Protein function and chromatin structure methods featured in Cold Spring Harbor Protocols

Two new methods for analyzing the roles played by proteins in cells are featured in the March issue of Cold Spring Harbor Protocols.

Thomas J. Wandless and colleagues from Stanford University provide detailed instructions for "Regulating Protein Stability in Mammalian Cells Using Small Molecules." This technique provides a rapid, reversible, and tunable method for studying the activity of a protein of interest in cells. The protein is attached to a destabilization domain, and the resulting fusion proteins are unstable and degraded, except in the presence of small ligands. The speed of small-molecule binding makes it an attractive alternative to studying gene function using RNA interference (RNAi). The method is freely accessible on the website for Cold Spring Harbor Protocols.

The second featured article for March looks at long-range chromosomal interactions and the proteins that mediate them. Stephen Baylin and colleagues from Johns Hopkins University contribute a method for the "Combined 3C-ChIP-Cloning (6C) Assay: A Tool to Unravel Protein Mediated Genome Architecture." 6C technology combines multiple techniques to identify the proteins that bridge distant genomic regions, while simultaneously identifying physical proximities. The method is also useful for determining if a candidate protein might mediate long-range interactions, both in cis and in trans in the nucleus. The 6C assay advances our understanding of chromatin folding and provides an important tool to examine the role of specific proteins in nuclear organization. This method is freely accessible on the website for Cold Spring Harbor Protocols.