Hot off the presses! Feb 01 Nat Rev Genet

The Feb 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(2):75 (2011)
  
• Development: Hourglass theory gets molecular approval | PDF (479 KB)
  - Nat Rev Genet 12(2):76 (2011)
  It was first observed two centuries ago that many animal embryos converge on a similar form during development, only to diverge afterwards. This temporal 'waist' in the so-called hourglass model of embryonic development is known as the 'phylotypic stage', and it is thought — controversially, given that it is based on subjective morphological comparisons — to represent an evolutionary conserved period.
• Genomics: No half measures for haplotypes | PDF (174 KB)
  - Nat Rev Genet 12(2):77 (2011)
  Individual human genomes are coming thick and fast, but they lack information on the combination of alleles along single chromosomes — the haplotype. Although common haplotypes can be identified using statistical and family-based approaches, direct methods for readily determining individual haplotypes would be extremely valuable for many areas of research, from population genetics to pharmacogenomics.
• Translational control | Evolution | Transcription | Disease genomics | PDF (119 KB)
  - Nat Rev Genet 12(2):77 (2011)
  A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress Chan, C. T. Y.et al. PLoS Genet. 6, e1001247 (2010)
• Human Disease: Next-generation sequencing of the next generation | PDF (211 KB)
  - Nat Rev Genet 12(2):78 (2011)
  There is great clinical demand for disease screening in utero using non-invasive techniques. A new study demonstrates the feasibility of genome-wide fetal genotyping using next-generation sequencing of the mother's blood.
• Evolution: How networks get new layers | PDF (205 KB)
  - Nat Rev Genet 12(2):78 (2011)
  A study in yeast provides the first explicit evidence for a possibly widespread mode of evolution in transcriptional regulatory networks — the insertion of new layers of control between existing regulatory relationships.In the yeasts Saccharomyces cerevisiae, Candida albicans and Kluyveromyces lactis, mating requires a set of haploid-specific genes (HSGs) that are regulated by the transcription factor a1–α2 (a heterodimer composed of two homeodomain proteins).
• Splicing | Evolution | Chromatin | PDF (120 KB)
  - Nat Rev Genet 12(2):78 (2011)
  Noisy splicing drives mRNA isoform diversity in human cells Pickrell, J. K.et al. PLoS Genet. 6, e1001236 (2010)
• Evolution: Young genes are essential too | PDF (158 KB)
  - Nat Rev Genet 12(2):79 (2011)
  The traditional wisdom in evolutionary genetics is that essential genes are usually the older ones that have been maintained over long evolutionary time frames. Two studies of young genes in species of Drosophila reveal that in fact essential genes are just as likely to be young, and that new genes can quickly integrate themselves into key pathways to take on essential roles.
• Epigenetics: Dad's diet lives on | PDF (120 KB)
  - Nat Rev Genet 12(2):80 (2011)
  Two recent studies in rodents show that unhealthy paternal diets can reprogramme gene expression in offspring, implicating epigenetics in these transgenerational effects.Ng and colleagues fed male rats a high-fat diet and looked for effects in their adult female offspring, which were fed a normal diet.
• Functional genomics: The modENCODE guide to the genome | PDF (214 KB)
  - Nat Rev Genet 12(2):80 (2011)
  Now that obtaining genome sequence is routine, assigning function is the current frontier. Vast data sets that are now available for the Caenorhabditis elegans and Drosophila melanogaster genomes — and which are described in a raft of new papers — show that large-scale collaborative efforts offer a way forward.
• Elucidating the inosinome: global approaches to adenosine-to-inosine RNA editing
  - Nat Rev Genet 12(2):81 (2011)
  Catalysed by members of the adenosine deaminase acting on RNA (ADAR) family of enzymes, adenosine-to-inosine (A-to-I) editing converts adenosines in RNA molecules to inosines, which are functionally equivalent to guanosines. Recently, global approaches to studying this widely conserved phenomenon have emerged. The use of bioinformatics, high-throughput sequencing and other approaches has increased the number of known editing sites by several orders of magnitude, and we now have a greater understanding of the control and the biological significance of editing. This Progress article reviews some of these recent global studies and their results.
• RNA sequencing: advances, challenges and opportunities
  - Nat Rev Genet 12(2):87 (2011)
  In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes. Recently, several developments in RNA-seq methods have provided an even more complete characterization of RNA transcripts. These developments include improvements in transcription start site mapping, strand-specific measurements, gene fusion detection, small RNA characterization and detection of alternative splicing events. Ongoing developments promise further advances in the application of RNA-seq, particularly direct RNA sequencing and approaches that allow RNA quantification from very small amounts of cellular materials.
• Gene silencing by microRNAs: contributions of translational repression and mRNA decay
  - Nat Rev Genet 12(2):99 (2011)
  Despite their widespread roles as regulators of gene expression, important questions remain about target regulation by microRNAs. Animal microRNAs were originally thought to repress target translation, with little or no influence on mRNA abundance, whereas the reverse was thought to be true in plants. Now, however, it is clear that microRNAs can induce mRNA degradation in animals and, conversely, translational repression in plants. Recent studies have made important advances in elucidating the relative contributions of these two different modes of target regulation by microRNAs. They have also shed light on the specific mechanisms of target silencing, which, although it differs fundamentally between plants and animals, shares some common features between the two kingdoms.
• Forest tree genomics: growing resources and applications
  - Nat Rev Genet 12(2):111 (2011)
  Over the past two decades, research in forest tree genomics has lagged behind that of model and agricultural systems. However, genomic research in forest trees is poised to enter into an important and productive phase owing to the advent of next-generation sequencing technologies, the enormous genetic diversity in forest trees and the need to mitigate the effects of climate change. Research on long-lived woody perennials is extending our molecular knowledge of complex life histories and adaptations to the environment — enriching a field that has traditionally drawn biological inference from a few short-lived herbaceous species.
• Silencing chromatin: comparing modes and mechanisms
  - Nat Rev Genet 12(2):123 (2011)
  Recent transcriptome analyses show that substantial proportions of eukaryotic genomes can be copied into RNAs, many of which do not encode protein sequences. However, cells have developed mechanisms to control and counteract the high transcriptional activity of RNA polymerases in order to achieve cell-specific gene activity or to prevent the expression of deleterious sequences. Here we compare how two silencing modes — the Polycomb system and heterochromatin — are targeted, established and maintained at different chromosomal locations and how DNA-binding proteins and non-coding RNAs connect these epigenetically stable and heritable structures to the sequence information of the DNA.
• Non-coding RNAs as regulators of embryogenesis
  - Nat Rev Genet 12(2):136 (2011)
  Non-coding RNAs (ncRNAs) are emerging as key regulators of embryogenesis. They control embryonic gene expression by several means, ranging from microRNA-induced degradation of mRNAs to long ncRNA-mediated modification of chromatin. Many aspects of embryogenesis seem to be controlled by ncRNAs, including the maternal–zygotic transition, the maintenance of pluripotency, the patterning of the body axes, the specification and differentiation of cell types and the morphogenesis of organs. Drawing from several animal model systems, we describe two emerging themes for ncRNA function: promoting developmental transitions and maintaining developmental states. These examples also highlight the roles of ncRNAs in ensuring a robust commitment to one of two possible cell fates.
• Triggers for genomic rearrangements: insights into genomic, cellular and environmental influences
  - Nat Rev Genet 12(2):150 (2011)
  Nature Reviews Genetics 11, 819–829 Figures 3 and 4 of the above article incorrectly showed 'microhomology-mediated break-induced repair' as a type of 'homology-directed repair'. This has been removed from both figures. In figure 3, 'microhomology-mediated break-induced replication' has been inserted under 'paused replication fork' followed by 'collapsed replication fork'. The corrected figures are available at http://www.nature.com/nrg/journal/v11/n12/full/nrg2883.html. In the first sentence of the 'Allelic and non-allelic homologous recombination' subsection (p824), gene conversion was incorrectly defined as a name for homologous recombination. This statement has been removed in the corrected version. The revised sentence reads: "Homologous recombination is a DNA double-strand break repair mechanism in which information from a template sequence is used to repair the damage." In the 'Allelic and non-allelic homologous recombination' subsection (p824–p826) and in figure 3, 'homologous recombination' was stated when the authors were specifically referring to allelic homologous recombination. 'Allelic' has been inserted into figure 3 (see link above) and these sentences: "Because allelic homologous recombination does not lead to rearrangements, it could be speculated that such a switch would not increase this form of genomic instability." "Allelic homologous recombination can be completed by synthesis-dependent strand annealing (SDSA) or double-strand break repair (DSBR) pathways." "Defects in the allelic homologous recombination pathway could result in non-allelic homologous recombination (NAHR), in which non-allelic sequences that share sequence similarity are used for repair." The authors apologize for these errors.