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 12(12):803 (2011)
  
• Regulatory RNA: Layer by layer | PDF (608 KB)
  - Nat Rev Genet 12(12):804 (2011)
  Between transcription and translation sits a whole host of regulatory RNAs, chiefly in the guise of microRNAs (miRNAs). Now we can add another regulatory layer: three papers published in Cell show that protein-coding and non-coding RNAs influence the interaction of miRNAs with their target RNAs and demonstrate the biological importance of this mechanism in the context of cancer.
• Molecular evolution: Dealing with nonsense | PDF (157 KB)
  - Nat Rev Genet 12(12):805 (2011)
  The high rate of transcription error in biological systems has led to the evolution of mechanisms for minimizing the effects of potentially deleterious mistakes, such as those that generate premature termination codons (PTCs). Many transcripts containing PTCs are degraded by the nonsense-mediated decay (NMD) pathway, but a study now highlights the existence of a complementary strategy to NMD that suppresses nonsense errors by preferentially avoiding codons that can easily be mutated to a stop codon.
• Microbiomes: Getting down to mechanism | PDF (209 KB)
  - Nat Rev Genet 12(12):806 (2011)
  A new study uses the fruit fly as a model to reveal the molecular basis of microbiomic influences on host development and metabolism.
• Epigenetics: Inheriting a long life | PDF (201 KB)
  - Nat Rev Genet 12(12):806 (2011)
  The epigenome is traditionally viewed as being 'reset' on passage through the germline. However, in a handful of cases, transgenerational inheritance of epigenetic information can occur, although there is limited molecular understanding of these events.
• Comparative genomics: Mammalian alignments reveal human functional elements | PDF (161 KB)
  - Nat Rev Genet 12(12):806 (2011)
  A new project has carried out whole-genome sequencing to enable comparative genomics across 29 mammalian species. The result is the mapping of human functional elements in unprecedented detail.
• Ethics watch: DNA theft: your genetic information at risk | PDF (216 KB)
  - Nat Rev Genet 12(12):808 (2011)
  Thanks to the rise of the personal genomics industry, learning about your genetic information is as easy as ordering a kit over the internet with a credit card, sending back a swab of cheek cells to a direct-to-consumer (DTC) testing company and waiting for an e-mail for the desired information. But what if your curiosity extends to the genetic information of others?
• Development: Transcriptional activation at the maternal-to-zygotic transition | PDF (109 KB)
  - Nat Rev Genet 12(12):805 (2011)
  The authors investigated control of transcriptional activation during the maternal-to-zygotic transition (MZT) in Drosophila melanogaster by performing chromatin immunoprecipitation followed by sequencing (ChIP–seq) for the transcription factor Zelda. They found pervasive binding of Zelda at genomic regions that are activated in the MZT, and they found that its binding is associated with open chromatin.
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  - Nat Rev Genet 12(12):805 (2011)
  
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  - Nat Rev Genet 12(12):807 (2011)
  
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  - Nat Rev Genet 12(12):807 (2011)
  
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  - Nat Rev Genet 12(12):807 (2011)
  
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  - Nat Rev Genet 12(12):807 (2011)
  
• Genetic contributions to behavioural diversity at the gene–environment interface
  - Nat Rev Genet 12(12):809 (2011)
  Recent work on behavioural variation within and between species has furthered our understanding of the genetic architecture of behavioural traits, the identities of relevant genes and the ways in which genetic variants affect neuronal circuits to modify behaviour. Here we review our understanding of the genetics of natural behavioural variation in non-human animals and highlight the implications of these findings for human genetics. We suggest that gene–environment interactions are central to natural genetic variation in behaviour and that genes affecting neuromodulatory pathways and sensory processing are preferred sites of naturally occurring mutations.
• Software for systems biology: from tools to integrated platforms
  - Nat Rev Genet 12(12):821 (2011)
  Understanding complex biological systems requires extensive support from software tools. Such tools are needed at each step of a systems biology computational workflow, which typically consists of data handling, network inference, deep curation, dynamical simulation and model analysis. In addition, there are now efforts to develop integrated software platforms, so that tools that are used at different stages of the workflow and by different researchers can easily be used together. This Review describes the types of software tools that are required at different stages of systems biology research and the current options that are available for systems biology researchers. We also discuss the challenges and prospects for modelling the effects of genetic changes on physiology and the concept of an integrated platform.
• Controlling gene expression in response to stress
  - Nat Rev Genet 12(12):833 (2011)
  Acute stress puts cells at risk, and rapid adaptation is crucial for maximizing cell survival. Cellular adaptation mechanisms include modification of certain aspects of cell physiology, such as the induction of efficient changes in the gene expression programmes by intracellular signalling networks. Recent studies using genome-wide approaches as well as single-cell transcription measurements, in combination with classical genetics, have shown that rapid and specific activation of gene expression can be accomplished by several different strategies. This article discusses how organisms can achieve generic and specific responses to different stresses by regulating gene expression at multiple stages of mRNA biogenesis from chromatin structure to transcription, mRNA stability and translation.
• Evolution of microRNA diversity and regulation in animals
  - Nat Rev Genet 12(12):846 (2011)
  In the past decade, microRNAs (miRNAs) have been uncovered as key regulators of gene expression at the post-transcriptional level. The ancient origin of miRNAs, their dramatic expansion in bilaterian animals and their function in providing robustness to transcriptional programmes suggest that miRNAs are instrumental in the evolution of organismal complexity. Advances in understanding miRNA biology, combined with the increasing availability of diverse sequenced genomes, have begun to reveal the molecular mechanisms that underlie the evolution of miRNAs and their targets. Insights are also emerging into how the evolution of miRNA-containing regulatory networks has contributed to organismal complexity.
• Non-coding RNAs in human disease
  - Nat Rev Genet 12(12):861 (2011)
  The relevance of the non-coding genome to human disease has mainly been studied in the context of the widespread disruption of microRNA (miRNA) expression and function that is seen in human cancer. However, we are only beginning to understand the nature and extent of the involvement of non-coding RNAs (ncRNAs) in disease. Other ncRNAs, such as PIWI-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), transcribed ultraconserved regions (T-UCRs) and large intergenic non-coding RNAs (lincRNAs) are emerging as key elements of cellular homeostasis. Along with microRNAs, dysregulation of these ncRNAs is being found to have relevance not only to tumorigenesis, but also to neurological, cardiovascular, developmental and other diseases. There is great interest in therapeutic strategies to counteract these perturbations of ncRNAs.
• Error prevention and mitigation as forces in the evolution of genes and genomes
  - Nat Rev Genet 12(12):875 (2011)
  Why are short introns rarely a multiple of three nucleotides long? Why do essential genes cluster? Why are genes in operons often lined up in the order in which they are needed in the encoded pathway? In this Opinion article, we argue that these and many other — ostensibly disparate — observations are all pieces of an emerging picture in which multiple aspects of gene anatomy and genome architecture have evolved in response to error-prone gene expression.
• Correspondence: Gene-by-environment experiments: a new approach to finding the missing heritability
  - Nat Rev Genet 12(12):881 (2011)