binding maps are needed to address these issues, and genome-wide mapping is now possible thanks to the technological advances of ChIP–chip and ChIP–seq. This Review discusses how recent genomic profiling of transcription factors gives insight into how binding specificity is achieved and what features of chromatin influence the ability of transcription factors to interact with the genome. It also suggests future experiments that may further our understanding of the causes and consequences of transcription factor–genome interactions.
• Applying mass spectrometry-based proteomics to genetics, genomics and network biology
  - Nat Rev Genet 10(9):617-627 (2009)
  The systematic and quantitative molecular analysis of mutant organisms that has been pioneered by studies on mutant metabolomes and transcriptomes holds great promise for improving our understanding of how phenotypes emerge. Unfortunately, owing to the limitations of classical biochemical analysis, proteins have previously been excluded from such studies. Here we review how technical advances in mass spectrometry-based proteomics can be applied to measure changes in protein abundance, posttranslational modifications and protein–protein interactions in mutants at the scale of the proteome. We finally discuss examples that integrate proteomics data with genomic and phenomic information to build network-centred models, which provide a promising route for understanding how phenotypes emerge.
• Microfluidic devices for measuring gene network dynamics in single cells
  - Nat Rev Genet 10(9):628-638 (2009)
  The dynamics governing gene regulation have an important role in determining the phenotype of a cell or organism. From processing extracellular signals to generating internal rhythms, gene networks are central to many time-dependent cellular processes. Recent technological advances now make it possible to track the dynamics of gene networks in single cells under various environmental conditions using microfluidic 'lab-on-a-chip' devices, and researchers are using these new techniques to analyse cellular dynamics and discover regulatory mechanisms. These technologies are expected to yield novel insights and allow the construction of mathematical models that more accurately describe the complex dynamics of gene regulation.
• Genetics in geographically structured populations: defining, estimating and interpreting FST
  - Nat Rev Genet 10(9):639-650 (2009)
  Wright's F-statistics, and especially FST, provide important insights into the evolutionary processes that influence the structure of genetic variation within and among populations, and they are among the most widely used descriptive statistics in population and evolutionary genetics. Estimates of FST can identify regions of the genome that have been the target of selection, and comparisons of FST from different parts of the genome can provide insights into the demographic history of populations. For these reasons and others, FST has a central role in population and evolutionary genetics and has wide applications in fields that range from disease association mapping to forensic science. This Review clarifies how FST is defined, how it should be estimated, how it is related to similar statistics and how estimates of FST should be interpreted.
• Systems genetics analysis of cancer susceptibility: from mouse models to humans
  Quigley D Balmain A - Nat Rev Genet 10(9):651-657 (2009)
  Genetic studies of cancer susceptibility have shown that most heritable risk cannot be explained by the main effects of common alleles. This may be due to unknown gene–gene or gene–environment interactions and the complex roles of many genes at different stages of cancer. Studies using mouse models of cancer suggest that methods that integrate genetic analysis and genomic networks with knowledge of cancer biology can help to extend our understanding of heritable cancer susceptibility.
• Erratum: Mitochondrial and plastid evolution in eukaryotes: an outsiders' perspective
  - Nat Rev Genet 10(9):657 (2009)
  On page 499 of the above article, an error was introduced into the section entitled "Reprogramming the IM permeome." The sentence in the published version that reads "These data show a major transition in organellogenesis that occurred when the hosts replaced all previous IM solute transporters of the endosymbionts with eukaryote-derived nuclearencoded solute carriers" should refer to the replacement of "most previous IM solute transporters". The editors apologize for the error.