Hot off the presses! Apr 01 Nat Rev Genet

The Apr 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:

• 
  - Nat Rev Genet 12(4):225 (2011)
  
• 
  - Nat Rev Genet 12(4):226 (2011)
  
• Evolution: Two-step adaptation | PDF (6,392 KB)
  - Nat Rev Genet 12(4):227 (2011)
  A study of how the sequence of the human influenza A virus has evolved over the past 40 years could help efforts to construct effective flu vaccines and drugs by improving predictions of which new mutations will arise and spread.The sequences encoding the surface proteins haemagglutinin (HA) and neuraminidase (NA) — which determine whether a virus can enter and exit human cells — are the most rapidly evolving portions of the viral genome.
• Small RNAs: Recycling for silencing | PDF (113 KB)
  - Nat Rev Genet 12(4):227 (2011)
  A relatively underexplored aspect of microRNAs (miRNAs) is what happens to them after regulation of their target. A recent study provides insights into how often miRNAs are 'reused' and how target regulation influences their decay.
• Human evolution: Sweep model is swept away | PDF (121 KB)
  - Nat Rev Genet 12(4):228 (2011)
  Efforts to identify the genetic basis of human-specific adaptations have mainly looked for evidence of classic selective sweeps, which happen when a new, advantageous mutation is rapidly fixed in a population. However, a new study suggests that classic selective sweeps have been rare in our recent evolution.
• Biotechnology: Seeds of no change | PDF (167 KB)
  - Nat Rev Genet 12(4):228 (2011)
  Apomixis — the development of an embryo in the absence of meiosis and fertilization — occurs naturally in some wild species of plant but has been difficult to engineer in major crop species, in which it would be the ideal way to conserve the traits of superior hybrid genotypes. Two new studies describe promising routes to achieving apomixis in Arabidopsis thaliana and maize, respectively, by using genetic mutants.
• Development | Gene networks | Stem cells | Evolution | PDF (86 KB)
  - Nat Rev Genet 12(4):228 (2011)
  Dynamics of Dpp signaling and proliferation control Wartlick, O.et al. Science 331, 1154–1159 (2011)A new mechanism is proposed to explain how tissue growth can occur uniformly in response to a morphogen concentration gradient.
• Development | Chromatin | Gene regulation | Mutagenesis | PDF (88 KB)
  - Nat Rev Genet 12(4):229 (2011)
  Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-Seq Lott, S. E.et al. PLoS Biol. 9, e1000590 (2011)
• Development: Budding potential | PDF (152 KB)
  - Nat Rev Genet 12(4):230 (2011)
  Developmental biology is moving towards systems approaches, which seek to build comprehensive and quantitative models of how tissues form. These approaches require integrated means of viewing cell movement and mixing during organogenesis, and this paper provides one such tool: a novel two-dimensional model of mouse limb bud growth that can chart cell movements and patterns of regulatory gene expression in time and space.
• 
  - Nat Rev Genet 12(4):230 (2011)
  
• Methods for making induced pluripotent stem cells: reprogramming à la carte
  - Nat Rev Genet 12(4):231 (2011)
  Pluripotent stem-cell lines can be obtained through the reprogramming of somatic cells from different tissues and species by ectopic expression of defined factors. In theory, these cells — known as induced pluripotent stem cells (iPSCs) — are suitable for various purposes, including disease modelling, autologous cell therapy, drug or toxicity screening and basic research. Recent methodological improvements are increasing the ease and efficiency of reprogramming, and reducing the genomic modifications required to complete the process. However, depending on the downstream applications, certain technologies have advantages over others. Here, we provide a comprehensive overview of the existing reprogramming approaches with the aim of providing readers with a better understanding of the reprogramming process and a basis for selecting the most suitable method for basic or clinical applications.
• From expression QTLs to personalized transcriptomics
  - Nat Rev Genet 12(4):277 (2011)
  Approaches that combine expression quantitative trait loci (eQTLs) and genome-wide association (GWA) studies are offering new functional information about the aetiology of complex human traits and diseases. Improved study designs — which take into account technological advances in resolving the transcriptome, cell history and state, population of origin and diverse endophenotypes — are providing insights into the architecture of disease and the landscape of gene regulation in humans. Furthermore, these advances are helping to establish links between cellular effects and organismal traits.
• Enhancer function: new insights into the regulation of tissue-specific gene expression
  - Nat Rev Genet 12(4):283 (2011)
  Enhancer function underlies regulatory processes by which cells establish patterns of gene expression. Recent results suggest that many enhancers are specified by particular chromatin marks in pluripotent cells, which may be modified later in development to alter patterns of gene expression and cell differentiation choices. These marks may contribute to the repertoire of epigenetic mechanisms responsible for cellular memory and determine the timing of transcription factor accessibility to the enhancer. Mechanistically, cohesin and non-coding RNAs are emerging as crucial players responsible for facilitating enhancer–promoter interactions at some genes. Surprisingly, these interactions may be required not only to facilitate initiation of transcription but also to activate the release of RNA polymerase II (RNAPII) from promoter-proximal pausing.