Jonathan W. Jarvik Associate Professor Ph.D., Massachusetts Institute of Technology Postdoctoral Appointment, Yale University jarvik@cmu.edu 412-268-3398 (Phone) 412-268-7129 (Fax) 261 Mellon Institute Department of Biological Sciences Carnegie Mellon University 4400 Fifth Avenue Pittsburgh, PA 15213

Gene and protein discovery are major endeavors in biology and medicine today. We have developed a new approach to gene and protein discovery - CD-tagging - that allows us to simultaneously tag gene, transcript and protein in a single biochemical event. This event is recombinational in nature, involving the insertion of a specially designed "CD-cassette" into genomic DNA. CD-tagging gives us the opportunity to identify and isolate new proteins or protein-containing structures, and, having done so, to readily retrieve and analyze the genes that encode them. An important feature of the process is that no sequences are lost from the tagged gene, transcript or protein, and so the liklihood of retaining normal regulation and biochemical function is high.

Our current activities are focused on CD-tagging mammalian cells with epitope, luciferase and GFP tags, thereby enabling quantitation and observation of the tagged protein in live cells, identification of the tagged gene and transcript by amplification and sequencing, and purification of the tagged protein by affinity capture.

Future efforts will focus on automating all phases of the CD-tagging system so as to obtain and characterize thousands of tagged genes and/or tagged cell lines in a period of weeks or months.

Examples of CD-tagged cell lines can be viewed at http://cdtag.bio.cmu.edu/ Additional information about CD-tagging activities at Carnegie Mellon can be viewed at the Berget web site and theMurphy web site.

Selected Publications

Chen X, Velliste M, Weinstein S, Jarvik JW and Murphy RF. Location proteomics - Building subcellular location trees from high resolution 3D fluorescence microscope images of randomly-tagged proteins. Procedures SPIE, 4962:298-306, 2003.

Jarvik JW, Fisher GW, Shi C, Hennen L, Hauser C, Adler S and Berget PB. In vivo functional proteomics: Mammalian genome annotation using CD-tagging. BioTechniques, 33:852-866, 2002.

Telmer CA, Berget PB, Ballou B, Murphy RF and Jarvik JW. Epitope tagging genomic DNA using a CD-tagging Tn10 minitransposon. BioTechniques, 32(2):422-432, 2002.

Nelson RW, Jarvik JW, Taillon BE and Tubbs KA. BIA/MS analysis of epitope tagged peptides directly from E. coli lysate: multiplex detection at sub-femtomole levels. Analytical Chemistry, 71:2858-2865, 1999.

Jarvik JW and Telmer CA. Epitope Tagging. Annual Review Genetics 32:601-618, 1998.