Saturday, June 4, 2011

Hot off the presses! Jun 01 TIG

The Jun 01 issue of the TIG is now up on Pubget (About TIG): 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:

  • Editorial Board
    - TIG 27(6):i (2011)
  • Interpretation of karyotype evolution should consider chromosome structural constraints
    - TIG 27(6):207-216 (2011)
    Comparative genetics, genomics and cytogenetics provide tools to trace the evolutionary history of extant genomes. Yet, the interpretation of rapidly increasing genomic data is not always done in agreement with constraints determined by chromosome structural features and by insights obtained from chromosome mutagenesis. The terms 'non-reciprocal chromosome translocation', 'chromosome fusion' and 'centromere shift' used to explain genomic differences among organisms are misleading and often do not correctly reflect the mechanisms of chromosome rearrangements underlying the evolutionary karyotypic variation. Here, we (re)interpret evolutionary genome alterations in a parsimonious way and demonstrate that results of comparative genomics and comparative chromosome painting can be explained on the basis of known primary and secondary chromosome rearrangements. Therefore, some widespread terms used in comparative and evolutionary genomics should be either avoided! (e.g. non-reciprocal translocation) or redefined (e.g. chromosome fusion and centromere shift).
  • Somatic mosaicism in healthy human tissues
    - TIG 27(6):217-223 (2011)
    From the fertilization of an egg until the death of an individual, somatic cells can accumulate genetic changes, such that cells from different tissues or even within the same tissue differ genetically. The presence of multiple cell clones with distinct genotypes in the same individual is referred to as 'somatic mosaicism'. Many endogenous factors such as mobile elements, DNA polymerase slippage, DNA double-strand break, inefficient DNA repair, unbalanced chromosomal segregation and some exogenous factors such as nicotine and UV exposure can contribute to the generation of somatic mutations, thereby leading to somatic mosaicism. Such changes can potentially affect the epigenetic patterns and levels of gene expression, and ultimately the phenotypes of cells. Although recent studies suggest that somatic mosaicism is widespread during normal development and aging, its implications for heightened disease risks are incompletely understood. Here, I discuss the origins, p! revalence and implications of somatic mosaicism in healthy human tissues.
  • Forkhead transcription factors: key players in health and disease
    - TIG 27(6):224-232 (2011)
    Forkhead box (FOX) proteins constitute an evolutionarily conserved family of transcription factors with a central role not only during development, but also in the adult organism. Thus, the misregulation and/or mutation of FOX genes often induce human genetic diseases, promote cancer or deregulate ageing. Indeed, germinal FOX gene mutations cause diseases ranging from infertility to language and/or speech disorders and immunological defects. Moreover, because of their central role in signalling pathways and in the regulation of homeostasis, somatic misregulation and/or mutation of FOX genes are associated with cancer. FOX proteins have undergone diversification in terms of their sequence, regulation and function. In addition to dedicated roles, evidence suggests that Forkhead factors have retained some functional redundancy. Thus, combinations of slightly defective alleles might induce disease phenotypes in humans, acting as quantitative trait loci. Uncovering such var! iants would be a big step towards understanding the functional interdependencies of different FOX members and their implications in complex pathologies.
  • MicroRegulators come of age in senescence
    - TIG 27(6):233-241 (2011)
    Cellular senescence was first reported five decades ago as a state of long-term growth inhibition in viable, metabolically active cells cultured in vitro. However, evidence that senescence occurs in vivo and underlies pathophysiologic processes has only emerged over the past few years. Coincident with this increased knowledge, understanding of the mechanisms that control senescent-cell gene expression programs has also recently escalated. Such mechanisms include a prominent group of regulatory factors (miRNA), a family of small, noncoding RNAs that interact with select target mRNAs and typically repress their expression. Here, we review recent reports that miRNAs are key modulators of cellular senescence, and we examine their influence upon specific senescence-regulatory proteins. We discuss evidence that dysregulation of miRNA-governed senescence programs underlies age-associated diseases, including cancer.
  • Emerging patterns of epigenomic variation
    - TIG 27(6):242-250 (2011)
    Fuelled by new sequencing technologies, epigenome mapping projects are revealing epigenomic variation at all levels of biological complexity, from species to cells. Comparisons of methylation profiles among species reveal evolutionary conservation of gene body methylation patterns, pointing to the fundamental role of epigenomes in gene regulation. At the human population level, epigenomic changes provide footprints of the effects of genomic variants within the vast nonprotein-coding fraction of the genome, and comparisons of the epigenomes of parents and their offspring point to quantitative epigenomic parent-of-origin effects confounding classical Mendelian genetics. At the organismal level, comparisons of epigenomes from diverse cell types provide insights into cellular differentiation. Finally, comparisons of epigenomes from monozygotic twins help dissect genetic and environmental influences on human phenotypes and longitudinal comparisons reveal aging-associated ep! igenomic drift. The development of new bioinformatic frameworks for comparative epigenome analysis is putting epigenome maps within the reach of researchers across a wide spectrum of biological disciplines.

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