YY1 is a multifunctional transcription factor capable of either activation or repression of transcription. The mechanisms underlying its bifunctionality are not well understood. Using a series of mutant YY1 proteins, expressed as GALA fusions, we have characterized domains responsible for transcriptional activation, activation suppression or masking, and repression. The YY1 activation domain resides in the first 100 amino acids of the amino terminus and requires amino acids 16-29 and 80-99 for maximal activity. Since the transcriptional silencing or repressive function of full length YY1 (414 amino acids) appears to be its default state, we were able to identify a minimum region in the carboxyl terminus of YY1, between amino acids 370 and 397, which upon deletion permits YY1 to function as a constitutive activator. This region is also required for transcriptional repression, as the carboxyl terminal 81 amino acids of YY1, amino acids 333-414 are sufficient to repress basal transcription. Deletion of the carboxy terminal 44 amino acids, which include zinc fingers 3 and 4, abolishes repression. However, detailed mutational analyses indicate that the normal structures of zinc fingers 3 and 4, although required for DNA binding, are not required for transcriptional repression. We also provide evidence that YY1 can be sequestered within the nucleus by virtue of its interaction with a large molecular weight complex. The region responsible for this interaction is bounded by amino acids 256 and 341, which we show to be the same region required for the compartmentalization of YY1 within the nuclear matrix. YY1 was also shown to potently repress activated transcription independent of it binding to DNA, by a mechanism which probably involves squelching of a limiting transcription factor. The region responsible for this effect was shown to reside between amino acids 333 and 370. This detailed functional mapping of YY1 should serve as an important basis for future studies aimed at understanding mechanistically its diverse transcriptional effects
