Multiple Structural Maintenance of Chromosome Complexes at Transcriptional Regulatory Elements

Transcription factors control cell-specific gene expression programs by binding regulatory elements and recruiting cofactors and the transcription apparatus to the initiation sites of active genes. One of these cofactors is cohesin, a structural maintenance of chromosomes (SMC) complex that is necessary for proper gene expression. We report that a second SMC complex, condensin II, is also present at transcriptional regulatory elements of active genes during interphase and is necessary for normal gene activity. Both cohesin and condensin II are associated with genes in euchromatin and not heterochromatin. The two SMC complexes and the SMC loading factor NIPBL are particularly enriched at super-enhancers, and the genes associated with these regulatory elements are especially sensitive to reduced levels of these complexes. Thus, in addition to their well-established functions in chromosome maintenance during mitosis, both cohesin and condensin II make important contributions to the functions of the key transcriptional regulatory elements during interphase. •Cohesin and condensin II occupancy of enhancers and promoters is NIPBL dependent•Condensin II is recruited to regulatory elements during transcription activation•Cohesin and condensin II occupy super-enhancers and mediate proper gene expression The SMC complexes cohesin and condensin II occupy enhancers and promoters in a NIPBL-dependent manner. Condensin II is recruited to active regulatory elements during transcription activation in interphase cells. Both cohesin and condensin II occupy super-enhancers and are required for proper gene expression.