The characterization of transcription factor com-plexes and their binding sites in the genome by affin-ity purification has yielded tremendous new insights into how genes are regulated. The affinity purification requires either the use of antibodies raised against the factor of interest itself or by high-affinity bind-ing of a C- or N-terminally added tag sequence to the factor. Unfortunately, fusing extra amino acids to the termini of a factor can interfere with its biolog-ical function or the tag may be inaccessible inside the protein. Here, we describe an effective solution to that problem by integrating the ‘tag ’ close to the nuclear localization sequence domain of the factor. We demonstrate the effectiveness of this approach with the transcription factors Fli-1 and Irf2bp2, which cannot be tagged at their extremities without loss of function. This resulted in the identification of novel proteins partners and a new hypothesis on the con-tribution of Fli-1 to hematopoiesis
