Notable

J.O. Korbel et al., "SHOT: A Web server for the construction of genome phylogenies," Trends in Genetics, 18[3]:158-62, March 1, 2002.

"This paper reports the results of phylogenetic analysis using whole genome comparisons and introduces a new Web server (named "SHOT") for further analysis by gene-content and gene-order methods. Among the results, the gene-content method showed Homo sapiens to be more closely related to Drosophila melanogaster than Caenorhabditis elegans, and both methods showed Halobacterium sp. to branch at the root of the Archaea."

Y. Fang et al., "Membrane protein microarrays," Journal of the American Chemical Society, 124[11]:2394-5, March 20, 2002.

"Almost half of all known drug targets are membrane-associated proteins, but there had been no efficient high throughput microarray assays developed for membrane proteins until the process reported in this paper. The authors used a quill pin printer to spot a mixture of lipids and various G-protein-coupled receptors onto chemically modified glass slides and found that the arrayed receptors were still able to bind specifically to their ligands."

G. Yona, M. Levitt, "Within the twilight zone: A sensitive profile-profile comparison tool based on information theory," Journal of Molecular Biology, 315[5]:1257-75, Feb. 1, 2002.

"This work describes a new method to detect homology between distantly related proteins by comparing profile models generated from multiple protein sequence alignments like those produced by PSI-BLAST. The authors give a symmetric information-theoretic measure of similarity between the columns of two profiles; construct a dynamic programming alignment algorithm around this measure to judge the similarity of two profiles; provide extensive empirical tests arguing that their method is more sensitive than, e.g. PSI-BLAST; and produce results in agreement with structural alignment. [...] I found the review of profile-profile similarity scores and the discussion and citations associated with the authors' new approach particularly valuable. Symmetrizing the Kullback-Leibler divergence, as the authors do here, is a problem that comes up in many different contexts, but this is the first example I know of where a solution to this problem was directly applied in a bioinformatics context."

N.R. Dudley et al., "Using RNA interference to identify genes required for RNA interference," Proceedings of the National Academy of Sciences, 99[7]:4191-6, April 2, 2002.

"Through an RNAi-based genetic screen in Caenorhabditis elegans, the authors have obtained evidence that chromatin may play a role in RNAi in animals, as it does in plants. The original purpose of the study was to find genes with essential roles in embryogenesis, but it soon became clear that some pools of injected dsRNAs behaved in an unexpected manner. Further analysis identified five genes, all encoding proteins predicted to associate with chromatin that are candidates in the RNAi mechanism. The authors speculate that dsRNA in animals might result in both homologous mRNA degradation and transcriptional silencing by recruiting protein complexes to the silenced locus."

T. Borggrefe et al., "Quantitation of the RNA polymerase II transcription machinery in yeast," Journal of Biological Chemistry, 276[50]:47,150-3, Dec. 14, 2001.

"Recently, tandem affinity purification (TAP) tagging has been employed for the successful purification of many macromolecular complexes from yeast Saccharomyces cerevisiae. This recent report from [Roger] Kornberg's laboratory [at Stanford University] has taken advantage of this tagging method to analyze the amounts of RNA polymerase II transcription proteins in crude yeast extracts. The tandem tag is normally placed at the C-terminal domain of a given gene so that the expression of the tagged gene is controlled by the gene's own promoter. Using the tag as a marker, the authors have demonstrated that comparable amounts of RNA polymerase II, TFIIE, and TFIIF; lower levels of TBP and TFIIB; but much lower levels of Mediator and TFIIH exist in the yeast extract. This ingenious approach could be extended to analyze the entire yeast proteome."

D. Mukherjee et al., "The mammalian exosome mediates the efficient degradation of mRNAs that contain AU-rich elements," European Molecular Biology Organization Journal, 21[1-2]:165-74, Jan.15, 2002.

"It is well recognized that mRNA stability can be regulated by unstable elements within transcripts. This paper shows that in vitro, these AU-rich elements (ARE) act to recruit the exosome for 3'-degradation. That 3'-degradation is the major pathway for mRNA degradation in mammalian cells is contrary to what has been observed in yeast, where 5'-decay predominates. This work is supported by two other recent papers by Chen et al. (Cell, 107:451-464, 2001) and Wang and Kiledjian (Cell, 107:751-62, 2001). However, whereas this paper shows that the exosome can interact directly with AREs, Chen et al. suggest that exosome recruitment is bridged by specific ARE-binding proteins."