Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal?

We compared the transcription regulatory interactions inferred from three high-throughput methods. Because these methods use different principles, they have few interactions in common, suggesting they capture distinct facets of the transcription regulatory program. We show that these methods uncover disparate biological phenomena: long-range interactions between telomeres and transcription factors, downstream effects of interference with ribosome biogenesis and a protein-aggregation response. Through a detailed analysis of the latter, we predict components of the system responding to protein-aggregation stress.