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Genome Technology s Peer Review: A Weekly Forum of Recently Published Journal Articles: Jan 18, 2005

Following is a description of a recently published research paper recommended by a scientist involved in integrated biology. The scientist, Marc Vidal, is an assistant professor of genetics at HarvardMedicalSchooland a researcher at the Dana-Farber Cancer Institute.


For a complete list of this month's recommended papers, read  Genome Technology, a GenomeWeb News sister publication.

"Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays." Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, Snyder M, Young RA, Bulyk ML.  Nature Genetics. 2004 Dec; 36(12):1331-9.

"In this paper, the authors discuss their development of a 'new DNA microarray-based technology, called protein binding microarrays' that provides for 'rapid, high-throughput characterization of the in vitro DNA binding-site sequence specificities of transcription factors in a single day,' according to the abstract. The scientists found the DNA binding sites for three yeast transcription factors, and they write that comparison of these proteins in vitro binding sites with their in vivo binding sites 'indicates that PBM-derived sequence specificities can accurately reflect in vivo DNA sequence specificities. In addition to previously identified targets, Abf1, Rap1, and Mig1 bound to 107, 90, and 75 putative new target intergenic regions, respectively, many of which were upstream of previously uncharacterized open reading frames.'


"By comparing sequences, the team found that several of the previously unidentified sites were highly conserved across five species of yeast; the authors predict that they are functional binding sites. The team also suggests that protein binding microarrays will be useful for tracking down cis regulatory elements as well as transcriptional regulatory networks."

Marc Vidal, Researcher, Dana-Farber Cancer Institute
Assistant Professor of Genetics,

The views expressed here do not necessarily represent the opinions of Genome Technology or GenomeWeb News.

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