Transcription promotes discrete long-range chromatin loops and 3D domains besides organizing cohesin-mediated folding

The multi-layered arrangement of eukaryotic genomes and chromosome spatial organization dynamics are of functional importance for gene expression, DNA replication and segregation. Cohesin is an essential instrument of chromosome folding by carrying out long range intra-chromatid DNA looping in addition to allowing timely chromosome segregation. Cohesin also ensures dynamic regulation of gene expression in mammals by promoting interaction between distal regulatory elements and promoters whereas transcription affects genome folding in multiple ways in multiple organisms. 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 apparition of DNA borders and loops, independently of cohesin, interfering in addition with cohesin mediated loop expansion. Examination of the interplay between transcription and SMC complexes such as cohesin on the genome 3D organization using HiC and ChIP-seq methods, yeast mutants, cell synchonisation, gene induction and protein depletion