Hot off the presses! Jan 01 Trends Genet

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Latest Articles Include:

• Editorial Board
  - Trends Genet 26(1):i (2010)
  
• The emergence of new genes on the young therian X
  Potrzebowski L Vinckenbosch N Kaessmann H - Trends Genet 26(1):1-4 (2010)
  Recent studies have revealed that our sex chromosomes differentiated relatively recently from ancestral autosomes in the common ancestor of placental and marsupial mammals (therians). Here, we show that the therian X started to accumulate new retroduplicate genes with overall sex-biased expression upon therian sex chromosome differentiation. This process reached its peak within the first 90 million years of sex chromosome evolution and then leveled off. Taken together, our observations suggest that the major sex-related functional remodeling of the X was completed relatively soon after the origination of therian sex chromosomes.
• Acquisition of prokaryotic genes by fungal genomes
  Marcet-Houben M Gabaldón T - Trends Genet 26(1):5-8 (2010)
  The relevance of horizontal gene transfer (HGT) in eukaryotes is a matter of debate. Recent analyses have shown clear examples in some species such as Candida parapsilosis, but broader surveys are lacking. To assess the impact of HGT in the fungal kingdom, we searched for prokaryotic-derived HGTs in 60 fully sequenced genomes. Using strict phylogenomic criteria, we detected 713 transferred genes. HGT affected most fungal clades, with particularly high rates in Pezizomycotina. Transferred genes included bacterial arsenite reductase, catalase, different racemases and peptidoglycan metabolism enzymes. Our results suggest an important role for HGT in fungal evolution.
• Paramutation: the tip of an epigenetic iceberg?
  Suter CM Martin DI - Trends Genet 26(1):9-14 (2010)
  Paramutation describes the transfer of an acquired epigenetic state to an unlinked homologous locus, resulting in a meiotically heritable alteration in gene expression. Early investigations of paramutation characterized a mode of change and inheritance distinct from mendelian genetics, catalyzing the concept of the epigenome. Numerous examples of paramutation and paramutation-like phenomena have now emerged, with evidence that implicates small RNAs in the transfer and maintenance of epigenetic states. In animals Piwi-interacting RNA (piRNA)-mediated retrotransposon suppression seems to drive a vast system of epigenetic inheritance with paramutation-like characteristics. The classic examples of paramutation might be merely informative aberrations of pervasive and broadly conserved mechanisms that use RNA to sense homology and target epigenetic modification. When viewed in this context, paramutation is only one aspect of a common and broadly distributed form of inheritan! ce based on epigenetic states.
• Why does dosage compensation differ between XY and ZW taxa?
  Naurin S Hansson B Bensch S Hasselquist D - Trends Genet 26(1):15-20 (2010)
  Recent studies have demonstrated an extensive male bias in the gene expression on Z chromosomes in species with a ZW sex determination (e.g. birds), suggesting that ZW females have incomplete dosage compensation. We propose that the extensive male bias on Z chromosomes is caused by the functional properties of male-adapted genes, which make them unsuitable for high expression in females, and that ZW females are dosage-compensated to a point where they have achieved enough compensation to maintain the integrity of critical networks. In ZW systems, Z chromosomes spend two-thirds of their evolutionary time in males, and pronounced sexual selection in males and the male mutation bias can interact and affect levels of sexual antagonism, causing more extensive male bias in gene expression on Z-linked genes. These patterns and processes contrast with those acting on genes on the X chromosome in XY species, and might help explain the discrepancies in the degree of sex-biased g! ene expression and dosage compensation in XY and ZW systems.
• A global view of genomic information – moving beyond the gene and the master regulator
  Mattick JS Taft RJ Faulkner GJ - Trends Genet 26(1):21-28 (2010)
  The current view of gene regulation in complex organisms holds that gene expression is largely controlled by the combinatoric actions of transcription factors and other regulatory proteins, some of which powerfully influence cell type. Recent large-scale studies have confirmed that cellular differentiation involves many different regulatory factors. However, other studies indicate that the genome is pervasively transcribed to produce a variety of short and long non-protein-coding RNAs, including those derived from retrotransposed sequences, which also play important roles in the epigenetic regulation of gene expression. The evidence suggests that ontogenesis requires interplay between state-specific regulatory proteins, multitasked effector complexes and target-specific RNAs that recruit these complexes to their sites of action. Moreover, the semi-continuous nature of the transcriptome prompts the reassessment of 'genes' as discrete entities and indicates that the ! mammalian genome might be more accurately viewed as islands of protein-coding information in a sea of cis- and trans-acting regulatory sequences.
• Therapeutic gene silencing strategies for polyglutamine disorders
  Scholefield J Wood MJ - Trends Genet 26(1):29-38 (2010)
  Dominantly inherited polyglutamine disorders are chronic neurodegenerative diseases therapeutically amenable to gene-specific silencing strategies. Several compelling nucleic acid-based approaches have recently been developed to block the expression of mutant proteins and prevent toxic neurodegenerative sequelae. With such approaches, avoiding potential side effects caused by the concomitant ablation of the normal protein is an important objective. Therefore, allele-specific gene silencing is highly desirable; however, retaining wild type function is complex given that the common CAG mutation cannot be directly targeted, and might not be necessary or justifiable in all cases. Insights from polyglutamine gene function studies and the further development of allele-specific and other gene silencing methodologies will be important to determine the optimal therapeutic strategy for each polyglutamine disorder.
• Mapping genes for plant structure, development and evolution: functional mapping meets ontology
  He Q Berg A Li Y Vallejos CE Wu R - Trends Genet 26(1):39-46 (2010)
  One of the fundamental tasks in biology is the identification of genes that control the structure and developmental pattern of complex traits and their responses to the environment during trait development. Functional mapping provides a statistical means for detecting quantitative trait loci (QTLs) that underlie developmental traits, such as growth trajectories, and for testing the interplay between gene action and development. Here we describe how functional mapping and studies of plant ontology can be integrated so as to elucidate the expression mechanisms of QTLs that control plant growth, morphology, development, and adaptation to changing environments. This approach can also be used to construct an evo-devo framework for inferring the evolution of developmental traits.