Hot off the presses! Dec 01 Nat Rev Genet

The Dec 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 11(12):813 (2010)
  
• Genomics: A picture worth 1000 Genomes | PDF (378 KB)
  - Nat Rev Genet 11(12):814 (2010)
  A cast of hundreds, if not quite thousands, of researchers worldwide have published their work on the pilot phase of the 1000 Genomes Project, building directly on the success of previous efforts of the Human Genome Project and the International HapMap Project. The 1000 Genome Project's stated goal is quite specific: “.
• Human disease: Bound to repeat | PDF (242 KB)
  - Nat Rev Genet 11(12):815 (2010)
  A new mechanism for variable penetrance has been uncovered by a study of the genomic binding of ATRX, a SWI/SNF family member that causes a human developmental disorder. This study also suggests intriguing links among non-B DNA structures, histone variant deposition and gene expression.
• Development: Strand-specific satellite expression | PDF (287 KB)
  - Nat Rev Genet 11(12):815 (2010)
  At fertilization, the paternal genome undergoes dramatic changes in its chromatin state, including the de novo establishment of epigenetic marks. By analysing pericentric heterochromatin (as a model for constitutive heterochromatin) in early mouse development, a new study provides insights into the mechanisms by which these changes could occur and how nuclear organization in the zygote is set up.
• Crop genetics: Resequencing sows the seeds | PDF (197 KB)
  - Nat Rev Genet 11(12):816 (2010)
  Next-generation sequencing is rapidly expanding our knowledge of genetic variation in crop plants. Recent resequencing studies in rice and maize illustrate the promise of this new phase of crop genomics to further our understanding of the genetic basis of agronomically important traits.
• Quantitative traits: Variants dragged down by their neighbours | PDF (272 KB)
  - Nat Rev Genet 11(12):816 (2010)
  How does selection shape the genetic variation that influences quantitative traits? Most models assume that selection acts on the specific loci that affect the trait in question. But, according to a recent study in Caenorhabditis elegans, selection at neighbouring loci can also have a crucial role.
• Development: Transposon-derived small RNAs control patterning | PDF (316 KB)
  - Nat Rev Genet 11(12):816 (2010)
  Early embryogenesis requires the precise orchestration of repression and degradation of maternal transcripts with activation of the embryo's genome. A new paper reveals that retrotransposon-derived Piwi-interacting RNAs (piRNAs) are involved in this switch in Drosophila melanogaster.
• Adaptation | Human genomics | Gene expression | Evolution | PDF (156 KB)
  - Nat Rev Genet 11(12):817 (2010)
  Adaptation Selective sweeps and parallel mutation in the adaptive recovery from deleterious mutation in Caenorhabditis elegans Denver, D. R. et al. Genome Res. 29 Oct 2010 (doi:10.
• Molecular evolution: Concealed connections | PDF (184 KB)
  - Nat Rev Genet 11(12):818 (2010)
  Many mutations are neglected by studies of molecular evolution â€" in particular, the non-synonymous protein changes that are not known to have functional or fitness consequences. A systematic study of the functional effects of non-synonymous amino-acid substitutions now suggests that a substantial portion of these variants are involved in hidden epistatic interactions.
• Development | X Inactivation | Microbial genetics | PDF (150 KB)
  - Nat Rev Genet 11(12):818 (2010)
  Development Evolution of the mammalian embryonic pluripotency gene regulatory network Fernandez-Tresguerres, B. et al. Proc. Natl Acad.
• Triggers for genomic rearrangements: insights into genomic, cellular and environmental influences
  - Nat Rev Genet 11(12):819 (2010)
  Genomic rearrangements are associated with many human genomic disorders, including cancers. It was previously thought that most genomic rearrangements formed randomly but emerging data suggest that many are nonrandom, cell type-, cell stage- and locus-specific events. Recent studies have revealed novel cellular mechanisms and environmental cues that influence genomic rearrangements. In this Review, we consider the multitude of influences on genomic rearrangements by grouping these influences into four categories: proximity of chromosomal regions in the nucleus, cellular stress, inappropriate DNA repair or recombination, and DNA sequence and chromatin features. The synergy of these triggers can poise a cell for rearrangements and here we aim to provide a conceptual framework for understanding the genesis of genomic rearrangements.
• Regulation of transcription in plants: mechanisms controlling developmental switches
  - Nat Rev Genet 11(12):830 (2010)
  Unlike animals, plants produce new organs throughout their life cycle using pools of stem cells that are organized in meristems. Although many key regulators of meristem and organ identities have been identified, it is still not well understood how they function at the molecular level and how they can switch an entire developmental programme in which thousands of genes are involved. Recent advances in the genome-wide identification of target genes controlled by key plant transcriptional regulators and their interactions with epigenetic factors provide new insights into general transcriptional regulatory mechanisms that control switches of developmental programmes and cell fates in complex organisms.
• Analysing biological pathways in genome-wide association studies
  - Nat Rev Genet 11(12):843 (2010)
  Genome-wide association (GWA) studies have typically focused on the analysis of single markers, which often lacks the power to uncover the relatively small effect sizes conferred by most genetic variants. Recently, pathway-based approaches have been developed, which use prior biological knowledge on gene function to facilitate more powerful analysis of GWA study data sets. These approaches typically examine whether a group of related genes in the same functional pathway are jointly associated with a trait of interest. Here we review the development of pathway-based approaches for GWA studies, discuss their practical use and caveats, and suggest that pathway-based approaches may also be useful for future GWA studies with sequencing data.
• Phenomics: the next challenge
  - Nat Rev Genet 11(12):855 (2010)
  A key goal of biology is to understand phenotypic characteristics, such as health, disease and evolutionary fitness. Phenotypic variation is produced through a complex web of interactions between genotype and environment, and such a 'genotype–phenotype' map is inaccessible without the detailed phenotypic data that allow these interactions to be studied. Despite this need, our ability to characterize phenomes — the full set of phenotypes of an individual — lags behind our ability to characterize genomes. Phenomics should be recognized and pursued as an independent discipline to enable the development and adoption of high-throughput and high-dimensional phenotyping.
• Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana
  - Nat Rev Genet 11(12):867 (2010)
  A major challenge in evolutionary biology and plant breeding is to identify the genetic basis of complex quantitative traits, including those that contribute to adaptive variation. Here we review the development of new methods and resources to fine-map intraspecific genetic variation that underlies natural phenotypic variation in plants. In particular, the analysis of 107 quantitative traits reported in the first genome-wide association mapping study in Arabidopsis thaliana sets the stage for an exciting time in our understanding of plant adaptation. We also argue for the need to place phenotype–genotype association studies in an ecological context if one is to predict the evolutionary trajectories of plant species.
• Predicting genetic predisposition in humans: the promise of whole-genome markers
  - Nat Rev Genet 11(12):880 (2010)
  Although genome-wide association studies have identified markers that are associated with various human traits and diseases, our ability to predict such phenotypes remains limited. A perhaps overlooked explanation lies in the limitations of the genetic models and statistical techniques commonly used in association studies. We propose that alternative approaches, which are largely borrowed from animal breeding, provide potential for advances. We review selected methods and discuss the challenges and opportunities ahead.
• Mechanisms of trinucleotide repeat instability during human development
  - Nat Rev Genet 11(12):886 (2010)
  In Table 1 in the above article, there was a mistake on the row starting with DM1 (myotonic dystrophy type 1). The 'Repeat number (disease)' column incorrectly stated <50, when it should have stated >50. The author apologizes for the error.