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For a comprehensive review of the most interesting recent articles published in the biological sciences, visit Faculty of 1000 Biology, an online literature awareness tool published by BioMed Central. Faculty of 1000 Biology systematically highlights exciting recent publications on the basis of recommendations of a faculty of well over 1,000 of the world's leading researchers. |
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Andrew D. Sharrocks
University of Manchester, United Kingdom
CELL BIOLOGY
 New Finding
 Tech Advance
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This study identifies the transcriptional control networks operative in muscle differentiation through using a powerful combination of ChIP and expression arrays. ChIP on chip array analysis is used to identify the targets of the myogenic transcription factors, MEF2, MyoD and Myogenin, during Muscle differentiation in vitro. This is coupled with microarray analysis to demonstrate differentiation-specific changes in gene expression to identify several novel areas in which myogenic transcription factors function including roles in promoting muscle repair and responses to stress and damage.
Evaluated 3 May 2005 |
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David States
University of Michigan School of Medicine, United States of America
GENOMICS & GENETICS
 Hypothesis
New Finding
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This pioneering paper begins to dissect the logic of transcriptional regulatory elements in higher eukaryotic genomes using synthetic enhancers and computational analysis to assess the rules governing element spacing, stoichiometry and affinity. Although progress has been made in regulatory element recognition, we lack a general understanding of how alterations in binding sites for short-range repressors or adjacent activators might affect transcription; thus, it is difficult to predict whether sequence changes introduced during evolution would affect enhancer function. These authors demonstrate that there is a rich set of rules that influence the activity of short-range repression and that these regulatory grammars may generalize across groups of DNA binding proteins.
Evaluated 21 Apr 2005 |
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Lawrence Chasin
Columbia University, United States of America
CELL BIOLOGY
Tech Advance
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A new, simple, clever, high-throughput method is described for determining the sequence motifs representing the binding sites for DNA-binding proteins. DNA fragments (600 bp) from complex mixtures (genomes) are bound to a purified protein in vitro; the bound DNA is hybridized to DNA microarrays, and the motifs are identified by bioinformatic methods. Any DNA and any DNA microarray can be used. I see no reason why this methodology could not be extended to RNA-binding proteins.
Evaluated 22 Apr 2005 |
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Michael Meisterernst
GSF - National Research Center for Environment and Health, Germany
CELL BIOLOGY
New Finding
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Holstege and colleagues analyze gene reprogramming at the transition from stationary phase to proliferation in yeast. As one main finding, they observe that genes harbour RNA polymerase II in quiescent cells, literally as if they were poised for rapid transcriptional activation. This finding reminds us that the occupancy of transcription factors on genes does not necessarily reveal a functional correlation to the present status of these genes. This may well complicate the interpretation of ChIP data.
Evaluated 3 May 2005 |
Jurg Bahler
The Wellcome Trust Sanger Institute, United Kingdom
CELL BIOLOGY
New Finding
 Controversial
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This paper challenges current models of transcriptional activation by showing that RNA polymerase II recruitment to promoters is not rate-limiting during quiescence, a common but understudied cellular state. Detailed gene expression profiling of yeast cells leaving and entering quiescence in response to nutrients revealed the induction of ~50% of all genes within a few minutes after re-feeding. Interestingly, RNA polymerase II was found to be pre-bound upstream of many of these rapid response genes throughout quiescence.
Evaluated 27 Apr 2005 |
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Mark D. Adams
Case Western Reserve University, United States of America
GENOMICS & GENETICS
New Finding
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Lateral gene transfer (LGT) into gamma-proteobacteria represents a significant source of genome diversity, but does not confound construction of organismal phylogenies, because of limited LGT among gamma-proteobacteria and vertical transmission of LGT genes once acquired. The overall validity of a gamma proteobacterial phylogenetic tree was demonstrated by accounting for LGT in each of 13 species. Laterally transferred genes come from a large pool of primarily non-gamma-proteobacterial species and once inserted are generally transmitted vertically. The approach of global accounting for gene gain and loss should be applicable to other groups of prokaryotic organisms. The large number of singleton LGT genes highlights the fact that there is still a huge amount of unsampled genome diversity.
Evaluated 29 Apr 2005 |
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