Hot off the presses! Mar 01

The Mar 01 issue of the is now up on Pubget (About ): 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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  - Nature reviews. Genetics 11(3):167 (2010)
  
• Evolution: Illusions of conservation | PDF (193 KB)
  - Nature reviews. Genetics 11(3):169 (2010)
  If a sequence or property appears to be conserved across evolutionary time it is often interpreted as being functionally important. But can apparently conserved patterns be produced by neutral or indirect forces? New simulations of regulatory element evolution show that they can.
• Complex disease: Rare treasures | PDF (151 KB)
  - Nature reviews. Genetics 11(3):170 (2010)
  Rare variants distributed across large genomic regions make a substantial contribution to the genetic basis of complex diseases, according to a simulated genome-wide association (GWA) study that is backed by real disease-mapping data. GWA studies are based on the assumption that complex diseases are caused by many common variants of small effect, and the signals observed in GWA studies are assumed to correspond to common variants.
• Human genomics: Into Africa | PDF (199 KB)
  - Nature reviews. Genetics 11(3):170 (2010)
  The steady increase in the number of individual human genome sequences is providing fine-scale insights into variation in the human genome. These insights inform us about human diversity and have important implications for medical applications of genomics.
• Evo–devo: Nasonia tools up | PDF (183 KB)
  - Nature reviews. Genetics 11(3):170 (2010)
  Evolutionary developmental biology (evoâ€"devo) research has been boosted in recent years by expansion in the range of genetically tractable model organisms that can be manipulated in the laboratory. The publication of the genome sequence of three species of the parasitoid wasp Nasonia â€" accompanied by a clutch of papers that have utilized the sequence data â€" is enabling the development of a sophisticated genetic tool kit for this emerging arthropod model.
• Evolution | Population genetics | Splicing | Genetic variation | PDF (154 KB)
  - Nature reviews. Genetics 11(3):171 (2010)
  Evolution Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content Hughes, J. F. et al. Nature 463, 536â€"539 (2010) The authors report the finished sequence of the male-specific region of the Y chromosome (MSY) in chimpanzees. Comparing the MSY sequence of chimpanzees and humans reveals that far from being an evolutionarily stagnant region of the genome, as previously assumed, the two MSYs have in fact been diverging rapidly over the past 6 million years.
• Small RNAs: An epigenetic silencing influence | PDF (227 KB)
  - Nature reviews. Genetics 11(3):172 (2010)
  MicroRNAs (miRNAs) regulate gene expression by base pairing with target RNAs, leading to their cleavage in plants or translational inhibition in animals. Now evidence has emerged that in moss, miRNAs can also silence gene expression at the transcriptional level by interacting with DNA, leading to methylation.
• Gene networks: Meaningful connections | PDF (360 KB)
  - Nature reviews. Genetics 11(3):172 (2010)
  The magnitude and direction of epistasis and the functional consequences of these geneâ€"gene interactions are fundamental to relating genotype to phenotype and thus for informing fields from human disease to speciation. The detailed analysis of global metabolic and genetic interactions in Escherichia coli and Saccharomyces cerevisiae highlights the potential of such surveys for functionally annotating the genome, and also overturns some widely held assumptions.
• Cellular defence: Human cells clear foreign DNA | PDF (162 KB)
  - Nature reviews. Genetics 11(3):172 (2010)
  Foreign DNA poses a security threat to cells â€" for example, by allowing pathogen proteins to be expressed or by disrupting the genome. A mechanism by which human cells clear foreign DNA has now been identified â€" the first time that a DNA restriction system analogous to that of bacteria has been demonstrated in eukaryotes.
• Genome evolution | Plant genetics | Epigenetics | Evo–devo | PDF (154 KB)
  - Nature reviews. Genetics 11(3):173 (2010)
  Genome evolution Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes Chen, C.-L. et al. Genome Res.
• The molecular evolutionary basis of species formation
  - Nature reviews. Genetics 11(3):175 (2010)
  All plant and animal species arise by speciation — the evolutionary splitting of one species into two reproductively incompatible species. But until recently our understanding of the molecular genetic details of speciation was slow in coming and largely limited to Drosophila species. Here, I review progress in determining the molecular identities and evolutionary histories of several new 'speciation genes' that cause hybrid dysfunction between species of yeast, flies, mice and plants. The new work suggests that, surprisingly, the first steps in the evolution of hybrid dysfunction are not necessarily adaptive.
• CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea
  - Nature reviews. Genetics 11(3):181 (2010)
  Sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. The importance of such pathways is highlighted by the extensive study of RNA interference (RNAi) and related processes in eukaryotes. In many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (CRISPRs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. CRISPR sequences provide an adaptive, heritable record of past infections and express CRISPR RNAs — small RNAs that target invasive nucleic acids. Here, we review the mechanisms of CRISPR interference and its roles in microbial physiology and evolution. We also discuss potential applications of this novel interference pathway.
• Principles and challenges of genome-wide DNA methylation analysis
  - Nature reviews. Genetics 11(3):191 (2010)
  Methylation of cytosine bases in DNA provides a layer of epigenetic control in many eukaryotes that has important implications for normal biology and disease. Therefore, profiling DNA methylation across the genome is vital to understanding the influence of epigenetics. There has been a revolution in DNA methylation analysis technology over the past decade: analyses that previously were restricted to specific loci can now be performed on a genome-scale and entire methylomes can be characterized at single-base-pair resolution. However, there is such a diversity of DNA methylation profiling techniques that it can be challenging to select one. This Review discusses the different approaches and their relative merits and introduces considerations for data analysis.
• Establishing, maintaining and modifying DNA methylation patterns in plants and animals
  - Nature reviews. Genetics 11(3):204 (2010)
  Cytosine DNA methylation is a stable epigenetic mark that is crucial for diverse biological processes, including gene and transposon silencing, imprinting and X chromosome inactivation. Recent findings in plants and animals have greatly increased our understanding of the pathways used to accurately target, maintain and modify patterns of DNA methylation and have revealed unanticipated mechanistic similarities between these organisms. Key roles have emerged for small RNAs, proteins with domains that bind methylated DNA and DNA glycosylases in these processes. Drawing on insights from both plants and animals should deepen our understanding of the regulation and biological significance of DNA methylation.
• Mammalian recombination hot spots: properties, control and evolution
  - Nature reviews. Genetics 11(3):221 (2010)
  Recombination, together with mutation, generates the raw material of evolution, is essential for reproduction and lies at the heart of all genetic analysis. Recent advances in our ability to construct genome-scale, high-resolution recombination maps and new molecular techniques for analysing recombination products have substantially furthered our understanding of this important biological phenomenon in humans and mice: from describing the properties of recombination hot spots in male and female meiosis to the recombination landscape along chromosomes. This progress has been accompanied by the identification of trans-acting systems that regulate the location and relative activity of individual hot spots.
• Correspondence: Inbreeding effects in the epigenetic era
  - Nature reviews. Genetics 11(3):234 (2010)
  Recent articles by Charlesworth and Willis (The genetics of inbreeding depression. Nature Rev.