Transcription promotes discrete long-range chromatin loops besides organizing cohesin-mediated DNA folding

The multi-layered arrangement of eukaryotic genomes and chromosome spatial organization dynamics are of functional importance for gene expression, DNA replication and segregation. SMC complexes are essential instruments of chromosome folding by carrying out long range intra-chromatid DNA looping. Cohesin, in addition to tether sister chromatids, also ensures dynamic regulation of gene expression in mammals by promoting interaction between distal regulatory elements and promoters whereas transcription affects genome folding in numerous organisms and in multiple 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 through DNA borders and loops. Transcription activation specifically induces appearance of DNA borders and loops, independently of SMC complexes, while also directly interfering in addition with cohesin-mediated loop expansion.