The study reveals that Mediator and Cohesin physically and functionally connect enhancers and core promoters of active genes in embryonic stem cells (ES cells), facilitating DNA looping between enhancers and promoters. Mediator, a transcriptional coactivator, forms a complex with Cohesin, which can form rings that connect DNA segments. The Cohesin loading factor Nipbl is associated with these complexes, enabling Cohesin loading at promoters. DNA looping is observed between enhancers and promoters occupied by Mediator and Cohesin. Mediator and Cohesin occupy different promoters in different cells, generating cell-type specific DNA loops linked to gene expression programs. Transcription factors control gene expression programs by interacting with coactivators and the transcription apparatus. Enhancer-bound transcription factors bind coactivators like Mediator and p300, which then bind the transcription initiation apparatus. This interaction implies that gene activation is accompanied by DNA loop formation. Chromosome Conformation Capture (3C) experiments confirm that some enhancers are brought into proximity of promoters during active transcription. The study used a small hairpin RNA (shRNA) library to screen for regulators of transcription and chromatin necessary for maintaining ES cell state. Mediator, Cohesin, and Nipbl were identified as key regulators. Knockdown of these proteins resulted in reduced Oct4 levels, loss of ES cell colony morphology, and increased expression of developmentally important transcription factors, indicating their essential roles in maintaining ES cell state. Mediator occupies enhancers and promoters of actively transcribed genes. ChIP-Seq analysis showed that Mediator is found at both enhancers and core promoters of actively transcribed genes. Mediator was detected at the enhancers and core promoters of Oct4 and Nanog genes, along with RNA polymerase II and TBP, supporting the model that Mediator bridges interactions between transcription factors at enhancers and the transcription initiation apparatus at core promoters. Cohesin co-occupies active genes with Mediator and Nipbl. ChIP-Seq data revealed that Cohesin occupies sites bound by CTCF and also the enhancer and core promoter sites bound by Mediator. Nipbl was found to occupy enhancer and core promoter regions bound by Mediator and Cohesin but not CTCF and Cohesin co-occupied sites, suggesting a specific association with Mediator/Cohesin sites. Mediator, Cohesin, and Nipbl co-occupy promoter regions of Oct4 and other active ES cell genes, suggesting they all contribute to transcription control. Knockdown of these proteins resulted in similar effects on gene expression, indicating their essential roles in normal expression of actively transcribed genes. The study shows that Mediator, Cohesin, and Nipbl interact and co-occupy thousands of sites in the ES cell genome, suggesting physical interactions. Crosslinking and immunoprecipitation experiments confirmed that these complexesThe study reveals that Mediator and Cohesin physically and functionally connect enhancers and core promoters of active genes in embryonic stem cells (ES cells), facilitating DNA looping between enhancers and promoters. Mediator, a transcriptional coactivator, forms a complex with Cohesin, which can form rings that connect DNA segments. The Cohesin loading factor Nipbl is associated with these complexes, enabling Cohesin loading at promoters. DNA looping is observed between enhancers and promoters occupied by Mediator and Cohesin. Mediator and Cohesin occupy different promoters in different cells, generating cell-type specific DNA loops linked to gene expression programs. Transcription factors control gene expression programs by interacting with coactivators and the transcription apparatus. Enhancer-bound transcription factors bind coactivators like Mediator and p300, which then bind the transcription initiation apparatus. This interaction implies that gene activation is accompanied by DNA loop formation. Chromosome Conformation Capture (3C) experiments confirm that some enhancers are brought into proximity of promoters during active transcription. The study used a small hairpin RNA (shRNA) library to screen for regulators of transcription and chromatin necessary for maintaining ES cell state. Mediator, Cohesin, and Nipbl were identified as key regulators. Knockdown of these proteins resulted in reduced Oct4 levels, loss of ES cell colony morphology, and increased expression of developmentally important transcription factors, indicating their essential roles in maintaining ES cell state. Mediator occupies enhancers and promoters of actively transcribed genes. ChIP-Seq analysis showed that Mediator is found at both enhancers and core promoters of actively transcribed genes. Mediator was detected at the enhancers and core promoters of Oct4 and Nanog genes, along with RNA polymerase II and TBP, supporting the model that Mediator bridges interactions between transcription factors at enhancers and the transcription initiation apparatus at core promoters. Cohesin co-occupies active genes with Mediator and Nipbl. ChIP-Seq data revealed that Cohesin occupies sites bound by CTCF and also the enhancer and core promoter sites bound by Mediator. Nipbl was found to occupy enhancer and core promoter regions bound by Mediator and Cohesin but not CTCF and Cohesin co-occupied sites, suggesting a specific association with Mediator/Cohesin sites. Mediator, Cohesin, and Nipbl co-occupy promoter regions of Oct4 and other active ES cell genes, suggesting they all contribute to transcription control. Knockdown of these proteins resulted in similar effects on gene expression, indicating their essential roles in normal expression of actively transcribed genes. The study shows that Mediator, Cohesin, and Nipbl interact and co-occupy thousands of sites in the ES cell genome, suggesting physical interactions. Crosslinking and immunoprecipitation experiments confirmed that these complexes