Abstract
The spatial organization of eukaryotic genomes and its dynamics are of functional importance for gene expression, DNA replication and segregation. SMC complexes are essential instruments of chromosome folding, enabling long-distance intra-chromatid DNA loops. The interplay between these processes is complex. For instance cohesin, in addition to tether sister chromatids, dynamically regulates gene expression in mammals by promoting interaction between distal regulatory elements and promoters, whereas transcription itself affects genome folding in many ways. Here, we comprehensively dissect the relative contributions of transcription and cohesin complexes, as well as their interplay, on the yeast S. cerevisiae genome organization. In particular, we show that transcription: (i) is not a motor required to push cohesin during DNA loop expansion, (ii) specifically induces the appearance of DNA loops independently of SMC complexes, and (iii) interferes with cohesin-mediated DNA loop expansion during their establishment.