Vertebrate Interactome Mapping
Intricate complexes built from macromolecules perform most eukaryotic cell functions. Understanding these complexes, and how they are assembled and regulated is the key to understanding cell function and malfunction in disease. The complete DNA sequences of many organisms determined by genome projects have provided “catalogs” of proteins made in each organism, but have revealed little or nothing about the specific function of each protein.
The “vertebrate interactome” is all of the interactions that molecules make with each other in a vertebrate cell. The goal of our research stream is to better understand the function of ribonucleoproteins (RNPs), which are complexes of RNA and protein that participate in gene expression. We are particularly interested in complexes that interact with and process RNA.
Students in our stream study proteins that have been implicated in RNA processing and metabolism in vertebrate cells, but whose functions are not well understood. The best way to begin investigating the function of a novel protein is to find out what other proteins it interacts with to form complexes.
Students in our stream study the interactions that specific proteins make with other macromolecules, principally RNA and protein while mediating functions in gene expression. They attach DNA sequences encoding an “affinity tag” (the TAP tag) after the last codon of a gene using molecular cloning techniques including PCR, and through targeted homologous recombination ("recombineering"). They then replace one copy of this gene with a tagged version in cultured animal cells (DT40 cells), again using trageted recombination.
The modified version of the gene will direct the DT40 cells to produce a protein with the TAP tag attached to its C-terminus. The TAP tag allows complexes to be isolated intact and purified from nuclei.
Studying these complexes allow us to map the interactome or “social network” of the nucleus, and to gain insight into the function of proteins about which little is currently known.
The videos below were made by students in prior years. During those years the stream used different methodology, but they still speak to the esprit de corps of the group.
Albert MacKrell (email@example.com)
School of Biological Sciences Website: http://www.biosci.utexas.edu/
Spring: Gives BIO 205L or CH 204 Credit.
Fall: Gives BIO 377 or CH 369K Credit.