RNA Pol II-based regulations of chromosome folding

The spatial organization of eukaryotic genomes and its dynamics are of functional importance for gene expression, DNA replication, and segregation. Structural maintenance of chromosome (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 tethering sister chromatids, dynamically regulates gene expression in mammals by promoting interactions 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, to yeast S. cerevisiae genome organization. In particular, we show that transcription (1) is not a motor required to push cohesin during DNA loop expansion, (2) specifically induces the appearance of DNA loops independently of SMC complexes, and (3) interferes with cohesin-mediated DNA loop expansion during their establishment.