A combination of transcription factors mediates inducible interchromosomal contacts.

Abstract

The genome forms specific three-dimensional contacts in response to cellular or environmental conditions. However, it remains largely unknown which proteins specify and mediate such contacts. Here we describe an assay, MAP-C (Mutation Analysis in Pools by Chromosome conformation capture), that simultaneously characterizes the effects of hundreds of <i>cis</i> or <i>trans</i>-acting mutations on a chromosomal contact. Using MAP-C, we show that inducible interchromosomal pairing between <i>HAS1pr-TDA1pr</i> alleles in saturated cultures of <i>Saccharomyces</i> yeast is mediated by three transcription factors, Leu3, Sdd4 (Ypr022c), and Rgt1. The coincident, combined binding of all three factors is strongest at the <i>HAS1pr-TDA1pr</i> locus and is also specific to saturated conditions. We applied MAP-C to further explore the biochemical mechanism of these contacts, and find they require the structured regulatory domain of Rgt1, but no known interaction partners of Rgt1. Altogether, our results demonstrate MAP-C as a powerful method for dissecting the mechanistic basis of chromosome conformation.